Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_017368436.1 BA79_RS17265 ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000691145.1:WP_017368436.1 Length = 571 Score = 169 bits (429), Expect = 1e-46 Identities = 98/236 (41%), Positives = 140/236 (59%), Gaps = 10/236 (4%) Query: 6 LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPES-- 63 +I E F+YR AE D V+L +YEGE + I G +GSGKSTLA +NGL+ P S Sbjct: 5 MIQFEHFGFKYRSQAEPTLKD-VNLTIYEGEKVLIAGPSGSGKSTLAHCINGLV-PASYK 62 Query: 64 ----GDIEVAGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEM 119 G + + G +E+++ + + +G V Q+PD QF+G TV +D+AF LEN+ V REEM Sbjct: 63 GSMEGSLHIGGKNAEKENIFSLSQLVGTVLQDPDGQFIGLTVGEDIAFTLENDQVTREEM 122 Query: 120 IERVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGRE 179 RV+ A K + L H LSGGQKQRVAIAGV+ DI++ DE + LDP + Sbjct: 123 KTRVEKAAKLTEVDGKLASSVHELSGGQKQRVAIAGVLVNDVDILLFDEPLASLDPATGK 182 Query: 180 EVLETVRHLKEQGMATVISITHDLNEA--AKADRIIVMNGGKKYAEGPPEEIFKLN 233 EV++ + L+++ TV+ + H L + DRIIV+N G A+ P+E+ N Sbjct: 183 EVIDLIDRLQKETKKTVVMVEHRLEDVLFRHVDRIIVVNDGTIAADMTPDELLASN 238 Score = 124 bits (311), Expect = 5e-33 Identities = 74/225 (32%), Positives = 127/225 (56%), Gaps = 4/225 (1%) Query: 6 LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65 L+ V ++ F Y L+ +S V +GE ++I G NG+GK+TL++ L P G Sbjct: 302 LLEVRELSFDY--PTRPNTLNNISFTVKKGEMISIAGANGAGKTTLSKVLCAFEKPTKGT 359 Query: 66 IEVAGIQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDW 125 I + G +T +++ + ++IG+V QNP+ + D+VA GL GV +++ +RV+ Sbjct: 360 IHLNGDDITGDTIKQRSERIGVVMQNPNQMISKQMIFDEVALGLVLRGVKEDDIKDRVER 419 Query: 126 AVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETV 185 +K + F + LS GQK+RV IA ++ P+IIILDE T+ D E++ + Sbjct: 420 VLKVCGLYPFRNWPISALSFGQKKRVTIASILVLEPEIIILDEPTAGQDFRHYTEMMTFL 479 Query: 186 RHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEI 229 L +QG+ T++ ITHD++ + R IV++ G+K A+ P ++ Sbjct: 480 EQLNQQGV-TILMITHDMHLMLEYTTRTIVISDGEKIADDTPAKV 523 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: 428 Number of extensions: 20 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 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