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 BPHYT_RS35660 BPHYT_RS35660 membrane protein
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__BFirm:BPHYT_RS35660 Length = 283 Score = 134 bits (338), Expect = 2e-36 Identities = 84/259 (32%), Positives = 133/259 (51%), Gaps = 9/259 (3%) Query: 18 LLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEA--FRPKFQNSVVLAVSATL 75 L P +++ TALK + I + P W +F W A F +NS V+++ +T Sbjct: 25 LFPFAVMLFTALKPASEIFVYPARWLPVHWQWSNFSDMWVAANFGVALRNSTVISLLSTA 84 Query: 76 LSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKSI-----GLYGS 130 L+ V Y LA++PFRG GL +L + +++ LF+ I L S Sbjct: 85 LALAVSLPAAYALARFPFRGRGLYRQFLLVTQMLSPILLVVGLFRLAAMIPYGDGNLVDS 144 Query: 131 LFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLSVPAFVV 190 G+++ + + I + +Y+ +P +L E+A ++G G V LPL+VPA VV Sbjct: 145 KIGVIVSYAAFNIAFAVWMLSSYFQTVPRDLEESAWLEGCGRTKAVFKVFLPLAVPAIVV 204 Query: 191 VAIWQFTQIWNEFLFAVTLTR-PESQPITVALAQLAGGE-AVKWNLPMAGAILAALPTLL 248 AI+ F WNEF TL R PE++ +TV + + G+ V+W+L MA + A LP + Sbjct: 205 TAIFTFINAWNEFAVVYTLIRSPENKTLTVQVTDMVAGKYVVQWHLVMAATLCATLPVSV 264 Query: 249 VYILLGRYFLRGLLAGSVK 267 V+ L RY ++GL G+VK Sbjct: 265 VFAWLQRYLVKGLALGAVK 283 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: 225 Number of extensions: 17 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: 268 Length of database: 283 Length adjustment: 25 Effective length of query: 243 Effective length of database: 258 Effective search space: 62694 Effective search space used: 62694 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