Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate PfGW456L13_4639 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
Query= uniprot:P70970 (276 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4639 Length = 254 Score = 132 bits (331), Expect = 1e-35 Identities = 79/221 (35%), Positives = 129/221 (58%), Gaps = 13/221 (5%) Query: 10 LYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKN----- 64 L ++ K G +++IG +GSGKST L+ +N L +P G +SL I+ K Sbjct: 19 LKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMSLDGQNIRMIKDRHGMHV 78 Query: 65 ---KDLKKLRKKVGIVFQFPEHQLFEE-TVLKDISFGPMN-FGVKKEDAEQKAREMLQLV 119 +L+++R ++ +VFQ L+ TVL++I+ P G +++AE +AR L V Sbjct: 79 ADANELQRIRTRLAMVFQ--HFNLWSHMTVLENITMAPRRVLGCDRKEAEDRARRYLDKV 136 Query: 120 GLSEELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELH 179 GL+ + D+ P LSGGQ +RVAIA LAM+PEV++ DEPT+ LDP E++ + L Sbjct: 137 GLAPRVADQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALDPELVGEVLKVIQGLA 196 Query: 180 QRGNLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDL 220 + G T I+VTH M A + +++ +H+G ++ G+P ++ Sbjct: 197 EEGR-TMIMVTHEMSFARKVSSQVLFLHQGLVEEEGAPEEV 236 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: 174 Number of extensions: 12 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: 254 Length adjustment: 25 Effective length of query: 251 Effective length of database: 229 Effective search space: 57479 Effective search space used: 57479 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: 47 (22.7 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