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 H281DRAFT_03126 H281DRAFT_03126 oligopeptide transport system ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Burk376:H281DRAFT_03126 Length = 333 Score = 302 bits (774), Expect = 7e-87 Identities = 164/327 (50%), Positives = 214/327 (65%), Gaps = 7/327 (2%) Query: 2 MELLNVNNLKVEFHRVEGI-VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINR 60 M LL V +L V F R EG V AV +S+ L G +LGIVGESGSGKS +V++LL L+ Sbjct: 1 MPLLEVKDLSVRFTRREGAPVDAVQRVSFSLEPGRTLGIVGESGSGKSQTVMALLGLLAG 60 Query: 61 NGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWH 120 NG V GEA++ G++LL +N+ L IRG I +IFQ+PMTSLNP + + Q+ E + H Sbjct: 61 NGN-VSGEALYRGENLLAMNEAALNKIRGDRIGMIFQDPMTSLNPFLTIERQMTETLQLH 119 Query: 121 RLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADE 180 R M +AR RAIE LE V IP+S +R YP +FSGGMRQRVMIAMAL P++LIADE Sbjct: 120 RKMSRRDARRRAIETLETVRIPDSARRIGMYPHEFSGGMRQRVMIAMALLSEPEILIADE 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---TLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEI 297 + P HPYT+GLLN+ + + L IPGNPP P + +GC F PRC++ + Sbjct: 240 SLFAAPTHPYTRGLLNALPRLTDSSDDDRPLQTIPGNPPLPGEVGAGCAFAPRCAYCSDQ 299 Query: 298 CQREEPPLVNISENHRV--ACHLIKGE 322 C++ P LV + + ACH GE Sbjct: 300 CRQSRPALVAADGDPQALRACHRPVGE 326 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: 277 Number of extensions: 13 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: 333 Length adjustment: 28 Effective length of query: 296 Effective length of database: 305 Effective search space: 90280 Effective search space used: 90280 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