Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS15600 BPHYT_RS15600 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__BFirm:BPHYT_RS15600 Length = 389 Score = 244 bits (623), Expect = 4e-69 Identities = 155/358 (43%), Positives = 207/358 (57%), Gaps = 52/358 (14%) Query: 110 IALIALLLYPMVVVAIKGPQGSLTYVDNFGIQIL----IYVMLAWGLNIVVGLAGLLDLG 165 I I ++ PM++ A G N+ +++L +YVMLA GLN+VVG AGLLDLG Sbjct: 28 ITAIFVIAAPMIIGAAGG---------NYWVRVLDFAMLYVMLALGLNVVVGFAGLLDLG 78 Query: 166 YVAFYAVGAYSYALLSSY----------------FGLSFWVLLPLSGIFAALWGVILGFP 209 Y+AFYAVGAY+ ALLSS + F +++P + AA +GVILG P Sbjct: 79 YIAFYAVGAYTSALLSSPHLSSQFEWIAHLAPNGLHVPFLIIVPCAMAVAAFFGVILGAP 138 Query: 210 VLRLRGDYLAIVTLAFGEIIRLVLINW---TDVTKGTFGISSIPKATLFGIPFDATAGGF 266 LRLRGDYLAIVTL FGEI+R+ L N ++T G GI+ I AG F Sbjct: 139 TLRLRGDYLAIVTLGFGEIVRIFLNNLDRPVNITNGPKGITGIDPVH---------AGDF 189 Query: 267 A-----KLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACR 321 + LF L S Y +LF L +L +V RL+ IGRAW A+REDEIA + Sbjct: 190 SLAQTHSLFGLQFPSVYSYYYLFVLA---ALLVIWVCTRLQHSRIGRAWAAIREDEIAAK 246 Query: 322 SLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSL 381 ++GINT KL AFA GA F G +G+ F + QGFVSPESF ES V+LA VVLGGMG + Sbjct: 247 AMGINTRNVKLLAFAMGASFGGLSGAMFGSFQGFVSPESFTLPESIVVLACVVLGGMGHI 306 Query: 382 TGIAIAAIVMVGGTELLREM--SFLKLIFGPDFT-PELYRMLIFGLAMVVVMLFKPRG 436 G+ + A+++ E LR ++FG + E+ R L++ LAMV++ML++ G Sbjct: 307 PGVILGAVLLAVLPEFLRSTMGPLQNMVFGHEIVDTEVIRQLVYALAMVLIMLYRSEG 364 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: 511 Number of extensions: 23 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: 389 Length adjustment: 32 Effective length of query: 431 Effective length of database: 357 Effective search space: 153867 Effective search space used: 153867 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: 51 (24.3 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