Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_019388681.1 P735_RS0114015 ATP-binding cassette domain-containing protein
Query= TCDB::Q9X272 (328 letters) >NCBI__GCF_000283015.1:WP_019388681.1 Length = 227 Score = 105 bits (262), Expect = 1e-27 Identities = 70/213 (32%), Positives = 118/213 (55%), Gaps = 16/213 (7%) Query: 12 PLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG 71 P+LQ D + QG ++ + +++EI +GE + L+G++G GKS+ +T+ L Sbjct: 4 PILQLKDASIF--QGDSLV--LSNVNVEINKGEFVYLIGKTGTGKSSFMKTLYGDLPLTE 59 Query: 72 GKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGT--- 128 G+ D+ NL +K++ R+K+ ++FQD ++ R I D L+ T Sbjct: 60 GEGHIVDFDLKNLKEKDIPYLRRKLGVVFQDF------KLLTDRTINDNLLFVLKATGWK 113 Query: 129 -KKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSAL 187 K + + RVEE+L V + + FPHE SGG+QQR+ IARAL NP+ I+ DEP L Sbjct: 114 DKDKMKTRVEEVLTKVDMKTKGFK-FPHELSGGEQQRVAIARALLNNPELILADEPTGNL 172 Query: 188 DVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVV 220 D +++++L++I K G + L H+ A++ Sbjct: 173 DPQTSVEVMEVLQDI-NKNGNTILMATHDYALL 204 Lambda K H 0.321 0.142 0.417 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: 194 Number of extensions: 12 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: 328 Length of database: 227 Length adjustment: 25 Effective length of query: 303 Effective length of database: 202 Effective search space: 61206 Effective search space used: 61206 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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