BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 033484
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HKS|A Chain A, Crystal Structure Of Eukaryotic Translation Initiation
Factor Eif-5a2 From Arabidopsis Thaliana
pdb|3HKS|B Chain B, Crystal Structure Of Eukaryotic Translation Initiation
Factor Eif-5a2 From Arabidopsis Thaliana
Length = 167
Score = 164 bits (415), Expect = 1e-41, Method: Compositional matrix adjust.
Identities = 78/95 (82%), Positives = 85/95 (89%), Gaps = 1/95 (1%)
Query: 8 FESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFN 67
FE+ +++GASKT+PQ AG IRK G+IVIK RPCKVVEVSTSKTGKHGHAKCHFV IDIF
Sbjct: 16 FEA-SESGASKTYPQSAGNIRKGGHIVIKNRPCKVVEVSTSKTGKHGHAKCHFVAIDIFT 74
Query: 68 GKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFV 102
KKLEDIVPSSHNCDVPHV R DYQLIDI+EDGFV
Sbjct: 75 AKKLEDIVPSSHNCDVPHVNRVDYQLIDITEDGFV 109
>pdb|3ER0|A Chain A, Crystal Structure Of The Full Length Eif5a From
Saccharomyces Cerevisiae
pdb|3ER0|B Chain B, Crystal Structure Of The Full Length Eif5a From
Saccharomyces Cerevisiae
Length = 167
Score = 147 bits (371), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 68/102 (66%), Positives = 84/102 (82%), Gaps = 2/102 (1%)
Query: 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHF 60
MSDEEH FE+ ADAG+S T+P Q +RKNG++VIK RPCK+V++STSKTGKHGHAK H
Sbjct: 11 MSDEEHTFET-ADAGSSATYPMQCSALRKNGFVVIKSRPCKIVDMSTSKTGKHGHAKVHL 69
Query: 61 VGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDISEDGFV 102
V IDIF GKKLED+ PS+HN +VP V R +YQL+DI +DGF+
Sbjct: 70 VAIDIFTGKKLEDLSPSTHNMEVPVVKRNEYQLLDI-DDGFL 110
>pdb|3CPF|A Chain A, Crystal Structure Of Human Eukaryotic Translation
Initiation Factor Eif5a
pdb|3CPF|B Chain B, Crystal Structure Of Human Eukaryotic Translation
Initiation Factor Eif5a
Length = 138
Score = 129 bits (325), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 58/87 (66%), Positives = 71/87 (81%), Gaps = 1/87 (1%)
Query: 16 ASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIV 75
S TFP Q +RKNG++V+KGRPCK+VE+STSKTGKHGHAK H VGIDIF GKK EDI
Sbjct: 1 GSATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDIC 60
Query: 76 PSSHNCDVPHVTRTDYQLIDISEDGFV 102
PS+HN DVP++ R D+QLI I +DG++
Sbjct: 61 PSTHNMDVPNIKRNDFQLIGI-QDGYL 86
>pdb|1X6O|A Chain A, Structural Analysis Of Leishmania Braziliensis Eukaryotic
Initiation Factor 5a
Length = 174
Score = 112 bits (279), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 55/111 (49%), Positives = 73/111 (65%), Gaps = 3/111 (2%)
Query: 1 MSDEEHHFESKADA-GASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCH 59
MSDE+H F + ASKT+P AG ++K GY+ I GRPCKV+++S SKTGKHGHAK
Sbjct: 9 MSDEDHDFSHQGGGDNASKTYPLAAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVS 68
Query: 60 FVGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDI--SEDGFVCSYFVL 108
V DIF G +LED PS+HN +VP V Y ++DI +ED + ++ L
Sbjct: 69 IVATDIFTGNRLEDQAPSTHNVEVPFVKTYTYSVLDIQANEDPSLPAHLSL 119
>pdb|1XTD|A Chain A, Structural Analysis Of Leishmania Mexicana Eukaryotic
Initiation Factor 5a
Length = 174
Score = 110 bits (274), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 55/110 (50%), Positives = 72/110 (65%), Gaps = 3/110 (2%)
Query: 2 SDEEHHFESKADA-GASKTFPQQAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHF 60
SDE+H F + ASKT+P AG ++K GY+ I GRPCKV+++S SKTGKHGHAK
Sbjct: 10 SDEDHDFAHQGGGDNASKTYPXAAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSI 69
Query: 61 VGIDIFNGKKLEDIVPSSHNCDVPHVTRTDYQLIDI--SEDGFVCSYFVL 108
V DIF G +LED PS+HN +VP V Y ++DI +ED + S+ L
Sbjct: 70 VATDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPNEDPSLPSHLSL 119
>pdb|1BKB|A Chain A, Initiation Factor 5a From Archebacterium Pyrobaculum
Aerophilum
Length = 136
Score = 68.9 bits (167), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 30/77 (38%), Positives = 47/77 (61%)
Query: 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82
+AG +++ Y+VI G PC+VVE+ SKTGKHG AK V + +F+G K +P +
Sbjct: 10 EAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVE 69
Query: 83 VPHVTRTDYQLIDISED 99
VP + + Q++ +S D
Sbjct: 70 VPIIEKFTAQILSVSGD 86
>pdb|2EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 136
Score = 65.9 bits (159), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 46/76 (60%)
Query: 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDV 83
G+++ Y++I G PC++V++S SK GKHG AK VGI IF K E + P+S +V
Sbjct: 13 VGSLKVGQYVMIDGVPCEIVDISVSKPGKHGGAKARVVGIGIFEKVKKEFVAPTSSKVEV 72
Query: 84 PHVTRTDYQLIDISED 99
P + R Q++ I D
Sbjct: 73 PIIDRRKGQVLAIMGD 88
>pdb|1EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 135
Score = 65.5 bits (158), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 46/76 (60%)
Query: 24 AGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDV 83
G+++ Y++I G PC++V++S SK GKHG AK VGI IF K E + P+S +V
Sbjct: 12 VGSLKVGQYVMIDGVPCEIVDISVSKPGKHGGAKARVVGIGIFEKVKKEFVAPTSSKVEV 71
Query: 84 PHVTRTDYQLIDISED 99
P + R Q++ I D
Sbjct: 72 PIIDRRKGQVLAIMGD 87
>pdb|1IZ6|A Chain A, Crystal Structure Of Translation Initiation Factor 5a From
Pyrococcus Horikoshii
pdb|1IZ6|B Chain B, Crystal Structure Of Translation Initiation Factor 5a From
Pyrococcus Horikoshii
pdb|1IZ6|C Chain C, Crystal Structure Of Translation Initiation Factor 5a From
Pyrococcus Horikoshii
Length = 138
Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 48/94 (51%), Gaps = 4/94 (4%)
Query: 23 QAGTIRKNGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82
Q ++ YI+I PC++V ++ S GKHG AK + IF+GK + P+S D
Sbjct: 8 QVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVD 67
Query: 83 VPHVTRTDYQLIDISEDGFVCSYFVLSCSFYLSF 116
VP + + Q+I I+ D + ++ Y +F
Sbjct: 68 VPIIDKKTAQVIAITPD----TVQIMDMETYETF 97
>pdb|1KHI|A Chain A, Crystal Structure Of Hex1
Length = 176
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 17/83 (20%)
Query: 3 DEEHHFESKADAGASKTFPQQAGT-----------IRKNGYIVIKGRPCKVVEVSTS-KT 50
D++ H +ADA T G+ IR ++++GRPC+V+ +STS T
Sbjct: 5 DDDAHGHVEADAAPRATTGTGTGSASQTVTIPCHHIRLGDILILQGRPCQVIRISTSAAT 64
Query: 51 GKHGHAKCHFVGIDIFNGKKLED 73
G+H ++G+D+F + E+
Sbjct: 65 GQH-----RYLGVDLFTKQLHEE 82
>pdb|1PEX|A Chain A, Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain
Length = 207
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 30 NGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVGID---IFNGKKLEDIVPSSH--NCDVP 84
NGY +++G P K+ E+ K K A HF +F+G ++ ++H + D P
Sbjct: 94 NGYDILEGYPKKISELGLPKEVKKISAAVHFEDTGKTLLFSGNQVWRYDDTNHIMDKDYP 153
Query: 85 HVTRTDY 91
+ D+
Sbjct: 154 RLIEEDF 160
>pdb|3T79|A Chain A, Ndc10: A Platform For Inner Kinetochore Assembly In
Budding Yeast
pdb|3T79|D Chain D, Ndc10: A Platform For Inner Kinetochore Assembly In
Budding Yeast
Length = 402
Score = 27.3 bits (59), Expect = 2.4, Method: Composition-based stats.
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 81 CDVPHVTRTDYQLIDISEDGFVCSYFVLSCSFYLSF 116
C + H ++ ++ L+ + F C F ++ +YL F
Sbjct: 175 CGLAHSSKPNFVLVPNFQSPFTCPIFTMAVYYYLRF 210
>pdb|3SQI|A Chain A, Dna Binding Domain Of Ndc10
Length = 534
Score = 27.3 bits (59), Expect = 2.4, Method: Composition-based stats.
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 81 CDVPHVTRTDYQLIDISEDGFVCSYFVLSCSFYLSF 116
C + H ++ ++ L+ + F C F ++ +YL F
Sbjct: 175 CGLAHSSKPNFVLVPNFQSPFTCPIFTMAVYYYLRF 210
>pdb|1VKN|A Chain A, Crystal Structure Of N-Acetyl-Gamma-Glutamyl-Phosphate
Reductase (Tm1782) From Thermotoga Maritima At 1.80 A
Resolution
pdb|1VKN|B Chain B, Crystal Structure Of N-Acetyl-Gamma-Glutamyl-Phosphate
Reductase (Tm1782) From Thermotoga Maritima At 1.80 A
Resolution
pdb|1VKN|C Chain C, Crystal Structure Of N-Acetyl-Gamma-Glutamyl-Phosphate
Reductase (Tm1782) From Thermotoga Maritima At 1.80 A
Resolution
pdb|1VKN|D Chain D, Crystal Structure Of N-Acetyl-Gamma-Glutamyl-Phosphate
Reductase (Tm1782) From Thermotoga Maritima At 1.80 A
Resolution
Length = 351
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 15/46 (32%)
Query: 53 HGHAKCHFVGIDIFNGKKLEDIVPS---------------SHNCDV 83
H AK ++ + GKKLE+I PS S NCDV
Sbjct: 36 HPEAKITYLSSRTYAGKKLEEIFPSTLENSILSEFDPEKVSKNCDV 81
>pdb|3E0D|A Chain A, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase
Iii Alpha-Subunit
pdb|3E0D|B Chain B, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase
Iii Alpha-Subunit
Length = 1220
Score = 25.8 bits (55), Expect = 5.8, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 41 KVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTD 90
+V+EV+ G + HA H G+ + + L D+VP + + VT+ D
Sbjct: 557 QVIEVAMRLEGLNRHASVHAAGV-VIAAEPLTDLVPLMRDQEGRPVTQYD 605
>pdb|2HPI|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-Ray Structure Of Dna Polymerase Iii
pdb|2HPM|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-ray Structure Of Dna Polymerase Iii
Length = 1220
Score = 25.8 bits (55), Expect = 5.8, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 41 KVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDVPHVTRTD 90
+V+EV+ G + HA H G+ + + L D+VP + + VT+ D
Sbjct: 557 QVIEVAMRLEGLNRHASVHAAGV-VIAAEPLTDLVPLMRDQEGRPVTQYD 605
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.137 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,822,009
Number of Sequences: 62578
Number of extensions: 142434
Number of successful extensions: 241
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 224
Number of HSP's gapped (non-prelim): 17
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)