Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 8500414 DvMF_1164 inner-membrane translocator (RefSeq)
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__Miya:8500414 Length = 358 Score = 155 bits (393), Expect = 1e-42 Identities = 105/350 (30%), Positives = 185/350 (52%), Gaps = 27/350 (7%) Query: 12 AVALLVLPLILQSFGNAWVRIADLALLY----VLLALGLNIVVGYAGLLDLGYVAFYAVG 67 A+A L L L+L + N + L++ ++ A LNIV GY G G+ F VG Sbjct: 9 ALAALCLGLVLLAQFNVIDQYTQTVLMFMGINIIFASSLNIVNGYMGEFSCGHAGFMCVG 68 Query: 68 AYLFALMASPHLADNFAAFAAMFPNGLHTSLW-IVIPVAALLAAFFGAMLGAPTLKLRGD 126 AY ++++ N A+ P L L+ +V+ VA L+++ FG ++ P+ + RGD Sbjct: 69 AYASSVLSVVLFTSNKLVGDALLPPELAPMLFPVVLIVAGLVSSVFGLLVALPSFRTRGD 128 Query: 127 YLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSV 186 YLAI+T+ I+ + NLD + GP+G + V + G+ D+ + Sbjct: 129 YLAIITIAANYIVISVIENLD----IIGGPRGFHGMKRV-INGMR----------DLVDI 173 Query: 187 TLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGAS 246 + ++ + SV I RL +S G+ A+ +DE+AA+ M ++T ++KL+AF + + Sbjct: 174 PWMFIWVILGTLFSVWILRRLVNSTYGKGISAVCQDEVAAEIMSVDTNHVKLVAFMVSSG 233 Query: 247 FGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRY 306 GV+GA++ G+V+P++F++++S + MV LGG+ + G ++ A+L + L E LR+ Sbjct: 234 LAGVAGALYAHVYGYVNPQAFNILKSTEGLVMVYLGGMASLSGSVMAAILFTLLLESLRF 293 Query: 307 VAGPLQA-------MTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPSPE 349 V L A + G S + + +LI L +I++M RP G+ + E Sbjct: 294 VIPGLDAALHAVNLLPAGYELSQVWKWVLIPLILILLMQFRPEGIMGNRE 343 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: 299 Number of extensions: 19 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: 358 Length of database: 358 Length adjustment: 29 Effective length of query: 329 Effective length of database: 329 Effective search space: 108241 Effective search space used: 108241 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