Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate BPHYT_RS22035 BPHYT_RS22035 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__BFirm:BPHYT_RS22035 Length = 332 Score = 304 bits (778), Expect = 2e-87 Identities = 166/326 (50%), Positives = 212/326 (65%), Gaps = 6/326 (1%) Query: 2 MELLNVNNLKVEFHRVEGI-VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINR 60 M LL V +L V F R EG V AV G+S+ L G +LGIVGESGSGKS +V++LL L+ Sbjct: 1 MPLLEVKDLSVRFTRREGAPVDAVQGVSFSLEAGRTLGIVGESGSGKSQTVMALLGLLAG 60 Query: 61 NGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWH 120 NG+ V G A + G++LL +N+ L IRG I +IFQ+PMTSLNP + + Q+ E + H Sbjct: 61 NGK-VSGSATYRGENLLTMNEASLNKIRGDRIGMIFQDPMTSLNPFLTIERQMTETLQLH 119 Query: 121 RLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADE 180 R M EAR RAIE LE V IP++ +R YP +FSGGMRQRVMIAMAL P++LIADE Sbjct: 120 RKMSRREARRRAIETLESVRIPDAARRIGMYPHEFSGGMRQRVMIAMALLSEPEILIADE 179 Query: 181 PTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVE 240 PTTALDVT+QAQI+ELL+EL E G ++I ITHD+ V CD ++ MYAG+ VE+A Sbjct: 180 PTTALDVTVQAQIIELLRELNRERGTAIILITHDMGVVAGLCDDVMVMYAGQTVEQASAA 239 Query: 241 EILKTPLHPYTKGLLNS--TLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEIC 298 + P HPYT GLLN+ L + L IPGNPP P + +GC F PRC + E C Sbjct: 240 ALFAAPTHPYTLGLLNALPRLTDDDDDRPLQTIPGNPPLPGEVGAGCAFAPRCGYCTERC 299 Query: 299 QREEPPLVNISENHRV--ACHLIKGE 322 + PPL +++ ACH GE Sbjct: 300 RESRPPLAASADHVDALRACHRPVGE 325 Lambda K H 0.320 0.139 0.401 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: 273 Number of extensions: 14 Number of successful extensions: 3 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: 324 Length of database: 332 Length adjustment: 28 Effective length of query: 296 Effective length of database: 304 Effective search space: 89984 Effective search space used: 89984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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