Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 8501894 DvMF_2609 inner-membrane translocator (RefSeq)
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__Miya:8501894 Length = 415 Score = 250 bits (638), Expect = 5e-71 Identities = 145/331 (43%), Positives = 199/331 (60%), Gaps = 44/331 (13%) Query: 14 ALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFAL 73 A LVLP ++ ++ I ALLYV+L LGLNIVVG +G L LGYVAFYAVGAY +A+ Sbjct: 100 AFLVLPWVVSTYQT---NIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYSYAI 156 Query: 74 MASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTL 133 + S NF W V+P+ +AA FG +LG P L+LRGDYLAIVTL Sbjct: 157 LNS-----NFGL-----------GFWSVLPIGGAMAALFGILLGFPVLRLRGDYLAIVTL 200 Query: 134 GFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLF 193 GFGEIIR+ L N + + GP G+ I+ + G+ L ++ T YYL Sbjct: 201 GFGEIIRLVLENWS---SFSQGPSGIANIERPGLLGMQLSVS--------DATTYIYYLI 249 Query: 194 LVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGA 253 L V+V+++ RL++SRIGRAW A+REDEIA +AMGI+ KL AF +GA + G +G Sbjct: 250 LAAVIVTILAVTRLKNSRIGRAWQALREDEIACQAMGIDITTTKLTAFALGACWAGFAGV 309 Query: 254 MFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQA 313 +F A F++P SF+ +ES M++AMVVLGG+G + GV +GA++L LPE LR + Sbjct: 310 IFAAKTTFINPASFTFLESAMVLAMVVLGGMGSVIGVSVGALVLILLPEYLRAFSE---- 365 Query: 314 MTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 R L+ M+++M+ RP+GL Sbjct: 366 ----------YRMLIFGATMVLMMVFRPQGL 386 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: 409 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 415 Length adjustment: 30 Effective length of query: 328 Effective length of database: 385 Effective search space: 126280 Effective search space used: 126280 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: 50 (23.9 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