Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate RR42_RS30240 RR42_RS30240 microcin ABC transporter ATP-binding protein
Query= uniprot:P70970 (276 letters) >FitnessBrowser__Cup4G11:RR42_RS30240 Length = 544 Score = 144 bits (364), Expect = 3e-39 Identities = 82/216 (37%), Positives = 128/216 (59%), Gaps = 4/216 (1%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQI-SLGSTVIQAGKKNKDL 67 A+ D+ ++ G V ++G +GSGKST+ + + L++P+ G+I + G ++ +A K+ D+ Sbjct: 307 AVQDVALAVHAGETVGIVGESGSGKSTVARCIARLIEPSAGEIWAQGRSMAKAAKR--DI 364 Query: 68 KKLRKKVGIVFQFPEHQLF-EETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGLSEELL 126 R+ V +VFQ P L +TV I GP+NFGV A +A E++ LV L+ + L Sbjct: 365 SAFRRTVQVVFQDPYRSLNPRQTVGASIVEGPLNFGVPARQAWARAEELMHLVRLNPDAL 424 Query: 127 DRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTT 186 R P E SGGQ +R+ IA LA DPEVL+ DE + LD + +I+ + ++ QR L Sbjct: 425 QRYPSEFSGGQRQRICIARALACDPEVLIADEAVSALDVSVQAQIIALLNDIQQRLKLGI 484 Query: 187 ILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFL 222 + +TH + A+ D +IVM +G I GS RD+FL Sbjct: 485 LFITHDLRVASQICDRVIVMRQGRIVEQGSARDIFL 520 Score = 84.7 bits (208), Expect = 4e-21 Identities = 66/227 (29%), Positives = 111/227 (48%), Gaps = 15/227 (6%) Query: 8 LALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPT----KGQISL-GSTVIQAGK 62 LA+ I+ + G + ++G +GSGKS + Q + GLL PT G+I L G +++A Sbjct: 30 LAVRHISFEVAPGRIMCLLGESGSGKSVIAQAVMGLLPPTLKPCAGRIELLGENLLEAST 89 Query: 63 KNKDLKKLRK-KVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAREMLQLVGL 121 + L+ LR + +VFQ P L + + AE++AR +L++ Sbjct: 90 RR--LRALRGVAMAMVFQEPMTALNPVMTCGAQVDEVLAWHTDLRPAERRAR-ILEIFAR 146 Query: 122 S-----EELLDRSPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFY 176 + E + P +LSGGQ +R+ IA + + P +L+ DEPT LD + EI+ + Sbjct: 147 TRLPEPERIYSAYPHQLSGGQRQRIVIAIAMILRPALLICDEPTTALDVTTQAEILKLIR 206 Query: 177 ELHQRGNLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLFLK 223 EL + +TH A AD++ V+ G + G P++ L+ Sbjct: 207 ELQAESGTAVLFITHDFGVVAEIADDVAVLQLGELIEQG-PKEAVLR 252 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: 315 Number of extensions: 16 Number of successful extensions: 4 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: 544 Length adjustment: 30 Effective length of query: 246 Effective length of database: 514 Effective search space: 126444 Effective search space used: 126444 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 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