Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Synpcc7942_2494 Synpcc7942_2494 putative branched-chain amino acid ABC transporter, permease protein
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__SynE:Synpcc7942_2494 Length = 307 Score = 136 bits (343), Expect = 6e-37 Identities = 100/309 (32%), Positives = 159/309 (51%), Gaps = 44/309 (14%) Query: 44 LGLNIVVGY-AGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVI 102 LGL++ + AG L L AFYA+G YL A++++ L + P +L + + Sbjct: 21 LGLSVYLPLMAGQLSLASPAFYALGGYLAAILSTKGLTAS--------PEYSVGALLLEM 72 Query: 103 PVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQI 162 +AA+ AA ++G P L+LRG YLAI T+ EI+R+ NL ++T G G Sbjct: 73 GLAAIAAAVLAFLVGYPVLRLRGIYLAIATIALVEIVRVVALNL----SITGGAVG---- 124 Query: 163 DSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIRED 222 +FG+ +S Y ++ L L++++V C+RLQ R G AIRED Sbjct: 125 ----IFGIPQ---------PFSSAVGYLWIALPLLLIAVAACWRLQQVRTGLVLAAIRED 171 Query: 223 EIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLG 282 E+AA A+ +NT K+LAF +GA + GA+ F +P + S+ +A V++G Sbjct: 172 ELAASAIAVNTTRYKVLAFVLGAVLASLVGAVSAHFLNTWNPRQGTFDASITFLAFVLIG 231 Query: 283 GIGHIPGVILGAVLLSALPEVLRYVA-------GPLQAMTDGRLDSAILRQLLIALAMII 335 G G +LG ++L+ALPE+LR + G + + DGRL L+ L +++ Sbjct: 232 GSRSAFGPVLGGMVLTALPELLRAIGSVPGLWPGLSRLLQDGRL-------LIFGLLLVL 284 Query: 336 IMLLRPRGL 344 + P+GL Sbjct: 285 GSIYFPQGL 293 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: 294 Number of extensions: 17 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: 307 Length adjustment: 28 Effective length of query: 330 Effective length of database: 279 Effective search space: 92070 Effective search space used: 92070 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