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= 008856
(551 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 30/110 (27%), Positives = 47/110 (42%), Gaps = 17/110 (15%)
Query: 254 EHLGIRYCPSLTCIFSKNELPATLESLEVGNLP-----------PSLKSLRVRYCSKLES 302
E GIR P+ L+SL++ N P P L+ L +R C+ L +
Sbjct: 191 EWTGIRSLPASIANLQ------NLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRN 244
Query: 303 IAERLDNNTSLETISIYNCENLKILPSGLHKLHQLREISIGSCGNLVSFP 352
L+ + + +C NL LP +H+L QL ++ + C NL P
Sbjct: 245 YPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLP 294
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 56/197 (28%), Positives = 80/197 (40%), Gaps = 29/197 (14%)
Query: 311 TSLETISIYNCENLKILPSGLHKLHQLREISIGSCGNLVSFPGGGLPCAKLTALEIYDCK 370
LET+++ L+ LP+ + L++LRE+SI +C L P P A A +
Sbjct: 127 AGLETLTLAR-NPLRALPASIASLNRLRELSIRACPELTELPE---PLASTDASGEH--- 179
Query: 371 RLKALPKGLHNLSTLQDLTIGGALLSLEEDGLPTNLHSLVIRGNMEIWKSMIEWGRGFHR 430
+GL NL +L+ G L L NL SL IR + + G H
Sbjct: 180 ------QGLVNLQSLRLEWTGIRSLPASIANL-QNLKSLKIRNS-----PLSALGPAIHH 227
Query: 431 FSSLRHLTIDGCDDDTMMVSFPLEDKRLGTVLRLPTTLTSLRIEDFPNLERLSSSIIDLR 490
L L + GC T + ++P + L L ++D NL L I L
Sbjct: 228 LPKLEELDLRGC---TALRNYP-------PIFGGRAPLKRLILKDCSNLLTLPLDIHRLT 277
Query: 491 NLTELVLRGCPKLKYFP 507
L +L LRGC L P
Sbjct: 278 QLEKLDLRGCVNLSRLP 294
Score = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 51/207 (24%), Positives = 90/207 (43%), Gaps = 22/207 (10%)
Query: 131 CEGLVKLPQSSFSLSSLREIEIFKCSSLVSFP-EVALPSKLKKIQIGECDALKSLPEAWM 189
GL +LP + + L + + + + L + P +A ++L+++ I C L LPE +
Sbjct: 113 AAGLXELPDTXQQFAGLETLTLAR-NPLRALPASIASLNRLRELSIRACPELTELPEP-L 170
Query: 190 CDTNSSLEILSIHGCRSLT--YIAAVQLPSSLKMLTIWYCDNIRTLTVEEGIQCXXXXXX 247
T++S E + +SL + LP+S+ L N+++L +
Sbjct: 171 ASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANL-----QNLKSLKIRNSPLSALGPAI 225
Query: 248 XXXXXXEHLGIRYCPSLTCIFSKNELPATLESLEVGNLPPSLKSLRVRYCSKLESIAERL 307
E L +R C +L +N P + G P LK L ++ CS L ++ +
Sbjct: 226 HHLPKLEELDLRGCTAL-----RNYPP-----IFGGRAP--LKRLILKDCSNLLTLPLDI 273
Query: 308 DNNTSLETISIYNCENLKILPSGLHKL 334
T LE + + C NL LPS + +L
Sbjct: 274 HRLTQLEKLDLRGCVNLSRLPSLIAQL 300
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 34/79 (43%), Gaps = 12/79 (15%)
Query: 430 RFSSLRHLTIDGCDDDTMMVSFPLEDKRLGTVLRLPTTLTSLRIEDFPNLERLSSSIIDL 489
R S L+H TID + P ++ + TLT R L L +SI L
Sbjct: 102 RLSHLQHXTIDAAG----LXELPDTXQQFAGL----ETLTLARNP----LRALPASIASL 149
Query: 490 RNLTELVLRGCPKLKYFPE 508
L EL +R CP+L PE
Sbjct: 150 NRLRELSIRACPELTELPE 168
>pdb|1G9U|A Chain A, Crystal Structure Of Yopm-leucine Rich Effector Protein
From Yersinia Pestis
pdb|1JL5|A Chain A, Novel Molecular Architecture Of Yopm-A Leucine-Rich
Effector Protein From Yersinia Pestis
Length = 454
Score = 37.4 bits (85), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 92/385 (23%), Positives = 141/385 (36%), Gaps = 89/385 (23%)
Query: 133 GLVKLPQSSFSLSSLREIEIFKCSSLVSFPEVALPSKLKKIQIGECD--ALKSLPE--AW 188
GL LP+ L SL + C+SL PE LP LK + + + AL LP +
Sbjct: 82 GLSSLPELPPHLESL----VASCNSLTELPE--LPQSLKSLLVDNNNLKALSDLPPLLEY 135
Query: 189 MCDTNSSLE------------ILSIHGCR---------SLTYIAA-----VQLP--SSLK 220
+ +N+ LE I+ + SL +IAA +LP +L
Sbjct: 136 LGVSNNQLEKLPELQNSSFLKIIDVDNNSLKKLPDLPPSLEFIAAGNNQLEELPELQNLP 195
Query: 221 MLTIWYCDNIRTLTVEEGIQCXXXXXXXXXXXXEHLGIRYCPSLTCIFSKNELPATLESL 280
LT Y DN + + E ++ P LT I++ N L TL
Sbjct: 196 FLTAIYADNNSLKKLPDLPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLLKTL--- 252
Query: 281 EVGNLPPSLKSLRVR--YCSKLESIAERLDNNTSLETISIYNCENLKILPSGLHKLH--- 335
+LPPSL++L VR Y + L + + L + +S L LP L+ L+
Sbjct: 253 --PDLPPSLEALNVRDNYLTDLPELPQSL----TFLDVSENIFSGLSELPPNLYYLNASS 306
Query: 336 -----------QLREISIGSCGNLVSFPGGGLPCAKLTALEIYDCKRLKALPKGLHNL-- 382
L E+++ S L+ P +L A + LP+ L L
Sbjct: 307 NEIRSLCDLPPSLEELNV-SNNKLIELPALPPRLERLIA-SFNHLAEVPELPQNLKQLHV 364
Query: 383 ------------STLQDLTIGGALLSLEEDGLPTNLHSLVIRGN-----MEIWKSMIEWG 425
+++DL + L + E LP NL L + N +I +S+ +
Sbjct: 365 EYNPLREFPDIPESVEDLRMNSHLAEVPE--LPQNLKQLHVETNPLREFPDIPESVEDLR 422
Query: 426 RGFHRFSS---LRHLTIDGCDDDTM 447
R H T D +DD
Sbjct: 423 MNSERVVDPYEFAHETTDKLEDDVF 447
>pdb|2D1T|A Chain A, Crystal Structure Of The Thermostable Japanese Firefly
Luciferase Red-Color Emission S286n Mutant Complexed
With High-Energy Intermediate Analogue
Length = 548
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%)
Query: 306 RLDNNTSLETISIYNCENLKILPSGLHKLHQLREISIGSCGNLVSFPGGGLPCAK 360
+ D T L+T+ Y C N+ ++P+ L++ ++ NLV GG P +K
Sbjct: 269 KFDEETFLKTLQDYKCTNVILVPTLFAILNKSELLNKYDLSNLVEIASGGAPLSK 323
>pdb|3ONM|A Chain A, Effector Binding Domain Of Lysr-Type Transcription Factor
Rovm From Y. Pseudotuberculosis
pdb|3ONM|B Chain B, Effector Binding Domain Of Lysr-Type Transcription Factor
Rovm From Y. Pseudotuberculosis
Length = 238
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 10/88 (11%)
Query: 426 RGFHRFSSLRHLTIDGCDDDTMMVSFPLEDKRLGTVLRLPTTLTSLRIEDFPNL-ERLSS 484
RG H +S++ I G DDT P R+ T+ P +R++ P + + LSS
Sbjct: 17 RGSHMYSNMEGSLIIGASDDTADTLLPFLLNRVATL--YPRLAIDVRVKRSPFIADMLSS 74
Query: 485 SIIDLRNLT-------ELVLRGCPKLKY 505
+DL T ++LR P L Y
Sbjct: 75 GEVDLAITTAKVDSHPHVILRTSPTLWY 102
>pdb|3TGQ|A Chain A, Crystal Structure Of Unliganded Hiv-1 Clade B Strain Yu2
Gp120 Core
pdb|3TGQ|B Chain B, Crystal Structure Of Unliganded Hiv-1 Clade B Strain Yu2
Gp120 Core
pdb|3TGQ|C Chain C, Crystal Structure Of Unliganded Hiv-1 Clade B Strain Yu2
Gp120 Core
pdb|3TGQ|D Chain D, Crystal Structure Of Unliganded Hiv-1 Clade B Strain Yu2
Gp120 Core
Length = 352
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 26 VWRSATDHLGSQNSVVCRDAS-NQVFLAGPLKPRIPKLEELKINNIQNETCIWKSH--NE 82
VW+ AT L + D + V+ P P +E+K+ N+ +WK++ +
Sbjct: 1 VWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVKLENVTENFNMWKNNMVEQ 60
Query: 83 LLQDICSLKRLTITSCPKL 101
+ +DI SL ++ C KL
Sbjct: 61 MHEDIISLWDQSLKPCVKL 79
>pdb|3ZYO|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
And Immunoglobulin Domain Of Netrin-G Ligand-3
Length = 411
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 122 RLEYLILSYCEGLVKLPQSSFSLSSLREIEIFKCSSLVSFPEVALP-SKLKKIQIGECDA 180
RLEY+ + EGLV L + + +L++I ++LV E+ L ++L I+ G
Sbjct: 143 RLEYISEAAFEGLVNLRYLNLGMCNLKDIP--NLTALVRLEELELSGNRLDLIRPGSFQG 200
Query: 181 LKSLPEAWM 189
L SL + W+
Sbjct: 201 LTSLRKLWL 209
>pdb|2RAR|A Chain A, X-Ray Crystallographic Structures Show Conservation Of A
Trigonal- Bipyramidal Intermediate In A
Phosphoryl-Transfer Superfamily.
pdb|2RAV|A Chain A, X-Ray Crystallographic Structures Show Conservation Of A
Trigonal- Bipyramidal Intermediate In A
Phosphoryl-Transfer Superfamily
Length = 261
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 13/69 (18%)
Query: 345 CGNLVSFPGGGLPCAKLTALEIYDCKRLKAL-----PKG-LHNLSTLQD-------LTIG 391
G LVSF +P + + ALE K LK PK ++NLS LQD +T+
Sbjct: 10 AGTLVSFETHRIPSSTIEALEAAHAKGLKIFIATGRPKAIINNLSELQDRNLIDGYITMN 69
Query: 392 GALLSLEED 400
GA + E+
Sbjct: 70 GAYCFVGEE 78
>pdb|3ZYN|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
pdb|3ZYN|B Chain B, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
Length = 321
Score = 29.6 bits (65), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 122 RLEYLILSYCEGLVKLPQSSFSLSSLREIEIFKCSSLVSFPEVALP-SKLKKIQIGECDA 180
RLEY+ + EGLV L + + +L++I ++LV E+ L ++L I+ G
Sbjct: 143 RLEYISEAAFEGLVNLRYLNLGMCNLKDIP--NLTALVRLEELELSGNRLDLIRPGSFQG 200
Query: 181 LKSLPEAWM 189
L SL + W+
Sbjct: 201 LTSLRKLWL 209
>pdb|1YMQ|A Chain A, Had Superfamily Phosphotransferase Substrate
Diversification: Structure And Function Analysis Of The
Had Subclass Iib Sugar Phosphatase Bt4131
pdb|2RB5|A Chain A, X-ray Crystallographic Structures Show Conservation Of A
Trigonal- Bipyramidal Intermediate In A
Phosphoryl-transfer Superfamily.
pdb|2RBK|A Chain A, X-ray Crystallographic Structures Show Conservation Of A
Trigonal- Bipyramidal Intermediate In A
Phosphoryl-transfer Superfamily
Length = 261
Score = 29.6 bits (65), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 13/68 (19%)
Query: 346 GNLVSFPGGGLPCAKLTALEIYDCKRLKAL-----PKG-LHNLSTLQD-------LTIGG 392
G LVSF +P + + ALE K LK PK ++NLS LQD +T+ G
Sbjct: 11 GTLVSFETHRIPSSTIEALEAAHAKGLKIFIATGRPKAIINNLSELQDRNLIDGYITMNG 70
Query: 393 ALLSLEED 400
A + E+
Sbjct: 71 AYCFVGEE 78
>pdb|4ECO|A Chain A, Crystal Structure Of A Hypothetical Protein (Bacegg_03329)
From Bacteroides Eggerthii Dsm 20697 At 2.70 A
Resolution
pdb|4ECO|B Chain B, Crystal Structure Of A Hypothetical Protein (Bacegg_03329)
From Bacteroides Eggerthii Dsm 20697 At 2.70 A
Resolution
Length = 636
Score = 28.9 bits (63), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 296 YCSKLESIAERLDNNTSLETISIYNCENLKILPSGLHKLHQLREISIG 343
Y + ++ + DN L + +YNC NL LP+ L L + + I++
Sbjct: 234 YAQQYKTEDLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEXQLINVA 281
>pdb|1ZAU|A Chain A, Adenylation Domain Of Nad+ Dependent Dna Ligase From
M.Tuberculosis
Length = 328
Score = 28.9 bits (63), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 41/96 (42%), Gaps = 7/96 (7%)
Query: 370 KRLKALPKGLHNLSTLQDLTIGGALLSLEEDGLPTNLHSLVIRGNMEIWKSMIEWGRGFH 429
+RL+ + GL ++ + T+ A L+L GLP + H+ + + + + WG H
Sbjct: 229 RRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRH 288
Query: 430 RFSSLRHLTIDGCDDDTMMVSFPLEDKRLGTVLRLP 465
IDG + V +RLG+ R P
Sbjct: 289 EVDH----EIDGV---VVKVDEVALQRRLGSTSRAP 317
>pdb|3SGI|A Chain A, Crystal Structure Of Dna Ligase A Brct Domain Deleted
Mutant Of Mycobacterium Tuberculosis
Length = 615
Score = 28.9 bits (63), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 28/121 (23%), Positives = 52/121 (42%), Gaps = 11/121 (9%)
Query: 370 KRLKALPKGLHNLSTLQDLTIGGALLSLEEDGLPTNLHSLVIRGNMEIWKSMIEWGRGFH 429
+RL+ + GL ++ + T+ A L+L GLP + H+ + + + + WG H
Sbjct: 229 RRLRMICHGLGHVEGFRPATLHQAYLALRAWGLPVSEHTTLATDLAGVRERIDYWGEHRH 288
Query: 430 RFSSLRHLTIDGCDDDTMMVSFPLEDKRLGTVLRLPTTLTSLRIEDFPNLERLSSSIIDL 489
IDG + V +RLG+ R P + + +P E + ++D+
Sbjct: 289 EVDH----EIDGV---VVKVDEVALQRRLGSTSRAPRWAIAYK---YPP-EEAQTKLLDI 337
Query: 490 R 490
R
Sbjct: 338 R 338
>pdb|2D1S|A Chain A, Crystal Structure Of The Thermostable Japanese Firefly
Luciferase Complexed With High-Energy Intermediate
Analogue
Length = 548
Score = 28.9 bits (63), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 28/55 (50%)
Query: 306 RLDNNTSLETISIYNCENLKILPSGLHKLHQLREISIGSCGNLVSFPGGGLPCAK 360
+ D T L+T+ Y C ++ ++P+ L++ ++ NLV GG P +K
Sbjct: 269 KFDEETFLKTLQDYKCTSVILVPTLFAILNKSELLNKYDLSNLVEIASGGAPLSK 323
>pdb|2D1Q|A Chain A, Crystal Structure Of The Thermostable Japanese Firefly
Luciferase Complexed With Mgatp
pdb|2D1R|A Chain A, Crystal Structure Of The Thermostable Japanese Firefly
Luciferase Complexed With Oxyluciferin And Amp
Length = 548
Score = 28.9 bits (63), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 28/55 (50%)
Query: 306 RLDNNTSLETISIYNCENLKILPSGLHKLHQLREISIGSCGNLVSFPGGGLPCAK 360
+ D T L+T+ Y C ++ ++P+ L++ ++ NLV GG P +K
Sbjct: 269 KFDEETFLKTLQDYKCTSVILVPTLFAILNKSELLNKYDLSNLVEIASGGAPLSK 323
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
0.320 0.137 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,219,172
Number of Sequences: 62578
Number of extensions: 588397
Number of successful extensions: 1183
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1161
Number of HSP's gapped (non-prelim): 32
length of query: 551
length of database: 14,973,337
effective HSP length: 104
effective length of query: 447
effective length of database: 8,465,225
effective search space: 3783955575
effective search space used: 3783955575
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)