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= psy2632
(374 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KGD|A Chain A, Crystal Structure Of E. Coli Rna 3' Cyclase
pdb|3KGD|B Chain B, Crystal Structure Of E. Coli Rna 3' Cyclase
pdb|3KGD|C Chain C, Crystal Structure Of E. Coli Rna 3' Cyclase
pdb|3KGD|D Chain D, Crystal Structure Of E. Coli Rna 3' Cyclase
Length = 358
Score = 168 bits (426), Expect = 4e-42, Method: Compositional matrix adjust.
Identities = 109/343 (31%), Positives = 167/343 (48%), Gaps = 22/343 (6%)
Query: 10 VLNIDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQ 69
++ +DG+ EGGGQILR A+ S + +P + +IRAGR KPGL QHL + A +IC
Sbjct: 24 MIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICG 83
Query: 70 GRLENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGG 129
+E A +GS ++F PG + G++ +AGS TL++Q LP L F+ G S++ V GG
Sbjct: 84 ATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGG 143
Query: 130 TNADMAPPIDYYIHLWRPVFCHFFNFNIDIHD----VRRGFFPKGGGEVNVDVTPVQYIR 185
T+ APP D+ + P+ I IH +R GF+P GGG V +V+PV
Sbjct: 144 TDNPSAPPADFIRRVLEPLLA-----KIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFN 198
Query: 186 PIELTQRGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSD 245
++L +RG + + G +AG + +A+ L S+ + + + L D
Sbjct: 199 TLQLGERGNIVQMRGEVLLAG-----VPRHVAEREIATLAGSFSLHEQNI----HNLPRD 249
Query: 246 KAIGNGSGVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQD 305
+ GN + + + T + G R S KE+ L E+ D
Sbjct: 250 QGPGNTVSLEVESENITERFF---VVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLAD 306
Query: 306 QLIVMMALAKGTSRVRVGQISLHTRTAIHIAELMTSAKFNIIE 348
QL++ MALA G V S H T I + E +F++IE
Sbjct: 307 QLVLPMALA-GAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIE 348
>pdb|1QMH|A Chain A, Crystal Structure Of Rna 3'-Terminal Phosphate Cyclase, An
Ubiquitous Enzyme With Unusual Topology
pdb|1QMH|B Chain B, Crystal Structure Of Rna 3'-Terminal Phosphate Cyclase, An
Ubiquitous Enzyme With Unusual Topology
Length = 347
Score = 168 bits (426), Expect = 4e-42, Method: Compositional matrix adjust.
Identities = 109/343 (31%), Positives = 167/343 (48%), Gaps = 22/343 (6%)
Query: 10 VLNIDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQ 69
++ +DG+ EGGGQILR A+ S + +P + +IRAGR KPGL QHL + A +IC
Sbjct: 5 MIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICG 64
Query: 70 GRLENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGG 129
+E A +GS ++F PG + G++ +AGS TL++Q LP L F+ G S++ V GG
Sbjct: 65 ATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGG 124
Query: 130 TNADMAPPIDYYIHLWRPVFCHFFNFNIDIHD----VRRGFFPKGGGEVNVDVTPVQYIR 185
T+ APP D+ + P+ I IH +R GF+P GGG V +V+PV
Sbjct: 125 TDNPSAPPADFIRRVLEPLLA-----KIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFN 179
Query: 186 PIELTQRGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSD 245
++L +RG + + G +AG + +A+ L S+ + + + L D
Sbjct: 180 TLQLGERGNIVQMRGEVLLAG-----VPRHVAEREIATLAGSFSLHEQNI----HNLPRD 230
Query: 246 KAIGNGSGVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQD 305
+ GN + + + T + G R S KE+ L E+ D
Sbjct: 231 QGPGNTVSLEVESENITERFF---VVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLAD 287
Query: 306 QLIVMMALAKGTSRVRVGQISLHTRTAIHIAELMTSAKFNIIE 348
QL++ MALA G V S H T I + E +F++IE
Sbjct: 288 QLVLPMALA-GAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIE 329
>pdb|1QMI|A Chain A, Crystal Structure Of Rna 3'-Terminal Phosphate Cyclase, An
Ubiquitous Enzyme With Unusual Topology
pdb|1QMI|B Chain B, Crystal Structure Of Rna 3'-Terminal Phosphate Cyclase, An
Ubiquitous Enzyme With Unusual Topology
pdb|1QMI|C Chain C, Crystal Structure Of Rna 3'-Terminal Phosphate Cyclase, An
Ubiquitous Enzyme With Unusual Topology
pdb|1QMI|D Chain D, Crystal Structure Of Rna 3'-Terminal Phosphate Cyclase, An
Ubiquitous Enzyme With Unusual Topology
Length = 347
Score = 166 bits (419), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 108/342 (31%), Positives = 164/342 (47%), Gaps = 22/342 (6%)
Query: 11 LNIDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQG 70
+ +DG+ EGGGQILR A+ S + +P + +IRAGR KPGL QHL + A +IC
Sbjct: 6 IALDGAQGEGGGQILRSALSLSXITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICGA 65
Query: 71 RLENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGGT 130
+E A +GS ++F PG + G++ +AGS TL++Q LP L F+ G S++ V GGT
Sbjct: 66 TVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGGT 125
Query: 131 NADMAPPIDYYIHLWRPVFCHFFNFNIDIHD----VRRGFFPKGGGEVNVDVTPVQYIRP 186
+ APP D+ + P+ I IH +R GF+P GGG V +V+PV
Sbjct: 126 DNPSAPPADFIRRVLEPLLA-----KIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFNT 180
Query: 187 IELTQRGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDK 246
++L +RG + G +AG + +A+ L S+ + + + L D+
Sbjct: 181 LQLGERGNIVQXRGEVLLAG-----VPRHVAEREIATLAGSFSLHEQNI----HNLPRDQ 231
Query: 247 AIGNGSGVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQDQ 306
GN + + + T + G R S KE+ L E+ DQ
Sbjct: 232 GPGNTVSLEVESENITERFF---VVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLADQ 288
Query: 307 LIVMMALAKGTSRVRVGQISLHTRTAIHIAELMTSAKFNIIE 348
L++ ALA G V S H T I + E +F++IE
Sbjct: 289 LVLPXALA-GAGEFTVAHPSCHLLTNIAVVERFLPVRFSLIE 329
>pdb|3TUT|A Chain A, Crystal Structure Of Rtca.Atp Binary Complex
pdb|3TUX|A Chain A, Crystal Structure Of Rtca.Atp.Mn Ternary Complex
pdb|3TV1|A Chain A, Crystal Structure Of Rtca.Amp Product Complex
pdb|3TV1|B Chain B, Crystal Structure Of Rtca.Amp Product Complex
pdb|3TW3|A Chain A, Crystal Structure Of Rtca.Atp.Co Ternary Complex
Length = 358
Score = 165 bits (417), Expect = 4e-41, Method: Compositional matrix adjust.
Identities = 108/343 (31%), Positives = 167/343 (48%), Gaps = 22/343 (6%)
Query: 10 VLNIDGSVLEGGGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQ 69
++ +DG+ EGGGQILR A+ S + +P + +IRAGR KPGL QHL + A +IC
Sbjct: 24 MIALDGAQGEGGGQILRSALSLSMITGQPFTITSIRAGRAKPGLLRQHLTAVKAATEICG 83
Query: 70 GRLENAHIGSTEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGG 129
+E A +GS ++F PG + G++ +AGS TL++Q LP L F+ G S++ V GG
Sbjct: 84 ATVEGAELGSQRLLFRPGTVRGGDYRFAIGSAGSCTLVLQTVLPALWFADGPSRVEVSGG 143
Query: 130 TNADMAPPIDYYIHLWRPVFCHFFNFNIDIHD----VRRGFFPKGGGEVNVDVTPVQYIR 185
T+ APP D+ + P+ I IH +R GF+P GGG V +V+PV
Sbjct: 144 TDNPSAPPADFIRRVLEPLLA-----KIGIHQQTTLLRHGFYPAGGGVVATEVSPVASFN 198
Query: 186 PIELTQRGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSD 245
++L +RG + + G +AG + +A+ L S+ + + + L D
Sbjct: 199 TLQLGERGNIVQMRGEVLLAG-----VPRHVAEREIATLAGSFSLHEQNI----HNLPRD 249
Query: 246 KAIGNGSGVYIFAATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQD 305
+ GN + + + T + G R S KE+ L E+ D
Sbjct: 250 QGPGNTVSLEVESENITERFF---VVGEKRVSAEVVAAQLVKEVKRYLASTAAVGEYLAD 306
Query: 306 QLIVMMALAKGTSRVRVGQISLHTRTAIHIAELMTSAKFNIIE 348
QL++ MALA G V S + T I + E +F++IE
Sbjct: 307 QLVLPMALA-GAGEFTVAHPSSNLLTNIAVVERFLPVRFSLIE 348
>pdb|3PQV|A Chain A, Cyclase Homolog
pdb|3PQV|B Chain B, Cyclase Homolog
pdb|3PQV|C Chain C, Cyclase Homolog
pdb|3PQV|D Chain D, Cyclase Homolog
Length = 365
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 75/355 (21%), Positives = 146/355 (41%), Gaps = 14/355 (3%)
Query: 21 GGQILRMAMVFSGLLHRPIHVFNIRAGRVKPGLAAQHLNGLIVAKDICQGR-LENAHIGS 79
G + R+ +V + L + I + IR+ + PGL ++ L + + + G +E ++ G+
Sbjct: 13 GSRNFRLRVVMATLSGKAIKIEKIRSDDLNPGLKDYEVSFLRLMEAVTNGSSIEISYTGT 72
Query: 80 TEIIFYPGNITSGNFYADSKTAGSVTLIMQVALPLLLFSSGQSQLIVKGGTNADMAPPID 139
T +IF PG IT G++ + V + L L FS + ++ +G T++ ID
Sbjct: 73 T-VIFRPGIITGGSYTHQCPNSKPVGYFAEPMLYLAPFSKKKFSILFRGITSSHNDAGID 131
Query: 140 YYIHLWRPVFCHFFNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIEL--TQRGELTA 197
P+ F +H ++RG P GGGEV++ V + +PI + + +++
Sbjct: 132 AIKWGLMPIMEKFGVRECALHTLKRGSPPLGGGEVHLVVDSL-IAQPITMHALDKTMISS 190
Query: 198 VWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTKLKITTYQLSSDKAIGNGSGVYIF 257
+ G ++ + V + M D A L + + + + S G G+ +
Sbjct: 191 IRGVSY-STRVSPSLVNRMIDGAKKVLKSASCEVNITADVWRGENSGKSP---GWGLTLV 246
Query: 258 AATSTGARYSGGCNGSPRTSPGECGLNAAKELWSSLCENICFDEHTQDQLIVMMALAK-G 316
A G R G P + G + A L + ++ + I+ M + K
Sbjct: 247 AENKQGWRIFSEAIGDAGDVPEDIGASVAYHLLEEISKSGVVGRNQLPLTILYMIIGKED 306
Query: 317 TSRVRVGQISLHTRTAIHIAELM----TSAKFNIIEHEDKSCIIECQGMGFVNKN 367
R+R+ + + R + ++ T ++ I +G+GF N N
Sbjct: 307 IGRLRITKDQIDERFVWLLRDIKKVFGTEILLKPVDDNTTDLIATIKGIGFTNTN 361
>pdb|2HFD|A Chain A, Nmr Structure Of Protein Hydrogenase-1 Operon Protein Hyae
From Escherichia Coli: Northeast Structural Genomics
Consortium Target Er415
Length = 140
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 224 LVKSYPDFKTKLKITTYQLSSDKAIGNGSGVYIFAATS--TGARYSGGCNG 272
L++ +PD+ ++ I L +AIG+ GV+ F AT TG Y G NG
Sbjct: 61 LLREFPDYTWQVAIA--DLEQSEAIGDRFGVFRFPATLVFTGGNYRGVLNG 109
>pdb|3KHK|A Chain A, Crystal Structure Of Type-I Restriction-Modification
System Methylation Subunit (Mm_0429) From
Methanosarchina Mazei.
pdb|3KHK|B Chain B, Crystal Structure Of Type-I Restriction-Modification
System Methylation Subunit (Mm_0429) From
Methanosarchina Mazei
Length = 544
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 208 VKMNTAQTMADTAYDYLVKSYPDFKTKL-KITTYQLSSDKAIG 249
VK+ + + D A+D + K+ P K L +I+ YQL +DK IG
Sbjct: 135 VKLRSVSWLIDNAFDDIEKANPKLKGILNRISQYQLDADKLIG 177
>pdb|2XH8|A Chain A, X-Ray Structure Of 119-141 Znua Deletion Mutant From
Salmonella Enterica
Length = 291
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 45/196 (22%), Positives = 82/196 (41%), Gaps = 23/196 (11%)
Query: 175 NVDVTPVQYIRPIELTQRGELTAVWGHAFVAGGVKMNTAQTMADTAYDYLVKSYPDFKTK 234
V + + ++P+ + GE H +++ + TA + + + + +S
Sbjct: 101 QVTIAQLADVKPLLMKGAGEYNM---HLWLSPEIARATAVAIHEKLVELMPQSRAKLDAN 157
Query: 235 LKITTYQLS-SDKAIGN------GSGVYIF------AATSTGARYSGGCNGSPRTSPGEC 281
LK QL+ +DK +GN G G ++F G G +P PG
Sbjct: 158 LKDFEAQLAATDKQVGNELAPLKGKGYFVFHDAYGYYEKHYGLTPLGHFTVNPEIQPGAQ 217
Query: 282 GLNAAKELWSSLCEN--ICFDEHTQDQLIVMMALAKGTSRVRVGQISLHTRTAIHIAELM 339
L+ E+ + L E C Q + V+ A+A+GTS VR+G + T I + +
Sbjct: 218 RLH---EIRTQLVEQKATCVFAEPQFRPAVVEAVARGTS-VRMGTLD-PLGTNIKLGKTS 272
Query: 340 TSAKFNIIEHEDKSCI 355
SA + + ++ SC+
Sbjct: 273 YSAFLSQLANQYASCL 288
>pdb|2XQV|A Chain A, The X-Ray Structure Of The Zn(Ii) Bound Znua From
Salmonella Enterica
pdb|2XY4|A Chain A, X-Ray Structure Of Znua-Wt From Salmonella Enterica
Length = 288
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 35/134 (26%), Positives = 59/134 (44%), Gaps = 13/134 (9%)
Query: 230 DFKTKLKITTYQLSSDKAIGNGSGVYIFA------ATSTGARYSGGCNGSPRTSPGECGL 283
DF+ +L T Q+ ++ A G G ++F G G +P PG L
Sbjct: 157 DFEAQLAATDKQVGNELAPLKGKGYFVFHDAYGYYEKHYGLTPLGHFTVNPEIQPGAQRL 216
Query: 284 NAAKELWSSLCEN--ICFDEHTQDQLIVMMALAKGTSRVRVGQISLHTRTAIHIAELMTS 341
+ E+ + L E C Q + V+ A+A+GTS VR+G + T I + + S
Sbjct: 217 H---EIRTQLVEQKATCVFAEPQFRPAVVEAVARGTS-VRMGTLDP-LGTNIKLGKTSYS 271
Query: 342 AKFNIIEHEDKSCI 355
A + + ++ SC+
Sbjct: 272 AFLSQLANQYASCL 285
>pdb|1DKI|A Chain A, Crystal Structure Of The Zymogen Form Of Streptococcal
Pyrogenic Exotoxin B Active Site (C47s) Mutant
pdb|1DKI|B Chain B, Crystal Structure Of The Zymogen Form Of Streptococcal
Pyrogenic Exotoxin B Active Site (C47s) Mutant
pdb|1DKI|C Chain C, Crystal Structure Of The Zymogen Form Of Streptococcal
Pyrogenic Exotoxin B Active Site (C47s) Mutant
pdb|1DKI|D Chain D, Crystal Structure Of The Zymogen Form Of Streptococcal
Pyrogenic Exotoxin B Active Site (C47s) Mutant
Length = 371
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 153 FNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQRGELTAVWGHAFVAGGV 208
F +N +H + RG F K E +D Q +P+ G+ V GHAFV G
Sbjct: 269 FGYNQSVHQINRGDFSKQDWEAQIDKELSQN-QPVYYQGVGK---VGGHAFVIDGA 320
>pdb|1PVJ|A Chain A, Crystal Structure Of The Streptococcal Pyrogenic Exotoxin
B (Speb)- Inhibitor Complex
pdb|1PVJ|B Chain B, Crystal Structure Of The Streptococcal Pyrogenic Exotoxin
B (Speb)- Inhibitor Complex
pdb|1PVJ|C Chain C, Crystal Structure Of The Streptococcal Pyrogenic Exotoxin
B (Speb)- Inhibitor Complex
pdb|1PVJ|D Chain D, Crystal Structure Of The Streptococcal Pyrogenic Exotoxin
B (Speb)- Inhibitor Complex
Length = 368
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 153 FNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQRGELTAVWGHAFVAGGV 208
F +N +H + RG F K E +D Q +P+ G+ V GHAFV G
Sbjct: 266 FGYNQSVHQINRGDFSKQDWEAQIDKELSQN-QPVYYQGVGK---VGGHAFVIDGA 317
>pdb|2JTC|A Chain A, 3d Structure And Backbone Dynamics Of Spe B
Length = 253
Score = 28.1 bits (61), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 153 FNFNIDIHDVRRGFFPKGGGEVNVDVTPVQYIRPIELTQRGELTAVWGHAFVAGG 207
F +N +H + RG F K E +D Q +P+ G+ V GHAFV G
Sbjct: 151 FGYNQSVHQINRGDFSKQDWEAQIDKELSQ-NQPVYYQGVGK---VGGHAFVIDG 201
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
0.322 0.138 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,486,329
Number of Sequences: 62578
Number of extensions: 484559
Number of successful extensions: 926
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 908
Number of HSP's gapped (non-prelim): 14
length of query: 374
length of database: 14,973,337
effective HSP length: 100
effective length of query: 274
effective length of database: 8,715,537
effective search space: 2388057138
effective search space used: 2388057138
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: 52 (24.6 bits)