Align ABC transporter permease (characterized, see rationale)
to candidate 8500415 DvMF_1165 inner-membrane translocator (RefSeq)
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Miya:8500415 Length = 306 Score = 202 bits (514), Expect = 8e-57 Identities = 111/307 (36%), Positives = 175/307 (57%), Gaps = 13/307 (4%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M+I +Q + N L GS YALIALGYT+VYG++ LINFAHG++ M+GA ++ ++ G Sbjct: 1 MEIFIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLLLGD 60 Query: 61 MPGA---PGWVILLLATIIACVVAATLNFVIEKVAYRPLR--SSPRLAPLITAIGMSILL 115 + G PGW L L + ++ A + +E++AYRPLR + RL +ITA+ ++L Sbjct: 61 LLGVFNLPGWAALALTVPLTMLLTAGVGVTLERIAYRPLRRKGAHRLYVVITALMCGLIL 120 Query: 116 QTLAMIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGR 175 + + + + + P M+ + G +T ++ ++ + L ++V T +G Sbjct: 121 ENGNLALLGASRRKLPDMVDKVVYTFGSVSVTNLKVWVIITAFLVFFLLQFIVTRTRIGM 180 Query: 176 AMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKA 235 AMRA A + LMG+ D +I TF++G+ A +AG+++A +Y MG + G KA Sbjct: 181 AMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGWKA 240 Query: 236 FTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTL 295 F AAV GGIG++ GA +GG LL IE + L S + D+FAF +L++IL Sbjct: 241 FIAAVVGGIGDIRGAFIGGFLLAFIE--------IMVAAFLPSTFRDLFAFTILLMILWQ 292 Query: 296 RPSGLLG 302 RP+GL G Sbjct: 293 RPTGLFG 299 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: 233 Number of extensions: 13 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: 306 Length adjustment: 27 Effective length of query: 282 Effective length of database: 279 Effective search space: 78678 Effective search space used: 78678 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