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 3607472 Dshi_0885 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Dino:3607472 Length = 322 Score = 209 bits (532), Expect = 7e-59 Identities = 116/301 (38%), Positives = 177/301 (58%), Gaps = 11/301 (3%) Query: 18 EGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKDLL 77 + I+ AV +S+ + + +VGESGSGKS ++ L+ + +G G DL Sbjct: 30 KAILTAVSDVSFDVEERTVYALVGESGSGKSTIGKMVVGLLQPS----EGSVKIGGTDLA 85 Query: 78 KLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAIELLE 137 + ++ DI +IFQ+P SLNP RV + EP+ + + + A LLE Sbjct: 86 RETDPAKLDLVRADIQMIFQDPFASLNPRWRVRDIINEPVS----ARGGDVKGLAERLLE 141 Query: 138 RVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIMELL 197 +VG+ +P +FSGG RQR+ IA ALA PKL++ DEPT+ALDV++QAQ++ L+ Sbjct: 142 QVGLAAEDAG--KFPHEFSGGQRQRICIARALASEPKLIVCDEPTSALDVSVQAQVLNLM 199 Query: 198 QELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGLLNS 257 +LK+E+G++ +FI+HDL+V + DRI +Y G++VEEA + + + P HPYT+ LL + Sbjct: 200 SDLKDEFGLTYLFISHDLTVVQHVADRIGVLYLGRLVEEADPDTLFENPRHPYTQMLLAA 259 Query: 258 TLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEPPLVNISENHRVACH 317 ++ G+++ P G P+P P+GC FHPRC A+ C E P L + RVACH Sbjct: 260 APKMDGFGREVEPPKGEIPDPINPPTGCAFHPRCPIAVARCSAERPELRPLG-GARVACH 318 Query: 318 L 318 L Sbjct: 319 L 319 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: 283 Number of extensions: 17 Number of successful extensions: 2 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: 322 Length adjustment: 28 Effective length of query: 296 Effective length of database: 294 Effective search space: 87024 Effective search space used: 87024 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