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_RS02325 AZOBR_RS02325 ABC transporter substrate-binding protein
Query= TCDB::Q9X268 (642 letters) >FitnessBrowser__azobra:AZOBR_RS02325 Length = 503 Score = 105 bits (261), Expect = 6e-27 Identities = 95/302 (31%), Positives = 142/302 (47%), Gaps = 34/302 (11%) Query: 67 KVVPAVCESYTVSEDGLTYTFYLRKDKRWSNGDPVTAYDFEFAWKRAASPETPTLPLWAS 126 KVVP + E + VS DGLTYTF+LRK ++ +G + D F+ RA E+ Sbjct: 80 KVVPGLAEKWEVSADGLTYTFHLRKGAKFHDGSDADSADVTFSLDRARGAES-------- 131 Query: 127 PVQYIKNVYDCKSGAKPLDELGVKALDDYTLQVTLSRPMPSFINMLVLGGAMPLHRKTVQ 186 V K + + GV+A D T+ VTLSRP F+ + G A + ++ Sbjct: 132 -VNAQKGYFAAIA--------GVEAPDARTVVVTLSRPDGLFLFHMASGDAAIVAPESAG 182 Query: 187 EHPEDWWKPEYFVGNGPYVIESFTPNYEIVLVRNKYYVGDFPGNVDRIV---LKAGGLGL 243 + + VG GP+ E + +VLVRN Y G P ++R+ + + Sbjct: 183 ANKQT------PVGTGPFKFERWVAGDRVVLVRNPDYDGPKPA-LERVTFRFISDPAAQV 235 Query: 244 QQYLAGEIDAV--FITAVGDYVFALKNKQLSKELHEESGVQWVGYEITRSLSPVFDDIRI 301 AG+ID+ F T F + + + G +G T + FDD+R+ Sbjct: 236 AALKAGDIDSFPQFDTYEALPQFR-DDGAFTVMVGTTEGETILG---TNNARKPFDDVRV 291 Query: 302 RKALAMAIDKKVLTDIVLGGMAIPTHAYCSPDSEIAEAVKGI-PYDPEQAKKLLAEAGYP 360 R+A+A AID+K L D VL G ++ P + G+ PYDP++AK LLAEAG P Sbjct: 292 RRAMAHAIDRKTLIDGVLFGNGAAIGSHFPPHRAGYVDLTGLYPYDPDKAKALLAEAGLP 351 Query: 361 NG 362 +G Sbjct: 352 DG 353 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: 783 Number of extensions: 39 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 642 Length of database: 503 Length adjustment: 36 Effective length of query: 606 Effective length of database: 467 Effective search space: 283002 Effective search space used: 283002 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