Align TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate SMa0106 SMa0106 ABC transporter permease
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__Smeli:SMa0106 Length = 273 Score = 192 bits (487), Expect = 9e-54 Identities = 94/258 (36%), Positives = 153/258 (59%), Gaps = 1/258 (0%) Query: 28 IGGVFVLILIALAILAPYIAPY-PYDEPHYIRAFEGPSKDFIFGTDALGRDLFSRILYSL 86 +G ++I ILAP+IAP+ P + + + P F FGTD GRD+++RILY Sbjct: 9 LGAGLTTLVILAGILAPWIAPFDPVLDADLMNSELPPDATFWFGTDGQGRDVYTRILYGA 68 Query: 87 RNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAFPTFLFNVILVTALG 146 + + +G SQ + IIG LG AG+ GGW D + ++M A P+ +F + ++ LG Sbjct: 69 QISLTVGIVSQVINSIIGVTLGMTAGYWGGWWDDLVNGFTNVMLAIPSLIFALAVMAVLG 128 Query: 147 RGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTFYIIRKHILPNMIGP 206 GL ++ +A+GLT W+ R+ R L LK+ +V+AA+ G I+ ILPNM+GP Sbjct: 129 PGLPSLLIALGLTNWSWTCRIARSSTLSLKSLGYVQAAQTLGYGDLRIMFTQILPNMMGP 188 Query: 207 ILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMAFPHLLIFPAVTFAF 266 ILV G+ A+++E+ L+ +G+G++PP PSWG+++ + ++ P + IFP + Sbjct: 189 ILVMATLGMGSAVLSEAALSFLGLGIQPPFPSWGSMLTDARQLIQLAPWVAIFPGLAIFL 248 Query: 267 TLISFTFLADGLRDAFNP 284 +++ F L DGLRD+ +P Sbjct: 249 SVLGFNLLGDGLRDSLDP 266 Lambda K H 0.331 0.147 0.457 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: 259 Number of extensions: 15 Number of successful extensions: 1 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: 289 Length of database: 273 Length adjustment: 26 Effective length of query: 263 Effective length of database: 247 Effective search space: 64961 Effective search space used: 64961 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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