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= 009803
(525 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|Q Chain Q, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
Length = 332
Score = 212 bits (540), Expect = 4e-55, Method: Compositional matrix adjust.
Identities = 128/329 (38%), Positives = 189/329 (57%), Gaps = 18/329 (5%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
SDP+R LLT EE+ L+ G++ + KL E +REV+ + G
Sbjct: 2 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 259 SPTFAQWAAAAGVDQRELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDL 315
+ + +EL+R L+ G + +I +N+RLV+SIAK Y G G++ DL
Sbjct: 62 TARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL 121
Query: 316 VQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK 375
+QEG +GL+R EKF+ + FKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE ++
Sbjct: 122 IQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLS 181
Query: 376 EARKQLYSENGRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 433
+QL E GR P+ EE+AEA G KR+ L + P SL+ IG ++ +
Sbjct: 182 RTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDF 241
Query: 434 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGV 493
I D + + + + E+LEK L L+ RE V++ R GL DGR TL+E+G GV
Sbjct: 242 IPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGV 301
Query: 494 SRERIRQIESSAFRKLK-NKKRTKHLMQY 521
+RERIRQIE+ A RKLK ++ RT+ L +
Sbjct: 302 TRERIRQIENKALRKLKYHESRTRKLRDF 330
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 438
Score = 209 bits (532), Expect = 3e-54, Method: Compositional matrix adjust.
Identities = 131/347 (37%), Positives = 194/347 (55%), Gaps = 33/347 (9%)
Query: 208 VDYSDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSER 255
V SDP+R LLT EE+ L+ G++ + KL E +REV+ +
Sbjct: 90 VSTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAK 149
Query: 256 CGGS------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRL 297
G+ P + V++ +EL+R L+ G + +I +N+RL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 298 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 357
V+SIAK Y G G++ DL+QEG +GL+R EKF+ + FKFSTYA WWI+QA+ ++++DQ
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 269
Query: 358 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGLSMKRLHAVLLSPKAP 415
+RTIR+P HMVE ++ +QL E GR P+ EE+AEA G KR+ L + P
Sbjct: 270 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 329
Query: 416 RSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFG 475
SL+ IG ++ + I D + + + + E+LEK L L+ RE V++ R G
Sbjct: 330 VSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKG 389
Query: 476 LEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLMQY 521
L DGR TL+E+G GV+RERIRQIE+ A RKLK ++ RT+ L +
Sbjct: 390 LIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDF 436
>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
Length = 423
Score = 204 bits (520), Expect = 8e-53, Method: Compositional matrix adjust.
Identities = 107/242 (44%), Positives = 152/242 (62%), Gaps = 3/242 (1%)
Query: 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 342
G + +I +N+RLV+SIAK Y G G++ DL+QEG +GL+R EKF+ + FKFSTYA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 343 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGL 400
WWI+QA+ ++++DQ+RTIR+P HMVE ++ +QL E GR P EE+AEA G
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 401 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 460
KR+ L + P SL+ IG ++ + I D + D + + E+LEK L
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLM 519
L+ RE V++ R GL DGR TL+E+G GV+RERIRQIE+ A RKLK ++ RT+ L
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLR 419
Query: 520 QY 521
+
Sbjct: 420 DF 421
>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|P Chain P, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|F Chain F, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|P Chain P, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|F Chain F, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|P Chain P, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|3EQL|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
Length = 423
Score = 204 bits (520), Expect = 8e-53, Method: Compositional matrix adjust.
Identities = 107/242 (44%), Positives = 152/242 (62%), Gaps = 3/242 (1%)
Query: 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 342
G + +I +N+RLV+SIAK Y G G++ DL+QEG +GL+R EKF+ + FKFSTYA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 343 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGL 400
WWI+QA+ ++++DQ+RTIR+P HMVE ++ +QL E GR P EE+AEA G
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 401 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 460
KR+ L + P SL+ IG ++ + I D + D + + E+LEK L
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLM 519
L+ RE V++ R GL DGR TL+E+G GV+RERIRQIE+ A RKLK ++ RT+ L
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLR 419
Query: 520 QY 521
+
Sbjct: 420 DF 421
>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|P Chain P, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 443
Score = 204 bits (519), Expect = 9e-53, Method: Compositional matrix adjust.
Identities = 107/242 (44%), Positives = 152/242 (62%), Gaps = 3/242 (1%)
Query: 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 342
G + +I +N+RLV+SIAK Y G G++ DL+QEG +GL+R EKF+ + FKFSTYA
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 343 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGL 400
WWI+QA+ ++++DQ+RTIR+P HMVE ++ +QL E GR P EE+AEA G
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 401 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 460
KR+ L + P SL+ IG ++ + I D + D + + E+LEK L
Sbjct: 320 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 379
Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLM 519
L+ RE V++ R GL DGR TL+E+G GV+RERIRQIE+ A RKLK ++ RT+ L
Sbjct: 380 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLR 439
Query: 520 QY 521
+
Sbjct: 440 DF 441
>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 613
Score = 187 bits (476), Expect = 9e-48, Method: Compositional matrix adjust.
Identities = 97/252 (38%), Positives = 153/252 (60%), Gaps = 4/252 (1%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 329
+++ RR++ G K +M+ +N+RLVISIAK Y G+ DL+QEG GL++ +K
Sbjct: 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 418
Query: 330 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHP 389
F+ +G+KFSTYA WWI+QA+ +S++DQ+RTIR+P HM+E ++ +Q+ E GR P
Sbjct: 419 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 478
Query: 390 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 449
EE+AE + ++ VL K P S++ IG +++ + I D E D +
Sbjct: 479 TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTE 538
Query: 450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 509
++ VL L RE +V+R RFG++ TL+E+G+ V+RERIRQIE+ A RKL
Sbjct: 539 SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 598
Query: 510 KNKKRTKHLMQY 521
++ R++ L +
Sbjct: 599 RHPSRSEVLRSF 610
>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|Y Chain Y, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 613
Score = 187 bits (476), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 97/252 (38%), Positives = 153/252 (60%), Gaps = 4/252 (1%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 329
+++ RR++ G K +M+ +N+RLVISIAK Y G+ DL+QEG GL++ +K
Sbjct: 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 418
Query: 330 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHP 389
F+ +G+KFSTYA WWI+QA+ +S++DQ+RTIR+P HM+E ++ +Q+ E GR P
Sbjct: 419 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 478
Query: 390 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 449
EE+AE + ++ VL K P S++ IG +++ + I D E D +
Sbjct: 479 TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTE 538
Query: 450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 509
++ VL L RE +V+R RFG++ TL+E+G+ V+RERIRQIE+ A RKL
Sbjct: 539 SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKL 598
Query: 510 KNKKRTKHLMQY 521
++ R++ L +
Sbjct: 599 RHPSRSEVLRSF 610
>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment Containing Regions 1.2 To 3.1
Length = 241
Score = 144 bits (363), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 89/240 (37%), Positives = 132/240 (55%), Gaps = 32/240 (13%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
SDP+R LLT EE+ L+ G++ + KL E +REV+ + G
Sbjct: 2 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 259 S------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRLVIS 300
+ P + V++ +EL+R L+ G + +I +N+RLV+S
Sbjct: 62 TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 121
Query: 301 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360
IAK Y G G++ DL+QEG +GL+R EKF+ + FKFSTYA WWI+QA+ ++++DQ+RT
Sbjct: 122 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 181
Query: 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSL 418
IR+P HMVE ++ +QL E GR P+ EE+AEA G KR+ L + P SL
Sbjct: 182 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241
>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tacaat)
pdb|3UGP|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2
Complexed With -10 Promoter Element Ssdna Oligo (Tataat)
pdb|4GOR|A Chain A, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
pdb|4GOR|B Chain B, Crystallographic Analysis Of An Rna-Polymerase
Sigma-Subunit Fragment Complexed With -10 Promoter
Element Ssdna: G-Quadruplex Formation And Crystal
Packing
Length = 245
Score = 144 bits (363), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 89/240 (37%), Positives = 132/240 (55%), Gaps = 32/240 (13%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
SDP+R LLT EE+ L+ G++ + KL E +REV+ + G
Sbjct: 6 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 65
Query: 259 S------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRLVIS 300
+ P + V++ +EL+R L+ G + +I +N+RLV+S
Sbjct: 66 TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 125
Query: 301 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360
IAK Y G G++ DL+QEG +GL+R EKF+ + FKFSTYA WWI+QA+ ++++DQ+RT
Sbjct: 126 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 185
Query: 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSL 418
IR+P HMVE ++ +QL E GR P+ EE+AEA G KR+ L + P SL
Sbjct: 186 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 245
>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2
pdb|3LES|B Chain B, 2f5 Epitope Scaffold Es2
pdb|3LEV|A Chain A, Hiv-1 Antibody 2f5 In Complex With Epitope Scaffold Es2
Length = 179
Score = 100 bits (248), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 43/89 (48%), Positives = 65/89 (73%), Gaps = 3/89 (3%)
Query: 274 RELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 330
+EL+R L+ G + +I +N+RLV+SIAK Y G G++ DL+QEG +GL+R EKF
Sbjct: 91 KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 150
Query: 331 DASKGFKFSTYAHWWIKQAVRKSLSDQSR 359
+ +GF FSTYA WWI+QA+ ++++DQ+R
Sbjct: 151 EYKRGFAFSTYATWWIRQAINRAIADQAR 179
>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
Escherichia Coli Rna Polymerase
Length = 339
Score = 94.4 bits (233), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 64/90 (71%), Gaps = 4/90 (4%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 329
+++ RR++ G K +M+ +N+RLVISIAK Y G+ DL+QEG GL++ +K
Sbjct: 250 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 309
Query: 330 FDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359
F+ +G+KFSTYA WWI+QA+ +S++DQ+R
Sbjct: 310 FEYRRGYKFSTYATWWIRQAITRSIADQAR 339
>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 73
Score = 88.6 bits (218), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 42/71 (59%), Positives = 55/71 (77%)
Query: 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
MKE LE VLDTL RE V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL+
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 511 NKKRTKHLMQY 521
+ R+K L +
Sbjct: 61 HPSRSKRLKDF 71
>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
Sigma Factor Spoiiab With The Sporulation Sigma Factor
Sigmaf
Length = 243
Score = 85.1 bits (209), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 66/240 (27%), Positives = 122/240 (50%), Gaps = 15/240 (6%)
Query: 274 RELRRRLNYGIL-CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA 332
+EL RR G +D++I N+RLV S+ + + G DL Q GC GL++ +KFD
Sbjct: 16 KELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDL 75
Query: 333 SKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNE 392
S KFSTYA I +++ L D T+++ + E ++++A+ +L GR P
Sbjct: 76 SYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVT 134
Query: 393 EVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN--LKPSEVIADPEAETAEDLLIKKF 450
E+A+ G+S + + + + P S+ + + N + + IAD + + F
Sbjct: 135 EIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEASW-------F 187
Query: 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
K L+K ++ L+ RER +V R+ + +T E+ +G+S+ ++ ++E + +K
Sbjct: 188 DKIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHIK 243
>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
Maritima
Length = 87
Score = 84.3 bits (207), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 40/72 (55%), Positives = 56/72 (77%)
Query: 447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 506
++ M+E+LEKVL TL+PRE V+R R+GL DG+ KTL+E+G+ V+RERIRQIE A
Sbjct: 4 MRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKAL 63
Query: 507 RKLKNKKRTKHL 518
RKL++ R+K+L
Sbjct: 64 RKLRHPSRSKYL 75
>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex
Length = 62
Score = 83.2 bits (204), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 39/61 (63%), Positives = 50/61 (81%)
Query: 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
MKE LE VLDTL RE V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL+
Sbjct: 1 MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 511 N 511
+
Sbjct: 61 H 61
>pdb|3N97|A Chain A, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma
Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna
pdb|3N97|D Chain D, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma
Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna
Length = 72
Score = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 35/69 (50%), Positives = 48/69 (69%)
Query: 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
E+LEK L L+ RE V++ R GL DGR TL+E+G GV+RERIRQIE+ A RKL++
Sbjct: 2 EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRHP 61
Query: 513 KRTKHLMQY 521
R++ L +
Sbjct: 62 SRSEKLRDF 70
>pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
Sigma Subunit Fragment, Region 4
pdb|1KU7|A Chain A, Crystal Structure Of Thermus Aquatics Rna Polymerase
Sigmaa Subunit Region 4 Bound To-35 Element Dna
pdb|1KU7|D Chain D, Crystal Structure Of Thermus Aquatics Rna Polymerase
Sigmaa Subunit Region 4 Bound To-35 Element Dna
Length = 73
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 37/70 (52%), Positives = 49/70 (70%), Gaps = 1/70 (1%)
Query: 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-N 511
E+LEK L L+ RE V++ R GL DGR TL+E+G GV+RERIRQIE+ A RKLK +
Sbjct: 2 EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61
Query: 512 KKRTKHLMQY 521
+ RT+ L +
Sbjct: 62 ESRTRKLRDF 71
>pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With
Sigma-Region4 Of Thermus Aquaticus Bound To Dna
Length = 73
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 37/70 (52%), Positives = 49/70 (70%), Gaps = 1/70 (1%)
Query: 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-N 511
E+LEK L L+ RE V++ R GL DGR TL+E+G GV+RERIRQIE+ A RKLK +
Sbjct: 2 EELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61
Query: 512 KKRTKHLMQY 521
+ RT+ L +
Sbjct: 62 ESRTRKLRDF 71
>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|C Chain C, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|E Chain E, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1RP3|G Chain G, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
Complex, Sigma-28FLGM
pdb|1SC5|A Chain A, Sigma-28(Flia)FLGM COMPLEX
Length = 239
Score = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 60/239 (25%), Positives = 113/239 (47%), Gaps = 35/239 (14%)
Query: 287 KDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAH 343
++++I + LV +IA N + ++++DL+ G GL++ + + Y
Sbjct: 14 REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73
Query: 344 WWIKQAVR---KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGL 400
IK A+ +SL SR +R E R+KE ++L + GR P +EEVA+ G+
Sbjct: 74 LRIKGAIYDYLRSLDFGSRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGI 127
Query: 401 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD---------PEAETAEDLLIKKFM 451
S + L ++LD KI + L EV D P + E+ +IK+ +
Sbjct: 128 STEELF---------KTLD-KINFSYILSLEEVFRDFARDYSELIPSSTNVEEEVIKREL 177
Query: 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
E +++ + L RE+ V++ F E +E+ +++ S R+ Q+++ A +L+
Sbjct: 178 TEKVKEAVSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLR 232
>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
Length = 81
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/64 (45%), Positives = 43/64 (67%)
Query: 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517
VL L RE +V+R RFG++ TL+E+G+ V+RERIRQIE+ A RKL++ R++
Sbjct: 15 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 74
Query: 518 LMQY 521
L +
Sbjct: 75 LRSF 78
>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
pdb|3T72|OO Chain o, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna
Transcription Activation Sub-Complex
Length = 99
Score = 56.2 bits (134), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/61 (47%), Positives = 42/61 (68%)
Query: 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517
VL L RE +V+R RFG++ TL+E+G+ V+RERIRQIE+ A RKL++ R++
Sbjct: 16 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 75
Query: 518 L 518
L
Sbjct: 76 L 76
>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of
Sigma 70, Rsd, In Complex With Sigma 70 Domain 4
Length = 68
Score = 55.8 bits (133), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/64 (45%), Positives = 43/64 (67%)
Query: 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517
VL L RE +V+R RFG++ TL+E+G+ V+RERIRQIE+ A RKL++ R++
Sbjct: 2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61
Query: 518 LMQY 521
L +
Sbjct: 62 LRSF 65
>pdb|3I2C|H Chain H, Crystal Structure Of Anti-Il-23 Antibody Cnto4088
Length = 222
Score = 33.5 bits (75), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 21/43 (48%), Positives = 27/43 (62%), Gaps = 4/43 (9%)
Query: 315 LVQEGCRGLV--RGAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
LVQ G GLV +G+ K A+ GF F+TYA W++QA K L
Sbjct: 4 LVQSG-GGLVQPKGSLKLSCAASGFNFNTYAMHWVRQAPGKGL 45
>pdb|3KR3|H Chain H, Crystal Structure Of Igf-Ii Antibody Complex
Length = 251
Score = 33.5 bits (75), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FS Y WW++QA K L
Sbjct: 23 AASGFTFSNYIMWWVRQAPGKGL 45
>pdb|3MZY|A Chain A, The Crystal Structure Of The Rna Polymerase Sigma-H Factor
F Fusobacterium Nucleatum To 2.5a
Length = 164
Score = 33.1 bits (74), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 309 GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ----AVRKS 353
G +DLVQEG GL++ + +D +K FS++A I++ A+RK+
Sbjct: 1 GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREXISAIRKA 48
>pdb|3BN9|D Chain D, Crystal Structure Of Mt-Sp1 In Complex With Fab Inhibitor
E2
pdb|3BN9|F Chain F, Crystal Structure Of Mt-Sp1 In Complex With Fab Inhibitor
E2
Length = 257
Score = 32.3 bits (72), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 27/43 (62%), Gaps = 4/43 (9%)
Query: 315 LVQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
LVQ G GLV+ G+ + A+ GF FS+YA W++QA K L
Sbjct: 4 LVQSG-GGLVKPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGL 45
>pdb|3HI5|H Chain H, Crystal Structure Of Fab Fragment Of Al-57
pdb|3HI6|H Chain H, Crystal Structure Of Intermediate Affinity I Domain Of
Integrin Lfa-1 With The Fab Fragment Of Its Antibody
Al-57
pdb|3HI6|X Chain X, Crystal Structure Of Intermediate Affinity I Domain Of
Integrin Lfa-1 With The Fab Fragment Of Its Antibody
Al-57
Length = 220
Score = 32.3 bits (72), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FS Y WW++QA K L
Sbjct: 23 AASGFTFSRYVMWWVRQAPGKGL 45
>pdb|3SO3|C Chain C, Structures Of Fab-Protease Complexes Reveal A Highly
Specific Non- Canonical Mechanism Of Inhibition
Length = 228
Score = 32.0 bits (71), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 27/43 (62%), Gaps = 4/43 (9%)
Query: 315 LVQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
LVQ G GLV+ G+ + A+ GF FS+YA W++QA K L
Sbjct: 4 LVQSG-GGLVKPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGL 45
>pdb|3TNN|H Chain H, Crystal Structure Of N5-I5 Fab, An Adcc Mediating And
Non-Neutralizing Cd4i Anti-Hiv- 1 Antibody.
pdb|3TNN|A Chain A, Crystal Structure Of N5-I5 Fab, An Adcc Mediating And
Non-Neutralizing Cd4i Anti-Hiv- 1 Antibody.
pdb|3TNN|C Chain C, Crystal Structure Of N5-I5 Fab, An Adcc Mediating And
Non-Neutralizing Cd4i Anti-Hiv- 1 Antibody.
pdb|3TNN|E Chain E, Crystal Structure Of N5-I5 Fab, An Adcc Mediating And
Non-Neutralizing Cd4i Anti-Hiv- 1 Antibody
Length = 226
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FSTYA W++QA K L
Sbjct: 23 AASGFTFSTYAMSWVRQAPGKGL 45
>pdb|1NL0|H Chain H, Crystal Structure Of Human Factor Ix Gla Domain In Complex
Of An Inhibitory Antibody, 10c12
pdb|3D69|H Chain H, Crystal Structure Of The Fab Fragment Of An Anti-Factor Ix
Antibody 10c12
pdb|3D69|B Chain B, Crystal Structure Of The Fab Fragment Of An Anti-Factor Ix
Antibody 10c12
Length = 224
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FSTYA W++QA K L
Sbjct: 23 AASGFTFSTYAMHWVRQAPGKGL 45
>pdb|1CK0|H Chain H, Anti-Anti-Idiotypic Antibody Against Human Angiotensin Ii,
Unliganded Form
pdb|2CK0|H Chain H, Anti-Anti-Idiotypic Antibody Against Human Angiotensin Ii,
Complex With A Synthetic Cyclic Peptide
pdb|3CK0|H Chain H, Anti-Anti-Idiotypic Antibody Against Human Angiotensin Ii,
Complex With Human Angiotensin Ii
Length = 219
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 316 VQEGCRGLV--RGAEKFD-ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATY 372
+QE GLV RG+ K A+ GF F+T A W++QA K L +R F+ ATY
Sbjct: 4 LQESGGGLVQPRGSLKLSCAASGFTFNTDAMNWVRQAPGKGLEWVARIRSKGFNF--ATY 61
Query: 373 RVKEARKQL 381
R +
Sbjct: 62 YADSVRDRF 70
>pdb|3ZTJ|G Chain G, Structure Of Influenza A Neutralizing Antibody Selected
From Cultures Of Single Human Plasma Cells In Complex
With Human H3 Influenza Haemagglutinin.
pdb|3ZTJ|I Chain I, Structure Of Influenza A Neutralizing Antibody Selected
From Cultures Of Single Human Plasma Cells In Complex
With Human H3 Influenza Haemagglutinin.
pdb|3ZTJ|K Chain K, Structure Of Influenza A Neutralizing Antibody Selected
From Cultures Of Single Human Plasma Cells In Complex
With Human H3 Influenza Haemagglutinin.
pdb|3ZTN|H Chain H, Structure Of Influenza A Neutralizing Antibody Selected
From Cultures Of Single Human Plasma Cells In Complex
With Human H1 Influenza Haemagglutinin
Length = 226
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FSTYA W++QA K L
Sbjct: 23 AASGFTFSTYAMHWVRQAPGKGL 45
>pdb|1I9I|H Chain H, Native Crystal Structure Of The Recombinant Monoclonal
Wild Type Anti-Testosterone Fab Fragment
pdb|1I9J|H Chain H, Testosterone Complex Structure Of The Recombinant
Monoclonal Wild Type Anti-Testosterone Fab Fragment
Length = 220
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 315 LVQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
LV+ G GLV+ G+ K A+ GF FSTYA W++Q K L
Sbjct: 4 LVESG-GGLVKPGGSLKLSCAASGFTFSTYALSWVRQTADKRL 45
>pdb|2GHW|B Chain B, Crystal Structure Of Sars Spike Protein Receptor Binding
Domain In Complex With A Neutralizing Antibody, 80r
pdb|2GHW|D Chain D, Crystal Structure Of Sars Spike Protein Receptor Binding
Domain In Complex With A Neutralizing Antibody, 80r
Length = 247
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 315 LVQEGCRGLVRGAEKF---DASKGFKFSTYAHWWIKQAVRKSL 354
LVQ G G+V+ + A+ GF FS+YA W++QA K L
Sbjct: 6 LVQSG-GGVVQPGKSLRLSCAASGFAFSSYAMHWVRQAPGKGL 47
>pdb|1DQL|H Chain H, Crystal Structure Of An Unliganded (Native) Fv From A
Human Igm Anti-Peptide Antibody
Length = 123
Score = 30.4 bits (67), Expect = 2.4, Method: Composition-based stats.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FS+YA W++QA K L
Sbjct: 23 AASGFTFSSYAMHWVRQAPGKGL 45
>pdb|1H3P|H Chain H, Structural Characterisation Of A Monoclonal Antibody
Specific For The Pres1 Region Of The Hepatitis B Virus
Length = 219
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 27/43 (62%), Gaps = 4/43 (9%)
Query: 315 LVQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
LV+ G GLV+ G+ K A+ GF FS+YA W++Q+ K L
Sbjct: 4 LVESG-GGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSPEKRL 45
>pdb|4GXU|M Chain M, Crystal Structure Of Antibody 1f1 Bound To The 1918
Influenza Hemagglutinin
pdb|4GXU|O Chain O, Crystal Structure Of Antibody 1f1 Bound To The 1918
Influenza Hemagglutinin
pdb|4GXU|Q Chain Q, Crystal Structure Of Antibody 1f1 Bound To The 1918
Influenza Hemagglutinin
pdb|4GXU|S Chain S, Crystal Structure Of Antibody 1f1 Bound To The 1918
Influenza Hemagglutinin
pdb|4GXU|U Chain U, Crystal Structure Of Antibody 1f1 Bound To The 1918
Influenza Hemagglutinin
pdb|4GXU|W Chain W, Crystal Structure Of Antibody 1f1 Bound To The 1918
Influenza Hemagglutinin
pdb|4GXV|H Chain H, Crystal Structure Of Anti-Influenza Virus Antibody 1f1
pdb|4GXV|I Chain I, Crystal Structure Of Anti-Influenza Virus Antibody 1f1
Length = 231
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FS+YA W++QA K L
Sbjct: 23 AASGFTFSSYAMHWVRQAPGKGL 45
>pdb|2QQN|H Chain H, Neuropilin-1 B1 Domain In Complex With A Vegf-Blocking Fab
Length = 230
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FS+YA W++QA K L
Sbjct: 23 AASGFTFSSYAMSWVRQAPGKGL 45
>pdb|3UX9|B Chain B, Structural Insights Into A Human Anti-Ifn Antibody
Exerting Therapeutic Potential For Systemic Lupus
Erythematosus
pdb|3UX9|D Chain D, Structural Insights Into A Human Anti-Ifn Antibody
Exerting Therapeutic Potential For Systemic Lupus
Erythematosus
Length = 256
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FS+YA W++QA K L
Sbjct: 157 AASGFTFSSYAMSWVRQAPGKGL 179
>pdb|2VXS|H Chain H, Structure Of Il-17a In Complex With A Potent, Fully Human
Neutralising Antibody
pdb|2VXS|I Chain I, Structure Of Il-17a In Complex With A Potent, Fully Human
Neutralising Antibody
pdb|2VXS|J Chain J, Structure Of Il-17a In Complex With A Potent, Fully Human
Neutralising Antibody
pdb|2VXS|K Chain K, Structure Of Il-17a In Complex With A Potent, Fully Human
Neutralising Antibody
Length = 225
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FS+YA W++QA K L
Sbjct: 23 AASGFTFSSYAMSWVRQAPGKGL 45
>pdb|2EIX|A Chain A, The Structure Of Physarum Polycephalum Cytochrome B5
Reductase
pdb|2EIX|B Chain B, The Structure Of Physarum Polycephalum Cytochrome B5
Reductase
Length = 243
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 429 KPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIG 488
+P ++ + + DL+IK + K + + +D LNP + VR G D + ++E+G
Sbjct: 61 RPYTPVSSDDEKGYFDLIIKVYEKGQMSQYIDHLNPGDFLQVRGPKGQFDYKPNMVKEMG 120
Query: 489 ELMG 492
+ G
Sbjct: 121 MIAG 124
>pdb|2GCY|B Chain B, Humanized Antibody C25 Fab Fragment
Length = 218
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 316 VQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
+QE GLV+ G+ + A+ GF FS Y +W++QA K L
Sbjct: 4 LQESGGGLVQPGGSLRLSCAASGFTFSDYYMYWVRQAPGKGL 45
>pdb|3QOS|H Chain H, Crystal Structure Of Human Germline Antibody 3-23B3
pdb|3QOS|B Chain B, Crystal Structure Of Human Germline Antibody 3-23B3
Length = 228
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FS+YA W++QA K L
Sbjct: 23 AASGFTFSSYAMSWVRQAPGKGL 45
>pdb|2IG2|H Chain H, Dir Primaerstruktur Des Kristallisierbaren Monoklonalen
Immunoglobulins Igg1 Kol. Ii. Aminosaeuresequenz Der L-
Kette, Lambda-Typ, Subgruppe I (German)
Length = 455
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 335 GFKFSTYAHWWIKQAVRKSL 354
GF FS+YA +W++QA K L
Sbjct: 26 GFIFSSYAMYWVRQAPGKGL 45
>pdb|1IGT|B Chain B, Structure Of Immunoglobulin
pdb|1IGT|D Chain D, Structure Of Immunoglobulin
Length = 444
Score = 29.6 bits (65), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 316 VQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
+QE GLV+ G+ K A+ GF FS Y +W++Q K L
Sbjct: 4 LQESGGGLVQPGGSLKLSCATSGFTFSDYYMYWVRQTPEKRL 45
>pdb|3KDM|H Chain H, Crystal Structure Of Human Anti-Steroid Fab 5f2 In Complex
With Testosterone
pdb|3KDM|B Chain B, Crystal Structure Of Human Anti-Steroid Fab 5f2 In Complex
With Testosterone
Length = 225
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FS+YA W++QA K L
Sbjct: 23 AASGFTFSSYAMSWVRQAPGKGL 45
>pdb|2RCJ|A Chain A, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|B Chain B, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|E Chain E, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|F Chain F, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|I Chain I, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|J Chain J, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|M Chain M, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|N Chain N, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|Q Chain Q, Solution Structure Of Human Immunoglobulin M
pdb|2RCJ|R Chain R, Solution Structure Of Human Immunoglobulin M
Length = 218
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 335 GFKFSTYAHWWIKQAVRKSL 354
GF FS+YA +W++QA K L
Sbjct: 26 GFIFSSYAMYWVRQAPGKGL 45
>pdb|1IGC|H Chain H, Igg1 Fab Fragment (Mopc21) Complex With Domain Iii Of
Protein G From Streptococcus
Length = 222
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 315 LVQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
LV+ G GLV+ G+ K A+ GF FS++ W++QA K L
Sbjct: 4 LVESG-GGLVQPGGSRKLSCAASGFTFSSFGMHWVRQAPEKGL 45
>pdb|3CFI|C Chain C, Nanobody-Aided Structure Determination Of The Epsi:epsj
Pseudopilin Heterdimer From Vibrio Vulnificus
pdb|3CFI|F Chain F, Nanobody-Aided Structure Determination Of The Epsi:epsj
Pseudopilin Heterdimer From Vibrio Vulnificus
pdb|3CFI|I Chain I, Nanobody-Aided Structure Determination Of The Epsi:epsj
Pseudopilin Heterdimer From Vibrio Vulnificus
pdb|3CFI|L Chain L, Nanobody-Aided Structure Determination Of The Epsi:epsj
Pseudopilin Heterdimer From Vibrio Vulnificus
Length = 116
Score = 29.6 bits (65), Expect = 4.6, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 316 VQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
+QE GLV+ G+ + A+ GF FS YA W++QA K L
Sbjct: 4 LQESGGGLVQPGGSLRLSCAASGFAFSGYAMSWVRQAPGKGL 45
>pdb|2FB4|H Chain H, Dir Primaerstruktur Des Kristallisierbaren Monoklonalen
Immunoglobulins Igg1 Kol. Ii. Aminosaeuresequenz Der L-
Kette, Lambda-Typ, Subgruppe I (German)
Length = 229
Score = 29.6 bits (65), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 335 GFKFSTYAHWWIKQAVRKSL 354
GF FS+YA +W++QA K L
Sbjct: 26 GFIFSSYAMYWVRQAPGKGL 45
>pdb|3GJE|H Chain H, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
pdb|3GJE|B Chain B, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
pdb|3GJF|H Chain H, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
pdb|3GJF|M Chain M, Rational Development Of High-Affinity T-Cell Receptor-Like
Antibodies
Length = 220
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 332 ASKGFKFSTYAHWWIKQAVRKSL 354
A+ GF FSTY W++QA K L
Sbjct: 23 AASGFTFSTYQMSWVRQAPGKGL 45
>pdb|2AAB|H Chain H, Structural Basis Of Antigen Mimicry In A Clinically
Relevant Melanoma Antigen System
Length = 243
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 315 LVQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
LV+ G GLV+ G+ K A+ GF FS++ W++QA K L
Sbjct: 4 LVESG-GGLVQPGGSRKLSCAASGFTFSSFGMHWVRQAPEKGL 45
>pdb|1KNO|B Chain B, Crystal Structure Of The Complex Of A Catalytic Antibody
Fab With A Transition State Analog: Structural
Similarities In Esterase-Like Abzymes
pdb|1KNO|D Chain D, Crystal Structure Of The Complex Of A Catalytic Antibody
Fab With A Transition State Analog: Structural
Similarities In Esterase-Like Abzymes
pdb|1KNO|F Chain F, Crystal Structure Of The Complex Of A Catalytic Antibody
Fab With A Transition State Analog: Structural
Similarities In Esterase-Like Abzymes
Length = 220
Score = 29.3 bits (64), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 315 LVQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
LV+ G GLV+ G+ K A+ GF FS++ W++QA K L
Sbjct: 4 LVESG-GGLVQPGGSRKLSCAASGFTFSSFGMHWVRQAPEKGL 45
>pdb|2GFB|B Chain B, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|D Chain D, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|F Chain F, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|H Chain H, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|J Chain J, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|L Chain L, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|N Chain N, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
pdb|2GFB|P Chain P, Crystal Structure Of A Catalytic Fab Having Esterase-Like
Activity
Length = 219
Score = 29.3 bits (64), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 315 LVQEGCRGLVR--GAEKFD-ASKGFKFSTYAHWWIKQAVRKSL 354
LV+ G GLV+ G+ K A+ GF FS++ W++QA K L
Sbjct: 4 LVESG-GGLVQPGGSRKLSCAASGFTFSSFGMHWVRQAPEKGL 45
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 0.128 0.355
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,382,732
Number of Sequences: 62578
Number of extensions: 437431
Number of successful extensions: 1437
Number of sequences better than 100.0: 61
Number of HSP's better than 100.0 without gapping: 45
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1377
Number of HSP's gapped (non-prelim): 61
length of query: 525
length of database: 14,973,337
effective HSP length: 103
effective length of query: 422
effective length of database: 8,527,803
effective search space: 3598732866
effective search space used: 3598732866
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)