Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate 3607646 Dshi_1055 ABC transporter related (RefSeq)
Query= uniprot:P70970 (276 letters) >FitnessBrowser__Dino:3607646 Length = 366 Score = 127 bits (320), Expect = 3e-34 Identities = 76/214 (35%), Positives = 125/214 (58%), Gaps = 10/214 (4%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68 AL ++ +I G Y ++G +G GK+TLL+ + G +PT+GQ+ L G+ L Sbjct: 23 ALRQVDLTIAAGEYFVLLGPSGGGKTTLLRTIGGFHRPTEGQVLLH------GRDMSHLP 76 Query: 69 KLRKKVGIVFQFPEHQLFEE-TVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLD 127 ++ +VFQ + LF TVL+++S+G G+ K A++KA M+ +VGL+ + Sbjct: 77 PDKRPTTMVFQ--AYALFPHMTVLQNVSYGLKVAGMDKATAQEKAAAMMDVVGLAG-FAE 133 Query: 128 RSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTI 187 R P ELSGGQ +RV +A L +D ++L+LDEP A LD + RK++ L ++ +T I Sbjct: 134 RKPHELSGGQQQRVQLARALVLDRDILLLDEPLAALDAQLRKDMCLELKHLQEKVGITFI 193 Query: 188 LVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221 VTH+ E+A AD + ++ G + G+ RD++ Sbjct: 194 HVTHNQEEAMTVADRIALVADGQLVEQGAARDIY 227 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: 226 Number of extensions: 9 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: 276 Length of database: 366 Length adjustment: 27 Effective length of query: 249 Effective length of database: 339 Effective search space: 84411 Effective search space used: 84411 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