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= 043161
(444 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MKT|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKT|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKU|A Chain A, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
pdb|3MKU|B Chain B, Structure Of A Cation-Bound Multidrug And Toxin Compound
Extrusion (Mate) Transporter
Length = 460
Score = 88.2 bits (217), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 90/412 (21%), Positives = 185/412 (44%), Gaps = 19/412 (4%)
Query: 33 FWTETVKMWKIATPIVFNILCNYGTNSFTNIFVGHIGEIELSSVTISLSV-IGTFSFGFM 91
+ E + K+ATP++ + G I G + I++++V+I+ S+ + + FG
Sbjct: 7 YKKEASNLIKLATPVLIASVAQTGMGFVDTIMAGGVSAIDMAAVSIAASIWLPSILFG-- 64
Query: 92 LGMGSALETLCGQAFGAGQVHMLGVYMQRSWLILSVTCVCLLPIYCFASPILKLLGQEEQ 151
+G+ AL + Q GAG+ H + + + ++ + V ++ + I++ + EE
Sbjct: 65 VGLLMALVPVVAQLNGAGRQHKIPFEVHQGLILALLVSVPIIAVLFQTQFIIRFMDVEEA 124
Query: 152 IADLAGQFTILTIPQLFSLAINFPTQKFLQAQSKVSAFAWIGFVALVVHIVMLYVFIY-- 209
+A + I + + + + F S IGF+ L+++I + ++F+Y
Sbjct: 125 MATKTVGYMHAVIFAVPAYLLFQALRSFTDGMSLTKPAMVIGFIGLLLNIPLNWIFVYGK 184
Query: 210 --VFDWGMTGAAIAYDISSWIIAIGQVIYVIGWCK-------ETWHGLSRAAFIEIWAFV 260
+ G G +A I WI+ + + Y++ + ET+H I ++
Sbjct: 185 FGAPELGGVGCGVATAIVYWIMLLLLLFYIVTSKRLAHVKVFETFHKPQPKELIRLF--- 241
Query: 261 RLSLASAVMLCLEIWYMMSIIILTGHLDNAIVAVGSLSVCMNLNGWEAMLFIGINAAISV 320
RL A L E+ + +L L + +VA + V +N + M + I AA+S+
Sbjct: 242 RLGFPVAAALFFEVTLFAVVALLVAPLGSTVVA--AHQVALNFSSLVFMFPMSIGAAVSI 299
Query: 321 RVSNELGLGHPRAAKYSVYVTVFQSLLIGVLFMVIILITKDYFAIIFTSSAELQQAVAKL 380
RV ++LG + A + V + L + ++ ++ ++ A+++T + + +L
Sbjct: 300 RVGHKLGEQDTKGAAIAANVGLMTGLATACITALLTVLFREQIALLYTENQVVVALAMQL 359
Query: 381 AFLLGITMVLNSVQPVISGVAIGGGWQAMVAYINIGSYYIFGLPLGYLLGYT 432
I +++VQ V +G G + + SY++ GLP GY+LG T
Sbjct: 360 LLFAAIYQCMDAVQVVAAGSLRGYKDMTAIFHRTFISYWVLGLPTGYILGMT 411
>pdb|4HUK|A Chain A, Mate Transporter Norm-ng In Complex With Tpp And Monobody
pdb|4HUL|A Chain A, Mate Transporter Norm-ng In Complex With Cs+ And Monobody
pdb|4HUM|A Chain A, Mate Transporter Norm-ng In Complex With Ethidium And
Monobody
pdb|4HUN|A Chain A, Mate Transporter Norm-ng In Complex With R6g And Monobody
Length = 459
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 85/423 (20%), Positives = 175/423 (41%), Gaps = 26/423 (6%)
Query: 31 SVFWTETVKMWKIATPIVFNILCNYGTNSFTNIFVGHIGEIELSSVTISLSVIGTFSFGF 90
SVF E + +A P++ + G + G G+ +L++V + S T F
Sbjct: 7 SVFLKEIRLLTALALPMLLAQVAQVGIGFVDTVMAGGAGKEDLAAVALGSSAFATVYITF 66
Query: 91 MLGMGSALETLCGQAFGAGQVHMLG-VYMQRSWLILSVTCVCLLPIYCFASPILKLLGQE 149
M G+ +AL + Q +GAG+ G Q W L + ++ ++ +P L
Sbjct: 67 M-GIMAALNPMIAQLYGAGKTGEAGETGRQGIWFGLILGIFGMILMWAAITPFRNWLTLS 125
Query: 150 EQIADLAGQFTILTIPQLFSLAINFPTQKFLQAQSKVSAFAWIGFVALVVHIVMLYVFIY 209
+ + Q+ + T + + ++ + + ++ + F A V+++ + Y+F+Y
Sbjct: 126 DYVEGTMAQYMLFTSLAMPAAMVHRALHAYASSLNRPRLIMLVSFAAFVLNVPLNYIFVY 185
Query: 210 VFDWGM-----TGAAIAYDISSWIIAIGQVIYVIGWCKETWH---GLSR-------AAFI 254
+GM G +A W A+ IY+ KE + GL+ A F
Sbjct: 186 G-KFGMPALGGAGCGVATMAVFWFSALALWIYI---AKEKFFRPFGLTAKFGKPDWAVFK 241
Query: 255 EIWAFVRLSLASAVMLCLEIWYMMSIIILTGHLDNAIVAVGSLSVCMNLNGWEAMLFIGI 314
+IW ++ + LE I+ L VA + V ++L+G M+ +
Sbjct: 242 QIW---KIGAPIGLSYFLEASAFSFIVFLIAPFGEDYVA--AQQVGISLSGILYMIPQSV 296
Query: 315 NAAISVRVSNELGLGHPRAAKYSVYVTVFQSLLIGVLFMVIILITKDYFAIIFTSSAELQ 374
+A +VR+ LG A+Y V++ ++ V+ ++ +++ + A ++ +
Sbjct: 297 GSAGTVRIGFSLGRREFSRARYISGVSLVSGWVLAVITVLSLVLFRSPLASMYNDDPAVL 356
Query: 375 QAVAKLAFLLGITMVLNSVQPVISGVAIGGGWQAMVAYINIGSYYIFGLPLGYLLGYTAN 434
+ + G+ + Q + S G + +I+ +++ GL GYLL Y +
Sbjct: 357 SIASTVLLFAGLFQPADFTQCIASYALRGYKVTKVPMFIHAAAFWGCGLLPGYLLAYRFD 416
Query: 435 LGV 437
+G+
Sbjct: 417 MGI 419
>pdb|1Q47|A Chain A, Structure Of The Semaphorin 3a Receptor-Binding Module
pdb|1Q47|B Chain B, Structure Of The Semaphorin 3a Receptor-Binding Module
Length = 495
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%)
Query: 222 YDISSWIIAIGQVIYVIGWCKETWHGLSRAAFIEIWAFVRLSLASAVMLCLE 273
YD+ +G V+ V+ KETWH L E+ F + SA+ L +
Sbjct: 421 YDVMFIGTDVGTVLKVVSVPKETWHDLEEVLLEEMTVFREPTTISAMELSTK 472
>pdb|4GZA|G Chain G, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
Length = 538
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%)
Query: 222 YDISSWIIAIGQVIYVIGWCKETWHGLSRAAFIEIWAFVRLSLASAVML 270
YD+ +G V+ V+ KETWH L E+ F + SA+ L
Sbjct: 429 YDVMFIGTDVGTVLKVVSVPKETWHDLEEVLLEEMTVFREPTTISAMEL 477
>pdb|4GZ8|A Chain A, Mouse Semaphorin 3a, Domains Sema-Psi-Ig
pdb|4GZ8|B Chain B, Mouse Semaphorin 3a, Domains Sema-Psi-Ig
Length = 667
Score = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%)
Query: 222 YDISSWIIAIGQVIYVIGWCKETWHGLSRAAFIEIWAFVRLSLASAVML 270
YD+ +G V+ V+ KETWH L E+ F + SA+ L
Sbjct: 429 YDVMFIGTDVGTVLKVVSVPKETWHDLEEVLLEEMTVFREPTTISAMEL 477
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
0.328 0.141 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,076,835
Number of Sequences: 62578
Number of extensions: 452721
Number of successful extensions: 1100
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1091
Number of HSP's gapped (non-prelim): 7
length of query: 444
length of database: 14,973,337
effective HSP length: 102
effective length of query: 342
effective length of database: 8,590,381
effective search space: 2937910302
effective search space used: 2937910302
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (25.0 bits)