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= 031387
(160 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 = 247 bits (630), Expect = 2e-66, Method: Compositional matrix adjust.
Identities = 116/150 (77%), Positives = 135/150 (90%), Gaps = 1/150 (0%)
Query: 8 FESKADAGASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFN 67
FE+ +++GASKT+PQ AG IRK G+IVIKNRPCKVVEVSTSKTGKHGHAKCHFV IDIF
Sbjct: 16 FEA-SESGASKTYPQSAGNIRKGGHIVIKNRPCKVVEVSTSKTGKHGHAKCHFVAIDIFT 74
Query: 68 GKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQI 127
KKLEDIVPSSHNCD PHV R DYQLIDI+EDGFVSLLT++G TKDDL+LPTD+ L +Q+
Sbjct: 75 AKKLEDIVPSSHNCDVPHVNRVDYQLIDITEDGFVSLLTDSGGTKDDLKLPTDDGLTAQM 134
Query: 128 KDGFAEGKDLVVTVMSSMGEEQICALKDIG 157
+ GF EGKD+VV+VMSSMGEEQICA+K++G
Sbjct: 135 RLGFDEGKDIVVSVMSSMGEEQICAVKEVG 164
>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 = 189 bits (479), Expect = 7e-49, Method: Compositional matrix adjust.
Identities = 91/155 (58%), Positives = 120/155 (77%), Gaps = 3/155 (1%)
Query: 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHF 60
MSDEEH FE+ ADAG+S T+P Q +RKNG++VIK+RPCK+V++STSKTGKHGHAK H
Sbjct: 11 MSDEEHTFET-ADAGSSATYPMQCSALRKNGFVVIKSRPCKIVDMSTSKTGKHGHAKVHL 69
Query: 61 VGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTD 120
V IDIF GKKLED+ PS+HN + P V R +YQL+DI +DGF+SL+ G+TKDD++ P
Sbjct: 70 VAIDIFTGKKLEDLSPSTHNMEVPVVKRNEYQLLDI-DDGFLSLMNMDGDTKDDVKAPEG 128
Query: 121 ENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKD 155
E L ++ F EGKDL+VT++S+MGEE + K+
Sbjct: 129 E-LGDSLQTAFDEGKDLMVTIISAMGEEAAISFKE 162
>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 = 163 bits (412), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 76/139 (54%), Positives = 106/139 (76%), Gaps = 2/139 (1%)
Query: 16 ASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIV 75
S TFP Q +RKNG++V+K RPCK+VE+STSKTGKHGHAK H VGIDIF GKK EDI
Sbjct: 1 GSATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDIC 60
Query: 76 PSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGK 135
PS+HN D P++ R D+QLI I +DG++SLL ++G ++DLRLP + +L +I+ + G+
Sbjct: 61 PSTHNMDVPNIKRNDFQLIGI-QDGYLSLLQDSGEVREDLRLP-EGDLGKEIEQKYDCGE 118
Query: 136 DLVVTVMSSMGEEQICALK 154
++++TV+S+M EE A+K
Sbjct: 119 EILITVLSAMTEEAAVAIK 137
>pdb|1X6O|A Chain A, Structural Analysis Of Leishmania Braziliensis Eukaryotic
Initiation Factor 5a
Length = 174
Score = 150 bits (378), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 76/166 (45%), Positives = 106/166 (63%), Gaps = 7/166 (4%)
Query: 1 MSDEEHHFESKADA-GASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCH 59
MSDE+H F + ASKT+P AG ++K GY+ I RPCKV+++S SKTGKHGHAK
Sbjct: 9 MSDEDHDFSHQGGGDNASKTYPLAAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVS 68
Query: 60 FVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDI--SED----GFVSLLTETGNTKD 113
V DIF G +LED PS+HN + P V Y ++DI +ED +SL+ + G +++
Sbjct: 69 IVATDIFTGNRLEDQAPSTHNVEVPFVKTYTYSVLDIQANEDPSLPAHLSLMDDEGESRE 128
Query: 114 DLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKDIGPK 159
DL +P D L +QIK+ F GKD++V V+S+MG EQ+ K+ K
Sbjct: 129 DLDMPPDPALATQIKEQFDSGKDVLVVVVSAMGTEQVLQTKNAAEK 174
>pdb|1XTD|A Chain A, Structural Analysis Of Leishmania Mexicana Eukaryotic
Initiation Factor 5a
Length = 174
Score = 139 bits (351), Expect = 6e-34, Method: Compositional matrix adjust.
Identities = 73/165 (44%), Positives = 102/165 (61%), Gaps = 7/165 (4%)
Query: 2 SDEEHHFESKADA-GASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHF 60
SDE+H F + ASKT+P AG ++K GY+ I RPCKV+++S SKTGKHGHAK
Sbjct: 10 SDEDHDFAHQGGGDNASKTYPXAAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSI 69
Query: 61 VGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDI--SED----GFVSLLTETGNTKDD 114
V DIF G +LED PS+HN + P V Y ++DI +ED +SL + G +++D
Sbjct: 70 VATDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPNEDPSLPSHLSLXDDEGESRED 129
Query: 115 LRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKDIGPK 159
L P D L +QIK+ F GK+++V V+S+ G EQ+ K+ K
Sbjct: 130 LDXPPDAALATQIKEQFDSGKEVLVVVVSAXGTEQVLQTKNAAEK 174
>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 = 70.1 bits (170), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 39/132 (29%), Positives = 65/132 (49%), Gaps = 5/132 (3%)
Query: 23 QAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82
Q ++ YI+I + PC++V ++ S GKHG AK + IF+GK + P+S D
Sbjct: 8 QVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVD 67
Query: 83 APHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVM 142
P + + Q+I I+ D + ET T +P D + +I+D EG + V
Sbjct: 68 VPIIDKKTAQVIAITPDTVQIMDMETYET---FEVPIDTGVADEIRDQLKEG--INVEYW 122
Query: 143 SSMGEEQICALK 154
++G +I +K
Sbjct: 123 ETLGRIKIMRIK 134
>pdb|2EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 136
Score = 65.9 bits (159), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 35/100 (35%), Positives = 54/100 (54%), Gaps = 3/100 (3%)
Query: 24 AGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDA 83
G+++ Y++I PC++V++S SK GKHG AK VGI IF K E + P+S +
Sbjct: 13 VGSLKVGQYVMIDGVPCEIVDISVSKPGKHGGAKARVVGIGIFEKVKKEFVAPTSSKVEV 72
Query: 84 PHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENL 123
P + R Q++ I D V ++ T + L LP E +
Sbjct: 73 PIIDRRKGQVLAIMGD-MVQIMDL--QTYETLELPIPEGI 109
>pdb|1EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 135
Score = 65.9 bits (159), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 35/100 (35%), Positives = 54/100 (54%), Gaps = 3/100 (3%)
Query: 24 AGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDA 83
G+++ Y++I PC++V++S SK GKHG AK VGI IF K E + P+S +
Sbjct: 12 VGSLKVGQYVMIDGVPCEIVDISVSKPGKHGGAKARVVGIGIFEKVKKEFVAPTSSKVEV 71
Query: 84 PHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENL 123
P + R Q++ I D V ++ T + L LP E +
Sbjct: 72 PIIDRRKGQVLAIMGD-MVQIMDL--QTYETLELPIPEGI 108
>pdb|1BKB|A Chain A, Initiation Factor 5a From Archebacterium Pyrobaculum
Aerophilum
Length = 136
Score = 65.1 bits (157), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 45/77 (58%)
Query: 23 QAGTIRKNGYIVIKNRPCKVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCD 82
+AG +++ Y+VI PC+VVE+ SKTGKHG AK V + +F+G K +P +
Sbjct: 10 EAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVE 69
Query: 83 APHVTRTDYQLIDISED 99
P + + Q++ +S D
Sbjct: 70 VPIIEKFTAQILSVSGD 86
>pdb|1KHI|A Chain A, Crystal Structure Of Hex1
Length = 176
Score = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 48/172 (27%), Positives = 85/172 (49%), Gaps = 27/172 (15%)
Query: 3 DEEHHFESKADAG-----------ASKTFPQQAGTIRKNGYIVIKNRPCKVVEVSTSK-T 50
D++ H +ADA AS+T IR ++++ RPC+V+ +STS T
Sbjct: 5 DDDAHGHVEADAAPRATTGTGTGSASQTVTIPCHHIRLGDILILQGRPCQVIRISTSAAT 64
Query: 51 GKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRT-------DYQLIDISEDGFVS 103
G+H ++G+D+F K+L + N V +T Y+++D+ +DG +
Sbjct: 65 GQH-----RYLGVDLFT-KQLHEESSFVSNPAPSVVVQTMLGPVFKQYRVLDM-QDGSIV 117
Query: 104 LLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLV-VTVMSSMGEEQICALK 154
+TETG+ K +L + +L ++++ F G+ V V V+S G E +K
Sbjct: 118 AMTETGDVKQNLPVIDQSSLWNRLQKAFESGRGSVRVLVVSDHGREMAVDMK 169
>pdb|3TB6|A Chain A, Structure Of The Effector-binding Domain Of Arabinose
Repressor Arar From Bacillus Subtilis
pdb|3TB6|B Chain B, Structure Of The Effector-binding Domain Of Arabinose
Repressor Arar From Bacillus Subtilis
Length = 298
Score = 30.0 bits (66), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 96 ISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGF 131
+SE G+ LLT T N D+ R ENLLSQ DG
Sbjct: 41 LSEQGYSMLLTSTNNNPDNERRGL-ENLLSQHIDGL 75
>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 = 27.3 bits (59), Expect = 3.8, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 41 KVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTD 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 = 27.3 bits (59), Expect = 3.8, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 41 KVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTD 90
+V+EV+ G + HA H G+ + + L D+VP + + VT+ D
Sbjct: 557 QVIEVAMRLEGLNRHASVHAAGV-VIAAEPLTDLVPLMRDQEGRPVTQYD 605
>pdb|2F59|A Chain A, Lumazine Synthase Ribh1 From Brucella Abortus (gene
Bruab1_0785, Swiss-prot Entry Q57dy1) Complexed With
Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h)
Pyrimidinedione
pdb|2F59|B Chain B, Lumazine Synthase Ribh1 From Brucella Abortus (gene
Bruab1_0785, Swiss-prot Entry Q57dy1) Complexed With
Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h)
Pyrimidinedione
pdb|2F59|C Chain C, Lumazine Synthase Ribh1 From Brucella Abortus (gene
Bruab1_0785, Swiss-prot Entry Q57dy1) Complexed With
Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h)
Pyrimidinedione
pdb|2F59|D Chain D, Lumazine Synthase Ribh1 From Brucella Abortus (gene
Bruab1_0785, Swiss-prot Entry Q57dy1) Complexed With
Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h)
Pyrimidinedione
pdb|2F59|E Chain E, Lumazine Synthase Ribh1 From Brucella Abortus (gene
Bruab1_0785, Swiss-prot Entry Q57dy1) Complexed With
Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h)
Pyrimidinedione
pdb|2I0F|A Chain A, Lumazine Synthase Ribh1 From Brucella Abortus (gene
Bruab1_0785, Swiss-prot Entry Q57dy1)
pdb|2I0F|B Chain B, Lumazine Synthase Ribh1 From Brucella Abortus (gene
Bruab1_0785, Swiss-prot Entry Q57dy1)
pdb|2I0F|C Chain C, Lumazine Synthase Ribh1 From Brucella Abortus (gene
Bruab1_0785, Swiss-prot Entry Q57dy1)
pdb|2I0F|D Chain D, Lumazine Synthase Ribh1 From Brucella Abortus (gene
Bruab1_0785, Swiss-prot Entry Q57dy1)
pdb|2I0F|E Chain E, Lumazine Synthase Ribh1 From Brucella Abortus (gene
Bruab1_0785, Swiss-prot Entry Q57dy1)
Length = 157
Score = 26.6 bits (57), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 73 DIVPSSHNCDAPHVTRTDYQ----LIDISEDGFVSLLTETGNTKDDLRLP 118
+ + S H DAPH+ + + L D DG + L E G T D + +P
Sbjct: 2 EFLMSKHEADAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVP 51
>pdb|2O6H|A Chain A, Lumazine Synthase Ribh1 From Brucella Melitensis (gene
Bmei1187, Swiss-prot Entry Q8ygh2) Complexed With
Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h)
Pyrimidinedione
pdb|2O6H|B Chain B, Lumazine Synthase Ribh1 From Brucella Melitensis (gene
Bmei1187, Swiss-prot Entry Q8ygh2) Complexed With
Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h)
Pyrimidinedione
pdb|2O6H|C Chain C, Lumazine Synthase Ribh1 From Brucella Melitensis (gene
Bmei1187, Swiss-prot Entry Q8ygh2) Complexed With
Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h)
Pyrimidinedione
pdb|2O6H|D Chain D, Lumazine Synthase Ribh1 From Brucella Melitensis (gene
Bmei1187, Swiss-prot Entry Q8ygh2) Complexed With
Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h)
Pyrimidinedione
pdb|2O6H|E Chain E, Lumazine Synthase Ribh1 From Brucella Melitensis (gene
Bmei1187, Swiss-prot Entry Q8ygh2) Complexed With
Inhibitor 5-nitro-6-(d- Ribitylamino)-2,4(1h,3h)
Pyrimidinedione
Length = 157
Score = 26.6 bits (57), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 73 DIVPSSHNCDAPHVTRTDYQ----LIDISEDGFVSLLTETGNTKDDLRLP 118
+ + S H DAPH+ + + L D DG + L E G T D + +P
Sbjct: 2 EFLMSKHEADAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVP 51
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
0.314 0.133 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,108,361
Number of Sequences: 62578
Number of extensions: 203465
Number of successful extensions: 335
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 316
Number of HSP's gapped (non-prelim): 18
length of query: 160
length of database: 14,973,337
effective HSP length: 91
effective length of query: 69
effective length of database: 9,278,739
effective search space: 640232991
effective search space used: 640232991
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)