Align ABC transporter permease (characterized, see rationale)
to candidate BPHYT_RS04440 BPHYT_RS04440 ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__BFirm:BPHYT_RS04440 Length = 291 Score = 167 bits (424), Expect = 2e-46 Identities = 96/304 (31%), Positives = 169/304 (55%), Gaps = 20/304 (6%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M ILLQ I +G+ LG +YA+IA GY + + +NF G+ LM+GAL + + + Sbjct: 1 MAILLQLIYSGIALGMIYAVIAFGYQLTFATSGTLNFGQGDALMLGALVGLTLVTL---- 56 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRP-LRSSPRLAPLITAIGMSILLQTLA 119 G W+++ L CV +E++ RP +R +++ I + I+ + +A Sbjct: 57 --GVNYWLMIPLV----CVFGLLQGAFVERIGVRPAIRIKSEFGWIMSTIALGIIFKNVA 110 Query: 120 MIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 +W + +P+ LP +P ++ GA + P ++L++G V + ++ + T G+A+ A Sbjct: 111 ENLWGRDDLRFPSPLPEAPLKVFGANVLPMELLVVGGALVMMLAVEFFNRKTIFGKAVVA 170 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 TA + A+LMG+ +VI+ ++ + ++ AA AG++ A T TMG + GLKAF A Sbjct: 171 TANDRDAAALMGINTGLVITFSYALSSLTAAFAGVLIAPLTLTGA-TMGAVLGLKAFAVA 229 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299 + GG+ + G VVGG++LG+ E T TG + + Y D+ ++L+I+L L+P+G Sbjct: 230 IIGGLSSGLGIVVGGVILGIAE--------TTTGFYISTGYKDVPGLVLLLIVLALKPAG 281 Query: 300 LLGE 303 L G+ Sbjct: 282 LFGK 285 Lambda K H 0.327 0.142 0.419 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: 209 Number of extensions: 14 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: 309 Length of database: 291 Length adjustment: 27 Effective length of query: 282 Effective length of database: 264 Effective search space: 74448 Effective search space used: 74448 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 (21.7 bits) S2: 48 (23.1 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