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= psy8848
(459 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TV9|A Chain A, Crystal Structure Of Putative Peptide Maturation Protein
From Shigella Flexneri
Length = 457
Score = 314 bits (804), Expect = 7e-86, Method: Compositional matrix adjust.
Identities = 163/448 (36%), Positives = 271/448 (60%), Gaps = 11/448 (2%)
Query: 12 IYSKSEFQQLAQDMLNYAKKIGASHS---SIEFNEGNGFSVFVRKGKIDVIEQNNDKNMN 68
+Y +S +++ ++ ++ A ++ + S + ++ G SV R G+++ +E N+D +
Sbjct: 18 LYFQSNARKILEEAVSTALELASGKSDGAEVAVSKTTGISVSTRYGEVENVEFNSDGALG 77
Query: 69 VIIYIQDGKKMFYGNSSTSDFCKKSLYDTINAAYNIARFTASDNFAGLPDENTLEMNPLD 128
+ +Y Q+ K G++S++D +++ T+ AA +IAR+T+ D AG+ D+ L + +
Sbjct: 78 ITVYHQNRK----GSASSTDLSPQAIARTVQAALDIARYTSPDPCAGVADKELLAFDAPN 133
Query: 129 FKLYTPWFLSIDDAKLIAYRCENEAFNFNSLIVNNENTGVTTQQSHFLLANSHGFMSGYP 188
L+ P +S D+A +A R E A + I N E + + NSHG + GY
Sbjct: 134 LDLFHPAEVSPDEAIELAARAEQAALQADKRITNTEGGSFNSHYGVKVFGNSHGXLQGYC 193
Query: 189 FSKHIISISPIAIKGKEMQRDNWYSSNSDPKKLDQPEIIGFYAAKRTISRLKAKKISTRK 248
++H + IA + + +RD Y+ L PE +G A+RT+SRL +K+ST K
Sbjct: 194 STRHSLFSCVIAEENGDXERDYAYTIGRAXSDLQTPEWVGADCARRTLSRLSPRKLSTXK 253
Query: 249 CPVLFEAPLAFELLNIFARLISGNSLYRKSTFLVDSLGKKIFSSHIQIIEDPHILGSFGS 308
PV+F +A L I+G S+YRKSTFL+DSLGK+I + I E PH+L S
Sbjct: 254 APVIFANEVATGLFGHLVGAIAGGSVYRKSTFLLDSLGKQILPDWLTIEEHPHLLKGLAS 313
Query: 309 SSFDNEGVKTQKRLVVKNGIIQGYFLSTYSAKKLGMKTTGNSGGAHHLIIISNKTKSSDN 368
+ FD+EGV+T++R ++K+GI+ + L++YSA+KLG+K+TG++GG H+ I +
Sbjct: 314 TPFDSEGVRTERRDIIKDGILTQWLLTSYSARKLGLKSTGHAGGIHNWRIAGQGL----S 369
Query: 369 LKEMLKKMNTGLLVTELMGDGINYITGDYSKGAFGYWIENGKIQYSVEEITISGKLQNMF 428
++ LK+ TGL+VTEL G G++ ITGDYS+GA G+W+ENG+IQY V EITI+G L++ +
Sbjct: 370 FEQXLKEXGTGLVVTELXGQGVSAITGDYSRGAAGFWVENGEIQYPVSEITIAGNLKDXW 429
Query: 429 KQIVAIGSDVLTRNSNTSGSILIENMII 456
+ IV +G+D+ TR++ GS+L+ I
Sbjct: 430 RNIVTVGNDIETRSNIQCGSVLLPEXKI 457
>pdb|3QTD|A Chain A, Crystal Structure Of Putative Modulator Of Gyrase (Pmba)
From Pseudomonas Aeruginosa Pao1
pdb|3QTD|B Chain B, Crystal Structure Of Putative Modulator Of Gyrase (Pmba)
From Pseudomonas Aeruginosa Pao1
pdb|3QTD|C Chain C, Crystal Structure Of Putative Modulator Of Gyrase (Pmba)
From Pseudomonas Aeruginosa Pao1
pdb|3QTD|D Chain D, Crystal Structure Of Putative Modulator Of Gyrase (Pmba)
From Pseudomonas Aeruginosa Pao1
Length = 449
Score = 301 bits (772), Expect = 4e-82, Method: Compositional matrix adjust.
Identities = 167/443 (37%), Positives = 263/443 (59%), Gaps = 8/443 (1%)
Query: 17 EFQQLAQDMLNYAKKIGASHSSIEFNEGNGFSVFVRKGKIDVIEQNNDKNMNVIIYIQDG 76
+ ++ + ++ A++ GAS + + G S VR+G+++ +E N D+ + +Y
Sbjct: 15 DLREQVEQIIAEARRQGASACEVAVSLEQGLSTSVRQGEVETVEFNRDQGFGITLYAGQR 74
Query: 77 KKMFYGNSSTSDFCKKSLYDTINAAYNIARFTASDNFAGLPDENTLEMNPLDFKLYTPWF 136
K G++STS + ++ +T+ AA IAR T+ D AGL D + LY PW
Sbjct: 75 K----GSASTSATGEAAIRETVAAALAIARHTSEDECAGLADAALXARELPELDLYHPWS 130
Query: 137 LSIDDAKLIAYRCENEAFNFNSLIVNNENTGVTTQQSHFLLANSHGFMSGYPFSKHIISI 196
LS + A A CE AF + + + T + T Q + NSHGF+ GY ++H +S
Sbjct: 131 LSPEQAVERALACEAAAFAADKRVTKADGTTLNTHQGCRVYGNSHGFIGGYASTRHSLSC 190
Query: 197 SPIAIKGKEMQRDNWYSSNSDPKKLDQPEIIGFYAAKRTISRLKAKKISTRKCPVLFEAP 256
IA + QRD WY N + L E IG AA+R SRL A+ + T + PVLF
Sbjct: 191 VXIAEGEGQXQRDYWYDVNRRGEALASAESIGRRAAERAASRLGARPVQTAEVPVLFAPE 250
Query: 257 LAFELLNIFARLISGNSLYRKSTFLVDSLGKKIFSSHIQIIEDPHILGSFGSSSFDNEGV 316
+A L F ISG SLYRKS+FL +LG+++F + I E PH++G+ GS+SFD++G+
Sbjct: 251 IAVGLFGHFLGAISGGSLYRKSSFLEGALGQRLFPEWLSIDERPHLVGALGSASFDSDGL 310
Query: 317 KTQKRLVVKNGIIQGYFLSTYSAKKLGMKTTGNSGGAHHLIIISNKTKSSDNLKEMLKKM 376
T + V+NG + Y L TYS +KLG+ +T N+GG H+L + + ++ ++++
Sbjct: 311 ATYAKPFVENGELVSYVLGTYSGRKLGLPSTANAGGVHNLFV----SHGDEDQAALIRRX 366
Query: 377 NTGLLVTELMGDGINYITGDYSKGAFGYWIENGKIQYSVEEITISGKLQNMFKQIVAIGS 436
GLLVTEL G G+N +TGDYS+GA GYW+ENG+IQ+ V+E+TI+ L+++F++IVA+G
Sbjct: 367 ERGLLVTELXGQGVNLVTGDYSRGAAGYWVENGEIQFPVQEVTIAANLRDLFRRIVAVGK 426
Query: 437 DVLTRNSNTSGSILIENMIIAGK 459
D+ R + +GS+L+E+ +AG+
Sbjct: 427 DIERRGNLHTGSVLVESXXVAGR 449
>pdb|1VPB|A Chain A, Crystal Structure Of A Putative Modulator Of Dna Gyrase
(Bt3649) From Bacteroides Thetaiotaomicron Vpi-5482 At
1.75 A Resolution
Length = 451
Score = 154 bits (389), Expect = 9e-38, Method: Compositional matrix adjust.
Identities = 127/448 (28%), Positives = 234/448 (52%), Gaps = 20/448 (4%)
Query: 17 EFQQLAQDMLNYAKKIGASHSSIEFNEGNGFSVFVRKGKIDVIEQNNDKNMNVIIYIQDG 76
E ++LAQ ++YA K G + + + S +R K+D ++Q ++ +++ +Y+ DG
Sbjct: 17 ENKKLAQWAMDYALKNGCQAAKVLLYSSSNTSFELRDAKMDRLQQASEGGLSLSLYV-DG 75
Query: 77 KKMFYGNSSTSDFCKKSLYDTINAAYNIARFTASDNFAGLPDENTL-EMNPLDFKLYTPW 135
+ YG+ ST+ +K L I + R+ A D L D + + D KLY
Sbjct: 76 R---YGSISTNRLNRKELETFIKNGIDSTRYLAKDEARVLADPSRYYKGGKPDLKLYDAK 132
Query: 136 FLSI--DDAKLIAYRCENEAFNFNSLIVN-NENTGVTTQQSHFLLANSHGFMSGYPFSKH 192
F S+ DD +A EA + I++ + G ++ L++N GF + +
Sbjct: 133 FASLNPDDKIEMAKAVAEEALGKDERIISVGSSYGDGEDFAYRLISN--GFEGETKSTWY 190
Query: 193 IISISPIAIKGKEMQRDN--WYSSNSDPKKLDQPEIIGFYAAKRTISRLKAKKISTRKCP 250
+S + I I+G+ R + WY S+ L + + IG A +R + +L KK+ + K
Sbjct: 191 SLS-ADITIRGEGEARPSAYWYESSLYMNDLIK-KGIGQKALERVLRKLGQKKVQSGKYT 248
Query: 251 VLFEAPLAFELLNIFARLISGNSLYRKSTFLVDSLGKKIFSSHIQIIEDPHILGSFGSSS 310
++ + + LL+ ++G++L +K++FL++ L +KI S + + ++PH++ + G+
Sbjct: 249 MVVDPMNSSRLLSPMISALNGSALQQKNSFLLNKLNEKIASDRLTLTDEPHLVKASGARY 308
Query: 311 FDNEGVKTQKRLVVKNGIIQGYFLSTYSAKKLGMKTTGNSGGAHHLIIISNKTKSSDNLK 370
FDNEG+ T++R + G++ YF+ TY+AKK+G+ T SG + ++ +K NL
Sbjct: 309 FDNEGIATERRSIFDKGVLNTYFIDTYNAKKMGVDPT-ISGSSILVMETGDK-----NLD 362
Query: 371 EMLKKMNTGLLVTELMGDGINYITGDYSKGAFGYWIENGKIQYSVEEITISGKLQNMFKQ 430
++ + G+LVT G N TGD+S G G+ IENGK+ V E+ ++G L ++
Sbjct: 363 GLIAGVEKGILVTGFNGGNNNSSTGDFSYGIEGFLIENGKLTQPVSEMNVTGNLITLWNS 422
Query: 431 IVAIGSDVLTRNSNTSGSILIENMIIAG 458
+VA G+D +S S++ E + +G
Sbjct: 423 LVATGNDPRLNSSWRIPSLVFEGVDFSG 450
>pdb|1VL4|A Chain A, Crystal Structure Of A Putative Modulator Of A Dna Gyrase
(Tm0727) From Thermotoga Maritima Msb8 At 1.95 A
Resolution
pdb|1VL4|B Chain B, Crystal Structure Of A Putative Modulator Of A Dna Gyrase
(Tm0727) From Thermotoga Maritima Msb8 At 1.95 A
Resolution
Length = 447
Score = 150 bits (378), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 85/254 (33%), Positives = 152/254 (59%), Gaps = 7/254 (2%)
Query: 210 NWYSSNSDPKKLDQPEIIGFYAAKRTISRLKAKKISTRKCPVLFEAPLAFELLNIFARLI 269
+WY P+ L+ PE IG AA+ IS + +K I + K PVL +L+ +F +I
Sbjct: 197 SWYELARTPEDLN-PEEIGKRAAEEAISLIGSKTIPSGKYPVLMRNTALLDLMEMFIPMI 255
Query: 270 SGNSLYRKSTFLVDSLGKKIFSSHIQIIEDPHILGSFGSSSFDNEGVKTQKRLVVKNGII 329
S ++ + + L LG+++ + + I + P+ S+ FD+EGV T ++ V++NG++
Sbjct: 256 SAENVQKNLSPLKGKLGEQVGNPAVSIKDLPYHPKGLSSTPFDDEGVPTTEKFVLENGVL 315
Query: 330 QGYFLSTYSAKKLGMKTTGNS--GGAHHLIIISNKTKSSDNLKEMLKKMNTGLLVTELMG 387
+ + + +A+K G++ TGN GG + ++ + S +E+LK+M+ G+++TE+ G
Sbjct: 316 KTFLHNLKTARKEGVEPTGNGFVGGIRPVNLMLMPGEKS--FEELLKEMDRGVVITEVEG 373
Query: 388 --DGINYITGDYSKGAFGYWIENGKIQYSVEEITISGKLQNMFKQIVAIGSDVLTRNSNT 445
G N I+G++S A GYW+ENG+I + VE+ITISG ++ ++IV +G+DV
Sbjct: 374 MHAGANSISGEFSLFAKGYWVENGEIAHGVEDITISGNFLDLLRKIVLVGNDVKVSQHTI 433
Query: 446 SGSILIENMIIAGK 459
+ S+L+E + +AGK
Sbjct: 434 APSVLVEVLDVAGK 447
>pdb|1MKY|A Chain A, Structural Analysis Of The Domain Interactions In Der, A
Switch Protein Containing Two Gtpase Domains
Length = 439
Score = 29.3 bits (64), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 62 NNDKNMNVIIYIQDGKK-MFYGNSSTSDFCKKSLYDTI---NAAYNIARF 107
N + ++++++ DGK+ + + S +DF +KS DTI N A N+ F
Sbjct: 77 NXIREADLVLFVVDGKRGITKEDESLADFLRKSTVDTILVANKAENLREF 126
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
0.317 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: 13,467,310
Number of Sequences: 62578
Number of extensions: 572660
Number of successful extensions: 1291
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1279
Number of HSP's gapped (non-prelim): 16
length of query: 459
length of database: 14,973,337
effective HSP length: 102
effective length of query: 357
effective length of database: 8,590,381
effective search space: 3066766017
effective search space used: 3066766017
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: 53 (25.0 bits)