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 SMa0105 SMa0105 ABC transporter permease
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__Smeli:SMa0105 Length = 311 Score = 198 bits (503), Expect = 2e-55 Identities = 110/317 (34%), Positives = 184/317 (58%), Gaps = 11/317 (3%) Query: 25 LKFLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKG 84 L+F L+R+L I ++VVV ++ +V+ + PG F A DP A L Sbjct: 2 LRFTLRRVLQIIPTVVVVALLIFVIFSVVPGTF-----AASLFADGRRAADPQMIARLN- 55 Query: 85 FEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFA 144 E +GLN PL ++ + Y+ F G SF + + DLI ++ + LA+++++FA Sbjct: 56 --EEFGLNKPLMERFVTYVTDLAQFDLGTSFRT-RQPVIDLINDRMWASLQLAIAAMIFA 112 Query: 145 LVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWE- 203 LV+ VPLG +AAL+ + +D M +V G+++P + + + ++ +F++ L WLP+ G+ Sbjct: 113 LVISVPLGFVAALRPGSVLDTVTMIGAVSGLSMPQFWLGLLMMYLFALQLNWLPSFGYGD 172 Query: 204 -GIRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVIMKHALRPS 262 R ILP + L + PLA +AR TR +LD LN DFIRTA++KG + V+ H R + Sbjct: 173 GSFRNLILPAVTLGVTPLALLARTTRAGVLDVLNADFIRTAHSKGMSEAKVVRWHVARNA 232 Query: 263 MIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTFILALTVMI 322 ++ +VT VG Q L+ V +E +F PG+G L ++ +RD P++ + ++ L ++ Sbjct: 233 LVLIVTTVGLQFGSLIGQAVVIEKLFAWPGIGSLLVDSVASRDIPVVQGTILVIVLWFLV 292 Query: 323 MNLIVDVLYAILDPRIK 339 +N VD++YA +DPRIK Sbjct: 293 INTAVDLIYAAIDPRIK 309 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: 300 Number of extensions: 17 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: 311 Length adjustment: 28 Effective length of query: 313 Effective length of database: 283 Effective search space: 88579 Effective search space used: 88579 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