Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate HSERO_RS19345 HSERO_RS19345 amino acid ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >FitnessBrowser__HerbieS:HSERO_RS19345 Length = 244 Score = 137 bits (344), Expect = 3e-37 Identities = 86/230 (37%), Positives = 138/230 (60%), Gaps = 10/230 (4%) Query: 6 LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65 ++ ++D+ ++ + L+GVSL V +G+ +AI+G +GSGKSTL R LNGL ++GD Sbjct: 4 IVKIKDL---HKSFGSNKVLNGVSLDVQKGQMVAIIGKSGSGKSTLLRCLNGLEKVDAGD 60 Query: 66 IEVAGIQL---TEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIER 122 I+V G + + ++ E+RK++G+VFQ+ N F TV ++ L E + Sbjct: 61 IQVCGHDIHHPDKLNLRELRKQVGIVFQS-YNLFPHLTVERNITLALTTIKKMSTEQAKT 119 Query: 123 VDWAVKQ-VNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEV 181 + V Q V +++ D P LSGGQ QRVAIA +A P++++ DE TS LDP EV Sbjct: 120 IAHKVLQLVGLENKKDAYPEQLSGGQAQRVAIARSLAMAPELMLFDEVTSALDPELTAEV 179 Query: 182 LETVRHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIF 230 L+ + L GM T++ +TH++ A K AD ++ M+ G+ + GPP+E+F Sbjct: 180 LKVMEDLARGGM-TMVLVTHEMAFARKLADVLVFMHQGQVWEIGPPDELF 228 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: 192 Number of extensions: 9 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: 244 Length adjustment: 25 Effective length of query: 256 Effective length of database: 219 Effective search space: 56064 Effective search space used: 56064 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