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 3610415 Dshi_3796 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Dino:3610415 Length = 333 Score = 270 bits (691), Expect = 3e-77 Identities = 140/285 (49%), Positives = 186/285 (65%) Query: 21 VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGRIVDGEAIFLGKDLLKLN 80 V AV+G+S+KL GE LGI+GESGSGKSV++ +LLRL+ + G+ G+D+L LN Sbjct: 21 VHAVNGVSFKLAPGEVLGILGESGSGKSVTLKTLLRLLPEKKTRIGGQVRVDGQDVLALN 80 Query: 81 KEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLMKNEEARERAIELLERVG 140 L + RG +S+IFQ+P +L+P+ +G Q+ E ++ H + +A RA+E+LE V Sbjct: 81 GRALADHRGGVVSMIFQDPALALDPVYTIGQQIAESVVRHEGLSQRDAMARALEMLELVR 140 Query: 141 IPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTTALDVTIQAQIMELLQEL 200 IP + +R YP + SGGMRQR MIA+ALAC PKLL+ADEPTTALD T+Q Q++ LL+EL Sbjct: 141 IPSAKRRLKAYPHEMSGGMRQRAMIALALACKPKLLLADEPTTALDATVQIQVLLLLREL 200 Query: 201 KEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEILKTPLHPYTKGLLNSTLE 260 ++E GM VIF+THD+ VA DR+ MYAG VE V EI++ HPYTKGLL + L Sbjct: 201 QKEMGMGVIFVTHDIGVAVEVSDRLAVMYAGSFVETGSVAEIIRDGRHPYTKGLLAANLV 260 Query: 261 IGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREEPPL 305 G L IPG PP P GC F PRC A E C + P+ Sbjct: 261 GAEPGTPLEAIPGAPPALHAPPVGCAFAPRCDRAREACASDPLPV 305 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: 267 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: 333 Length adjustment: 28 Effective length of query: 296 Effective length of database: 305 Effective search space: 90280 Effective search space used: 90280 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