Align TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate GFF2861 HP15_2805 permease protein, ABC-type oligopeptide transporter
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__Marino:GFF2861 Length = 306 Score = 174 bits (441), Expect = 2e-48 Identities = 93/259 (35%), Positives = 146/259 (56%), Gaps = 6/259 (2%) Query: 28 IGGVFVLILIALAILAPYIAPY-PYDEPHYIRAF-----EGPSKDFIFGTDALGRDLFSR 81 IG +L++ A+ AP++AP+ PY + +R EG S +++ GTD LGRD SR Sbjct: 40 IGFGILLVMAVFAVFAPWLAPHDPYLQNLPMRMLPPVWVEGGSWEYLLGTDHLGRDYMSR 99 Query: 82 ILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAFPTFLFNVIL 141 I+Y R + IG G+ + ++IG LG +AG+ GGW+D+ + +V A P+ L + L Sbjct: 100 IIYGARISMTIGIGAATIGMVIGVTLGLIAGYFGGWLDQAVNFLVTCQLAVPSLLLIMAL 159 Query: 142 VTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTFYIIRKHILP 201 V +G+ + + IG T W + R L L+ +FV AA+A G S F I K +LP Sbjct: 160 VFVIGQSITVVIFVIGATHWVFYLVVTRSATLRLRELDFVAAAQAMGCSKFQIAVKEVLP 219 Query: 202 NMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMAFPHLLIFPA 261 N++ I+V V A++ E+ L+ +G+G+ P+PSWG +I EG M P L+I P Sbjct: 220 NLVNQIMVIFTLEVAVAILNEATLSFLGLGIPSPIPSWGLMIAEGKQAMFFQPWLVILPG 279 Query: 262 VTFAFTLISFTFLADGLRD 280 ++ +I+ L DG+RD Sbjct: 280 ISLFILVIAINLLGDGVRD 298 Lambda K H 0.331 0.147 0.457 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: 234 Number of extensions: 10 Number of successful extensions: 1 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: 289 Length of database: 306 Length adjustment: 26 Effective length of query: 263 Effective length of database: 280 Effective search space: 73640 Effective search space used: 73640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 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