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= 038122
(130 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4HTG|A Chain A, Porphobilinogen Deaminase From Arabidopsis Thaliana
Length = 320
Score = 177 bits (448), Expect = 2e-45, Method: Compositional matrix adjust.
Identities = 99/177 (55%), Positives = 109/177 (61%), Gaps = 48/177 (27%)
Query: 2 EEALINGEIDIAVHSMKDVPTYLLDKTILPCNLQRE------------------------ 37
+EALING IDIAVHSMKDVPTYL +KTILPCNL RE
Sbjct: 78 DEALINGHIDIAVHSMKDVPTYLPEKTILPCNLPREDVRDAFICLTAATLAELPAGSVVG 137
Query: 38 ------------------------GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVTN 73
GNVQ RL KL G +QATL ALAGLK L+MTENV +
Sbjct: 138 TASLRRKSQILHKYPALHVEENFRGNVQTRLSKLQGGKVQATLLALAGLKRLSMTENVAS 197
Query: 74 ILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVVCERAFLGTLDGSC 130
IL +D+ML AVAQGAIGIAC ++D KMA YL SLNHEETR A+ CERAFL TLDGSC
Sbjct: 198 ILSLDEMLPAVAQGAIGIACRTDDDKMATYLASLNHEETRLAISCERAFLETLDGSC 254
>pdb|1PDA|A Chain A, Structure Of Porphobilinogen Deaminase Reveals A Flexible
Multidomain Polymerase With A Single Catalytic Site
Length = 313
Score = 76.3 bits (186), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 60/178 (33%), Positives = 77/178 (43%), Gaps = 51/178 (28%)
Query: 2 EEALINGEIDIAVHSMKDVPTYL--------------------------LDKTILPC--- 32
E AL+ DIAVHSMKDVP LD LP
Sbjct: 67 EVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDA--LPAGSI 124
Query: 33 ----NLQRE----------------GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVT 72
+L+R+ GNV RL KL+ G A + A+AGLK L + +
Sbjct: 125 VGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIR 184
Query: 73 NILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVVCERAFLGTLDGSC 130
LP + L AV QGA+GI C +D + + L +LNH ET V ERA L+G+C
Sbjct: 185 AALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGAC 242
>pdb|2YPN|A Chain A, Hydroxymethylbilane Synthase
pdb|1GTK|A Chain A, Time-Resolved And Static-Ensemble Structural Chemistry Of
Hydroxymethylbilane Synthase
Length = 313
Score = 75.9 bits (185), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 60/178 (33%), Positives = 76/178 (42%), Gaps = 51/178 (28%)
Query: 2 EEALINGEIDIAVHSMKDVPTYL--------------------------LDKTILPC--- 32
E AL+ DIAVHSMKDVP LD LP
Sbjct: 67 EVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDA--LPAGSI 124
Query: 33 ----NLQRE----------------GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVT 72
+L+R+ GNV RL KL+ G A + A+AGLK L + +
Sbjct: 125 VGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIR 184
Query: 73 NILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVVCERAFLGTLDGSC 130
LP + L AV QGA+GI C +D + + L +LNH ET V ERA L+G C
Sbjct: 185 AALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGGC 242
>pdb|1YPN|A Chain A, Reduced Form Hydroxymethylbilane Synthase (K59q Mutant)
Crystal Structure After 2 Hours In A Flow Cell
Determined By Time-Resolved Laue Diffraction
Length = 313
Score = 75.9 bits (185), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 60/178 (33%), Positives = 76/178 (42%), Gaps = 51/178 (28%)
Query: 2 EEALINGEIDIAVHSMKDVPTYL--------------------------LDKTILPC--- 32
E AL+ DIAVHSMKDVP LD LP
Sbjct: 67 EVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDA--LPAGSI 124
Query: 33 ----NLQRE----------------GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVT 72
+L+R+ GNV RL KL+ G A + A+AGLK L + +
Sbjct: 125 VGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIR 184
Query: 73 NILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVVCERAFLGTLDGSC 130
LP + L AV QGA+GI C +D + + L +LNH ET V ERA L+G C
Sbjct: 185 AALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGGC 242
>pdb|1AH5|A Chain A, Reduced Form Selenomethionine-Labelled Hydroxymethylbilane
Synthase Determined By Mad
Length = 313
Score = 72.4 bits (176), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 59/178 (33%), Positives = 75/178 (42%), Gaps = 51/178 (28%)
Query: 2 EEALINGEIDIAVHSMKDVPTYL--------------------------LDKTILPC--- 32
E AL+ DIAVHS KDVP LD LP
Sbjct: 67 EVALLENRADIAVHSXKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDA--LPAGSI 124
Query: 33 ----NLQRE----------------GNVQARLRKLNEGVIQATLSALAGLKCLNMTENVT 72
+L+R+ GNV RL KL+ G A + A+AGLK L + +
Sbjct: 125 VGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIR 184
Query: 73 NILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVVCERAFLGTLDGSC 130
LP + L AV QGA+GI C +D + + L +LNH ET V ERA L+G C
Sbjct: 185 AALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAXNTRLEGGC 242
>pdb|3EQ1|A Chain A, The Crystal Structure Of Human Porphobilinogen Deaminase
At 2.8a Resolution
pdb|3EQ1|B Chain B, The Crystal Structure Of Human Porphobilinogen Deaminase
At 2.8a Resolution
Length = 361
Score = 66.6 bits (161), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 55/180 (30%), Positives = 79/180 (43%), Gaps = 51/180 (28%)
Query: 2 EEALINGEIDIAVHSMKDVPTYL-------------------------LDKTI--LP--- 31
E AL E+D+ VHS+KD+PT L + KT+ LP
Sbjct: 82 EHALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEKS 141
Query: 32 ----------CNLQR----------EGNVQARLRKLNEGV-IQATLSALAGLKCLNMTEN 70
LQR +GN+ RLRKL+E A + A AGL+ +
Sbjct: 142 VVGTSSLRRAAQLQRKFPHLEFRSIQGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNR 201
Query: 71 VTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVVCERAFLGTLDGSC 130
V IL ++ + AV QGA+G+ + D+ + +G L+ ET + ERAFL L+G C
Sbjct: 202 VGQILHPEECMYAVGQGALGVEVRAKDQDILDLVGVLHDPETLLRCIAERAFLRHLEGGC 261
>pdb|3ECR|A Chain A, Structure Of Human Porphobilinogen Deaminase
pdb|3ECR|B Chain B, Structure Of Human Porphobilinogen Deaminase
Length = 364
Score = 65.9 bits (159), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 55/180 (30%), Positives = 79/180 (43%), Gaps = 51/180 (28%)
Query: 2 EEALINGEIDIAVHSMKDVPTYL-------------------------LDKTI--LP--- 31
E AL E+D+ VHS+KD+PT L + KT+ LP
Sbjct: 85 EHALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEKS 144
Query: 32 ----------CNLQRE----------GNVQARLRKLNEGV-IQATLSALAGLKCLNMTEN 70
LQR+ GN+ RLRKL+E A + A AGL+ +
Sbjct: 145 VVGTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNR 204
Query: 71 VTNILPIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVVCERAFLGTLDGSC 130
V IL ++ + AV QGA+G+ + D+ + +G L+ ET + ERAFL L+G C
Sbjct: 205 VGQILHPEECMYAVGQGALGVEVRAKDQDILDLVGVLHDPETLLRCIAERAFLRHLEGGC 264
>pdb|3UDW|C Chain C, Crystal Structure Of The Immunoreceptor Tigit In Complex
With Poliovirus Receptor (PvrCD155NECL-5) D1 Domain
pdb|3UDW|D Chain D, Crystal Structure Of The Immunoreceptor Tigit In Complex
With Poliovirus Receptor (PvrCD155NECL-5) D1 Domain
Length = 118
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 11 DIAVHSMKDVPTYLLDKTILPCNLQ 35
D+ V + VP +L D LPC LQ
Sbjct: 1 DVVVQAPTQVPGFLGDSVTLPCYLQ 25
>pdb|1DGI|R Chain R, Cryo-Em Structure Of Human Poliovirus(Serotype
1)complexed With Three Domain Cd155
pdb|1NN8|R Chain R, Cryoem Structure Of Poliovirus Receptor Bound To
Poliovirus
pdb|1NN8|S Chain S, Cryoem Structure Of Poliovirus Receptor Bound To
Poliovirus
pdb|1NN8|T Chain T, Cryoem Structure Of Poliovirus Receptor Bound To
Poliovirus
Length = 302
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 11 DIAVHSMKDVPTYLLDKTILPCNLQ 35
D+ V + VP +L D LPC LQ
Sbjct: 1 DVVVQAPTQVPGFLGDSVTLPCYLQ 25
>pdb|4FQP|A Chain A, Crystal Structure Of Human Nectin-Like 5 Full Ectodomain
(D1-D3)
Length = 313
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 11 DIAVHSMKDVPTYLLDKTILPCNLQ 35
D+ V + VP +L D LPC LQ
Sbjct: 1 DVVVQAPTQVPGFLGDSVTLPCYLQ 25
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 65 LNMTE-NVTNIL-PIDDMLLAVAQGAIGIACTSNDKKMAKYLGSLNHEETRQAVVCERAF 122
N+TE NV L P+ + + + + A G +K ++ N EE +QA+ C R +
Sbjct: 20 FNVTEKNVMEFLAPLKPVAIRIVRNAHG------NKTGYIFVDFSNEEEVKQALKCNREY 73
Query: 123 LG 124
+G
Sbjct: 74 MG 75
>pdb|3J0C|A Chain A, Models Of E1, E2 And Cp Of Venezuelan Equine Encephalitis
Virus Tc-83 Strain Restrained By A Near Atomic
Resolution Cryo-Em Map
pdb|3J0C|D Chain D, Models Of E1, E2 And Cp Of Venezuelan Equine Encephalitis
Virus Tc-83 Strain Restrained By A Near Atomic
Resolution Cryo-Em Map
pdb|3J0C|G Chain G, Models Of E1, E2 And Cp Of Venezuelan Equine Encephalitis
Virus Tc-83 Strain Restrained By A Near Atomic
Resolution Cryo-Em Map
pdb|3J0C|J Chain J, Models Of E1, E2 And Cp Of Venezuelan Equine Encephalitis
Virus Tc-83 Strain Restrained By A Near Atomic
Resolution Cryo-Em Map
Length = 442
Score = 25.4 bits (54), Expect = 8.3, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 29/67 (43%)
Query: 41 QARLRKLNEGVIQATLSALAGLKCLNMTENVTNILPIDDMLLAVAQGAIGIACTSNDKKM 100
A K + +QA L+ G + T V P++ + + G + A T D+K+
Sbjct: 118 HAEAYKAHTASVQAFLNITVGEHSIVTTVYVNGETPVNFNGVKITAGPLSTAWTPFDRKI 177
Query: 101 AKYLGSL 107
+Y G +
Sbjct: 178 VQYAGEI 184
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
0.318 0.134 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,350,095
Number of Sequences: 62578
Number of extensions: 111690
Number of successful extensions: 348
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 328
Number of HSP's gapped (non-prelim): 19
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)