Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_019557545.1 F612_RS0109555 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000381085.1:WP_019557545.1 Length = 397 Score = 133 bits (335), Expect = 5e-36 Identities = 85/221 (38%), Positives = 126/221 (57%), Gaps = 6/221 (2%) Query: 16 YRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTE 75 + K ++ S +VY GE ++G +GSGKSTL R LN LI P G+I + G +T+ Sbjct: 38 FAKTGNTVGVNNASFEVYAGEIFVVMGLSGSGKSTLVRLLNRLIEPTEGNIWIDGQNITQ 97 Query: 76 ESVWEVR----KKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVN 131 S E+R KKI MVFQ+ TV ++ AFGL +G + + + A++QV Sbjct: 98 MSDKELRQARRKKISMVFQS-FALLPHMTVIENAAFGLTLDGFNKNQAQKEALDALEQVG 156 Query: 132 MQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQ 191 + + P LSGG +QRV IA +A +I+++DEA S LDP+ R E+ + + L+E+ Sbjct: 157 LGTHANSYPSELSGGMQQRVGIARALATGSEIMLMDEAFSALDPLIRTEMQDELVKLQEK 216 Query: 192 GMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIFK 231 T+I I+HDL+EA + DRI +M G G PEEI + Sbjct: 217 NHRTIIFISHDLDEAMRIGDRIAIMEQGNIVQVGTPEEILR 257 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: 12 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: 397 Length adjustment: 28 Effective length of query: 253 Effective length of database: 369 Effective search space: 93357 Effective search space used: 93357 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 Apr 09 2024. 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