Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BPHYT_RS15595 BPHYT_RS15595 ABC transporter
Query= uniprot:Q1MCU2 (292 letters) >FitnessBrowser__BFirm:BPHYT_RS15595 Length = 257 Score = 206 bits (524), Expect = 4e-58 Identities = 122/264 (46%), Positives = 166/264 (62%), Gaps = 12/264 (4%) Query: 9 MSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTM 68 MSD+ L V+ ++ +FGGL A+++ E K G I LIGPNGAGKTT FN ITG Y P Sbjct: 1 MSDNIRLSVKGVNKRFGGLQALSEVGLEIKSGQIYGLIGPNGAGKTTFFNVITGLYTPDS 60 Query: 69 GMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKAS 128 G + G+ Y + +++ K A +ARTFQNIRLF G+T LEN++V +H + + Sbjct: 61 GEFKLD---GENYTPTAV--YQVAK-AGIARTFQNIRLFGGMTALENVMVGRHVR----T 110 Query: 129 GYTILGLIGVGPYKR-EAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMC 187 + ++G + P +R E E E A LE + AD + +L YG QRRLEIARA+ Sbjct: 111 KHGLIGAVFQTPAERKEEREIKERAIELLEYVGIAQYADYTSRNLSYGHQRRLEIARALA 170 Query: 188 TGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEY 247 T P+LL LDEPAAG+N E L LL IRA+ G +ILLIEHD+ +VM + + + VL+Y Sbjct: 171 TDPKLLALDEPAAGMNATEKVELTKLLDKIRAD-GKTILLIEHDVKLVMGLCNQMTVLDY 229 Query: 248 GQKISDGTPDHVKNDPRVIAAYLG 271 G+ I+ G P V+ DP+VI AYLG Sbjct: 230 GKVIAQGLPQDVQKDPKVIEAYLG 253 Lambda K H 0.318 0.136 0.386 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: 220 Number of extensions: 7 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: 292 Length of database: 257 Length adjustment: 25 Effective length of query: 267 Effective length of database: 232 Effective search space: 61944 Effective search space used: 61944 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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