Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Dino:3607124 Length = 338 Score = 125 bits (315), Expect = 1e-33 Identities = 78/209 (37%), Positives = 123/209 (58%), Gaps = 4/209 (1%) Query: 23 RALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEVR 82 +AL ++L + +GE++ VG +G GKSTL R L GL SG IE+ G +T +V Sbjct: 17 QALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVT--TVEPAD 74 Query: 83 KKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPHH 142 + + MVFQ+ + TVR+++ FG++ NG + ER+ A + + ++D+LD++P Sbjct: 75 RDLAMVFQSYA-LYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQLEDYLDRKPGQ 133 Query: 143 LSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISITHD 202 LSGGQ+QRVAI I P + + DE S LD R ++ + L +Q AT+I +THD Sbjct: 134 LSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTHD 193 Query: 203 LNEA-AKADRIIVMNGGKKYAEGPPEEIF 230 EA AD+I+V+N G+ G P +++ Sbjct: 194 QVEAMTMADKIVVLNRGRIEQVGSPMDLY 222 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: 237 Number of extensions: 9 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: 281 Length of database: 338 Length adjustment: 27 Effective length of query: 254 Effective length of database: 311 Effective search space: 78994 Effective search space used: 78994 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: 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