Align ABC transporter permease (characterized, see rationale)
to candidate WP_028998315.1 H537_RS0113285 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000430725.1:WP_028998315.1 Length = 290 Score = 174 bits (441), Expect = 2e-48 Identities = 102/310 (32%), Positives = 172/310 (55%), Gaps = 23/310 (7%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M L+Q + +GL +G++YAL ALG+T++Y +INFA G+ LM+G GM+ A Sbjct: 1 MSDLMQFVFSGLTIGAIYALAALGFTLIYNASGVINFAQGDFLMLG--------GMIAAA 52 Query: 61 MPGA--PGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTL 118 + GA P V ++L+ +AC V + ++ + A RP + ++ +I IG SI +Q + Sbjct: 53 LLGANMPYGVAIVLS--VACTVL--VGVILYRWAIRPAGEASAVSLIIVTIGASIFIQGV 108 Query: 119 AMIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMR 178 ++ N P ++ GA++ P + + GV A+ + + V T G+AM Sbjct: 109 VQVVLGKNQHTLPAFSGDEALQVLGAYVLPQSLWMCGVAALLVVACVVFFRRTLSGKAML 168 Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238 A A N A +G+ ++ +F + A+L A+AG++ A+ T + +G + G+K F A Sbjct: 169 AVAANRLAARAVGIPTTRILQLSFGLSALLGAVAGVV-AAPITTTVYDIGLMLGMKGFVA 227 Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298 A GG+G+ GAVVGG+++GL+EA+ +GY+ S Y D F+++I++L P Sbjct: 228 ATLGGLGSPLGAVVGGLIVGLLEALIAGYV--------SSAYKDAVPFVLIIVVLLAMPH 279 Query: 299 GLLGERVADR 308 GL G RV +R Sbjct: 280 GLFGARVTER 289 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: 231 Number of extensions: 13 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: 309 Length of database: 290 Length adjustment: 27 Effective length of query: 282 Effective length of database: 263 Effective search space: 74166 Effective search space used: 74166 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