Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate WP_000942251.1 HK29_RS01475 amino acid ABC transporter ATP-binding protein
Query= uniprot:P40735 (281 letters) >NCBI__GCF_000382825.1:WP_000942251.1 Length = 254 Score = 139 bits (350), Expect = 6e-38 Identities = 90/256 (35%), Positives = 150/256 (58%), Gaps = 18/256 (7%) Query: 6 LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65 ++ VE I + ER+ L+ V+LQV +G+ + I+G +GSGK+T R LN L +SG Sbjct: 1 MLQVEHIAKTF---GERQVLEDVNLQVNQGDVVVILGPSGSGKTTFLRCLNHLEKADSGR 57 Query: 66 IEVAG-----IQLTEESVWEVRKKIGMVFQNPDNQFVGTTVRDDVAFGL-ENNGVPREEM 119 + +AG +L+++ + E+R+K VFQ+ N F T +++ GL VP+EE Sbjct: 58 LTLAGKTYDLAKLSKKDILEIRQKTAFVFQHY-NLFANKTALENILEGLIVARKVPKEEA 116 Query: 120 IERVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGRE 179 ++R + A+++V + + D P LSGGQ+QR+ IA IA +P++I+LDE TS LDP Sbjct: 117 LKRAESALEKVGLLAYKDYYPSQLSGGQQQRIGIARAIAVKPEVILLDEPTSALDPELVG 176 Query: 180 EVLETVRHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIFKLNKE--- 235 +VL+ ++ L +G+ T++ +TH++ A A+ +I M+GG+ E P + F +E Sbjct: 177 DVLDVLKQLAGEGV-TMVVVTHEMGFARDVANHVIFMDGGRIVEENNPHDFFSRPQEERT 235 Query: 236 ---LVRIGLDLPFSFQ 248 L RI D +S + Sbjct: 236 KQFLARILSDASYSVE 251 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: 204 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: 254 Length adjustment: 25 Effective length of query: 256 Effective length of database: 229 Effective search space: 58624 Effective search space used: 58624 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 24 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