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= 007612
(596 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 = 102 bits (254), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 118/493 (23%), Positives = 195/493 (39%), Gaps = 73/493 (14%)
Query: 46 ILLNQGLATLAFFGVGVNLVLFLTRVL------QQNNAEAANNVSKWTGTVYIFSLVGAF 99
I+ ++ +F+G+ L FL L + A A + + VY F L+G +
Sbjct: 17 IIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLGGW 76
Query: 100 LSDSYWGRFKTCAIFQXXXXXXXXXXXXXXXXXXXRPRGCGNELTPCGTHSSLEICL--- 156
++D ++G++ T L C H+ L I
Sbjct: 77 IADRFFGKYNTILWL---------------------------SLIYCVGHAFLAIFEHSV 109
Query: 157 --FYLSIYFVALGNGGYQPNIATFGADQYDEEDAKEGHSKVAFFSYFYLALNLGSLFSNT 214
FY ++ +ALG+GG +P +++F DQ+D+ + F FY +N GS F++
Sbjct: 110 QGFYTGLFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDMFYFTINFGSFFASL 166
Query: 215 ILGYFEDEGMWALGFWVSTGSAFAALVLFLAGTTRYRHFKPSGNPLARFCQVIVAATKKW 274
+ A+ F + F A V F G RY H P F VI +A
Sbjct: 167 SMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLTK 226
Query: 275 RVHLSAEGEDLYVIDANDSS-------TNGNRNMLHTHGFKFLDRAAYISSRDLDEQKQG 327
G L +I ++ T G L + +S L+ ++
Sbjct: 227 VEGKGNIGLVLALIGGVSAAYALVNIPTLGIVAGLCCAMVLVMGFVGAGASLQLERARKS 286
Query: 328 CSNPWRLCPVTQVEEVKCILRLLPIWLCTILYSVVFTQMASLFVEQGAAMKTTVSNFRIP 387
P V+ V+ +LR+L ++ + +F Q AS ++ Q M V
Sbjct: 287 H-------PDAAVDGVRSVLRILVLFALVTPFWSLFDQKASTWILQANDM---VKPQWFE 336
Query: 388 PASMSSFDILSVAAFIFLYRRVIEPLAGGIRKKNSKGLTELQRMGIGLVIAIVAMLAAGI 447
PA M + + L V I V+ P I + K LT L++MG G+ I ++ + G
Sbjct: 337 PAMMQALNPLLVMLLIPFNNFVLYP---AIERMGVK-LTALRKMGAGIAITGLSWIVVGT 392
Query: 448 VECYRLKYAKTECKHCEGASSLSIFWQVPQYALIGASEVFMYVAQLEFFNAQAPDGLKSF 507
++ +G S+LSIFWQ+ YAL+ EV + LEF +QAP +K
Sbjct: 393 IQL-----------MMDGGSALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGT 441
Query: 508 GSALCMTSISLGN 520
+ S+++GN
Sbjct: 442 IMSFWTLSVTVGN 454
>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 = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 50/104 (48%), Gaps = 6/104 (5%)
Query: 160 SIYFVALGNGGYQPNIATFGADQYDEEDAKEGHSKVAFFSYFYLALNLGSLFSNTILGYF 219
SI + +G G +PN++T YDE D + A FS F +NLG+ + I+G
Sbjct: 114 SIILIIIGTGFLKPNVSTLVGTLYDEHDRRRD----AGFSIFVFGINLGAFIAPLIVGAA 169
Query: 220 EDEGMWALGFWVSTGSAFAALVLFLAG--TTRYRHFKPSGNPLA 261
++ + + F ++ F L+++ G T H+ +PLA
Sbjct: 170 QEAAGYHVAFSLAAIGMFIGLLVYYFGGKKTLDPHYLRPTDPLA 213
>pdb|2W18|A Chain A, Crystal Structure Of The C-Terminal Wd40 Domain Of Human
Palb2
Length = 356
Score = 28.9 bits (63), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 5/95 (5%)
Query: 277 HLSAEGEDLYVIDANDSSTNGNRNMLHTHGFKFLDRAAYISSRDLDEQKQGCSNPWRLCP 336
H+S E + + A+DS GN ++ K + + + ++ GC P C
Sbjct: 3 HMSVEQTETAELPASDSINPGNLQLVSE--LKNPSGSCSVDVSAMFWERAGCKEP---CI 57
Query: 337 VTQVEEVKCILRLLPIWLCTILYSVVFTQMASLFV 371
+T E+V + + L W LY+ F ++ L +
Sbjct: 58 ITACEDVVSLWKALDAWQWEKLYTWHFAEVPVLQI 92
>pdb|3EU7|A Chain A, Crystal Structure Of A Palb2 BRCA2 COMPLEX
Length = 356
Score = 28.9 bits (63), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 5/95 (5%)
Query: 277 HLSAEGEDLYVIDANDSSTNGNRNMLHTHGFKFLDRAAYISSRDLDEQKQGCSNPWRLCP 336
H+S E + + A+DS GN ++ K + + + ++ GC P C
Sbjct: 3 HMSVEQTETAELPASDSINPGNLQLVSE--LKNPSGSCSVDVSAMFWERAGCKEP---CI 57
Query: 337 VTQVEEVKCILRLLPIWLCTILYSVVFTQMASLFV 371
+T E+V + + L W LY+ F ++ L +
Sbjct: 58 ITACEDVVSLWKALDAWQWEKLYTWHFAEVPVLQI 92
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 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,941,641
Number of Sequences: 62578
Number of extensions: 671267
Number of successful extensions: 1467
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1456
Number of HSP's gapped (non-prelim): 13
length of query: 596
length of database: 14,973,337
effective HSP length: 104
effective length of query: 492
effective length of database: 8,465,225
effective search space: 4164890700
effective search space used: 4164890700
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)