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 Ac3H11_4827 Dipeptide transport system permease protein DppB (TC 3.A.1.5.2)
Query= TCDB::Q9X269 (341 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4827 Length = 320 Score = 192 bits (487), Expect = 1e-53 Identities = 110/325 (33%), Positives = 186/325 (57%), Gaps = 24/325 (7%) Query: 27 FLLKRLLTIAISMVVVIVITYVLMWLAPGNFFELQRVRDAIARVTTPDDPAYQATLKGFE 86 F LKR T+ +++ ++ ++++ + PGN ++ DA +P+ A A+ Sbjct: 4 FFLKRFATLLATLIGASIVVFLVLEILPGNAAQMLMGPDA-----SPEAVAALAS----- 53 Query: 87 ERYGLNNPLWKQILMYLKGAVVFKFGPSFSDPARNIEDLIKEKFPITFTLALSSILFALV 146 + GL+ P + ++ G VV G S++ + + DL+ E+ +T LAL +++ V Sbjct: 54 -KLGLDQPASLRYWQWVSGLVVGNMGDSYAYSSP-VLDLVLERLALTVPLALMAMVITTV 111 Query: 147 VGVPLGILAALKKNTWIDYTAMTVSVIGVAIPSYVVAVFLILIFSIYLGWLPTSGWEG-- 204 + + G+ AA + N D M ++ IG+AIP++ A+ LIL+FS+ L W G+ G Sbjct: 112 LALAAGVYAASRHNKVGDVGVMGLAQIGIAIPNFWFAILLILLFSVKLQWFSAGGFPGWT 171 Query: 205 ----------IRTKILPTIALALGPLASVARFTRVSLLDTLNQDFIRTAYAKGGDDRTVI 254 ++ +LP IALA+ A +AR TR ++L+ L +DF+RTA AKG R + Sbjct: 172 EDAGGSPLEALKALLLPAIALAVVQAAILARITRSAVLEVLREDFVRTARAKGLTQRAAL 231 Query: 255 MKHALRPSMIPLVTIVGPQMAYLMVGTVWVENIFRIPGLGQLFANAAVTRDYPLLVTSTF 314 H LR +MIP++T++G Q A L+ GT+ VEN+F +PGLG+L + RD ++ Sbjct: 232 WGHVLRNAMIPVITVMGLQFANLLAGTIVVENVFYLPGLGRLIFQSISNRDLIVVRNCVM 291 Query: 315 ILALTVMIMNLIVDVLYAILDPRIK 339 +LA V+I+N +VD+LYA++DPR+K Sbjct: 292 LLATMVVIVNFVVDILYAVIDPRVK 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: 290 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: 320 Length adjustment: 28 Effective length of query: 313 Effective length of database: 292 Effective search space: 91396 Effective search space used: 91396 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