Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 208248 DVU2742 high-affinity branched chain amino acid ABC transporter, permease protein
Query= uniprot:A0A165KER0 (358 letters) >MicrobesOnline__882:208248 Length = 358 Score = 156 bits (394), Expect = 9e-43 Identities = 107/361 (29%), Positives = 189/361 (52%), Gaps = 30/361 (8%) Query: 1 MKNTKTNWIIGAVALLVLPLILQSFGNAWVRIADLALLYV----LLALGLNIVVGYAGLL 56 M+N N ++ A+ LLV+ L FG + ++ L+++ + A LNIV GY G Sbjct: 1 MRNYTLNIVLAALCLLVVGL--SQFG-VLDQYSETVLMFIGINIIFAASLNIVNGYMGEF 57 Query: 57 DLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLW-IVIPVAALLAAFFGAM 115 G+ F VGAY+ +L++ +N AA+ P L L+ +VI + +AA FG + Sbjct: 58 SCGHAGFMCVGAYVSSLLSVTLFTNNKLLGAALLPPELAPLLFPVVIAIGGFVAAGFGLL 117 Query: 116 LGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKR 175 + P+ + RGDYLAI+T+ I+ + NL+ GP+G + V + G+ Sbjct: 118 VALPSFRTRGDYLAIITIAANYIVISLIENLE----FIGGPRGFHGMKKV-INGMR---- 168 Query: 176 LEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRN 235 D+ + L+ + S+ + RL S G+ A+ +DE+AA+ M ++T + Sbjct: 169 ------DLADIPWMLIWVLLGTLFSLWLLRRLVTSTYGKGISAVCQDEVAAEIMSVDTNH 222 Query: 236 MKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAV 295 +KL AF + + GV+G ++ G+V+P++F++++S + MV LGG+ + G ++ A+ Sbjct: 223 IKLTAFMVSSGLAGVAGGLYAHIFGYVNPQAFNILKSTEGLVMVYLGGMASLSGSVMSAI 282 Query: 296 LLSALPEVLRYVAGPLQA-------MTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPSP 348 L + L E LR+V L + + DG S I + ++I L +I++M RP G+ + Sbjct: 283 LFTLLIESLRFVIPGLDSVLHSVGLLPDGYELSQIWKWVIIPLILILLMQFRPEGIMGNR 342 Query: 349 E 349 E Sbjct: 343 E 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: 333 Number of extensions: 24 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: 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