Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate H281DRAFT_01522 H281DRAFT_01522 amino acid ABC transporter substrate-binding protein, PAAT family
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__Burk376:H281DRAFT_01522 Length = 260 Score = 145 bits (367), Expect = 7e-40 Identities = 98/285 (34%), Positives = 145/285 (50%), Gaps = 31/285 (10%) Query: 3 VKRTTAAKTLIGAVLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPEL 62 VK+ AA T+ A+L +I A AKDW T+ ++ Y P+ GKL GF+ +L Sbjct: 1 VKKLLAALTV--ALLATVSI---GAHAKDWSTIRFGVDASYPPFESKGSDGKLVGFDIDL 55 Query: 63 VANLCERIKLQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPAT 122 +C R+K +C V D+DGMIP L+A KFD ++ ++S+TP+R + +AFS TP Sbjct: 56 GNEICARLKAKCVWVENDFDGMIPALKAKKFDGVLSSMSMTPQRAEQVAFSSKLFNTPTR 115 Query: 123 FAVADAKVLPKAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGF 182 A G+G++ PT ++ LKGKT+G++ GT+ + + Sbjct: 116 LV---------AKKGSGIL----------PTAES----LKGKTVGVEQGTIQETYAKTYW 152 Query: 183 KDI-ATIRVYKTSPERDLDLANGRIDASFDDVTYYAANIDK-KETASIVMAGPKIGGP-I 239 + A + Y+ + DL +GR+DA+ D K A G + P I Sbjct: 153 EPKGAKVVPYQNQDQVYADLLSGRLDAALQDAVQAEIGFLKTPRGAGFDFVGKNLDDPKI 212 Query: 240 WGPGEGLAFRKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDV 284 G G G+ RK+D DLKAK D AI+ + DGT KKL K+F DV Sbjct: 213 LGNGAGIGMRKEDTDLKAKVDKAIADIIKDGTYKKLEKKYFDFDV 257 Lambda K H 0.316 0.134 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 215 Number of extensions: 8 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 286 Length of database: 260 Length adjustment: 25 Effective length of query: 261 Effective length of database: 235 Effective search space: 61335 Effective search space used: 61335 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory