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 207955 DVU2461 oligopeptide ABC transporter, permease protein
Query= TCDB::Q9X269 (341 letters) >MicrobesOnline__882:207955 Length = 339 Score = 200 bits (508), Expect = 5e-56 Identities = 121/334 (36%), Positives = 184/334 (55%), Gaps = 28/334 (8%) Query: 25 LKFLLKRLLTIAISMVVVIV-ITYVLMW---LAPGNFFELQRVRDAIARVTTPDDPAYQA 80 L L +R+L MVVV + IT + W LAPG+ +L+ TT + A Sbjct: 9 LTALARRMLRKLAWMVVVFLGITVICFWVIHLAPGSPTDLE---------TTMNPLAGAE 59 Query: 81 TLKGFEERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSS 140 K E YGL+ PL+ Q +L V FG S S R + + I+E+ P+T + +++ Sbjct: 60 ARKRLESIYGLDQPLYVQYAQWLGRLVRLDFGNSMSSDGRPVMERIRERLPLTVGMNVAA 119 Query: 141 ILFALVVGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTS 200 + L++ VP+G+ +A + W D + IG A+P + +A+ L+L F I+LGWLP S Sbjct: 120 LFLTLLLAVPIGVASAHWQGGWFDRGMTVLVFIGFAMPGFWLALLLMLFFGIHLGWLPLS 179 Query: 201 GWEGI---------------RTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYA 245 G + R LP G LA ++RF R ++L+ L QD+I TA A Sbjct: 180 GLTSLDYATLSPWGKFLDVARHLALPLFIYTFGSLAGMSRFMRSAMLEVLRQDYILTARA 239 Query: 246 KGGDDRTVIMKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRD 305 KG RTVI +HALR +++P++TI+G + L+ G+V +E+IF +PGLGQLF A + RD Sbjct: 240 KGLPTRTVIFRHALRNALLPVITILGLSLPGLIGGSVIIESIFALPGLGQLFYTAVMARD 299 Query: 306 YPLLVTSTFILALTVMIMNLIVDVLYAILDPRIK 339 YPL++ + + A+ NLI D+ Y + DPRI+ Sbjct: 300 YPLIMGNLVLGAVLTQAGNLIADLCYGLADPRIR 333 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: 306 Number of extensions: 13 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: 339 Length adjustment: 28 Effective length of query: 313 Effective length of database: 311 Effective search space: 97343 Effective search space used: 97343 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 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