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= 045562
(525 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 = 100 bits (250), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 119/495 (24%), Positives = 197/495 (39%), Gaps = 98/495 (19%)
Query: 40 RSALFIIGVEMAERFAYYGVSSNLITYLTGPLAQST------ATAAENVNAWSGVASLLP 93
R +II E ERF++YG+ + L +L L S A A + +++ P
Sbjct: 12 RQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFP 71
Query: 94 LFGAFLADSFLGRYRAIIIXXXXXXXXXXXXXXXXXXXXXXXXECQNTSCSANQFQVIF- 152
L G ++AD F G+Y I+ C + F IF
Sbjct: 72 LLGGWIADRFFGKYNTILWLSLIY-------------------------CVGHAFLAIFE 106
Query: 153 -----FFFSLYLIALGQGGHKPCVQAFGADQFDSQHPLESKLKSSFFNWWYFGMCMGTFV 207
F+ L+LIALG GG KP V +F DQFD + L F+ +YF + G+F
Sbjct: 107 HSVQGFYTGLFLIALGSGGIKPLVSSFMGDQFDQSN---KSLAQKAFDMFYFTINFGSFF 163
Query: 208 TLTVLNYIQDNLNWILGFGIPCILMVIALVVFLLGTKIYRYSLKGEEKSPFLRIGQVFVT 267
+ + N + FGIP +LM +A V F LG K Y + + E K P F+
Sbjct: 164 ASLSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIH-MPPEPKDP-----HGFLP 217
Query: 268 AVRNWRITPSAIALEEEARGT------LPHQSSEQFKFLNK-----------ALLASNGS 310
+R SA+ + E +G L S + +N A++ G
Sbjct: 218 VIR------SALLTKVEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGF 271
Query: 311 KGYG---------KVCSVGEVEEAKALLRLVPIWTTCLVYAIVFAQSSTFFTKQGVTMDR 361
G G K V+ +++LR++ ++ + +F Q ++ + Q M
Sbjct: 272 VGAGASLQLERARKSHPDAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDM-- 329
Query: 362 SVVADFQIPAASLQSFISLAIVLTIPIYDRIFVPIARTFTRKPAGITMLQRIGTGMFLSA 421
V A +Q+ L ++L IP + + P R +T L+++G G+
Sbjct: 330 --VKPQWFEPAMMQALNPLLVMLLIPFNNFVLYP---AIERMGVKLTALRKMGAGI---- 380
Query: 422 ASMTGATLVEMKRLKTAEEYGLVDKPNVTIPMSVWWLIPQYALLGVSEAFTMVGLQEFFY 481
++TG + + + ++ + G +S++W I YALL E EF Y
Sbjct: 381 -AITGLSWIVVGTIQLMMDGGSA--------LSIFWQILPYALLTFGEVLVSATGLEFAY 431
Query: 482 DQVPTELRSVGLSLY 496
Q P ++ +S +
Sbjct: 432 SQAPKAMKGTIMSFW 446
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 53/209 (25%), Positives = 86/209 (41%), Gaps = 31/209 (14%)
Query: 41 SALFIIGVEMAERFAYYGVSSNLITYL-----TGPLAQSTATAAENVNAWSGVASLLPLF 95
S LF+ EM ERF+YYG+ + L+ Y+ TG L + ATAA + ++ + L
Sbjct: 16 STLFM--TEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLSGTI 73
Query: 96 GAFLADSFLGRYRAIIIXXXXXXXXXXXXXXXXXXXXXXXXECQNTSCSANQFQVIFFFF 155
G F+AD +G A+ A F F
Sbjct: 74 GGFVADRIIGARPAVFWGGVLI--------------------MLGHIVLALPFGASALFG 113
Query: 156 SLYLIALGQGGHKPCVQAFGADQFDSQHPLESKLKSSFFNWWYFGMCMGTFVTLTVLNYI 215
S+ LI +G G KP V +D + + + F+ + FG+ +G F+ ++
Sbjct: 114 SIILIIIGTGFLKPNVSTLVGTLYDEH----DRRRDAGFSIFVFGINLGAFIAPLIVGAA 169
Query: 216 QDNLNWILGFGIPCILMVIALVVFLLGTK 244
Q+ + + F + I M I L+V+ G K
Sbjct: 170 QEAAGYHVAFSLAAIGMFIGLLVYYFGGK 198
>pdb|2ZZR|A Chain A, Crystal Structure Of Unsaturated Glucuronyl Hydrolase From
Streptcoccus Agalactiae
Length = 397
Score = 28.9 bits (63), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 24/56 (42%)
Query: 178 QFDSQHPLESKLKSSFFNWWYFGMCMGTFVTLTVLNYIQDNLNWILGFGIPCILMV 233
+ + + +E LK + N YFG T T + + DN W GF C+ +
Sbjct: 25 KIEVEEAIEKALKQLYINIDYFGEEYPTPATFNNIYKVMDNTEWTNGFWTGCLWLA 80
>pdb|3VXD|A Chain A, Crystal Structure Of Unsaturated Glucuronyl Hydrolase
Mutant D115n From Streptcoccus Agalactiae
pdb|3VXD|B Chain B, Crystal Structure Of Unsaturated Glucuronyl Hydrolase
Mutant D115n From Streptcoccus Agalactiae
pdb|3VXD|C Chain C, Crystal Structure Of Unsaturated Glucuronyl Hydrolase
Mutant D115n From Streptcoccus Agalactiae
pdb|3VXD|D Chain D, Crystal Structure Of Unsaturated Glucuronyl Hydrolase
Mutant D115n From Streptcoccus Agalactiae
Length = 398
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 24/56 (42%)
Query: 178 QFDSQHPLESKLKSSFFNWWYFGMCMGTFVTLTVLNYIQDNLNWILGFGIPCILMV 233
+ + + +E LK + N YFG T T + + DN W GF C+ +
Sbjct: 26 KIEVEEAIEKALKQLYINIDYFGEEYPTPATFNNIYKVMDNTEWTNGFWTGCLWLA 81
>pdb|3ANI|A Chain A, Crystal Structure Of Unsaturated Glucuronyl Hydrolase
Mutant D175n From Streptcoccus Agalactiae
pdb|3ANK|A Chain A, Crystal Structure Of Unsaturated Glucuronyl Hydrolase
Mutant D175n From Streptcoccus Agalactiae Complexed With
Dglca-Galnac6s
Length = 398
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 24/56 (42%)
Query: 178 QFDSQHPLESKLKSSFFNWWYFGMCMGTFVTLTVLNYIQDNLNWILGFGIPCILMV 233
+ + + +E LK + N YFG T T + + DN W GF C+ +
Sbjct: 26 KIEVEEAIEKALKQLYINIDYFGEEYPTPATFNNIYKVMDNTEWTNGFWTGCLWLA 81
>pdb|3ANJ|A Chain A, Crystal Structure Of Unsaturated Glucuronyl Hydrolase From
Streptcoccus Agalactiae
Length = 398
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 24/56 (42%)
Query: 178 QFDSQHPLESKLKSSFFNWWYFGMCMGTFVTLTVLNYIQDNLNWILGFGIPCILMV 233
+ + + +E LK + N YFG T T + + DN W GF C+ +
Sbjct: 26 KIEVEEAIEKALKQLYINIDYFGEEYPTPATFNNIYKVMDNTEWTNGFWTGCLWLA 81
>pdb|3H8I|A Chain A, The First X-Ray Structure Of A Sulfide:quinone
Oxidoreductase: Insights Into Sulfide Oxidation
Mechanism
pdb|3H8I|B Chain B, The First X-Ray Structure Of A Sulfide:quinone
Oxidoreductase: Insights Into Sulfide Oxidation
Mechanism
pdb|3H8L|A Chain A, The First X-Ray Structure Of A Sulfide:quinone
Oxidoreductase: Insights Into Sulfide Oxidation
Mechanism
pdb|3H8L|B Chain B, The First X-Ray Structure Of A Sulfide:quinone
Oxidoreductase: Insights Into Sulfide Oxidation
Mechanism
Length = 409
Score = 28.5 bits (62), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 426 GATLVEMKRLKTAEEYGLVDKPNVTIPMSVWWLIPQYALLGVSEAFTMVGLQEFFYDQVP 485
G LV ++K E+ +VD+ TIP + L+P Y + T + + + +P
Sbjct: 232 GIKLVHNFKIKEIREHEIVDEKGNTIPADITILLPPYTGNPALKNSTPDLVDDGGF--IP 289
Query: 486 TELRSVGLSLYLSIFGVGS 504
T+L V + Y +++ VG
Sbjct: 290 TDLNMVSIK-YDNVYAVGD 307
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
0.324 0.138 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,795,480
Number of Sequences: 62578
Number of extensions: 527161
Number of successful extensions: 1495
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1483
Number of HSP's gapped (non-prelim): 10
length of query: 525
length of database: 14,973,337
effective HSP length: 103
effective length of query: 422
effective length of database: 8,527,803
effective search space: 3598732866
effective search space used: 3598732866
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: 54 (25.4 bits)