Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 176 bits (447), Expect = 6e-49 Identities = 99/304 (32%), Positives = 171/304 (56%), Gaps = 4/304 (1%) Query: 35 EYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDLSVGS 94 E LI +++ A ++ F + N+ + S + +++ M + +R DLSV + Sbjct: 10 ETLLIAAILLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVAA 69 Query: 95 TVAFAGVLCAMV-LNATGNTFIAIVA-AVAAGGVIGFVNGAVIAYLRINALITTLATMEI 152 +A G++ +MV + A G + I+A A+ G ++G NG ++ L+I ++ TL TM I Sbjct: 70 NLALTGMVVSMVNVAAPGLPIVVILAIAIGLGTLLGMFNGLLVWKLQIPPIVVTLGTMTI 129 Query: 153 VRGLGFIVSHGQAVGVS--SDTFIALGGLSFFGVSLPIWVTLLCFIVFGVMLNQTVYGRN 210 RG+ F++S G+ V S F A G+ + W+ +L I+F +++ +T GR Sbjct: 130 FRGIIFLISDGKWVNSHEMSPAFKAFPRAELLGLPVLSWIAILAVILFTIVMTRTTLGRA 189 Query: 211 TLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAQGFELNVI 270 A GGNP A+ AGI+V +T+ + F I GA+ L G + SR + A GFEL+V+ Sbjct: 190 FYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVSRFAVSYVDIAGGFELDVV 249 Query: 271 SACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAILLAAVLLDQ 330 +ACV+GGVS++GG T+ G ++G L +G ++N + +++I F+Q + G ++ AV L+ Sbjct: 250 AACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPFWQLAISGGAIIIAVALNA 309 Query: 331 LKNR 334 NR Sbjct: 310 QANR 313 Lambda K H 0.326 0.139 0.396 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: 251 Number of extensions: 12 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: 338 Length of database: 327 Length adjustment: 28 Effective length of query: 310 Effective length of database: 299 Effective search space: 92690 Effective search space used: 92690 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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