Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_035131541.1 Q763_RS04180 ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000769915.1:WP_035131541.1 Length = 562 Score = 114 bits (286), Expect = 4e-30 Identities = 77/215 (35%), Positives = 122/215 (56%), Gaps = 14/215 (6%) Query: 16 YRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTE 75 + +D + +A++ VS ++YEGE L +VG +G GKSTL A+ L +G I G LT+ Sbjct: 321 FGRDVKFKAVNNVSFKIYEGETLGLVGESGCGKSTLGNAILQLDKATAGSILYKGQDLTK 380 Query: 76 ES---VWEVRKKIGMVFQNPDNQF-----VGTTVRDDV-AFGLENNGVPREEMIERVDWA 126 S + E+RK+I ++FQ+P + VG + + + GL N R E + Sbjct: 381 LSASAIRELRKEIQIIFQDPYSSLNPRITVGKAIMEPMKVHGLYKNDRERREKTIEI--- 437 Query: 127 VKQVNM-QDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETV 185 +K+V + ++ ++ PH SGGQ+QRV IA IA +P +I+ DE+ S LD + +VL + Sbjct: 438 LKRVGLGEEHFNRYPHEFSGGQRQRVGIARTIALQPKLIVCDESVSALDISVQAQVLNLL 497 Query: 186 RHLKEQGMATVISITHDLNEAA-KADRIIVMNGGK 219 LKE T I I+HDL +D+++VMN G+ Sbjct: 498 NELKENFGFTYIFISHDLAVVKYMSDQVLVMNKGQ 532 Score = 94.7 bits (234), Expect = 4e-24 Identities = 74/248 (29%), Positives = 129/248 (52%), Gaps = 24/248 (9%) Query: 4 NQLISVEDIVFRYRKDAERRAL-DGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPE 62 + L+++ I RK+ + + + + + E L IVG +GSGKS + A+ GL LP+ Sbjct: 3 DSLLNINHITISARKEGQWTPIVHDSTFTLEQNEILGIVGESGSGKSVTSLAVMGL-LPK 61 Query: 63 S------GDIEVAGIQLTEESVWEVRK----KIGMVFQNPDNQF-----VGTTVRDDVAF 107 G I G +++ + E+R I M+FQ P + G V + Sbjct: 62 GILQVTQGSIAFEGRDISQLTTREMRNIRGNDIAMIFQEPMSSLNPSLKCGYQVEEIFK- 120 Query: 108 GLENNGVPREEM---IERVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDII 164 E+ + + E+ + + VK N + ++ PH +SGGQKQRV IA IA +P I+ Sbjct: 121 --EHTSLSKREIKATVLSLFEKVKLPNPEKIYNRYPHEISGGQKQRVMIAMAIACKPKIL 178 Query: 165 ILDEATSMLDPIGREEVLETVRHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAE 223 I DE T+ LD ++E++ ++ L+++ ++I I+HDL+ ++ A+R++VM G + Sbjct: 179 IADEPTTALDVTVQKEIILLLKELQQETKMSIIFISHDLSLVSEIANRVLVMYKGNIVEQ 238 Query: 224 GPPEEIFK 231 G EIF+ Sbjct: 239 GVATEIFE 246 Lambda K H 0.316 0.135 0.383 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: 347 Number of extensions: 23 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 281 Length of database: 562 Length adjustment: 31 Effective length of query: 250 Effective length of database: 531 Effective search space: 132750 Effective search space used: 132750 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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