Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate 209324 DVU0388 amino acid ABC transporter, ATP-binding protein
Query= uniprot:P70970 (276 letters) >MicrobesOnline__882:209324 Length = 255 Score = 137 bits (345), Expect = 2e-37 Identities = 86/220 (39%), Positives = 129/220 (58%), Gaps = 7/220 (3%) Query: 7 RLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKD 66 R L D++ + G +IG +G+GKSTLLQ +N L+ P G +SL + A +K D Sbjct: 21 RPILRDVSLDVDRGQLKVLIGPSGAGKSTLLQCINHLILPDAGTVSLEGRAVDAHRK-AD 79 Query: 67 LKKLRKKVGIVFQFPEHQLFEET-VLKDISFGPMNF-GVKKEDAEQKAREMLQLVGLSEE 124 L R++VG++FQ E LF+ L ++S G+ + A ++A L+ VGLS Sbjct: 80 LYAFRQQVGMIFQ--EFNLFDHLDALSNVSIALRKVRGMSRAAARERAMAELERVGLSSR 137 Query: 125 LLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNL 184 P +LSGGQ +RVAIA LAMDP+V++LDEPT+ LDP E++ + +L +G + Sbjct: 138 HA-LYPAQLSGGQKQRVAIARALAMDPKVMLLDEPTSALDPELVGEVLAVIRDL-AKGGM 195 Query: 185 TTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKG 224 T ++ TH M+ A A A+E++ M +G I GSP +L G Sbjct: 196 TMVMATHQMDFARALANEIVFMERGAIIERGSPAELLAPG 235 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: 162 Number of extensions: 8 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: 255 Length adjustment: 25 Effective length of query: 251 Effective length of database: 230 Effective search space: 57730 Effective search space used: 57730 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: 47 (22.7 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