Align ABC transporter permease (characterized, see rationale)
to candidate WP_011767453.1 AZO_RS18720 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000061505.1:WP_011767453.1 Length = 310 Score = 371 bits (952), Expect = e-107 Identities = 186/310 (60%), Positives = 243/310 (78%), Gaps = 1/310 (0%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M+ L+QQ INGLV+GS+YALIALGYTMVYGI+ LINFAHG+VLM+GA+T+ + + G Sbjct: 1 METLIQQTINGLVIGSVYALIALGYTMVYGILGLINFAHGDVLMVGAMTALQTMLFLMGV 60 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 PG V+L +A ++A V+ + F +E++AYR LR++PRLAPLITAIGMS LLQT+AM Sbjct: 61 APGMSPLVMLTIALLVAIPVSMLIGFTMERLAYRRLRNAPRLAPLITAIGMSFLLQTIAM 120 Query: 121 IIWKPNYKPYPTMLPSSPFE-IGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 IIW NY +P ++ ++P + + G F+TP QI+I+ V+A+ + L LV+ T +GRAMRA Sbjct: 121 IIWGRNYHTFPQLISTTPLQPVEGVFVTPVQIVIVIVSALLMIGLTLLVSRTRIGRAMRA 180 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 TAEN R ASLMGV + VI+ TF+IGA LAA+AG+MYASNYG A + MGF+PGLKAFTAA Sbjct: 181 TAENHRTASLMGVDTNAVIAFTFVIGAGLAAVAGVMYASNYGIAHYGMGFMPGLKAFTAA 240 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299 V GGIGNL GA+VGG++LGL+E+ G+GYI LT G L S Y DIFAF++L ++L RP+G Sbjct: 241 VLGGIGNLGGAMVGGVVLGLVESFGAGYIEHLTFGFLNSSYQDIFAFLILGLVLIFRPTG 300 Query: 300 LLGERVADRA 309 LLGERV+DRA Sbjct: 301 LLGERVSDRA 310 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: 310 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: 310 Length adjustment: 27 Effective length of query: 282 Effective length of database: 283 Effective search space: 79806 Effective search space used: 79806 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