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 7025499 Shewana3_2653 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__ANA3:7025499 Length = 335 Score = 159 bits (402), Expect = 9e-44 Identities = 99/310 (31%), Positives = 169/310 (54%), Gaps = 16/310 (5%) Query: 24 PQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPD----GGKIFFEGK 79 P G+ ++A++ +S+ + GE GLVGESG G+S L R IL + P+ ++ ++G Sbjct: 16 PHGR--VRALEKVSLTLNAGEIHGLVGESGSGRSLLARAILGIPGPNWTITADRMMWDGN 73 Query: 80 DITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRV-- 136 ++ + KE + M +IFQDP GSL+P TVG + + + ++ K Sbjct: 74 NLMAMTSKERRNLMGSDMAMIFQDPSGSLDPSQTVGSQLMQAMPKNPKAYFWQKHKHAKL 133 Query: 137 --EELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQ 192 ++ L VGI ++ + S+ E S G+ Q++ IA A+A P+ ++ DEP +++++S Q Sbjct: 134 TAQKWLHKVGIKNPQKVMLSYAWELSEGECQKVMIAMAIANQPRLLIADEPTNSMELSTQ 193 Query: 193 AQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPY 252 AQI LL ++ Q +S L I+H L + ++V+Y G+++E G +++ P HPY Sbjct: 194 AQIFRLLSQLNQLQNVSILIISHELETLAQWCDHLSVLYCGQVMESGPTEELINQPYHPY 253 Query: 253 TRALLKSVPKIPW-DGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTE 311 T+ALL ++P + K +L G P+ LP GCR RC E + C +P L+ Sbjct: 254 TKALLDNMPDYSGIEAHKAIMPTLPGSAPALQHLPIGCRLGPRCPEAQKKCV-NQPSLSH 312 Query: 312 VEKNHFVSCH 321 + +F +CH Sbjct: 313 LRDRYF-ACH 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: 266 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: 335 Length adjustment: 28 Effective length of query: 300 Effective length of database: 307 Effective search space: 92100 Effective search space used: 92100 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