Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 7023651 Shewana3_0880 ABC transporter related (RefSeq)
Query= uniprot:P40735 (281 letters) >FitnessBrowser__ANA3:7023651 Length = 241 Score = 134 bits (337), Expect = 2e-36 Identities = 83/224 (37%), Positives = 131/224 (58%), Gaps = 6/224 (2%) Query: 16 YRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTE 75 ++ + L G++ + +GE ++++G +GSGKST R +N L P GDIE+ G +T Sbjct: 8 HKSYGDNAVLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLEKPTQGDIEIEGQSITA 67 Query: 76 ES--VWEVRKKIGMVFQNPDNQFVGTTVRDDVAFG-LENNGVPREEMIERVDWAVKQVNM 132 + V ++R+K+GMVFQN N F TV ++ + + + E + + QV + Sbjct: 68 KDACVDKLRQKVGMVFQN-FNLFPHKTVLQNITLAPVSLKLMTQAEADNKALALLTQVGL 126 Query: 133 QDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQG 192 QD + P LSGGQKQRVAIA +A PD+++ DE TS LDP +VL+ ++ L ++G Sbjct: 127 QDKANAYPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDPEMVGDVLDVMKDLAQKG 186 Query: 193 MATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIFKLNKE 235 M T++ +TH++ A +DR+I M+GG PEE+F KE Sbjct: 187 M-TMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEELFTRPKE 229 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: 157 Number of extensions: 6 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: 241 Length adjustment: 24 Effective length of query: 257 Effective length of database: 217 Effective search space: 55769 Effective search space used: 55769 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