Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_011972867.1 MAEO_RS00720 ATP-binding cassette domain-containing protein
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000017185.1:WP_011972867.1 Length = 281 Score = 185 bits (470), Expect = 8e-52 Identities = 109/267 (40%), Positives = 169/267 (63%), Gaps = 7/267 (2%) Query: 6 LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65 +I +DIV++Y ALD ++ V +G+ +A++G NG+GKSTL NG++ P+SG Sbjct: 3 IIEAKDIVYKYPDGT--LALDRANISVEKGDMVALLGPNGAGKSTLFLHFNGILKPKSGK 60 Query: 66 IEVAG--IQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERV 123 I + G I+ +S+ EVRK +G+VFQN D+Q TV+ DVAFG N G+ EE+ +RV Sbjct: 61 ILLKGAPIKYDAKSLMEVRKTVGIVFQNSDDQLFAPTVKQDVAFGPLNLGLKEEEVEKRV 120 Query: 124 DWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLE 183 A+K+V M+ F ++ PHHLSGGQK+RVAIAG++A P+I++LDE T+ LDP+G ++++ Sbjct: 121 KEALKEVGMEGFENKPPHHLSGGQKKRVAIAGILAMHPEIMVLDEPTAGLDPMGASKIMK 180 Query: 184 TVRHLKEQGMATVISITHDLN-EAAKADRIIVMNGGKKYAEGPPEEIFKLNKELVRIGLD 242 + L ++G+ +IS THD++ A++I VM K G EE+F K + L Sbjct: 181 LLYKLNKEGITIIIS-THDVDLVPIYANKIFVMGKTKIVKSGTVEEVFSDIKTIRSANLR 239 Query: 243 LPFSFQLSQLL-RENGLALEENHLTQE 268 LP L ++L R+ G+ L+ + E Sbjct: 240 LPRVAHLIEVLNRKEGIDLKMGYTIGE 266 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: 221 Number of extensions: 8 Number of successful extensions: 2 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: 281 Length adjustment: 26 Effective length of query: 255 Effective length of database: 255 Effective search space: 65025 Effective search space used: 65025 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