Align ABC transporter permease (characterized, see rationale)
to candidate WP_028583915.1 G494_RS0106725 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000429965.1:WP_028583915.1 Length = 296 Score = 147 bits (370), Expect = 4e-40 Identities = 95/310 (30%), Positives = 155/310 (50%), Gaps = 24/310 (7%) Query: 2 DILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAM 61 D+ Q + G+ G++YA++A+G+ ++Y +INFA GE +M+G + + S + M Sbjct: 4 DLFFQYLFAGVTYGAIYAIVAIGFNIIYNTTGIINFAQGEFVMLGGMIAIS----LHQVM 59 Query: 62 PGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMI 121 P L LA +A + + IE + R L+S L +I IG+SILL+ A+ Sbjct: 60 P-------LPLAITLAVALTMVIGAAIEIIFIRWLQSPSVLRLIIITIGVSILLREAALH 112 Query: 122 IWKPNYKPYPTMLPS--SPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 IW + + P + S +G ++P + ++ + +A L +T GR MRA Sbjct: 113 IWGESIRSLPYFYGNEISSISLGSVHLSPQVLWVIAACGIMVAGLSLFFKYTPTGREMRA 172 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAG-IMYASNYGTAQHTMGFLPGLKAFTA 238 + N A L G+ +++ +F++ A + A+AG +M Y Q+ G +K FT Sbjct: 173 CSANRTAAILCGISTRNMVTLSFMLSAGIGAVAGCVMSPITY--TQYDSGTGLAIKGFTV 230 Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298 A+ GG+GN AV GILLG+IEA + + D A +L+ IL ++P Sbjct: 231 AILGGLGNSMAAVAAGILLGIIEAFSVSVVPLA--------FQDAIAITILLAILFVKPH 282 Query: 299 GLLGERVADR 308 GL G VA R Sbjct: 283 GLFGSSVAAR 292 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: 183 Number of extensions: 7 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: 296 Length adjustment: 27 Effective length of query: 282 Effective length of database: 269 Effective search space: 75858 Effective search space used: 75858 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 24 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