Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 8501378 DvMF_2110 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Miya:8501378 Length = 316 Score = 265 bits (676), Expect = 1e-75 Identities = 140/309 (45%), Positives = 197/309 (63%), Gaps = 17/309 (5%) Query: 29 ILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGK-------DI 81 +L+AVDG+S+ + G TLGLVGESGCGKSTL R ++ LL P G++ +G+ D Sbjct: 8 VLRAVDGVSLTLDRGRTLGLVGESGCGKSTLARMVVGLLPPSAGQVLLDGRLFAGTDGDA 67 Query: 82 TNL----NDKEMKPYRKK----MQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERR 133 N + ++ R + +Q++FQDP SLNP+ TVG I + L + + ERR Sbjct: 68 ANGGASGHSADLAISRAEAAQLVQMVFQDPFSSLNPRRTVGASIGEALAVAGV-PGPERR 126 Query: 134 KRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQA 193 +V ++L +VG+ E + +PHEFSGGQ+QR+ +ARAL +P +VCDEPVS+LD S+QA Sbjct: 127 AKVADMLQLVGLRAEHADRYPHEFSGGQRQRVAVARALITHPALVVCDEPVSSLDASVQA 186 Query: 194 QIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYT 253 Q+++LL E+Q+ MG++YLFI+H+L VV H+S VAVMYLGK+VE D +F P HPYT Sbjct: 187 QVLNLLRELQEHMGLAYLFISHDLGVVGHMSDHVAVMYLGKVVEEAPRDVLFAAPAHPYT 246 Query: 254 RALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVE 313 RALL SVP + ++ +L G+LPSPI P GC F RC + +C + P V Sbjct: 247 RALLASVP-VRDPSRRAEHPALSGDLPSPIAPPPGCPFHPRCPQVMDVCRRQVPGWHVVA 305 Query: 314 KNHFVSCHL 322 + CHL Sbjct: 306 EGQHARCHL 314 Lambda K H 0.321 0.142 0.417 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: 273 Number of extensions: 11 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: 328 Length of database: 316 Length adjustment: 28 Effective length of query: 300 Effective length of database: 288 Effective search space: 86400 Effective search space used: 86400 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