Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate SMa2067 SMa2067 sulfate/thiosulfate binding protein
Query= uniprot:P70970 (276 letters) >FitnessBrowser__Smeli:SMa2067 Length = 347 Score = 138 bits (348), Expect = 1e-37 Identities = 85/218 (38%), Positives = 126/218 (57%), Gaps = 14/218 (6%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68 AL D+ I G +A++G +GSGK+TLL+ + GL PT+G I G A K+ Sbjct: 17 ALVDVTLDILSGELIALLGPSGSGKTTLLRLIAGLESPTEGMIFFGDE--DASKRTVQ-- 72 Query: 69 KLRKKVGIVFQFPEHQLFEE-TVLKDISFG----PMNFGVKKEDAEQKAREMLQLVGLSE 123 + +G VFQ + LF TVL +++FG P N + ++A +++ LV LS Sbjct: 73 --ERNIGFVFQ--HYALFRHMTVLDNVTFGLKVRPANRRPPAAEIRRRALDLIDLVQLSG 128 Query: 124 ELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGN 183 L R P +LSGGQ +RVA+A +A++P VL+LDEP LD + RKE+ E+H R Sbjct: 129 -LEKRYPAQLSGGQRQRVALARAMAVEPSVLLLDEPFGALDAQVRKELRRWLREIHDRTG 187 Query: 184 LTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221 TT+ VTH E+A AD ++VM KG I+ G+P +++ Sbjct: 188 YTTLFVTHDQEEALELADRVVVMSKGAIEQVGTPDEIY 225 Lambda K H 0.318 0.136 0.380 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: 216 Number of extensions: 14 Number of successful extensions: 2 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: 276 Length of database: 347 Length adjustment: 27 Effective length of query: 249 Effective length of database: 320 Effective search space: 79680 Effective search space used: 79680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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