Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate SMa0711 SMa0711 ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__Smeli:SMa0711 Length = 276 Score = 150 bits (380), Expect = 2e-41 Identities = 91/267 (34%), Positives = 134/267 (50%), Gaps = 6/267 (2%) Query: 6 LYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEAFRPKFQ- 64 LY L ++ G L P+Y + +TAL A I WP P W +F RP F Sbjct: 11 LYAGLAVVCGVLLFPIYWLFVTALSTLAEIRQLPPSFWPAEPQWSTFAKVGTE-RPIFLW 69 Query: 65 --NSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFM 122 NS + A+ + LS +V GY L+++ +G L IL +P ++IPLF Sbjct: 70 LWNSTLAALGSVALSMVVSVFAGYSLSRFSVKGGRSLGLFILTAKMLPATLLVIPLFGIF 129 Query: 123 KSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILP 182 +S+GL GSL+ LVL H IP T + + Y+ IP EL +AA +DG G V+LP Sbjct: 130 RSMGLIGSLWSLVLAHATLIIPFTTWMLKGYFDTIPRELEQAAMVDGCSPLGALFRVVLP 189 Query: 183 LSVPAFVVVAIWQFTQIWNEFLFAVT-LTRPE-SQPITVALAQLAGGEAVKWNLPMAGAI 240 ++ P A++ F W ++ +A T LT + S + + + G WN A A+ Sbjct: 190 VATPGLAATALYAFVLSWADYAYARTFLTNAQGSWTANLGITTMKGEYVTDWNEISAAAV 249 Query: 241 LAALPTLLVYILLGRYFLRGLLAGSVK 267 ALP +L+Y+ L RY + GL AG+ K Sbjct: 250 FIALPIILIYLFLERYLVGGLTAGAEK 276 Lambda K H 0.330 0.146 0.461 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: 260 Number of extensions: 22 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: 268 Length of database: 276 Length adjustment: 25 Effective length of query: 243 Effective length of database: 251 Effective search space: 60993 Effective search space used: 60993 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 (21.8 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