Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate 3609043 Dshi_2432 Monosaccharide-transporting ATPase (RefSeq)
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Dino:3609043 Length = 327 Score = 168 bits (426), Expect = 2e-46 Identities = 105/324 (32%), Positives = 173/324 (53%), Gaps = 19/324 (5%) Query: 14 KEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAG 73 +E + +L+LLA+I + P F++ NL+++ +S I++A+G +I+T+ DLS Sbjct: 9 RETLLIAAILLLLALIASRFPAFIAPSNLAHVFNDTSPLILLAIGQMIVILTRCIDLSVA 68 Query: 74 RQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVT 133 + L +V + + N P + PI +++ I +G ++G+ NGL++ L + Sbjct: 69 ANLALTGMVVSMV-------NVAAPGL---PIVVILAIAIGLGTLLGMFNGLLVWKLQIP 118 Query: 134 PFITTLGTMIIVYGINSLYYD--FVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYAL 191 P + TLGTM I GI L D +V + +S F F + + LG LS+I A+ Sbjct: 119 PIVVTLGTMTIFRGIIFLISDGKWVNSHEMS---PAFKAFPRAEL-LGLPVLSWI---AI 171 Query: 192 IAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAG 251 +AV ++ +T G+ +A GGNP AA +G++VG + +SG G L Sbjct: 172 LAVILFTIVMTRTTLGRAFYAAGGNPHAATYAGIDVGKTQFWAFTISGALAGLTGYLWVS 231 Query: 252 RIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPY 311 R + ++ +ELD +AACV+GGVS GGVGTV G + G + +I L + ++P+ Sbjct: 232 RFAVSYVDIAGGFELDVVAACVIGGVSIMGGVGTVGGALLGALFLGIIKNALPVVDISPF 291 Query: 312 WQYIIKGAIIIFAVALDSLKYARK 335 WQ I G II AVAL++ +K Sbjct: 292 WQLAISGGAIIIAVALNAQANRKK 315 Lambda K H 0.327 0.143 0.415 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: 265 Number of extensions: 15 Number of successful extensions: 3 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: 336 Length of database: 327 Length adjustment: 28 Effective length of query: 308 Effective length of database: 299 Effective search space: 92092 Effective search space used: 92092 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