Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= uniprot:P70970 (276 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 131 bits (329), Expect = 3e-35 Identities = 80/213 (37%), Positives = 123/213 (57%), Gaps = 2/213 (0%) Query: 8 LALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDL 67 +A+ D N SI EG ++G +GSGKSTLL+ +N L++PT G++ + T I + L Sbjct: 41 VAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDIAKVSDKELL 100 Query: 68 KKLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLD 127 + RK++ +VFQ L +VL +I+FG GVKK + EQKA E +QLVGL + + Sbjct: 101 QIRRKELAMVFQ-NFGLLPHRSVLHNIAFGLELQGVKKGEREQKAMESMQLVGL-KGYEN 158 Query: 128 RSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTI 187 + ELSGG +RV +A LA +PEVL++DE + LDP R ++ D L + T + Sbjct: 159 QMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQSKMKKTIV 218 Query: 188 LVTHSMEDAAAYADEMIVMHKGTIQASGSPRDL 220 +TH + +A D + +M G I G+ ++ Sbjct: 219 FITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEI 251 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: 268 Number of extensions: 14 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: 408 Length adjustment: 28 Effective length of query: 248 Effective length of database: 380 Effective search space: 94240 Effective search space used: 94240 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: 49 (23.5 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