Align ABC transporter permease (characterized, see rationale)
to candidate BWI76_RS15335 BWI76_RS15335 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Koxy:BWI76_RS15335 Length = 524 Score = 117 bits (293), Expect = 6e-31 Identities = 98/315 (31%), Positives = 151/315 (47%), Gaps = 29/315 (9%) Query: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63 LL Q GL LGS+ L ALG + YG++ +IN AHGE+LMIGA +SC + Q Sbjct: 228 LLGQAFMGLSLGSVLLLAALGLAITYGLLGVINMAHGEMLMIGA---YSCWLVQQALAQL 284 Query: 64 APGWVIL--LLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSI-LLQTLAM 120 AP W+ L+A +A ++ + +E+ R L P L L+ G+S+ L+Q + M Sbjct: 285 APQWLAFYPLIALPVAFLITGGIGMALERTVIRHLYGRP-LETLLATWGISLMLIQLVRM 343 Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQIL---ILGVTAVALASLVY---LVNHTNLG 174 + N + + + + GG + P IL L V A L L++ +N T LG Sbjct: 344 LFGAQNVE-----VANPAWLSGGVQVLPNLILPWNRLAVLAFVLLVLLFTWLTLNKTRLG 398 Query: 175 RAMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLK 234 +RA +N +A+ GV V F +G+ +A + G+ S G +G + Sbjct: 399 MNVRAVTQNRAMAACCGVPTGRVDMLAFGLGSGIAGLGGVA-LSQLGNVGPELGQGYIID 457 Query: 235 AFTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILT 294 +F V GG+G LAG+V LG+ I +G + G +L +++I+ + Sbjct: 458 SFLVVVLGGVGQLAGSVAAAFGLGIFNKILEPQMGAVLGKIL--------ILVLIILFIQ 509 Query: 295 LRPSGL--LGERVAD 307 RP GL L RV D Sbjct: 510 KRPQGLFALKGRVID 524 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: 316 Number of extensions: 13 Number of successful extensions: 1 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: 524 Length adjustment: 31 Effective length of query: 278 Effective length of database: 493 Effective search space: 137054 Effective search space used: 137054 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 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