Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_4985 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4985 Length = 345 Score = 156 bits (394), Expect = 1e-42 Identities = 106/297 (35%), Positives = 158/297 (53%), Gaps = 23/297 (7%) Query: 142 ILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAAL 201 + I V A GLNI+ G GL+ LG AF +GAY+ A+L + G F + L G A L Sbjct: 51 VSINVASATGLNILTGYTGLVSLGQAAFMGLGAYTVAVLETKVGTPFVLNLLAGGFVAML 110 Query: 202 WGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDA 261 G+++G P LR++G YLAI T+A I + NW T GT G+ S+P A LFG+ D Sbjct: 111 GGIVVGIPSLRVKGLYLAIATIAASFIAHFIFANW-KFTGGTGGL-SVPPAKLFGMALDT 168 Query: 262 TAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACR 321 + L++LI+ + +L L R +GRA+ A+R+ +I+ Sbjct: 169 S------------------FRLYWLIVPVTILMLLGAANLFRTRVGRAFIAIRDRDISAE 210 Query: 322 SLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSL 381 LGI + KL +F + +AG AG +A V+PESF L S LA +++GGMGS+ Sbjct: 211 VLGIPLLRYKLLSFGLSSFYAGVAGGLWAYFFRVVTPESFPLLMSIFFLAAIIVGGMGSI 270 Query: 382 TGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPEL--YRMLIFGLAMVVVMLFKPRG 436 G + A+ M ELL+ + L + G + T L R +IFGL ++ ++F+P G Sbjct: 271 LGGILGAVFMTMVPELLKLVVDL-MPGGSELTVLLSPVRTVIFGLLIIGFLVFEPHG 326 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: 459 Number of extensions: 28 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: 345 Length adjustment: 31 Effective length of query: 432 Effective length of database: 314 Effective search space: 135648 Effective search space used: 135648 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 17 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