Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_170920503.1 B9A12_RS09210 energy-coupling factor transporter ATPase
Query= uniprot:P40735 (281 letters) >NCBI__GCF_900176285.1:WP_170920503.1 Length = 571 Score = 153 bits (386), Expect = 1e-41 Identities = 91/228 (39%), Positives = 135/228 (59%), Gaps = 5/228 (2%) Query: 22 RRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEV 81 R+AL + L ++EGE +A++GHNGSGK+TLAR L+GL P G + G L+ E + ++ Sbjct: 32 RQALRHIDLSIHEGERIAVLGHNGSGKTTLARVLSGLAPPTQGRVLFQGDPLSRERLEDL 91 Query: 82 RKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPH 141 R+++G +FQ+PD+Q TV DDV FGL N VP +E ER A+ + ++ + PH Sbjct: 92 RQRVGFLFQDPDDQLFCPTVLDDVLFGLLNFQVPPKEAEERARKALAAMGLEAEAHRAPH 151 Query: 142 HLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISITH 201 HLS GQ++R A+A ++A PD++ILDE T+ +DP E +L V LK+ T+I I+H Sbjct: 152 HLSYGQRKRAALAAILALEPDVLILDEPTANMDPTS-EALLSKV--LKDY-PGTLICISH 207 Query: 202 D-LNEAAKADRIIVMNGGKKYAEGPPEEIFKLNKELVRIGLDLPFSFQ 248 D L R +V+ G + + E + L GLD F FQ Sbjct: 208 DILFLYGLCTRAVVLQAGGIHHDTSFERLISHRASLQEHGLDFTFRFQ 255 Score = 125 bits (314), Expect = 2e-33 Identities = 87/260 (33%), Positives = 149/260 (57%), Gaps = 12/260 (4%) Query: 9 VEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEV 68 +E + F Y AL+ VS QV GE LA+VG NG+GKSTLA L G I +G + Sbjct: 312 LEMLGFSYAYGDGTVALENVSFQVGRGERLALVGPNGAGKSTLAACLAG-IRWGTGQYLL 370 Query: 69 AGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVK 128 G ++ + + +G+VFQ+ +Q V + D+VAFGL N G P + ++V + Sbjct: 371 DGRKVEGAFRRNLWRHVGLVFQDSADQMVCSRCGDEVAFGLRNLGWPESRIRKKVQAMLH 430 Query: 129 QVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHL 188 ++ F D+ P HLSGG+++R+A+A V+A P+++ILDE T+ LDP +++L+ L Sbjct: 431 WAGLEGFEDRVPQHLSGGERKRLALAAVLAMEPEVLILDEPTAGLDPQTEQKLLQ----L 486 Query: 189 KEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIFKLNKELVRI-GLDLPFS 246 ++ AT++ I+HD+ + DR ++M+ G + + P F +++ L + GLD + Sbjct: 487 LDEVEATLVLISHDVCFVSMLTDRTLLMHRG-RIVDDLPTGKFLVDRNLHSLYGLDFTYY 545 Query: 247 FQLSQLLRENGLALEENHLT 266 + + +++ L+E+H T Sbjct: 546 NRCCREIQD----LQEDHRT 561 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: 396 Number of extensions: 25 Number of successful extensions: 4 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: 571 Length adjustment: 31 Effective length of query: 250 Effective length of database: 540 Effective search space: 135000 Effective search space used: 135000 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 Apr 09 2024. 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