Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_170920503.1 B9A12_RS09210 energy-coupling factor transporter ATPase
Query= uniprot:P70970 (276 letters) >NCBI__GCF_900176285.1:WP_170920503.1 Length = 571 Score = 142 bits (358), Expect = 2e-38 Identities = 89/238 (37%), Positives = 132/238 (55%), Gaps = 11/238 (4%) Query: 4 PFERLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKK 63 P R AL I+ SI EG +AV+GH GSGK+TL + L+GL PT+G++ + + Sbjct: 29 PNGRQALRHIDLSIHEGERIAVLGHNGSGKTTLARVLSGLAPPTQGRVLFQGDPLSRER- 87 Query: 64 NKDLKKLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSE 123 L+ LR++VG +FQ P+ QLF TVL D+ FG +NF V ++AE++AR+ L +GL Sbjct: 88 ---LEDLRQRVGFLFQDPDDQLFCPTVLDDVLFGLLNFQVPPKEAEERARKALAAMGLEA 144 Query: 124 ELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGN 183 E R+P LS GQ +R A+A +LA++P+VL+LDEPTA +DP + + + Sbjct: 145 E-AHRAPHHLSYGQRKRAALAAILALEPDVLILDEPTANMDPTSEALLSKVLKDYPG--- 200 Query: 184 LTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETIKFQ 241 T I ++H + +V+ G I S L + GLD T +FQ Sbjct: 201 -TLICISHDILFLYGLCTRAVVLQAGGIHHDTSFERLISHRASLQEHGLDF--TFRFQ 255 Score = 116 bits (291), Expect = 1e-30 Identities = 78/227 (34%), Positives = 123/227 (54%), Gaps = 12/227 (5%) Query: 8 LALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDL 67 +AL +++ + G +A++G G+GKSTL L G+ T + G V A ++N Sbjct: 326 VALENVSFQVGRGERLALVGPNGAGKSTLAACLAGIRWGTGQYLLDGRKVEGAFRRN--- 382 Query: 68 KKLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLD 127 L + VG+VFQ Q+ +++FG N G + +K + ML GL E D Sbjct: 383 --LWRHVGLVFQDSADQMVCSRCGDEVAFGLRNLGWPESRIRKKVQAMLHWAGL-EGFED 439 Query: 128 RSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTI 187 R P LSGG+ +R+A+A VLAM+PEVL+LDEPTAGLDP+ ++++ + E+ T + Sbjct: 440 RVPQHLSGGERKRLALAAVLAMEPEVLILDEPTAGLDPQTEQKLLQLLDEV----EATLV 495 Query: 188 LVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAG-WGLD 233 L++H + + D ++MH+G I P FL + +GLD Sbjct: 496 LISHDVCFVSMLTDRTLLMHRGRI-VDDLPTGKFLVDRNLHSLYGLD 541 Lambda K H 0.318 0.136 0.380 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: 420 Number of extensions: 25 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 276 Length of database: 571 Length adjustment: 31 Effective length of query: 245 Effective length of database: 540 Effective search space: 132300 Effective search space used: 132300 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 (21.7 bits) S2: 50 (23.9 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