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 GFF1851 HP15_1808 peptide ABC transporter, permease protein
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Marino:GFF1851 Length = 361 Score = 145 bits (367), Expect = 1e-39 Identities = 104/360 (28%), Positives = 174/360 (48%), Gaps = 52/360 (14%) Query: 27 FLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRD-------AIARVT-------- 71 ++L+RL I +++ ++++ +V++ APG E Q + + A+AR + Sbjct: 4 YILRRLALIIPTLIGIMLLNFVIVQAAPGGPVE-QLIAEMEGHGGSALARASGGGTGGEV 62 Query: 72 ------------TPDDPAYQATLKGFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPA 119 PD+ LK E YG + P ++ L F FG SF Sbjct: 63 ADSSGDTRGSRGIPDE-----LLKEIEVMYGFDKPAHERFFKMLGDYATFNFGDSFFRE- 116 Query: 120 RNIEDLIKEKFPITFTLALSSILFALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPS 179 +++ DLI +K P++ +L L S L + +PLGI A+ + D + V+G AIP Sbjct: 117 KSVIDLIIDKMPVSISLGLWSTLIIYFISIPLGIRKAVTDGSRFDVWTSSAIVVGYAIPG 176 Query: 180 YVVAVFLILIFS--IYLGWLPTSGWEGIR-------TKI--------LPTIALALGPLAS 222 ++ A+ LI++F+ Y W P G KI LP A +G A+ Sbjct: 177 FLFAILLIVLFAGGSYFDWFPLRGLTSSNFDELTWYQKIGDYFWHLALPVTANVIGGFAT 236 Query: 223 VARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPSM-IPLVTIVGPQMAYLMVGT 281 + T+ S LD + + ++ TA AKG D + V+ H R +M I + ++ G +A G+ Sbjct: 237 LTLLTKNSFLDEIGKQYVVTARAKGLDQKEVLYGHVFRNAMLIVIASLPGVLVALFFTGS 296 Query: 282 VWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMNLIVDVLYAILDPRIKLD 341 + +E IF + GLG L AA+ RDYP++ + +I L +I+ LI D+ Y ++DPRI + Sbjct: 297 LLIEVIFSLDGLGLLGFEAALNRDYPVIFGTLYIFTLMGLILKLISDITYVLVDPRIDFE 356 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: 306 Number of extensions: 18 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: 341 Length of database: 361 Length adjustment: 29 Effective length of query: 312 Effective length of database: 332 Effective search space: 103584 Effective search space used: 103584 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: 49 (23.5 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