Align ABC transporter permease (characterized, see rationale)
to candidate WP_011385948.1 AMB_RS18170 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000009985.1:WP_011385948.1 Length = 297 Score = 164 bits (415), Expect = 2e-45 Identities = 94/306 (30%), Positives = 167/306 (54%), Gaps = 14/306 (4%) Query: 3 ILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMP 62 +LLQ ++NGL++G++Y ++A+ + ++Y Q++NFA GE L+IGA T W + M Sbjct: 5 LLLQLLVNGLIVGTLYGVVAMCFVLIYKSTQVVNFAQGEFLLIGAWTCWWLVTSM----- 59 Query: 63 GAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMII 122 P +V + + V L ++ RPL P ++ ++ IG+SI Q + I Sbjct: 60 ALPFYVAFPMTFLFMMVFGIALQMIV----LRPLIGEPVISVIMVTIGLSIFFQAVMKSI 115 Query: 123 WKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAE 182 + +P+P + P +I G + P ++ L V+ V + + ++ +G AMRATA Sbjct: 116 FGVWAQPFPEIFPVKSVDILGLSVQPAYLMSLVVSIVIMGLFAWFFKYSRMGLAMRATAF 175 Query: 183 NPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFG 242 N +VA +G+ V + + I A+++A+AG++ G + F G+K F A + G Sbjct: 176 NQQVAQSLGISVKAVFATAWAISAMVSALAGVVVGMVNGVSSALSFF--GIKVFPAVIVG 233 Query: 243 GIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLG 302 G+ ++ GAV+GG+++G++E + G LG+ YT + F VL+IIL ++P GL G Sbjct: 234 GLDSIIGAVLGGLIIGVLENLAEYADGQYLH--LGNLYT-VAPFYVLVIILMIKPYGLFG 290 Query: 303 ERVADR 308 + +R Sbjct: 291 TKTIER 296 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: 215 Number of extensions: 7 Number of successful extensions: 3 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: 297 Length adjustment: 27 Effective length of query: 282 Effective length of database: 270 Effective search space: 76140 Effective search space used: 76140 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: 48 (23.1 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