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= 039943
(581 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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 106/515 (20%), Positives = 191/515 (37%), Gaps = 107/515 (20%)
Query: 26 RTLPFIIANEAFERMASMG----LMPNMI--LYLCGEYNMETTAGTNVLLIWTAATNFLP 79
R +P+IIA+EA ER + G L P ++ L L + +V + F P
Sbjct: 12 RQIPYIIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFP 71
Query: 80 IIGAFLADSCVGRYPMIGFGCITYLLGVVLLWLTTILSQAQPPACDQLRSDCESATWSQX 139
++G ++AD G+Y I LWL+ I A + ++
Sbjct: 72 LLGGWIADRFFGKYNTI-------------LWLSLIYCVGH--AFLAIFEHSVQGFYTG- 115
Query: 140 XXXXXXXXXXXXXXXXXXXXXXAFGAEQLEKGDENKSKGALQSYFSWYYVSVLASSMVAV 199
+F +Q ++ +++ ++ A F +Y ++ S A
Sbjct: 116 ------LFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA----FDMFYFTINFGSFFAS 165
Query: 200 TCIVYIQDNLGWKVGFGVPAVIXXXXXXXXXXXXPFY----------------------- 236
+ + N G V FG+P V+ Y
Sbjct: 166 LSMPLLLKNFGAAVAFGIPGVLMFVATVFFWLGRKRYIHMPPEPKDPHGFLPVIRSALLT 225
Query: 237 -VQSKANTSLLTGLIQVLVASYKNRHIKLSSQTTEEMYHPRKGSMLLVPSENLRCLNKAC 295
V+ K N L+ LI + A+Y +I P G + + C
Sbjct: 226 KVEGKGNIGLVLALIGGVSAAYALVNI------------PTLGIVAGL------CCAMVL 267
Query: 296 IIKHPGQDSTPD-RRASNPWSLCTVDQVEE-LKALI---KVIPLWSTGIMIAVTISQSSF 350
++ G ++ RA VD V L+ L+ V P WS + ++S
Sbjct: 268 VMGFVGAGASLQLERARKSHPDAAVDGVRSVLRILVLFALVTPFWS------LFDQKAST 321
Query: 351 PVLQASTMDRHITPNFEIPSGSFGIFTIITVILWIGFYDRILQPIASKIRGKPCQLRLKQ 410
+LQA+ M + P + P+ + V+L I F + +L P ++ K LR
Sbjct: 322 WILQANDM---VKPQWFEPA-MMQALNPLLVMLLIPFNNFVLYPAIERMGVKLTALR--- 374
Query: 411 RMGIGLLFSTASMAAWAITETVRRNIAINEGISDDPRAVVKMSAMW-VLPYHVLSGLAMA 469
+MG G+ + S W + T++ + ++ G + +S W +LPY +L+ +
Sbjct: 375 KMGAGIAITGLS---WIVVGTIQ--LMMDGGSA--------LSIFWQILPYALLTFGEVL 421
Query: 470 FNMIGQIEFYYSELPRSMSSIASALHGLGMSVASL 504
+ G +EF YS+ P++M + L ++V +L
Sbjct: 422 VSATG-LEFAYSQAPKAMKGTIMSFWTLSVTVGNL 455
>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 = 33.9 bits (76), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 8/92 (8%)
Query: 24 GLRTLPFIIANEAFERMASMGLMPNMILYL-----CGEYNMETTAGTNVLLIWTAATNFL 78
GL TL E +ER + G+ ++ Y+ G+ ++ +++ I+ +
Sbjct: 14 GLSTL---FMTEMWERFSYYGMRAILLYYMWFLISTGDLHITRATAASIMAIYASMVYLS 70
Query: 79 PIIGAFLADSCVGRYPMIGFGCITYLLGVVLL 110
IG F+AD +G P + +G + +LG ++L
Sbjct: 71 GTIGGFVADRIIGARPAVFWGGVLIMLGHIVL 102
>pdb|4IGJ|A Chain A, Crystal Structure Of Maleylacetoacetate Isomerase From
Anaeromyxobacter Dehalogenans 2cp-1, Target Efi-507175
pdb|4IGJ|B Chain B, Crystal Structure Of Maleylacetoacetate Isomerase From
Anaeromyxobacter Dehalogenans 2cp-1, Target Efi-507175
Length = 242
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 271 EMYHPRKGSMLLVPSENLRCLNKACIIKHPGQDSTPDRRASNP 313
++Y+ R+ + L P LR +++AC P Q + PDR+ P
Sbjct: 193 QLYNARRFGLDLEPYPTLRRVDEACAALAPFQAAHPDRQPDAP 235
>pdb|3H53|A Chain A, Crystal Structure Of Human Alpha-N-Acetylgalactosaminidase
pdb|3H53|B Chain B, Crystal Structure Of Human Alpha-N-Acetylgalactosaminidase
pdb|3H54|A Chain A, Crystal Structure Of Human
Alpha-N-Acetylgalactosaminidase,Complex With Galnac
pdb|3H54|B Chain B, Crystal Structure Of Human
Alpha-N-Acetylgalactosaminidase,Complex With Galnac
pdb|3H55|A Chain A, Crystal Structure Of Human
Alpha-N-Acetylgalactosaminidase, Complex With Galactose
pdb|3H55|B Chain B, Crystal Structure Of Human
Alpha-N-Acetylgalactosaminidase, Complex With Galactose
pdb|3IGU|A Chain A, Crystal Structure Of Human
Alpha-n-acetylgalactosaminidase, Covalent Intermediate
pdb|3IGU|B Chain B, Crystal Structure Of Human
Alpha-n-acetylgalactosaminidase, Covalent Intermediate
pdb|4DO4|A Chain A, Pharmacological Chaperones For Human
Alpha-N-Acetylgalactosaminidase
pdb|4DO4|B Chain B, Pharmacological Chaperones For Human
Alpha-N-Acetylgalactosaminidase
pdb|4DO5|A Chain A, Pharmacological Chaperones For Human
Alpha-N-Acetylgalactosaminidase
pdb|4DO5|B Chain B, Pharmacological Chaperones For Human
Alpha-N-Acetylgalactosaminidase
pdb|4DO6|A Chain A, Pharmacological Chaperones For Human
Alpha-N-Acetylgalactosaminidase
pdb|4DO6|B Chain B, Pharmacological Chaperones For Human
Alpha-N-Acetylgalactosaminidase
Length = 400
Score = 29.3 bits (64), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 26/53 (49%)
Query: 376 FTIITVILWIGFYDRILQPIASKIRGKPCQLRLKQRMGIGLLFSTASMAAWAI 428
+++++++ W + ILQP+A + L G+ L S A MA W +
Sbjct: 206 WSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTV 258
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
0.322 0.135 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,475,150
Number of Sequences: 62578
Number of extensions: 558830
Number of successful extensions: 1035
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1030
Number of HSP's gapped (non-prelim): 6
length of query: 581
length of database: 14,973,337
effective HSP length: 104
effective length of query: 477
effective length of database: 8,465,225
effective search space: 4037912325
effective search space used: 4037912325
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)