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= 030552
(175 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 = 237 bits (604), Expect = 3e-63, Method: Compositional matrix adjust.
Identities = 116/165 (70%), Positives = 135/165 (81%), Gaps = 16/165 (9%)
Query: 8 FESKADAGASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGK 67
FE+ +++GASKT+PQ AG IRK G+IVIKNRPCK VVEVSTSKTGK
Sbjct: 16 FEA-SESGASKTYPQSAGNIRKGGHIVIKNRPCK---------------VVEVSTSKTGK 59
Query: 68 HGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTK 127
HGHAKCHFV IDIF KKLEDIVPSSHNCD PHV R DYQLIDI+EDGFVSLLT++G TK
Sbjct: 60 HGHAKCHFVAIDIFTAKKLEDIVPSSHNCDVPHVNRVDYQLIDITEDGFVSLLTDSGGTK 119
Query: 128 DDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKDIG 172
DDL+LPTD+ L +Q++ GF EGKD+VV+VMSSMGEEQICA+K++G
Sbjct: 120 DDLKLPTDDGLTAQMRLGFDEGKDIVVSVMSSMGEEQICAVKEVG 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 = 179 bits (454), Expect = 8e-46, Method: Compositional matrix adjust.
Identities = 91/170 (53%), Positives = 120/170 (70%), Gaps = 18/170 (10%)
Query: 1 MSDEEHHFESKADAGASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEV 60
MSDEEH FE+ ADAG+S T+P Q +RKNG++VIK+RPCK +V++
Sbjct: 11 MSDEEHTFET-ADAGSSATYPMQCSALRKNGFVVIKSRPCK---------------IVDM 54
Query: 61 STSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLL 120
STSKTGKHGHAK H V IDIF GKKLED+ PS+HN + P V R +YQL+DI +DGF+SL+
Sbjct: 55 STSKTGKHGHAKVHLVAIDIFTGKKLEDLSPSTHNMEVPVVKRNEYQLLDI-DDGFLSLM 113
Query: 121 TETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKD 170
G+TKDD++ P E L ++ F EGKDL+VT++S+MGEE + K+
Sbjct: 114 NMDGDTKDDVKAPEGE-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 = 153 bits (386), Expect = 5e-38, Method: Compositional matrix adjust.
Identities = 76/154 (49%), Positives = 106/154 (68%), Gaps = 17/154 (11%)
Query: 16 ASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHF 75
S TFP Q +RKNG++V+K RPCK +VE+STSKTGKHGHAK H
Sbjct: 1 GSATFPMQCSALRKNGFVVLKGRPCK---------------IVEMSTSKTGKHGHAKVHL 45
Query: 76 VGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTD 135
VGIDIF GKK EDI PS+HN D P++ R D+QLI I +DG++SLL ++G ++DLRLP +
Sbjct: 46 VGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGI-QDGYLSLLQDSGEVREDLRLP-E 103
Query: 136 ENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALK 169
+L +I+ + G+++++TV+S+M EE A+K
Sbjct: 104 GDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIK 137
>pdb|1X6O|A Chain A, Structural Analysis Of Leishmania Braziliensis Eukaryotic
Initiation Factor 5a
Length = 174
Score = 140 bits (352), Expect = 5e-34, Method: Compositional matrix adjust.
Identities = 76/181 (41%), Positives = 106/181 (58%), Gaps = 22/181 (12%)
Query: 1 MSDEEHHFESKADA-GASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVE 59
MSDE+H F + ASKT+P AG ++K GY+ I RPCK V++
Sbjct: 9 MSDEDHDFSHQGGGDNASKTYPLAAGALKKGGYVCINGRPCK---------------VID 53
Query: 60 VSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDI--SED--- 114
+S SKTGKHGHAK V DIF G +LED PS+HN + P V Y ++DI +ED
Sbjct: 54 LSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEVPFVKTYTYSVLDIQANEDPSL 113
Query: 115 -GFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKDIGP 173
+SL+ + G +++DL +P D L +QIK+ F GKD++V V+S+MG EQ+ K+
Sbjct: 114 PAHLSLMDDEGESREDLDMPPDPALATQIKEQFDSGKDVLVVVVSAMGTEQVLQTKNAAE 173
Query: 174 K 174
K
Sbjct: 174 K 174
>pdb|1XTD|A Chain A, Structural Analysis Of Leishmania Mexicana Eukaryotic
Initiation Factor 5a
Length = 174
Score = 129 bits (325), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 73/180 (40%), Positives = 102/180 (56%), Gaps = 22/180 (12%)
Query: 2 SDEEHHFESKADA-GASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEV 60
SDE+H F + ASKT+P AG ++K GY+ I RPCK V+++
Sbjct: 10 SDEDHDFAHQGGGDNASKTYPXAAGALKKGGYVCINGRPCK---------------VIDL 54
Query: 61 STSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTDYQLIDI--SED---- 114
S SKTGKHGHAK V DIF G +LED PS+HN + P V Y ++DI +ED
Sbjct: 55 SVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEVPFVKTFTYSVLDIQPNEDPSLP 114
Query: 115 GFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLVVTVMSSMGEEQICALKDIGPK 174
+SL + G +++DL P D L +QIK+ F GK+++V V+S+ G EQ+ K+ K
Sbjct: 115 SHLSLXDDEGESREDLDXPPDAALATQIKEQFDSGKEVLVVVVSAXGTEQVLQTKNAAEK 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 = 59.7 bits (143), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 39/147 (26%), Positives = 65/147 (44%), Gaps = 20/147 (13%)
Query: 23 QAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFN 82
Q ++ YI+I + PC+ +V ++ S GKHG AK + IF+
Sbjct: 8 QVSKLKPGRYIIIDDEPCR---------------IVNITVSSPGKHGSAKARIEAVGIFD 52
Query: 83 GKKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQI 142
GK + P+S D P + + Q+I I+ D + ET T +P D + +I
Sbjct: 53 GKVRSIVKPTSAEVDVPIIDKKTAQVIAITPDTVQIMDMETYET---FEVPIDTGVADEI 109
Query: 143 KDGFAEGKDLVVTVMSSMGEEQICALK 169
+D EG + V ++G +I +K
Sbjct: 110 RDQLKEG--INVEYWETLGRIKIMRIK 134
>pdb|2EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 136
Score = 56.2 bits (134), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 35/115 (30%), Positives = 54/115 (46%), Gaps = 18/115 (15%)
Query: 24 AGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNG 83
G+++ Y++I PC ++V++S SK GKHG AK VGI IF
Sbjct: 13 VGSLKVGQYVMIDGVPC---------------EIVDISVSKPGKHGGAKARVVGIGIFEK 57
Query: 84 KKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENL 138
K E + P+S + P + R Q++ I D V ++ T + L LP E +
Sbjct: 58 VKKEFVAPTSSKVEVPIIDRRKGQVLAIMGD-MVQIMDL--QTYETLELPIPEGI 109
>pdb|1EIF|A Chain A, Eukaryotic Translation Initiation Factor 5a From
Methanococcus Jannaschii
Length = 135
Score = 56.2 bits (134), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 35/115 (30%), Positives = 54/115 (46%), Gaps = 18/115 (15%)
Query: 24 AGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFNG 83
G+++ Y++I PC ++V++S SK GKHG AK VGI IF
Sbjct: 12 VGSLKVGQYVMIDGVPC---------------EIVDISVSKPGKHGGAKARVVGIGIFEK 56
Query: 84 KKLEDIVPSSHNCDAPHVTRTDYQLIDISEDGFVSLLTETGNTKDDLRLPTDENL 138
K E + P+S + P + R Q++ I D V ++ T + L LP E +
Sbjct: 57 VKKEFVAPTSSKVEVPIIDRRKGQVLAIMGD-MVQIMDL--QTYETLELPIPEGI 108
>pdb|1BKB|A Chain A, Initiation Factor 5a From Archebacterium Pyrobaculum
Aerophilum
Length = 136
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 45/92 (48%), Gaps = 15/92 (16%)
Query: 23 QAGTIRKNGYIVIKNRPCKPQVFKFPSFSLHSKQVVEVSTSKTGKHGHAKCHFVGIDIFN 82
+AG +++ Y+VI PC+ VVE+ SKTGKHG AK V + +F+
Sbjct: 10 EAGELKEGSYVVIDGEPCR---------------VVEIEKSKTGKHGSAKARIVAVGVFD 54
Query: 83 GKKLEDIVPSSHNCDAPHVTRTDYQLIDISED 114
G K +P + P + + Q++ +S D
Sbjct: 55 GGKRTLSLPVDAQVEVPIIEKFTAQILSVSGD 86
>pdb|1KHI|A Chain A, Crystal Structure Of Hex1
Length = 176
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 49/187 (26%), Positives = 85/187 (45%), Gaps = 42/187 (22%)
Query: 3 DEEHHFESKADAG-----------ASKTFPQQAGTIRKNGYIVIKNRPCKPQVFKFPSFS 51
D++ H +ADA AS+T IR ++++ RPC
Sbjct: 5 DDDAHGHVEADAAPRATTGTGTGSASQTVTIPCHHIRLGDILILQGRPC----------- 53
Query: 52 LHSKQVVEVSTSK-TGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRT------ 104
QV+ +STS TG+H ++G+D+F K+L + N V +T
Sbjct: 54 ----QVIRISTSAATGQH-----RYLGVDLFT-KQLHEESSFVSNPAPSVVVQTMLGPVF 103
Query: 105 -DYQLIDISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGFAEGKDLV-VTVMSSMGE 162
Y+++D+ +DG + +TETG+ K +L + +L ++++ F G+ V V V+S G
Sbjct: 104 KQYRVLDM-QDGSIVAMTETGDVKQNLPVIDQSSLWNRLQKAFESGRGSVRVLVVSDHGR 162
Query: 163 EQICALK 169
E +K
Sbjct: 163 EMAVDMK 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 = 0.70, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 111 ISEDGFVSLLTETGNTKDDLRLPTDENLLSQIKDGF 146
+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 = 30.0 bits (66), Expect = 0.76, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 55 KQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTD 105
+QV+EV+ G + HA H G+ + + L D+VP + + VT+ D
Sbjct: 556 RQVIEVAMRLEGLNRHASVHAAGV-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 = 30.0 bits (66), Expect = 0.76, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 55 KQVVEVSTSKTGKHGHAKCHFVGIDIFNGKKLEDIVPSSHNCDAPHVTRTD 105
+QV+EV+ G + HA H G+ + + L D+VP + + VT+ D
Sbjct: 556 RQVIEVAMRLEGLNRHASVHAAGV-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 = 8.4, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 88 DIVPSSHNCDAPHVTRTDYQ----LIDISEDGFVSLLTETGNTKDDLRLP 133
+ + 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 = 8.8, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 88 DIVPSSHNCDAPHVTRTDYQ----LIDISEDGFVSLLTETGNTKDDLRLP 133
+ + 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
0.315 0.133 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,548,527
Number of Sequences: 62578
Number of extensions: 220914
Number of successful extensions: 380
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 356
Number of HSP's gapped (non-prelim): 16
length of query: 175
length of database: 14,973,337
effective HSP length: 92
effective length of query: 83
effective length of database: 9,216,161
effective search space: 764941363
effective search space used: 764941363
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)