Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 3608584 Dshi_1978 inner-membrane translocator (RefSeq)
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__Dino:3608584 Length = 317 Score = 113 bits (283), Expect = 6e-30 Identities = 96/321 (29%), Positives = 150/321 (46%), Gaps = 29/321 (9%) Query: 30 VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAM 89 V A +A + + LGLN+ G GL + G VAF+ G Y ++ A + F Sbjct: 9 VFFATIASILAIAVLGLNLHWGNTGLFNGGVVAFFGAGGYATLILGGTPQAAHLGGFG-- 66 Query: 90 FPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHP 149 P GL +VI A LLA G + T++LR DYLAI T G + F N + + Sbjct: 67 LPYGLALLGGLVI--AGLLAWLVGLL----TIRLRHDYLAIATFG---VAVAFENLVRNA 117 Query: 150 VNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICY---- 205 L G GL + + G Y F V+ ++I Y Sbjct: 118 QRLAGGASGLRGFERPLADTIPPG-------------LAYNAAFFAFVLAALIATYLGLE 164 Query: 206 RLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPE 265 RL GR AIREDE AA+A+G + ++L AF +G+ G++GA++ F F+SP+ Sbjct: 165 RLIRGPFGRLLRAIREDETAARALGKSPDRIRLTAFVIGSVILGLAGALYATFYAFISPQ 224 Query: 266 SFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRLDSAILR 325 + + I AM+++GG G+ G I GA L+ + A + +L + ++ Sbjct: 225 DVLPILTFQIWAMLIVGGAGNNRGAIAGAFLIWGAWTASGWALSRF-APIEVQLYTGSIQ 283 Query: 326 QLLIALAMIIIMLLRPRGLWP 346 +LI ++ ++L RP+GL+P Sbjct: 284 FVLIGCVIVGMLLWRPQGLFP 304 Lambda K H 0.328 0.144 0.430 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: 309 Number of extensions: 19 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: 358 Length of database: 317 Length adjustment: 28 Effective length of query: 330 Effective length of database: 289 Effective search space: 95370 Effective search space used: 95370 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