Align TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate SM_b21197 SM_b21197 oligopeptide uptake ABC transporter permease
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Smeli:SM_b21197 Length = 307 Score = 244 bits (623), Expect = 2e-69 Identities = 130/319 (40%), Positives = 195/319 (61%), Gaps = 15/319 (4%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 + F+L+RL + ++ +V+ I++ LM APG F L+R P +T++ Sbjct: 2 ISFILRRLASAVPTLFIVVTISFFLMRFAPGGPFNLER-------------PLPPSTMEN 48 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 Y L+ PLW+Q YL AV FGPS+ N+ LI + P + L ++L A Sbjct: 49 LMRTYHLDQPLWRQYATYLGNAVTGDFGPSYIYHDNNVAQLIGKGLPYSMELGFYALLLA 108 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWE- 203 +V GV G +AAL++N+++D+ M+VS IGV +P++VV L LIF+I L WLP GW Sbjct: 109 VVGGVITGTIAALRQNSFLDFAVMSVSTIGVTVPNFVVGPVLTLIFAIVLAWLPAGGWGD 168 Query: 204 -GIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPS 262 +R ILP IALAL LA AR TR S+++ LN D IRTA A G R V++ HA+R + Sbjct: 169 GSLRFLILPMIALALPQLAVFARLTRGSMIEALNTDHIRTAKAYGLPSRAVVVTHAMRGA 228 Query: 263 MIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMI 322 M+P+V+ + P A L+ G+ VE IF IPG+G+ F A+ RDY L++ + ++A+ V++ Sbjct: 229 MLPVVSYLAPCAAALLTGSAVVETIFTIPGVGRYFVLGAINRDYTLVMGTVILIAIFVIL 288 Query: 323 MNLIVDVLYAILDPRIKLD 341 NL+VD+LY +LDPR++ D Sbjct: 289 FNLLVDILYGLLDPRVRHD 307 Lambda K H 0.328 0.143 0.429 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: 275 Number of extensions: 16 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: 341 Length of database: 307 Length adjustment: 28 Effective length of query: 313 Effective length of database: 279 Effective search space: 87327 Effective search space used: 87327 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