Align ABC transporter permease (characterized, see rationale)
to candidate AZOBR_RS29670 AZOBR_RS29670 ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__azobra:AZOBR_RS29670 Length = 290 Score = 187 bits (475), Expect = 3e-52 Identities = 102/296 (34%), Positives = 162/296 (54%), Gaps = 18/296 (6%) Query: 5 LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGA 64 LQ ++N +VLG YAL+ +G T+++GI++++NF HGE+ GA ++ GMM G Sbjct: 5 LQHLLNAVVLGGTYALLGIGLTLIFGIMRVVNFTHGELYTFGAYMAYMLAGMM-----GL 59 Query: 65 PGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWK 124 ++ L +A ++ + A + F + RPL+ + ++ IG I +Q ++W Sbjct: 60 NFFMSLAMAAVLGMALGALIEFTL----LRPLKGADIDTTMLVMIGAGIAMQAGEQLVWG 115 Query: 125 PNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAENP 184 K P+ P+ P +G + ++ +LGV + L L+N T LG AMRAT ++P Sbjct: 116 GVAKSVPSPFPTEPVVLGSVSVGMNRLFVLGVALLLLGGFYLLINRTKLGVAMRATFQDP 175 Query: 185 RVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGI 244 A+LMGV ++ + TF +G+ LAA AG + + TMG L LKAF + GG+ Sbjct: 176 DTAALMGVNRGLMYTLTFALGSGLAATAGALLGPIF-VVTPTMGDLVALKAFAIVILGGL 234 Query: 245 GNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GN+ GA +GG +L L E G+GY L S Y D F+++I +L +RP GL Sbjct: 235 GNIPGATIGGFVLALAEEFGAGY--------LSSGYRDAMGFLLIIAVLIVRPQGL 282 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: 214 Number of extensions: 12 Number of successful extensions: 3 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: 290 Length adjustment: 27 Effective length of query: 282 Effective length of database: 263 Effective search space: 74166 Effective search space used: 74166 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