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 3609212 Dshi_2598 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Dino:3609212 Length = 312 Score = 161 bits (408), Expect = 2e-44 Identities = 96/307 (31%), Positives = 156/307 (50%), Gaps = 8/307 (2%) Query: 32 LLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKGFEERYGL 91 LL + + + T+ L+W APG+ AIA + + + L G Sbjct: 9 LLRALVVLTGAALATFALLWHAPGD------PALAIAEARYGQNVSKEV-LDFIRAEAGF 61 Query: 92 NNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFALVVGVPL 151 ++ W +L + FG S S R++ + TF LAL S+ L V VPL Sbjct: 62 DDGFWTAFWAWLAPLMQGDFGQS-SVNGRDVWPDLVTAMSYTFPLALVSLALGLAVSVPL 120 Query: 152 GILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWEGIRTKILP 211 ++A + +W+D A+ ++ +GVAIP++ + + LIL+F++ LGWLP G E ILP Sbjct: 121 ALIATRRPGSWLDRGAVALASVGVAIPAFWLGLLLILLFAVQLGWLPAMGAETTTHSILP 180 Query: 212 TIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPSMIPLVTIVG 271 + L G AS+ R R +L+ Q F+ +G R + H + +P+VT++G Sbjct: 181 AMTLGFGVAASLTRIIRSGILEARGQPFLPAFTRRGVARRDIARDHVAPHAAVPVVTVLG 240 Query: 272 PQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMIMNLIVDVLY 331 ++A+L+ G V VE IF PGLG NA RD+P + + A+ +++NL +D++Y Sbjct: 241 LELAFLLEGLVVVEVIFARPGLGSFLVNAIFARDFPKVQAVVILAAVVFVVVNLAIDLIY 300 Query: 332 AILDPRI 338 LDPR+ Sbjct: 301 RSLDPRV 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: 330 Number of extensions: 21 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: 341 Length of database: 312 Length adjustment: 28 Effective length of query: 313 Effective length of database: 284 Effective search space: 88892 Effective search space used: 88892 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