Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate GFF3770 PGA1_262p01740 putative peptide ABC transporter, ATP-binding protein
Query= uniprot:P70970 (276 letters) >FitnessBrowser__Phaeo:GFF3770 Length = 309 Score = 132 bits (331), Expect = 1e-35 Identities = 67/213 (31%), Positives = 124/213 (58%), Gaps = 2/213 (0%) Query: 10 LYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLKK 69 L ++ ++++G A++G +GSGK+T+++ + GL G + I+ G K + Sbjct: 20 LAGVSFTVEQGETYAMVGESGSGKTTVIRAIAGLAPAQAGSVKFDGQEIR-GISEKAFRP 78 Query: 70 LRKKVGIVFQFPEHQLFEETVLKDISFGPMNF-GVKKEDAEQKAREMLQLVGLSEELLDR 128 LRK + ++FQ P L ++++ P G+K D E +A+ +L+LV L DR Sbjct: 79 LRKDIAMMFQDPTGSLSPRLTIRNLITEPYKIQGMKDRDLEAEAKRLLELVNLPAHFADR 138 Query: 129 SPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTIL 188 P++LSGGQ RRV +A LA++P++++ DEPTAGLD + E++++ +L +R L+ ++ Sbjct: 139 YPYQLSGGQARRVGVARALALEPKLILADEPTAGLDVSVQGELLNLLNDLRERLGLSMVI 198 Query: 189 VTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221 +TH++ AD M +++ G + G+ +F Sbjct: 199 ITHNLNVVRHVADRMGILYLGRLVEEGTTEAIF 231 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: 209 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: 309 Length adjustment: 26 Effective length of query: 250 Effective length of database: 283 Effective search space: 70750 Effective search space used: 70750 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