Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= uniprot:P70970 (276 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 126 bits (316), Expect = 7e-34 Identities = 77/219 (35%), Positives = 128/219 (58%), Gaps = 9/219 (4%) Query: 6 ERLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNK 65 ++ A+ DI+ I+EGS A++G GSGK+TLL+ + GL P KG+I I GK Sbjct: 17 KQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKGEIVFSGQTIVNGKSA- 75 Query: 66 DLKKLRKKVGIVFQFPEHQLFEE-TVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEE 124 L +++VG++FQ E+ LF + T+L+++ + +A Q A + L L GL E+ Sbjct: 76 -LPANQREVGVIFQ--EYALFPQMTLLENVREA---LHQESRNARQIAMDSLALAGL-ED 128 Query: 125 LLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNL 184 P +LS GQ +R A+A LA P++L+LD+P LD R + EI + ++ + + Sbjct: 129 SFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDIRDIVKATGI 188 Query: 185 TTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLK 223 T I+ +H +DA + AD + ++HKG +Q G+P +++ K Sbjct: 189 TAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKK 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: 225 Number of extensions: 13 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: 345 Length adjustment: 27 Effective length of query: 249 Effective length of database: 318 Effective search space: 79182 Effective search space used: 79182 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