Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate WP_086509707.1 BZY95_RS09540 ABC transporter ATP-binding protein
Query= uniprot:P70970 (276 letters) >NCBI__GCF_002151265.1:WP_086509707.1 Length = 540 Score = 142 bits (359), Expect = 1e-38 Identities = 82/219 (37%), Positives = 131/219 (59%), Gaps = 2/219 (0%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLK 68 AL D++ ++ G V ++G +GSGKSTL + + L +P G +SL T A K +L+ Sbjct: 303 ALDDVSFTLAPGETVGIVGESGSGKSTLGRCVVRLERPDSGSLSLSGTDFSA-LKGDELR 361 Query: 69 KLRKKVGIVFQFPEHQLF-EETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELLD 127 + R++V ++FQ P L V I+ GPM GV + A Q+A E+L+LVGL +D Sbjct: 362 RERRRVQMIFQDPYASLNPRHRVGYAIAQGPMANGVPRRQAMQQAEELLELVGLGAVAVD 421 Query: 128 RSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTI 187 R P E SGGQ +R+ IA LA++PE++V DE + LD + +++++ EL Q+ +L+ + Sbjct: 422 RYPHEFSGGQRQRIGIARALALNPELIVADEAVSALDVSIQAQVLELLEELKQKLSLSLL 481 Query: 188 LVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLKGEE 226 +TH + AA D +IVM G I G+ +++FL+ E Sbjct: 482 FITHDLRVAAQICDSIIVMQHGRIVEQGTAQEVFLRPRE 520 Score = 101 bits (251), Expect = 4e-26 Identities = 63/220 (28%), Positives = 112/220 (50%), Gaps = 8/220 (3%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLL----KPTKGQISLGSTVIQAGKKN 64 A+ +++ + G + V+G +GSGKS + GLL +PT G++ + A + Sbjct: 26 AVEEVSYDVARGEIMCVVGESGSGKSMAANAVMGLLPKGVRPTAGEVLFDGQNLLALNEK 85 Query: 65 KDLKKLRKKVGIVFQFPEHQL--FEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLS 122 + K ++G++FQ P L + + + ++KA +L+ VG+ Sbjct: 86 QHRKLRGLRIGMIFQEPMTALNPLMRVGAQIAEVFEAHGKYSSRERQEKALALLEEVGIP 145 Query: 123 E--ELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQ 180 E + + PF+LSGGQ +RV IA LA++PE+L+ DEPT LD + +I+++ +L Q Sbjct: 146 EPDKAIRAYPFQLSGGQRQRVMIAMALALEPELLIADEPTTALDVTTQAQILELIRDLQQ 205 Query: 181 RGNLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDL 220 R + + +TH A A + VM G + G+ R++ Sbjct: 206 RRGMAVMFITHDFGVVAEVATRVCVMRYGRVVELGTAREV 245 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: 317 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 276 Length of database: 540 Length adjustment: 30 Effective length of query: 246 Effective length of database: 510 Effective search space: 125460 Effective search space used: 125460 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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