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 AZOBR_RS21775 AZOBR_RS21775 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__azobra:AZOBR_RS21775 Length = 329 Score = 302 bits (773), Expect = 8e-87 Identities = 152/307 (49%), Positives = 205/307 (66%) Query: 2 MELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61 M LL++ NL VEF G +AVDGI +++GE +GIVGESGSGKSV+ L+++ L+ N Sbjct: 1 MPLLDIKNLSVEFTTRAGTFRAVDGIDLTVDEGEVVGIVGESGSGKSVTSLAVMGLLGSN 60 Query: 62 GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121 G +V F GKDLL ++ + R I GKD++++FQ PMTSLNP VG Q+ME + H Sbjct: 61 GTVVADRMRFGGKDLLAMSPSQRRKITGKDVAMVFQEPMTSLNPCFTVGFQIMETLKVHE 120 Query: 122 LMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEP 181 + + R RAIELLE+VGIP R +P Q SGGM QRVMIA+A+AC+P+LL+ADEP Sbjct: 121 GLSGKALRNRAIELLEQVGIPAPESRLSAFPHQLSGGMNQRVMIAIAIACNPRLLVADEP 180 Query: 182 TTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEE 241 TTALDVTIQ QI++LL L++E GM++I ITHD+ V R++ MYAG++ E PV+ Sbjct: 181 TTALDVTIQKQILDLLVRLQKERGMALILITHDMGVVAETAQRVVVMYAGQVAETRPVDA 240 Query: 242 ILKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQRE 301 + K P HPYT LL++ E ++L IPG P P GC F+PRC FA + C+ E Sbjct: 241 LFKAPRHPYTGALLDALPERALGKRRLPTIPGVVPGIGDRPQGCLFNPRCRFATDRCRIE 300 Query: 302 EPPLVNI 308 P L ++ Sbjct: 301 RPALFDV 307 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: 258 Number of extensions: 6 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: 329 Length adjustment: 28 Effective length of query: 296 Effective length of database: 301 Effective search space: 89096 Effective search space used: 89096 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: 48 (23.1 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