Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate Ac3H11_909 Sulfate and thiosulfate import ATP-binding protein CysA (EC 3.6.3.25)
Query= uniprot:P70970 (276 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_909 Length = 374 Score = 130 bits (328), Expect = 3e-35 Identities = 79/218 (36%), Positives = 130/218 (59%), Gaps = 14/218 (6%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68 AL D++ I+ G +A++G +G GK+TLL+ + GL G I +G+ D+ Sbjct: 17 ALRDVSLDIQSGELIALLGPSGCGKTTLLRIIAGLETADVGTIHF------SGEDTTDVH 70 Query: 69 KLRKKVGIVFQFPEHQLFEE-TVLKDISFG----PMNFGVKKEDAEQKAREMLQLVGLSE 123 + VG VFQ + LF TV ++++FG P + + ++K ++L+LV L + Sbjct: 71 VRERNVGFVFQ--HYALFRHMTVFENVAFGLRVKPRSERPSEAQIKKKVMDLLKLVQL-D 127 Query: 124 ELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGN 183 L +R P +LSGGQ +R+A+A LA++P+VL+LDEP LD + RKE+ LH + Sbjct: 128 WLAERYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLRRLHDELH 187 Query: 184 LTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221 +T+I VTH E+A AD ++V+++G I+ SGSP+ ++ Sbjct: 188 VTSIFVTHDQEEALEVADRVVVINQGRIEQSGSPQQVW 225 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: 229 Number of extensions: 13 Number of successful extensions: 2 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: 374 Length adjustment: 28 Effective length of query: 248 Effective length of database: 346 Effective search space: 85808 Effective search space used: 85808 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