Align ABC transporter permease (characterized, see rationale)
to candidate GFF4156 HP15_4096 inner-membrane translocator
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Marino:GFF4156 Length = 292 Score = 141 bits (356), Expect = 2e-38 Identities = 94/300 (31%), Positives = 151/300 (50%), Gaps = 23/300 (7%) Query: 11 GLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAPGWVIL 70 GL +G +YALIALG+ ++Y ++INFA GE++M A + G M+ W+ L Sbjct: 13 GLAMGGLYALIALGFVIIYKATRVINFAIGEIMMFAAYLFLAFAGGME-----MSPWIAL 67 Query: 71 LLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWKPNYKPY 130 LA I + L VIEK RP+ ++ ++ IG++ +L L IW + + Sbjct: 68 PLAVIGGSI----LGGVIEKTMIRPMLGESPISVVMVTIGIASILVGLVEFIWTADPQLL 123 Query: 131 PTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLV--NHTNLGRAMRATAENPRVAS 188 P LP P IG ++ P + G + +VYL+ + G A+RATA + A Sbjct: 124 PNFLPREPVFIGELYLAPK--IAYGFLIGSALLIVYLLYFRFSRGGVALRATASDQAAAY 181 Query: 189 LMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGIGNLA 248 MG+ V + ++ G++ A++AG++ A+ G + G + GL + GG+ ++ Sbjct: 182 SMGINVRRVFNMAWVFGSLAASLAGVLVAATGGLSPQ-FGII-GLSVLVVVIVGGLDSIL 239 Query: 249 GAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLGERVADR 308 GA+V G+ +G +E T+ G LG Y F+VL IIL +RP GL G +R Sbjct: 240 GALVAGVFIGWLE--------TVAGAYLGGEYRMPATFLVLAIILVIRPYGLFGTHEIER 291 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: 239 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: 292 Length adjustment: 27 Effective length of query: 282 Effective length of database: 265 Effective search space: 74730 Effective search space used: 74730 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