Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_097070748.1 CRO22_RS13790 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_900217815.1:WP_097070748.1 Length = 358 Score = 125 bits (315), Expect = 2e-33 Identities = 97/302 (32%), Positives = 154/302 (50%), Gaps = 21/302 (6%) Query: 140 IQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYS-YALLSSYFGLSFWVLLPLSGIF 198 + LIY + A GLNI+VG AG + LG F AVGAY+ Y L++++ + F+ + L+G Sbjct: 54 VPFLIYAIAAIGLNILVGFAGQVSLGTGGFMAVGAYAVYKLMTAFPEVPFFFHVILAGGV 113 Query: 199 AALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTD--VTKGTFGISSIPKATLFG 256 A GV+ G P LR++G YLA+ TLA + + L N G + P T+ G Sbjct: 114 TACVGVLFGLPSLRIKGFYLAVATLA-AQFFLVWLFNKVPWFYNYSASGQITAPDRTMLG 172 Query: 257 IPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALRED 316 I +SA K +LF L++ L A V L R +GR W A+R+ Sbjct: 173 IYITGAQ-----------TSAVAK-YLFCLVILT--LVALVARNLTRGTVGRKWMAIRDM 218 Query: 317 EIACRSLGINTVTTKLTAFATGAMFAGFAGS-FFAARQGFVS-PESFVFLESAVILAIVV 374 +IA +G+N +T K+TAFA + F G AG+ F+ G E+F +S ++L +V+ Sbjct: 219 DIAAEIIGVNPLTAKVTAFAVSSFFIGIAGALLFSVYLGAAEVGEAFGINKSFLVLFMVI 278 Query: 375 LGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKP 434 +GG+GS+ G A +V L+ + + D L ++I G +++ ++ +P Sbjct: 279 IGGLGSIFGSFAGAAFLVLLPVFLKNVLVGAFGWPTDVAAHL-ELMIVGALIILFLIVEP 337 Query: 435 RG 436 G Sbjct: 338 HG 339 Lambda K H 0.330 0.145 0.432 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: 478 Number of extensions: 27 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: 463 Length of database: 358 Length adjustment: 31 Effective length of query: 432 Effective length of database: 327 Effective search space: 141264 Effective search space used: 141264 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 (21.8 bits) S2: 50 (23.9 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