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 8501683 DvMF_2401 nickel transporter permease NikB (RefSeq)
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Miya:8501683 Length = 313 Score = 171 bits (432), Expect = 3e-47 Identities = 102/318 (32%), Positives = 171/318 (53%), Gaps = 17/318 (5%) Query: 27 FLLKRLLTIAISMVVVIVITYVLMWLAPGN----FFELQRVRDAIARVTTPDDPAYQATL 82 ++LKRL + +++V V+ ++L+ A G+ + L R+ P D A Sbjct: 4 YILKRLAALIPLLLLVSVVVFLLLRAAQGDPAMAYLRLSRI--------PPTDEALATAR 55 Query: 83 KGFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSIL 142 + E L+ PLW+Q +L AV FG S+ R + + P T LA +++L Sbjct: 56 RMLE----LDLPLWEQYARWLARAVTGDFGNSYVT-GRPVLGEVLHYLPATLQLAGAALL 110 Query: 143 FALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGW 202 L+V +PLG+ AAL ++ +D A +S V++P++ + L+ +F++ LGWLP G Sbjct: 111 LTLIVSIPLGVGAALHRDRPLDNAARALSFTSVSLPNFWLGFLLVWLFAVKLGWLPALGR 170 Query: 203 EGIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPS 262 G+ +LP + L+L + R R SLL+ ++ I A A+G +R V+ +H + S Sbjct: 171 GGLEHLVLPAVTLSLMSMGINTRLIRASLLENMHARHIMYARARGISERGVVWRHMFKNS 230 Query: 263 MIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMI 322 +IP++T +G + L+ G V VE +F PG+G+ +A RDYP+L ++ ++ Sbjct: 231 LIPVLTSLGMHVGELLGGAVIVETVFAWPGVGRYAVSAVYNRDYPILQCFMLLMTAIFVL 290 Query: 323 MNLIVDVLYAILDPRIKL 340 NL VD+LYA DPRI+L Sbjct: 291 CNLAVDILYAWADPRIRL 308 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: 265 Number of extensions: 10 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: 313 Length adjustment: 28 Effective length of query: 313 Effective length of database: 285 Effective search space: 89205 Effective search space used: 89205 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