Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 5210736 Shew_3164 ABC transporter-related protein (RefSeq)
Query= uniprot:P40735 (281 letters) >FitnessBrowser__PV4:5210736 Length = 241 Score = 120 bits (302), Expect = 2e-32 Identities = 77/218 (35%), Positives = 122/218 (55%), Gaps = 14/218 (6%) Query: 21 ERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLT--EESV 78 + + L G+ + GE ++++G +GSGKST R +N L P G+I + G +T + + Sbjct: 13 DNQVLKGIDESIARGEVVSVIGPSGSGKSTFLRCINLLEQPTQGEIVIDGQSITAPDACI 72 Query: 79 WEVRKKIGMVFQNPDNQFVGTTVRDDVAF-----GLENNGVPREEMIERVDWAVKQVNMQ 133 ++R+K+GMVFQN N F TV+ ++ GL E + +D QV + Sbjct: 73 DKLRQKVGMVFQN-FNLFPHKTVQQNITLAPVKLGLMTQAEADSEAMRLLD----QVGLS 127 Query: 134 DFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGM 193 D P LSGGQKQRVAIA +A +P++++ DE TS LDP +VL+ ++ L + GM Sbjct: 128 DKASAYPASLSGGQKQRVAIARALAMKPELMLFDEPTSALDPEMVGDVLDVMKQLAQAGM 187 Query: 194 ATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIF 230 T++ +TH++ A +DR+I M+GG P +F Sbjct: 188 -TMVIVTHEMGFAKDVSDRVIFMDGGYVVESNVPALLF 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: 160 Number of extensions: 8 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: 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