Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate PfGW456L13_3150 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)
Query= uniprot:P40735 (281 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3150 Length = 372 Score = 138 bits (347), Expect = 2e-37 Identities = 85/207 (41%), Positives = 123/207 (59%), Gaps = 6/207 (2%) Query: 28 VSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEVR----K 83 VSLQV GE I+G +GSGKSTL R LN LI P +G I V G +L+ + ++R + Sbjct: 56 VSLQVRRGEIFCIMGLSGSGKSTLIRLLNKLITPSAGKIVVKGKELSSLNAAQLREVRAR 115 Query: 84 KIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQEPHHL 143 IGMVFQ+ TV ++ AFGLE GV + E + + A+ +V + D++ + P L Sbjct: 116 HIGMVFQSVA-LLPNRTVLENTAFGLEVQGVGKAERYKVAEQALAKVGLSDWMSRYPSEL 174 Query: 144 SGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMATVISITHDL 203 SGG +QRV +A I A P++I++DE S LDP+ R ++ + R L ++ + + ITHDL Sbjct: 175 SGGMQQRVGLARAITADPEVILMDEPFSALDPLIRRQLQDEFRQLTKELGKSAVFITHDL 234 Query: 204 NEAAK-ADRIIVMNGGKKYAEGPPEEI 229 +EA + DRI +M G G EEI Sbjct: 235 DEAIRIGDRIAIMKDGAIIQVGTAEEI 261 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: 248 Number of extensions: 13 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: 372 Length adjustment: 28 Effective length of query: 253 Effective length of database: 344 Effective search space: 87032 Effective search space used: 87032 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