Align ABC transporter permease (characterized, see rationale)
to candidate 3607106 Dshi_0528 Monosaccharide-transporting ATPase (RefSeq)
Query= uniprot:A0A166R405 (325 letters) >FitnessBrowser__Dino:3607106 Length = 334 Score = 141 bits (355), Expect = 3e-38 Identities = 91/306 (29%), Positives = 156/306 (50%), Gaps = 17/306 (5%) Query: 27 LLAMVALFSVLS----SHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVLA 82 L+ MV +F ++S FLS +++A Q P+ +LA+ MT ++ GGIDLSV + Sbjct: 17 LIIMVFVFGLMSVLSPDRFLSSQNLTSMAFQFPEFAILALAMTIAMMTGGIDLSVVGIAN 76 Query: 83 LAASAVSVAILGWGWSVLPAA----------LLGMAVAALAGTITGSITVAWRIPSFIVS 132 L+A ++ + + + +PAA + + A+AG I GS+ + +P + + Sbjct: 77 LSAVVAALILTHFSNAEMPAAQSAIWLAIAITAALCIGAIAGLINGSLVAFFGLPPILAT 136 Query: 133 LGVLEMARGLAYQMTGSRTAYIG--DAFAWLSNPIAFGISPSFIIALLIIFIAQAVLTRT 190 LG + G A MTG +A +G D A + N G+ I+ ++ F+ VLTRT Sbjct: 137 LGSGLVFTGFAIAMTGG-SAVMGFPDTVALIGNATLAGVPVPLILFAVLAFLLHLVLTRT 195 Query: 191 VFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGSGL 250 FG + G N A A I+ + V+ + G+ A +A L +SR +A + GS Sbjct: 196 AFGLRVTMYGANPLAALYAAIDINRMLLKVYVIAGMFASVAGLIIMSRANSAKADYGSSY 255 Query: 251 ELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVA 310 L + V+GG + GG G VI VL + L++GL +G + + +I GA++++ Sbjct: 256 LLLAVLIAVLGGVNPYGGYGRVIGVVLAVLSMQFLSSGLNMLGVSNFARELIWGALLILV 315 Query: 311 VVLDTY 316 +V++T+ Sbjct: 316 MVINTH 321 Lambda K H 0.325 0.139 0.393 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: 254 Number of extensions: 13 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: 325 Length of database: 334 Length adjustment: 28 Effective length of query: 297 Effective length of database: 306 Effective search space: 90882 Effective search space used: 90882 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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