Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_058929662.1 AU252_RS04330 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_001484605.1:WP_058929662.1 Length = 322 Score = 140 bits (354), Expect = 5e-38 Identities = 95/309 (30%), Positives = 160/309 (51%), Gaps = 16/309 (5%) Query: 145 YVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGV 204 Y + A GL + G +GLL+ G F AVGAY +A+ + FG+ F+V L ++ I +A++ + Sbjct: 22 YALAALGLAVHFGYSGLLNFGQAGFMAVGAYGFAISTLTFGVPFFVGLVIAVICSAIFAM 81 Query: 205 ILGFPVLRLRGDYLAIVTLAFGEIIRLVLI--NWTDVTKGTFGISSIPKATLFGIPFDAT 262 +LG P LRLR DYLAIVT+A EI+R ++ T VT G+++ PF Sbjct: 82 LLGIPTLRLRADYLAIVTIAAAEIVRYIVTTNQLTAVTGSANGLAAFEGGFYAMNPF--P 139 Query: 263 AGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRS 322 AG + + + + ++ + L++ C L L R P GR + +REDE A RS Sbjct: 140 AGSYMGMNN---RDFFIRVVGWGLVIICCTLVWL----LMRSPWGRVLKGIREDENAVRS 192 Query: 323 LGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLT 382 LG N K+ A G + AG F +G V P ++ + + ++LGG+G++ Sbjct: 193 LGKNVYAYKMQALIMGGVLGALAGMIFTLPRGAVQPANYGTELTFFLYTCLLLGGLGTVL 252 Query: 383 GIAIAAIVMVGGTELLREMSFLKLIFGP-----DFTPELYRMLIFGLAMVVVMLFKPRGF 437 G I A++ L + + + + G R ++ G+A++++M+F+P+G Sbjct: 253 GPVIGAMIFWVVLSLTQGILYGLIESGAVTWLNTVQAGQLRYILVGVALMLLMIFRPQGV 312 Query: 438 VGSREPTAF 446 G+++ AF Sbjct: 313 FGNKKELAF 321 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: 457 Number of extensions: 32 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: 463 Length of database: 322 Length adjustment: 30 Effective length of query: 433 Effective length of database: 292 Effective search space: 126436 Effective search space used: 126436 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 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