Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate 14789 b0652 glutamate and aspartate transporter subunit (NCBI)
Query= uniprot:P70970 (276 letters) >FitnessBrowser__Keio:14789 Length = 241 Score = 135 bits (340), Expect = 8e-37 Identities = 86/216 (39%), Positives = 124/216 (57%), Gaps = 13/216 (6%) Query: 10 LYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLKK 69 L D + +K+G V V G +GSGKSTL++ +NGL +G+I++ V+ K DL K Sbjct: 17 LTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVDGIVVN--DKKTDLAK 74 Query: 70 LRKKVGIVFQ----FPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEEL 125 LR +VG+VFQ FP + E L + + K A +KA ++L+ VGLS Sbjct: 75 LRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRD----KAPAREKALKLLERVGLSAHA 130 Query: 126 LDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLT 185 ++ P +LSGGQ +RVAIA L MDP ++ DEPT+ LDP E++D+ EL G +T Sbjct: 131 -NKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVMVELANEG-MT 188 Query: 186 TILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221 ++VTH M A A+ +I M +G I SP+D F Sbjct: 189 MMVVTHEMGFARKVANRVIFMDEGKI-VEDSPKDAF 223 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: 153 Number of extensions: 6 Number of successful extensions: 4 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: 241 Length adjustment: 24 Effective length of query: 252 Effective length of database: 217 Effective search space: 54684 Effective search space used: 54684 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