Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 8502039 DvMF_2752 inner-membrane translocator (RefSeq)
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__Miya:8502039 Length = 330 Score = 199 bits (505), Expect = 1e-55 Identities = 132/335 (39%), Positives = 184/335 (54%), Gaps = 47/335 (14%) Query: 12 AVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71 AV + VLPL+L + W + LY +LAL LNI++G AGL +G+ AFYAVGAY+ Sbjct: 13 AVVVAVLPLLLDPY---WTDVFVSIGLYSVLALSLNIILGQAGLFHMGHAAFYAVGAYVT 69 Query: 72 ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131 A+ A+ LW +P A L AA F ++ P + LRGDYL IV Sbjct: 70 AI------ANTMWGVPV---------LW-AMPFAGLAAALFAMVVARPIIHLRGDYLLIV 113 Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYY 191 T+G EI+RI L N + LT G G +FG+ R +FGF I +YY Sbjct: 114 TIGIVEIVRIALIN--NVFGLTGGANG--------IFGIS---RPMLFGFKIAKPVHFYY 160 Query: 192 LFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVS 251 L V S+++ RL++SR GRA I+ED+ AA+ G+N + KL AF +GA + G++ Sbjct: 161 LVWAYVACSILLFRRLENSRFGRALNYIKEDDTAAEGSGVNIASYKLWAFVLGAFWAGMT 220 Query: 252 GAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPL 311 G ++ A +SPESFS ESV++ A+V+LGG G GV+LGA LL LPE R Sbjct: 221 GTIYAAKMTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGLPEFFR------ 273 Query: 312 QAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346 + A R L LAM+++M+ RP+G+ P Sbjct: 274 --------EFASARMLAFGLAMVVMMIFRPQGMLP 300 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: 300 Number of extensions: 16 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: 330 Length adjustment: 29 Effective length of query: 329 Effective length of database: 301 Effective search space: 99029 Effective search space used: 99029 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