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 Ac3H11_2051 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2051 Length = 348 Score = 284 bits (726), Expect = 3e-81 Identities = 147/322 (45%), Positives = 208/322 (64%), Gaps = 1/322 (0%) Query: 2 MELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61 M LL V NL VEF G ++A+D IS+ + GE LG+VGESG+GKS++ +++ L+ Sbjct: 12 MSLLEVKNLVVEFPGRRGTLRALDDISFSIAPGEILGVVGESGAGKSLTGAAIIGLLEPP 71 Query: 62 GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121 GR+ G+ + G+ + L+ EE+R+IRG+ I IFQ+P+TSLNP+ VG Q+ E I+ H Sbjct: 72 GRVASGQILLEGQRIDNLSNEEMRHIRGRRIGAIFQDPLTSLNPLYTVGRQLTETILAHL 131 Query: 122 LMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEP 181 + EAR+RAI LL+ GIP + +R +YP QFSGGMRQRV+IA+ALA PKL++ADEP Sbjct: 132 PVTPAEARQRAIALLKDTGIPAAEERIDHYPHQFSGGMRQRVVIALALAAEPKLIVADEP 191 Query: 182 TTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEE 241 TTALDV+IQAQI+ LL+ + + G +V+ ITHD+ V CDR+ +YAG++ E PV + Sbjct: 192 TTALDVSIQAQIITLLKNICKSRGAAVMLITHDMGVIAETCDRVAVLYAGRVAEIGPVHD 251 Query: 242 ILKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQRE 301 ++ P HPYT GL+ S ++ ++L I G P P GC ++PRC + C E Sbjct: 252 VINKPSHPYTSGLMASIPDMTMDRERLNQIDGAMPRLNAIPKGCAYNPRCPQTFDRCMTE 311 Query: 302 EPPLVNISENHRVACHLIKGES 323 P L+ R AC L G S Sbjct: 312 RPDLMPAGST-RAACWLHAGAS 332 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: 285 Number of extensions: 12 Number of successful extensions: 1 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: 348 Length adjustment: 28 Effective length of query: 296 Effective length of database: 320 Effective search space: 94720 Effective search space used: 94720 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