Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate GFF71 PS417_00360 methionine ABC transporter ATP-binding protein
Query= uniprot:P70970 (276 letters) >FitnessBrowser__WCS417:GFF71 Length = 335 Score = 130 bits (327), Expect = 4e-35 Identities = 89/270 (32%), Positives = 147/270 (54%), Gaps = 18/270 (6%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68 AL+ + S++ G +IGH+G+GKSTLL+ +N L +P+ G+I++ + A N L+ Sbjct: 20 ALHSTSLSVENGQVFGLIGHSGAGKSTLLRLINRLEEPSGGKITVDGEEVTALDAN-GLR 78 Query: 69 KLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFG--VKKEDAEQKAREMLQLVGLSEELL 126 + R++VG++FQ + L +TV +++ P+ + +++ +Q+ E+L VGLS+ Sbjct: 79 RFRQQVGMIFQH-FNLLASKTVADNVAL-PLTLAGELSRKEIDQRVAELLARVGLSDHA- 135 Query: 127 DRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTT 186 + P +LSGGQ +RV IA LA P++L+ DE T+ LDP+ ++ + E+++ LT Sbjct: 136 KKYPAQLSGGQKQRVGIARALATKPKILLCDEATSALDPQTTASVLQLLAEINRELKLTI 195 Query: 187 ILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEEMAGWGLDLPETIKFQRHLEA 246 +L+TH M+ D++ VM G I GS D+FL + P T +F + E Sbjct: 196 VLITHEMDVIRRVCDQVAVMDAGVIVEQGSVADVFLHPKH--------PTTKRFVQESEQ 247 Query: 247 ALGVRFNEPMLTIEDAAAEI-RALFQGEKT 275 V NE I R FQGE T Sbjct: 248 ---VDENEQRDDFAHVPGRIVRLTFQGEAT 274 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: 205 Number of extensions: 11 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: 276 Length of database: 335 Length adjustment: 27 Effective length of query: 249 Effective length of database: 308 Effective search space: 76692 Effective search space used: 76692 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: 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