Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= uniprot:P40735 (281 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 123 bits (308), Expect = 7e-33 Identities = 76/219 (34%), Positives = 126/219 (57%), Gaps = 8/219 (3%) Query: 17 RKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEE 76 +K + +AL ++L + EGE + ++G +GSGK+TL R + GL +SG I +T+ Sbjct: 10 KKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFGNRDVTQV 69 Query: 77 SVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLE----NNGVPREEMIERVDWAVKQVNM 132 V + +++G VFQN F TV D+VAFGLE + E+ +RV ++ V + Sbjct: 70 HVRD--RRVGFVFQNYA-LFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLLEMVQL 126 Query: 133 QDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQG 192 + P LSGGQKQR+A+A +A +P++++LDE LD R+E+ +R L ++ Sbjct: 127 GHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSLHDEL 186 Query: 193 MATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIF 230 T + +THD +EA + +DR++VM+ G P E++ Sbjct: 187 KFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELY 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: 272 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: 376 Length adjustment: 28 Effective length of query: 253 Effective length of database: 348 Effective search space: 88044 Effective search space used: 88044 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: 48 (23.1 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