Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate CA265_RS16020 CA265_RS16020 ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Pedo557:CA265_RS16020 Length = 250 Score = 120 bits (302), Expect = 2e-32 Identities = 82/229 (35%), Positives = 124/229 (54%), Gaps = 9/229 (3%) Query: 6 LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65 +I ++DI Y+ + L G+S + EG I+G +GSGK+TL + + GL P+SG Sbjct: 1 MIEIKDI---YKSFSGNDVLQGISGKFEEGVTNLIIGGSGSGKTTLLKCMVGLHQPDSGS 57 Query: 66 IEVAG---IQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLEN-NGVPREEMIE 121 + G +T E EVRK+IGM+FQ F TV +++ F L R+E +E Sbjct: 58 VLYDGRDFTPMTYEQRIEVRKEIGMLFQG-SALFDSMTVEENIMFPLNMFTDQSRKEKLE 116 Query: 122 RVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEV 181 RVD+ +++VN+ P LSGG K+RV IA I+ P + DE S LDP + Sbjct: 117 RVDFCLERVNLAGKNKLFPAELSGGMKKRVGIARAISMNPKYLFCDEPNSGLDPKTSIVI 176 Query: 182 LETVRHLKEQGMATVISITHDLNEA-AKADRIIVMNGGKKYAEGPPEEI 229 E ++ + E+ T I +THD+N D I+ ++ GKK+ EG +EI Sbjct: 177 DELIQEITEEYKTTTIVVTHDMNSVMGIGDYILFLHEGKKFWEGSNKEI 225 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: 198 Number of extensions: 14 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: 250 Length adjustment: 25 Effective length of query: 256 Effective length of database: 225 Effective search space: 57600 Effective search space used: 57600 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: 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