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= 008231
(573 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter.
pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
Family Transporter
Length = 524
Score = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 102/426 (23%), Positives = 171/426 (40%), Gaps = 31/426 (7%)
Query: 152 LYAALYTIALGGGGIKSNVSGFGSDQFDTSDPK-EEKAMIFFFNRFYFAISIGSLFAVIV 210
Y L+ IALG GGIK VS F DQFD S+ +KA F+ FYF I+ GS FA +
Sbjct: 112 FYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA----FDMFYFTINFGSFFASLS 167
Query: 211 LVYVQDNVGRGWGYGISAGTMVVAAAILLIGTPWY-----RFKKPRGSPLTVIWRVLLLA 265
+ + N G +GI M VA +G Y K P G L VI LL
Sbjct: 168 MPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGF-LPVIRSALLTK 226
Query: 266 WKKRSH---PYPDHPSLLNEYQNAKVPHTEKFKCLDKAAIIEDNAV---ANENKNNSWIV 319
+ + + + Y +P L A ++ V A+ +
Sbjct: 227 VEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERARKS 286
Query: 320 STVTEVEEVKMVLKLLPIWATCILFWTVYSQMTTFTVEQATFMNRKIGSFTVPSGXXXXX 379
V+ V+ VL++L ++A FW+++ Q + + QA N +
Sbjct: 287 HPDAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQA---NDMVKPQWFEPAMMQAL 343
Query: 380 XXXXXXXXXXXNEKVFVPLARKITHSIQGMTSLQRVGTGLIFSVIAMIVSAVIEQQRRET 439
N V P ++ +T+L+++G G+ + ++ IV I+
Sbjct: 344 NPLLVMLLIPFNNFVLYPAIERMGVK---LTALRKMGAGIAITGLSWIVVGTIQLMMDGG 400
Query: 440 SVQKHIQISAFWLVPQYFLVGAGEAFVYVGQLEFFIREGPERMKSMSTGLFLSAISMG-M 498
S +S FW + Y L+ GE V LEF + P+ MK + ++++G +
Sbjct: 401 SA-----LSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGNL 455
Query: 499 FVSSMLVSIVDKITNKHWLRSNLNKGKLNNFYWLLAVLGLLNFMVFLFFAMKHQYNVQHR 558
+V VS+ + +++ ++ F++ A +L +VF +A +Q +R
Sbjct: 456 WVLLANVSVKSPTVTEQIVQTGMSVTAFQMFFF--AGFAILAAIVFALYARSYQMQDHYR 513
Query: 559 VKGDKE 564
E
Sbjct: 514 QATGSE 519
>pdb|1L8K|A Chain A, T Cell Protein-Tyrosine Phosphatase Structure
Length = 314
Score = 36.6 bits (83), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 10/100 (10%)
Query: 259 WRVLLLAWKKRSHPYPDHPSLLNEYQNAKVPHTEKFKCLDKAAIIEDNAVANENKNNSWI 318
W+ L L + SH YP ++ AK P + + + V +N N +I
Sbjct: 18 WQPLYLEIRNESHDYP--------HRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYI 69
Query: 319 VSTVTEVEEVKM--VLKLLPIWATCILFWTVYSQMTTFTV 356
+++ ++EE + +L P+ TC FW + Q T V
Sbjct: 70 NASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAV 109
>pdb|4APS|A Chain A, Crystal Structure Of A Pot Family Peptide Transporter In
An Inward Open Conformation.
pdb|4APS|B Chain B, Crystal Structure Of A Pot Family Peptide Transporter In
An Inward Open Conformation
Length = 491
Score = 34.3 bits (77), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 79/365 (21%), Positives = 142/365 (38%), Gaps = 64/365 (17%)
Query: 25 DRSKT--GGWLAAGLILGTELSERICAMGISMNLVTYL-----VGDLHLSSAKSATIVTN 77
D+ KT G L + TE+ ER G+ L+ Y+ GDLH++ A +A+I+
Sbjct: 3 DKGKTFFGQPLGLSTLFMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIM-- 60
Query: 78 FMXXXXXXXXXXXXXXXXXXXRYLTVAIFASVTAL--VVGLLTSATSIPSMRPPQ-CDDY 134
AI+AS+ L +G A I RP
Sbjct: 61 --------------------------AIYASMVYLSGTIGGFV-ADRIIGARPAVFWGGV 93
Query: 135 RRKHHQCIEANGKQLAMLYAALYTIALGGGGIKSNVSGFGSDQFDTSDPKEEKAMIFFFN 194
+ A + L+ ++ I +G G +K NVS +D D + + F+
Sbjct: 94 LIMLGHIVLALPFGASALFGSIILIIIGTGFLKPNVSTLVGTLYDEHDRRRDAG----FS 149
Query: 195 RFYFAISIGSLFAVIVLVYVQDNVGRGWGYGISAGTMVVAAAILLIG-----TPWYRFKK 249
F F I++G+ A +++ Q+ G + ++A M + + G P Y
Sbjct: 150 IFVFGINLGAFIAPLIVGAAQEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPT 209
Query: 250 PRGSPLTVIWRVLLLAWKKRSHPYPDHPSLLNEYQNAKVPHTEKFKCLDKAAIIEDNAVA 309
+P V + LL+ + ++N +P ++ I+ A+A
Sbjct: 210 DPLAPEEV--KPLLVKVSLAVAGFIAIIVVMNLVGWNSLP-----AYINLLTIV---AIA 259
Query: 310 NENKNNSWIVSTV--TEVEEVKMVLKLLPIWATCILFWTVYSQMTTFTVEQATFMNRKIG 367
+W++S+V T E +++V +P++ +LFW + Q +V ATF ++
Sbjct: 260 IPVFYFAWMISSVKVTSTEHLRVV-SYIPLFIAAVLFWAIEEQG---SVVLATFAAERVD 315
Query: 368 SFTVP 372
S P
Sbjct: 316 SSWFP 320
>pdb|2FEA|A Chain A, Crystal Structure Of Mtnx Phosphatase From Bacillus
Subtilis At 2.00 A Resolution
pdb|2FEA|B Chain B, Crystal Structure Of Mtnx Phosphatase From Bacillus
Subtilis At 2.00 A Resolution
Length = 236
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 262 LLLAWKKRSHPYPDHPSLLNEYQNAKVPHTEKFKCLDKAAIIEDNAVANENKNNSWIV-- 319
LL ++ Y +H S N+Y + PH+ K C ++ + + + ++ N +I+
Sbjct: 110 LLEGIVEKDRIYCNHASFDNDYIHIDWPHSCKGTCSNQCGCCKPSVIHELSEPNQYIIXI 169
Query: 320 -STVTEVEEVKM 330
+VT+VE K+
Sbjct: 170 GDSVTDVEAAKL 181
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
0.323 0.136 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,217,034
Number of Sequences: 62578
Number of extensions: 582553
Number of successful extensions: 918
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 914
Number of HSP's gapped (non-prelim): 15
length of query: 573
length of database: 14,973,337
effective HSP length: 104
effective length of query: 469
effective length of database: 8,465,225
effective search space: 3970190525
effective search space used: 3970190525
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)