Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= uniprot:P70970 (276 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 119 bits (297), Expect = 1e-31 Identities = 83/215 (38%), Positives = 121/215 (56%), Gaps = 16/215 (7%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISL-GSTVIQAGKKNKDL 67 AL ++ I +G +A++G +GSGK+TLL+ + GL P GQ+ G V A Sbjct: 17 ALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFDGQDVTYASAA---- 72 Query: 68 KKLRKKVGIVFQFPEHQLFEE-TVLKDISFG-PMNFGVKKEDAEQKAR---EMLQLVGLS 122 ++VG VFQ ++ LF+ TV K+I+FG + G K + AR E+L+LV L Sbjct: 73 ---ARRVGFVFQ--QYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLKLVEL- 126 Query: 123 EELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRG 182 E L R P +LSGGQ +RVA++ LA+ P VL+LDEP LD RK + +H Sbjct: 127 EGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRVHDAT 186 Query: 183 NLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSP 217 +TTI VTH E+A AD + +++ G I+ G+P Sbjct: 187 GVTTIFVTHDQEEALELADRVAILNNGRIEQIGTP 221 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: 169 Number of extensions: 8 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: 339 Length adjustment: 27 Effective length of query: 249 Effective length of database: 312 Effective search space: 77688 Effective search space used: 77688 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