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 5210054 Shew_2501 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__PV4:5210054 Length = 337 Score = 165 bits (417), Expect = 2e-45 Identities = 98/310 (31%), Positives = 175/310 (56%), Gaps = 16/310 (5%) Query: 24 PQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPD----GGKIFFEGK 79 P G+ +KA++ +S+ + GE GLVGESG G++ L + IL + + ++ ++G+ Sbjct: 16 PHGR--VKALERVSLTLNPGEVHGLVGESGSGRTLLAKAILGIPGHNWTIQADRMMWDGQ 73 Query: 80 DITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI----GTKKERRK 134 ++ +++ E + +M +IFQDP+ SL+P + VG I + + +K ++RK Sbjct: 74 NLMDMSPSERRVLMGSEMAMIFQDPISSLDPAIAVGTQIIEAMPENKELPWWKRGSDKRK 133 Query: 135 RVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQ 192 + ++ L VGI ++ ++S+ E S G+ Q++ IA A+A P+ ++ DEP ++++V Q Sbjct: 134 KAQQWLHKVGIKETQKIMSSYAWELSDGECQKVMIAIAVANQPRLLIADEPTNSMEVRTQ 193 Query: 193 AQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPY 252 AQI LL ++ Q +S L I+H L + ++ VMY G+++E G + NP HPY Sbjct: 194 AQIFRLLSKLNQLQNVSILLISHELETLSQWCDRLTVMYSGQVMESGVTSDVIANPYHPY 253 Query: 253 TRALLKSVPKIP-WDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTE 311 T+ALL ++P + K +L G P+ LP GCR RC + + +C +P L Sbjct: 254 TKALLDNIPDYSNPEHHKTMMQTLPGSAPALQHLPIGCRLGPRCPQAQKLCV-NQPSLCH 312 Query: 312 VEKNHFVSCH 321 +K+ + +CH Sbjct: 313 -QKDRYFACH 321 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: 278 Number of extensions: 17 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: 337 Length adjustment: 28 Effective length of query: 300 Effective length of database: 309 Effective search space: 92700 Effective search space used: 92700 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