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 SMc03127 SMc03127 ABC transporter permease
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Smeli:SMc03127 Length = 308 Score = 204 bits (520), Expect = 2e-57 Identities = 112/315 (35%), Positives = 187/315 (59%), Gaps = 13/315 (4%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 ++F+L RL+ I+++ V+ +V++ ++ D + PD P Q + Sbjct: 2 IRFVLVRLMRAVITILAVVTFAFVVLRMSG----------DPAQVMLGPDVP--QDAVDA 49 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 F + +GL+ P+W Q L Y+K FG S D A + L+ E+ P T L L +++ Sbjct: 50 FRKTWGLDQPIWIQYLAYIKSIFTGDFGVSMRDKASALH-LVLERVPATLQLTLPALILK 108 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWEG 204 L++G+P G+ AAL + ++ D +T+++IG +PS+V+ + L+LIFS+ LG LP+ G + Sbjct: 109 LMIGIPAGVYAALHRQSFADRGVITLAIIGFTVPSFVMGLVLVLIFSVLLGVLPSGGQDT 168 Query: 205 IRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPSMI 264 ILPTI +++G + +ARF+R ++++ L Q +IRTA AKG R VI HAL + + Sbjct: 169 WMHGILPTITMSIGGIGILARFSRSAMIEVLGQPYIRTASAKGLKWRDVIWSHALPNAAV 228 Query: 265 PLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMN 324 P+VTIVG + L+ G V VE+IF PG+G+L + RD ++ I+A +++ N Sbjct: 229 PIVTIVGFMVGSLIAGAVVVESIFSWPGIGRLLIVSVSNRDLAVVQCILLIIAAAMVMSN 288 Query: 325 LIVDVLYAILDPRIK 339 L+VD+LY LDPR++ Sbjct: 289 LVVDLLYGWLDPRLR 303 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: 294 Number of extensions: 14 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: 308 Length adjustment: 28 Effective length of query: 313 Effective length of database: 280 Effective search space: 87640 Effective search space used: 87640 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