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 WP_084295488.1 C8J29_RS21175 ABC transporter permease
Query= TCDB::Q9X269 (341 letters) >NCBI__GCF_003046325.1:WP_084295488.1 Length = 317 Score = 206 bits (524), Expect = 6e-58 Identities = 108/328 (32%), Positives = 193/328 (58%), Gaps = 20/328 (6%) Query: 22 MRFLKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQAT 81 M L+FL++R+++ + VV ++T+ L+ + PG D A + + A Q Sbjct: 1 MTVLRFLIRRMVSAVPVLFVVSLVTFALIAIVPG---------DVTAELAGAEATAEQRA 51 Query: 82 LKGFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSI 141 + ++ GLN PL++Q L + + G S+ ++ D + E+ P+T +LA ++ Sbjct: 52 V--LRDQLGLNQPLYQQALRWYGNLLQGDLGHSYL-LNMSVTDAVLERLPVTLSLAGLAL 108 Query: 142 LFALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSG 201 + A+V+GV LG+LAA++ ++W+D M+V++IG+++P + + + +I +FS+ L W PT G Sbjct: 109 VLAVVLGVLLGVLAAIRHDSWVDQGTMSVALIGLSVPDFWLGLIMISVFSVGLAWFPTGG 168 Query: 202 WEGI--------RTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTV 253 + R+ LP +ALA + +AR TR S+L+ + QD+IRTA AKG TV Sbjct: 169 YVPFSEDALGWARSMALPALALAFTQMGVIARMTRSSMLEVMGQDYIRTARAKGMRRHTV 228 Query: 254 IMKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTST 313 + KHALR +++P++T++G L+ G V +E++F +PG+G+L A RD+P++ Sbjct: 229 VFKHALRNALVPVITVIGVMTGVLLGGAVVIESVFSLPGVGRLIIGAIQRRDFPIIQGGL 288 Query: 314 FILALTVMIMNLIVDVLYAILDPRIKLD 341 I A + +N++VD+ Y DPR++ D Sbjct: 289 LITASLFVFVNILVDLAYGWFDPRVRND 316 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: 307 Number of extensions: 12 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: 317 Length adjustment: 28 Effective length of query: 313 Effective length of database: 289 Effective search space: 90457 Effective search space used: 90457 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 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