Align ABC transporter permease (characterized, see rationale)
to candidate SM_b20604 SM_b20604 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Smeli:SM_b20604 Length = 537 Score = 142 bits (359), Expect = 1e-38 Identities = 94/297 (31%), Positives = 156/297 (52%), Gaps = 14/297 (4%) Query: 6 QQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAP 65 Q I GL LGS+ L A+G + +G++ +IN AHGE++M+GA T++ +++ + P Sbjct: 243 QNIWYGLSLGSVLLLAAIGLAITFGVMGIINMAHGEMVMLGAYTTFLVQDVVRTSFPHLF 302 Query: 66 GWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWKP 125 W L +A +A +V + +E+ R L P L L+ G+S++LQ I+ P Sbjct: 303 EWS-LAIALPLAFLVTGAVGLALERGVIRFLYGRP-LETLLATWGISLILQQTVRTIFGP 360 Query: 126 NYKPY--PTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAEN 183 + P+ + S FE+GG IT ++ I+ A+L++L+ T +G MRA +N Sbjct: 361 TNREVGNPSWM-SGAFELGGLAITWNRLWIIVFALAVFAALLFLLKKTPMGLQMRAVTQN 419 Query: 184 PRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGG 243 R+AS MG++ V + TF +G+ +A IAG+ S +G + +F VFGG Sbjct: 420 RRMASSMGIRTPWVDALTFALGSGIAGIAGVA-LSQIDNVSPNLGQGYIIDSFMVVVFGG 478 Query: 244 IGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 +GNL G +VG LG++ Y G + G +L +++I+ + RP GL Sbjct: 479 VGNLWGTLVGAFSLGILNKFLEPYAGAVLGKIL--------VLVLIILFIQKRPRGL 527 Lambda K H 0.327 0.142 0.419 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: 313 Number of extensions: 9 Number of successful extensions: 2 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: 309 Length of database: 537 Length adjustment: 31 Effective length of query: 278 Effective length of database: 506 Effective search space: 140668 Effective search space used: 140668 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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