Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate HSERO_RS02995 HSERO_RS02995 ABC transporter permease
Query= BRENDA::P68183 (296 letters) >FitnessBrowser__HerbieS:HSERO_RS02995 Length = 291 Score = 57.8 bits (138), Expect = 3e-13 Identities = 64/210 (30%), Positives = 92/210 (43%), Gaps = 28/210 (13%) Query: 100 VALSTTCAYAFARMRFPGKATLLKGMLIFQM-FPAVLSLVALYALFDRLGEYIPFIGLNT 158 +A+S R RFPG+A LL ML F + FP V+ + L R G IG T Sbjct: 91 LAISVFVGLFLQRHRFPGQALLL-AMLTFPLAFPGVVVGFMVIMLAGRQG----LIGALT 145 Query: 159 HG----GVIFAY-LGGIALH---------VWTIKGYFETIDSSLEEAAALDGATPWQAFR 204 +G ++FAY L G+ L + T+ E +D SLEEAA GA PWQ Sbjct: 146 NGLFGESLVFAYSLAGLFLGYLYFSIPRVILTVVAAAEKLDPSLEEAARSLGARPWQVLL 205 Query: 205 LVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNPQNYLWGDFA 264 V+LP +P L + F ++ A L +++ + + Y Y +FA Sbjct: 206 HVVLPALLPALVSSGAICFATSVGAFGTAFTLAANIDVLPMTI----YNEFTGY--ANFA 259 Query: 265 AAAVMSALPITIVFLLAQRWLVNGLTAGGV 294 AA +S + I + + L LT GV Sbjct: 260 TAASLSIVLGVITWAVLA--LARSLTGSGV 287 Lambda K H 0.328 0.141 0.435 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: 224 Number of extensions: 14 Number of successful extensions: 2 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: 296 Length of database: 291 Length adjustment: 26 Effective length of query: 270 Effective length of database: 265 Effective search space: 71550 Effective search space used: 71550 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: 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