Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_028999965.1 H537_RS0124590 sugar ABC transporter ATPase
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000430725.1:WP_028999965.1 Length = 592 Score = 149 bits (375), Expect = 3e-40 Identities = 102/338 (30%), Positives = 164/338 (48%), Gaps = 44/338 (13%) Query: 105 RHFLKIALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDL 164 RH + + ++A L + + G G+ Y+ + Y + A G+N++VG +G L Sbjct: 5 RHVIGVVVVAGAL-----IGLTGQIGNDYYL-RIAFTMCTYYLCAAGMNVLVGFSGQKSL 58 Query: 165 GYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLA 224 G +A GAY+ ALLS++ +S W+LLPL+ + AA GV++ P LR++G YLA+VTLA Sbjct: 59 GQAGLFAAGAYAAALLSTHTDISPWLLLPLAAVAAAACGVLIALPSLRVKGPYLAMVTLA 118 Query: 225 FGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLF 284 FG +I ++ WT+V G G+ + T G P + ++ I Sbjct: 119 FGVVIEKLVSEWTEVFGGAQGLYGVKSLTWQGEPLTT------------LQWVWFSI--- 163 Query: 285 YLILALCMLTAYVTIRLRRM---PIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMF 341 L+A V I LR + GRA +L+ DEIA S+G+ K+ AF A+ Sbjct: 164 -------GLSAVVHILLRNVLTGRFGRALLSLQADEIASSSVGVRVYRAKVMAFVIAAVT 216 Query: 342 AGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREM 401 G AG+ A + +++ + F S IL +V+LGG GSL G + A+V+ LL Sbjct: 217 CGIAGAMVAQQNQYINSDFVTFHLSIFILLLVLLGGSGSLMGPLVGAVVLTAIDALLSRW 276 Query: 402 SFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVG 439 + + ++G ++ + PRG G Sbjct: 277 PAV-------------QHFVYGALLLFALYVMPRGVTG 301 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: 642 Number of extensions: 37 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: 463 Length of database: 592 Length adjustment: 35 Effective length of query: 428 Effective length of database: 557 Effective search space: 238396 Effective search space used: 238396 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: 52 (24.6 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