Score E
Sequences producing significant alignments: (bits) Value
pir||T29322 hypothetical protein M01E11.5 - Caenorhabditis ... 477 e-134
pir||T25767 hypothetical protein F46F11.2 - Caenorhabditis ... 338 3e-92
pir||T19920 hypothetical protein Y39A1C.3 - Caenorhabditis ... 125 6e-28
sp|P41824|YBFH_APLCA Y-BOX FACTOR HOMOLOG (APY1) >gi|409419... 108 6e-23
dbj|BAA19850.1| (AB003336) Y box protein 2 [Carassius auratus] 104 1e-21
sp|P21574|YB56_XENLA CYTOPLASMIC RNA-BINDING PROTEIN P56 (Y... 103 2e-21
pir||B38274 Y box-binding protein 2 - African clawed frog >... 103 2e-21
gb|AAA59949.1| (M83234) DNA-binding protein [Homo sapiens] 102 3e-21
gb|AAB94768.1| (AF038994) Y box transcription factor [Mus m... 102 3e-21
pir||A23677 Y box-binding protein 1 - rat >gi|203999|gb|AAA... 102 3e-21
pir||A40498 Y box-binding protein YB-1 - human >gi|340419|g... 102 3e-21
gb|AAC62774.1| (AF093129) zfY1 [Danio rerio] 102 3e-21
sp|P16991|YB1_HUMAN Y BOX BINDING PROTEIN-1 (Y-BOX TRANSCRI... 102 3e-21
sp|P27817|YB1_MOUSE Y BOX BINDING PROTEIN-1 (Y-BOX TRANSCRI... 102 3e-21
sp|P21573|YB1_XENLA Y BOX BINDING PROTEIN-1 (Y-BOX TRANSCRI... 102 3e-21
pir||I58195 Y box-binding protein 1 - mouse >gi|199821|gb|A... 102 3e-21
ref|NP_035862.1| Y box protein 1 >gi|111259|pir||S22822 tra... 102 3e-21
pir||PS0015 DNA-binding protein B - human (fragment) >gi|18... 102 3e-21
pir||A55971 Y box-binding protein 1 - rabbit >gi|608518|gb|... 102 3e-21
gb|AAA75476.1| (U33197) mYB-1b [Mus musculus] 102 3e-21
ref|NP_004550.1| nuclease sensitive element binding protein... 102 3e-21
gb|AAA40906.1| (M69138) putative [Rattus norvegicus] 102 3e-21
pir||S34426 nuclease sensitive element-binding protein 1 - ... 102 3e-21
sp|Q06066|YB1_CHICK Y BOX BINDING PROTEIN-1 (Y-BOX TRANSCRI... 101 6e-21
dbj|BAA03376.1| (D14485) dbpA murine homologue [Mus musculus] 101 6e-21
sp|P45441|YB54_XENLA CYTOPLASMIC RNA-BINDING PROTEIN P54 (Y... 101 6e-21
dbj|BAA05380.1| (D26328) similar to dbpB/YB-1 of mouse [Gal... 101 6e-21
gb|AAA75475.1| (U33196) mYB-1a [Mus musculus] 101 6e-21
gb|AAB01787.1| (U43513) Y-Box binding protein [Columba livia] 101 6e-21
ref|NP_003642.1| cold shock domain protein A >gi|2135012|pi... 101 8e-21
pir||I53354 DNA-binding protein A - human >gi|950340|gb|AAA... 101 8e-21
pir||PS0014 DNA-binding protein A - human (fragment) >gi|18... 101 8e-21
gb|AAF61741.1| (AF246224) RNA binding protein MSY4 [Mus mus... 101 8e-21
sp|P16989|DBPA_HUMAN DNA-BINDING PROTEIN A (COLD SHOCK DOMA... 101 8e-21
dbj|BAA19849.1| (AB003335) Y box protein 1 [Carassius auratus] 101 8e-21
sp|Q62764|DBPA_RAT DNA-BINDING PROTEIN A (COLD SHOCK DOMAIN... 101 8e-21
gb|AAF72335.1|AF171061_1 (AF171061) Y-box protein ZONAB-A [... 101 1e-20
gb|AAC34193.1| (L35549) Y-box binding protein [Mus musculus... 100 1e-20
sp|Q00436|YB3_XENLA B BOX BINDING PROTEIN (YB3 PROTEIN) >gi... 100 2e-20
pir||S51608 RYB-a protein - rat >gi|505133|dbj|BAA05907.1| ... 100 2e-20
pir||S48055 RYB-a protein - rat 100 2e-20
gb|AAF72336.1|AF171062_1 (AF171062) Y-box protein ZONAB-B [... 99 3e-20
ref|NP_058571.1| Y box protein 2 >gi|4071321|gb|AAC98673.1|... 99 4e-20
ref|NP_057066.1| germ cell specific Y-box binding protein >... 99 5e-20
pir||T21689 hypothetical protein F33A8.3 - Caenorhabditis e... 98 7e-20
gb|AAA64706.1| (U23162) Rous sarcoma virus transcription en... 97 2e-19
gb|AAB80761.1| (AF022769) Y-box binding protein A [Columba ... 96 4e-19
gb|AAC98674.1| (AF073955) Y-box protein MSY2 isoform a [Mus... 94 1e-18
gb|AAF49961.1| (AE003542) yps gene product [Drosophila mela... 93 3e-18
gb|AAB94634.1| (U49120) Y-box protein [Drosophila melanogas... 90 3e-17
Alignments
>pir||T29322 hypothetical protein M01E11.5 - Caenorhabditis elegans
gb|AAB37828.1| (U80450) coded for by C. elegans cDNA yk110a1.5; coded for by C.
elegans cDNA yk141e7.5; coded for by C. elegans cDNA
yk167a8.5; coded for by C. elegans cDNA yk47h6.5; coded
for by C. elegans cDNA yk110a1.3; coded for by C.
elegans cDNA yk167a8.3; stro>
Length = 265
Score = 477 bits (1215), Expect = e-134
Identities = 246/265 (92%), Positives = 246/265 (92%)
Query: 1 MSDTANTAVEVDEQVIEKKLDDLSIGKKRSPSKDDTSKHRLPAAERIRIWEEEQKAKIVL 60
MSDTANTAVEVDEQVIEKKLDDLSIGKKRSPSKDDTSKHRLPAAERIRIWEEEQKAKIVL
Sbjct: 1 MSDTANTAVEVDEQVIEKKLDDLSIGKKRSPSKDDTSKHRLPAAERIRIWEEEQKAKIVL 60
Query: 61 TAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLADEEEVLFDLV 120
TAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLADEEEVLFDLV
Sbjct: 61 TAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLADEEEVLFDLV 120
Query: 121 DGKNGPEAANVTGPAGVNVSGSKYRHQLLSRFRKNRKPKIVVGEDFDSKETEKLVEAPAV 180
DGKNGPEAANVTGPAGVNVSGSKYRHQLLSRFRKNRKPKIVVGEDFDSKETEKLVEAPAV
Sbjct: 121 DGKNGPEAANVTGPAGVNVSGSKYRHQLLSRFRKNRKPKIVVGEDFDSKETEKLVEAPAV 180
Query: 181 AMEXXXXXXXXXXXXXXXXXXXGAGDAADSSATTESLGTSSETASPDSKSCTKIISEEAG 240
AME GAGDAADSSATTESLGTSSETASPDSKSCTKIISEEAG
Sbjct: 181 AMEKKKQRKQRKNKNRKQKDQKGAGDAADSSATTESLGTSSETASPDSKSCTKIISEEAG 240
Query: 241 LSKIDRCDSALDDAGLGAQLIDAQI 265
LSKIDRCDSALDDAGLGAQLIDAQI
Sbjct: 241 LSKIDRCDSALDDAGLGAQLIDAQI 265
>pir||T25767 hypothetical protein F46F11.2 - Caenorhabditis elegans
gb|AAB42263.1| (U88173) contains strong similarity to a cold-shock domain
(PS:PS00352) [Caenorhabditis elegans]
Length = 267
Score = 338 bits (858), Expect = 3e-92
Identities = 174/267 (65%), Positives = 203/267 (75%), Gaps = 2/267 (0%)
Query: 1 MSDTANTAVEVDEQVIEKKLDDLSIGKKRSPSKDDTS--KHRLPAAERIRIWEEEQKAKI 58
MSDTAN AVE+ E+ +E+KL++LS+ K +PS + K RLP AERIR+WEEEQK+K
Sbjct: 1 MSDTANAAVEIGEEALEQKLEELSVQDKTTPSNSEEKMRKRRLPTAERIRLWEEEQKSKT 60
Query: 59 VLTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLADEEEVLFD 118
+T GLQGKVKWYSVLRRYGFISR+DGEKD+FVHQTAI+KS TEKFYLRTL D+EEVLFD
Sbjct: 61 AITTGLQGKVKWYSVLRRYGFISRNDGEKDIFVHQTAIAKSATEKFYLRTLGDDEEVLFD 120
Query: 119 LVDGKNGPEAANVTGPAGVNVSGSKYRHQLLSRFRKNRKPKIVVGEDFDSKETEKLVEAP 178
LV+GKNGPEAANVTGP G NV GS+YRH+LLSRFRKNRKP+ V + K E
Sbjct: 121 LVEGKNGPEAANVTGPNGDNVIGSRYRHKLLSRFRKNRKPRASVDGEESQSTDAKPQEMS 180
Query: 179 AVAMEXXXXXXXXXXXXXXXXXXXGAGDAADSSATTESLGTSSETASPDSKSCTKIISEE 238
A A + GAGDAADSSA TES ++S+ ASPDSKSC+KII+EE
Sbjct: 181 ADAEKKKPRKQRKNRNRKSKAQQKGAGDAADSSAVTESSESASDVASPDSKSCSKIITEE 240
Query: 239 AGLSKIDRCDSALDDAGLGAQLIDAQI 265
AGLSK+DRCDSAL +AGLGAQ IDAQI
Sbjct: 241 AGLSKVDRCDSALGEAGLGAQPIDAQI 267
>pir||T19920 hypothetical protein Y39A1C.3 - Caenorhabditis elegans
emb|CAA97783.1| (Z73424) similar to 'Cold-shock' DNA-binding domain~cDNA EST
EMBL:D75839 comes from this gene~cDNA EST EMBL:T01941
comes from this gene [Caenorhabditis elegans]
emb|CAA19509.1| (AL023839) similar to 'Cold-shock' DNA-binding domain~cDNA EST
EMBL:D75839 comes from this gene~cDNA EST EMBL:T01941
comes from this gene [Caenorhabditis elegans]
Length = 294
Score = 125 bits (310), Expect = 6e-28
Identities = 62/117 (52%), Positives = 85/117 (71%), Gaps = 3/117 (2%)
Query: 40 RLPAAERIRIWEEEQKAKIVLTAGLQGKVKWYSVLRRYGFISR---SDGEKDVFVHQTAI 96
R P ++++ EE+ +K V+ G++G VKW+SV RYGF++R +D +D FVHQTAI
Sbjct: 65 RPPYEDQMKKLEEDLASKKVIETGVKGHVKWFSVRGRYGFVARDKPTDENEDFFVHQTAI 124
Query: 97 SKSDTEKFYLRTLADEEEVLFDLVDGKNGPEAANVTGPAGVNVSGSKYRHQLLSRFR 153
+KS T KFYLRTL D+E V+FD+V+G GPEAANVTGP G NV GS++ LL+ +R
Sbjct: 125 TKSSTIKFYLRTLDDDEPVVFDIVEGLKGPEAANVTGPDGENVRGSRFARTLLTHWR 181
>sp|P41824|YBFH_APLCA Y-BOX FACTOR HOMOLOG (APY1)
gb|AAA60373.1| (U02684) Y-Box factor [Aplysia californica]
Length = 253
Score = 108 bits (267), Expect = 6e-23
Identities = 53/93 (56%), Positives = 70/93 (74%), Gaps = 1/93 (1%)
Query: 52 EEQKAKIVLTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLAD 111
EEQK K ++ + + G VKW++V YGFI+R D ++DVFVHQTAI K++ K YLR++ D
Sbjct: 21 EEQKEKKIIASQVSGTVKWFNVKSGYGFINRDDTKEDVFVHQTAIVKNNPRK-YLRSVGD 79
Query: 112 EEEVLFDLVDGKNGPEAANVTGPAGVNVSGSKY 144
E+V FD+V+G+ G EAANVTGP G NV GSKY
Sbjct: 80 GEKVEFDVVEGEKGNEAANVTGPEGSNVQGSKY 112
>dbj|BAA19850.1| (AB003336) Y box protein 2 [Carassius auratus]
Length = 297
Score = 104 bits (256), Expect = 1e-21
Identities = 53/109 (48%), Positives = 74/109 (67%), Gaps = 2/109 (1%)
Query: 51 EEEQKAKIVLTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLA 110
E+ Q + V+ G++G VKW++V YGFI+R+D ++DVFVHQTAI K++ KF LR++
Sbjct: 8 EQPQPERKVIATGVEGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKF-LRSVG 66
Query: 111 DEEEVLFDLVDGKNGPEAANVTGPAGVNVSGSKYRHQLLSRFRKNRKPK 159
D E V FD+V+ G EAANVTGP G+ V GS+Y RFR+ P+
Sbjct: 67 DGEVVEFDVVEAAKGSEAANVTGPGGIPVKGSRYAPN-KRRFRRRFYPR 114
>sp|P21574|YB56_XENLA CYTOPLASMIC RNA-BINDING PROTEIN P56 (Y BOX BINDING PROTEIN-2)
(Y-BOX TRANSCRIPTION FACTOR) (MRNP4)
Length = 336
Score = 103 bits (254), Expect = 2e-21
Identities = 55/106 (51%), Positives = 73/106 (67%), Gaps = 4/106 (3%)
Query: 54 QKAKIVLTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLADEE 113
Q K VL +QG VKW++V YGFI+R+D ++DVFVHQTAI K++ KF LR++ D E
Sbjct: 32 QANKKVLATQVQGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKF-LRSVGDGE 90
Query: 114 EVLFDLVDGKNGPEAANVTGPAGVNVSGSKY---RHQLLSRFRKNR 156
V FD+V+G+ G EAANVTGP GV V GS++ R + RF + R
Sbjct: 91 TVEFDVVEGEKGAEAANVTGPGGVPVKGSRFAPNRRRFRRRFYRPR 136
>pir||B38274 Y box-binding protein 2 - African clawed frog
gb|AAA49716.1| (M59454) DNA-binding protein [Xenopus laevis]
Length = 336
Score = 103 bits (254), Expect = 2e-21
Identities = 55/106 (51%), Positives = 73/106 (67%), Gaps = 4/106 (3%)
Query: 54 QKAKIVLTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLADEE 113
Q K VL +QG VKW++V YGFI+R+D ++DVFVHQTAI K++ KF LR++ D E
Sbjct: 32 QANKKVLATQVQGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKF-LRSVGDGE 90
Query: 114 EVLFDLVDGKNGPEAANVTGPAGVNVSGSKY---RHQLLSRFRKNR 156
V FD+V+G+ G EAANVTGP GV V GS++ R + RF + R
Sbjct: 91 TVEFDVVEGEKGAEAANVTGPGGVPVKGSRFAPNRRRFRRRFYRPR 136
>gb|AAA59949.1| (M83234) DNA-binding protein [Homo sapiens]
Length = 320
Score = 102 bits (253), Expect = 3e-21
Identities = 57/132 (43%), Positives = 82/132 (61%), Gaps = 3/132 (2%)
Query: 54 QKAKIVLTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLADEE 113
++ K V+ + G VKW++V YGFI+R+D ++DVFVHQTAI K++ K YLR++ D E
Sbjct: 46 RRDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRK-YLRSVGDGE 104
Query: 114 EVLFDLVDGKNGPEAANVTGPAGVNVSGSKYR--HQLLSRFRKNRKPKIVVGEDFDSKET 171
V FD+V+G+ G EAANVTGP GV V GSKY R+ + R P +++ + E+
Sbjct: 105 TVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSES 164
Query: 172 EKLVEAPAVAME 183
+ E A E
Sbjct: 165 GEKNEGSESAPE 176
>gb|AAB94768.1| (AF038994) Y box transcription factor [Mus musculus]
Length = 299
Score = 102 bits (252), Expect = 3e-21
Identities = 57/129 (44%), Positives = 80/129 (61%), Gaps = 3/129 (2%)
Query: 57 KIVLTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLADEEEVL 116
K V+ + G VKW++V YGFI+R+D ++DVFVHQTAI K++ K YLR++ D E V
Sbjct: 27 KKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRK-YLRSVGDGETVE 85
Query: 117 FDLVDGKNGPEAANVTGPAGVNVSGSKYR--HQLLSRFRKNRKPKIVVGEDFDSKETEKL 174
FD+V+G+ G EAANVTGP GV V GSKY R+ + R P +++ + E+ +
Sbjct: 86 FDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEK 145
Query: 175 VEAPAVAME 183
E A E
Sbjct: 146 NEGSESAPE 154
>pir||A23677 Y box-binding protein 1 - rat
gb|AAA41108.1| (M57299) enhancer factor-1-alpha [Rattus norvegicus]
Length = 322
Score = 102 bits (252), Expect = 3e-21
Identities = 57/129 (44%), Positives = 80/129 (61%), Gaps = 3/129 (2%)
Query: 57 KIVLTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTLADEEEVL 116
K V+ + G VKW++V YGFI+R+D ++DVFVHQTAI K++ K YLR++ D E V
Sbjct: 50 KKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRK-YLRSVGDGETVE 108
Query: 117 FDLVDGKNGPEAANVTGPAGVNVSGSKYR--HQLLSRFRKNRKPKIVVGEDFDSKETEKL 174
FD+V+G+ G EAANVTGP GV V GSKY R+ + R P +++ + E+ +
Sbjct: 109 FDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEK 168
Query: 175 VEAPAVAME 183
E A E
Sbjct: 169 NEGSESAPE 177
Database: nr
Posted date: Jul 9, 2000 11:06 PM
Number of letters in database: 162,524,432
Number of sequences in database: 517,904
Lambda K H
0.309 0.128 0.346
Gapped
Lambda K H
0.270 0.0470 0.230
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 74082674
Number of Sequences: 517904
Number of extensions: 2819110
Number of successful extensions: 8114
Number of sequences better than 10.0: 193
Number of HSP's better than 10.0 without gapping: 130
Number of HSP's successfully gapped in prelim test: 63
Number of HSP's that attempted gapping in prelim test: 7849
Number of HSP's gapped (non-prelim): 203
length of query: 265
length of database: 162,524,432
effective HSP length: 63
effective length of query: 202
effective length of database: 129,896,480
effective search space: 26239088960
effective search space used: 26239088960
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 42 (21.7 bits)
S2: 70 (31.7 bits)
