Align ABC transporter permease (characterized, see rationale)
to candidate WP_058929184.1 AU252_RS01305 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_001484605.1:WP_058929184.1 Length = 288 Score = 141 bits (356), Expect = 2e-38 Identities = 95/309 (30%), Positives = 166/309 (53%), Gaps = 24/309 (7%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 MD L+Q +NGL LG+ YAL+ALG+++V+G++ +INFAHG ++G ++S +M G Sbjct: 1 MDTLVQATVNGLALGAQYALLALGFSLVFGVLGVINFAHGAFYVLGGYFTYS---LMTGL 57 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 G P LA I A + A + +V+E + + + LI ++G ++ Sbjct: 58 --GLP----YALALIAAVLGVAAVGYVMELLLIEKIVDNHE-GTLIVSLGFYFVVIAALT 110 Query: 121 IIWKPNYKPYPTMLP-SSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 + + P + P P S + G +I +++++ V+AVA+ L +L+ + G A+RA Sbjct: 111 LFYGP--EAVPVRFPVDSVLRLEGFYIPVARLIVIAVSAVAVLGLWFLLYRSKHGIALRA 168 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 +EN VA++ G++P + + A LA +AG + + T + +G + +F Sbjct: 169 LSENRDVATMQGLRPRVYFPLAVALSAALAGLAGGLVTPIF-TLEPPVGEAALMVSFLVV 227 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYI-GTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298 V GG+G+L GA + +GL+EAI Y+ G+LT LL F++++ +L RPS Sbjct: 228 VLGGLGSLVGAASAAVGVGLVEAIAGTYLDGSLTRLLL---------FVIVLALLLFRPS 278 Query: 299 GLLGERVAD 307 G+ G + D Sbjct: 279 GIAGRSLRD 287 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: 200 Number of extensions: 8 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: 288 Length adjustment: 27 Effective length of query: 282 Effective length of database: 261 Effective search space: 73602 Effective search space used: 73602 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 Apr 09 2024. 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