Align TM1746, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate AZOBR_RS21760 AZOBR_RS21760 peptide ABC transporter substrate-binding protein
Query= TCDB::Q9X268 (642 letters) >FitnessBrowser__azobra:AZOBR_RS21760 Length = 533 Score = 119 bits (299), Expect = 3e-31 Identities = 102/318 (32%), Positives = 147/318 (46%), Gaps = 35/318 (11%) Query: 64 GGVKVVPAVCESYTVSEDGLTYTFYLRKDKRW-SNGD-----PVTAYDFEFAWKRAASPE 117 GG KVVP + E + VSEDGLTYTF+LRK +W SN D A D +++ R + Sbjct: 66 GGTKVVPGLAEKWEVSEDGLTYTFHLRKGVKWHSNNDFKPTRDANADDVLWSFNRQWKKD 125 Query: 118 TPTLPLWASPVQYIKNVYDCKSGAKPLDELGVKALDDYTLQVTLSRPMPSFINMLVLGGA 177 P + Y ++ A P ++ +DDYT++ TL++ FI L A Sbjct: 126 HPFHKVSGGAYDYFNDM------AMPDLLKSIEKVDDYTVKFTLNKVEAPFIANL----A 175 Query: 178 MPLHRKTVQEHPEDWWKPEYF-------VGNGPYVIESFTPNYEIVLVRNKYYVGDFPG- 229 MP E+ E K +G GP+ F + ++R K + + G Sbjct: 176 MPFAPIQSAEYAEALQKKNQIDKIDQAPIGTGPF---QFVAYQKDAVIRYKAFEPYWGGK 232 Query: 230 -NVDRIVLKAGGLGLQQYL---AGEIDAVFITAVGDYVFALKNKQLSKELHEESGVQWVG 285 +D +V +Y AGE V D K+ ++ L E+ G+ VG Sbjct: 233 AQLDNLVFAITPDAAVRYAKLKAGECHIVPYPNPADLEAMKKDSAIT--LMEQEGLN-VG 289 Query: 286 YEITRSLSPVFDDIRIRKALAMAIDKKVLTDIVLGGMAIPTHAYCSPDS-EIAEAVKGIP 344 Y FDD+R+R+AL MAIDKK + D V G +P P + ++ P Sbjct: 290 YLAFNVTKKPFDDVRVRRALNMAIDKKAVVDAVYQGAGVPAKNPIPPTMWSYNKEIEDYP 349 Query: 345 YDPEQAKKLLAEAGYPNG 362 YDPE+AKKLLAEAG+P+G Sbjct: 350 YDPERAKKLLAEAGFPDG 367 Lambda K H 0.319 0.138 0.431 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: 978 Number of extensions: 47 Number of successful extensions: 4 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: 642 Length of database: 533 Length adjustment: 37 Effective length of query: 605 Effective length of database: 496 Effective search space: 300080 Effective search space used: 300080 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 (21.7 bits) S2: 53 (25.0 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