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= psy195
(691 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 = 174 bits (440), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 122/403 (30%), Positives = 188/403 (46%), Gaps = 76/403 (18%)
Query: 10 MLSPSEQPKYPKAVFFIVINEFCERFCYYGMRTVLSLYMHLVLLYD------EKTATVMF 63
M SP + PK+P+ + +I+ +E CERF +YGMR +L+ ++ LL A +F
Sbjct: 1 MNSPVDAPKWPRQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVF 60
Query: 64 HIWTGLCYFFPLFGGIIADTYLGKFLTIVILSIVYLGGNVLLTVTAIDPLNIPKRTFTLV 123
H + YFFPL GG IAD + GK+ TI+ LS++Y G+ L + + F
Sbjct: 61 HSFVIGVYFFPLLGGWIADRFFGKYNTILWLSLIYCVGHAFLAI-----FEHSVQGF-YT 114
Query: 124 GLLLIAVGTGGIKPCVSSFGGDQFIVPEQSAQLEKFFSLFYFSINAGSLISTFITPIFRH 183
GL LIA+G+GGIKP VSSF GDQF +S +K F +FYF+IN GS ++ P+
Sbjct: 115 GLFLIALGSGGIKPLVSSFMGDQFDQSNKSLA-QKAFDMFYFTINFGSFFASLSMPLL-- 171
Query: 184 DMQCFGQEACFPLAFGVPALLMFLAIIVFIIGKPMYKINKP------------------- 224
++ FG +AFG+P +LMF+A + F +G+ Y P
Sbjct: 172 -LKNFGAA----VAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTK 226
Query: 225 ---KGNVALEV-----------------------FQCTIRAIKNKFKTKKSERTKEHWLD 258
KGN+ L + C + + S + L+
Sbjct: 227 VEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQ-----LE 281
Query: 259 YANDKYDQGTIEDIKTXXXXXXXXXXXXXXWALFDQQGSRWTFQANRMDGRVFGTSLEIK 318
A + ++ +++ W+LFDQ+ S W QAN M + +
Sbjct: 282 RARKSHPDAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDMVKPQW-----FE 336
Query: 319 PDQMQLINPLLILTFIPLFQYVIYPLVDKCGLN-RPLRKLTVG 360
P MQ +NPLL++ IP +V+YP +++ G+ LRK+ G
Sbjct: 337 PAMMQALNPLLVMLLIPFNNFVLYPAIERMGVKLTALRKMGAG 379
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 35/113 (30%), Positives = 55/113 (48%), Gaps = 12/113 (10%)
Query: 580 LKDDSSNKVSMLWLFPQYIIITAAEIMFSITGFEFAFTQAPVSMKSAVSACWLLTTAFGN 639
L D + +S+ W Y ++T E++ S TG EFA++QAP +MK + + W L+ GN
Sbjct: 395 LMMDGGSALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTVGN 454
Query: 640 LIVAI----VAEAKIFEN--------QAYEFLLFASLMVVDMGVFALLAMRYK 680
L V + V + E A++ FA ++ VFAL A Y+
Sbjct: 455 LWVLLANVSVKSPTVTEQIVQTGMSVTAFQMFFFAGFAILAAIVFALYARSYQ 507
>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 = 71.2 bits (173), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 62/194 (31%), Positives = 94/194 (48%), Gaps = 23/194 (11%)
Query: 28 INEFCERFCYYGMRTVLSLYMHLV-----LLYDEKTATVMFHIWTGLCYFFPLFGGIIAD 82
+ E ERF YYGMR +L YM + L TA + I+ + Y GG +AD
Sbjct: 20 MTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTIGGFVAD 79
Query: 83 TYLGKFLTIVILSIVYLGGNVLLTVTAIDPLNIPKRTFTLVG-LLLIAVGTGGIKPCVSS 141
+G V+ GG VL+ + I L +P L G ++LI +GTG +KP VS+
Sbjct: 80 RIIGA------RPAVFWGG-VLIMLGHIV-LALPFGASALFGSIILIIIGTGFLKPNVST 131
Query: 142 FGGDQFIVPEQSAQLEKFFSLFYFSINAGSLISTFITPIFRHDMQCFGQEACFPLAFGVP 201
G + E + + FS+F F IN G+ FI P+ Q + A + +AF +
Sbjct: 132 LVGTLY--DEHDRRRDAGFSIFVFGINLGA----FIAPLIVGAAQ---EAAGYHVAFSLA 182
Query: 202 ALLMFLAIIVFIIG 215
A+ MF+ ++V+ G
Sbjct: 183 AIGMFIGLLVYYFG 196
Score = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 583 DSSNKVSMLWLFPQYIIITAAEIMFSITGFEFAFTQAPVSMKSAVSACWLLTTAFGN 639
+S KVS LWL + ++ E++ S G AP + S + + W L+++ G+
Sbjct: 379 GTSGKVSPLWLVGSWALVILGEMLISPVGLSVTTKLAPKAFNSQMMSMWFLSSSVGS 435
>pdb|1Y07|A Chain A, Crystal Structure Of The Superoxide Reductase From
Treponema Pallidum
pdb|1Y07|B Chain B, Crystal Structure Of The Superoxide Reductase From
Treponema Pallidum
pdb|1Y07|C Chain C, Crystal Structure Of The Superoxide Reductase From
Treponema Pallidum
pdb|1Y07|D Chain D, Crystal Structure Of The Superoxide Reductase From
Treponema Pallidum
Length = 128
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 516 GFYQDIDLPTG---ACYTEYIEGIPAGVYEVRSENKVLKSNMELQDDNVYVLNLNTEASP 572
GF+ +D P G AC +E + +P G + E + + + V V ++ +P
Sbjct: 15 GFFLGMDAPAGSSVACGSEVLRAVPVGTVDAAKEKHIPVVEVHGHEVKVKVGSVAHPMTP 74
Query: 573 EHRTA 577
EH A
Sbjct: 75 EHYIA 79
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
0.325 0.140 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,663,792
Number of Sequences: 62578
Number of extensions: 737523
Number of successful extensions: 1598
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1583
Number of HSP's gapped (non-prelim): 8
length of query: 691
length of database: 14,973,337
effective HSP length: 106
effective length of query: 585
effective length of database: 8,340,069
effective search space: 4878940365
effective search space used: 4878940365
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.8 bits)