Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_041670877.1 RSPH17029_RS18130 amino acid ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000015985.1:WP_041670877.1 Length = 242 Score = 131 bits (330), Expect = 1e-35 Identities = 83/212 (39%), Positives = 128/212 (60%), Gaps = 6/212 (2%) Query: 23 RALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTE--ESVWE 80 + L VSL V +GE + + G +GSGKSTL R +N L + +SG I V G+++T+ +++ Sbjct: 15 QVLHDVSLDVRKGERVVVCGPSGSGKSTLIRCINRLEVHQSGQIFVKGLEMTDNVKNIDT 74 Query: 81 VRKKIGMVFQNPDNQFVGTTVRDDVAFG-LENNGVPREEMIERVDWAVKQVNMQDFLDQE 139 +R+ IGMVFQN N F TV +++ G + + + + +++V + + + Sbjct: 75 IRRHIGMVFQN-FNLFPHLTVLENLTLGPMLTRQMKKSAAEDLAMHFLRKVRIPEQSGKY 133 Query: 140 PHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISI 199 P LSGGQ+QRVAIA + P+I++ DE TS LDP +EVL+T+ L E GM T+I + Sbjct: 134 PLQLSGGQQQRVAIARSLCMEPEIMLFDEPTSALDPEMIKEVLDTMIELAESGM-TMIVV 192 Query: 200 THDLNEA-AKADRIIVMNGGKKYAEGPPEEIF 230 TH++ A AD ++ M G+K GPPEE F Sbjct: 193 THEMGFARTVADNVVFMADGRKVESGPPEEFF 224 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: 173 Number of extensions: 8 Number of successful extensions: 4 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: 242 Length adjustment: 25 Effective length of query: 256 Effective length of database: 217 Effective search space: 55552 Effective search space used: 55552 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 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