Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate 3606891 Dshi_0321 ABC transporter related (RefSeq)
Query= uniprot:P70970 (276 letters) >FitnessBrowser__Dino:3606891 Length = 258 Score = 122 bits (307), Expect = 6e-33 Identities = 78/214 (36%), Positives = 121/214 (56%), Gaps = 8/214 (3%) Query: 10 LYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLKK 69 L DIN ++ G + + G +GSGKSTL++ +N L + G I++ T++ + KN D Sbjct: 33 LRDINLTVYRGERIVICGPSGSGKSTLIRCINALEEHQAGSITVDGTLLSSDLKNIDT-- 90 Query: 70 LRKKVGIVFQFPEHQLFEE-TVLKDISFGPMNFG-VKKEDAEQKAREMLQLVGLSEELLD 127 +R +VG+ FQ LF T+L++ + P+ K++AE A L+ V + ++ + Sbjct: 91 IRSEVGMCFQ--HFNLFPHLTILENCTLAPIWVRKTPKKEAEATAMHFLEKVKIPDQA-N 147 Query: 128 RSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTI 187 + P +LSGGQ +RVAIA L M P +++ DEPT+ LDP KE++D EL + G +T I Sbjct: 148 KYPGQLSGGQQQRVAIARSLCMRPRIMLFDEPTSALDPEMIKEVLDTMIELAEEG-MTMI 206 Query: 188 LVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221 VTH M A A+ +I M G I P + F Sbjct: 207 CVTHEMGFARQVANRVIFMDAGQIVEQNEPEEFF 240 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: 149 Number of extensions: 6 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: 258 Length adjustment: 25 Effective length of query: 251 Effective length of database: 233 Effective search space: 58483 Effective search space used: 58483 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