Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 143 bits (360), Expect = 7e-39 Identities = 82/209 (39%), Positives = 131/209 (62%), Gaps = 4/209 (1%) Query: 24 ALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEVRK 83 ALD + L + GE+L ++G +G GK+T+ R ++G P SG++ + G + V ++ Sbjct: 22 ALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRINGQVVNR--VPPEQR 79 Query: 84 KIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPHHL 143 ++ VFQN F TVRD+VAFGL+ GV +E RV A++ V++++F D++P L Sbjct: 80 QVNTVFQNYA-LFPHMTVRDNVAFGLKMQGVAADETARRVLDALRMVHLENFADRKPRQL 138 Query: 144 SGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISITHDL 203 SGGQ+QRVAIA + P +++LDE S LD R+++ ++HL+ Q T + +THD Sbjct: 139 SGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQLGITFVFVTHDQ 198 Query: 204 NEA-AKADRIIVMNGGKKYAEGPPEEIFK 231 EA A +DR++VMN G+ G P+EI++ Sbjct: 199 EEAFAMSDRVVVMNEGRIEQIGAPKEIYE 227 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: 282 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: 399 Length adjustment: 28 Effective length of query: 253 Effective length of database: 371 Effective search space: 93863 Effective search space used: 93863 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: 49 (23.5 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