Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate AZOBR_RS23030 AZOBR_RS23030 ABC transporter ATP-binding protein
Query= uniprot:P70970 (276 letters) >FitnessBrowser__azobra:AZOBR_RS23030 Length = 554 Score = 137 bits (344), Expect = 7e-37 Identities = 77/211 (36%), Positives = 123/211 (58%), Gaps = 2/211 (0%) Query: 12 DINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGKKNKDLKKLR 71 D++ +I +G V ++G +GSGKSTL + + GL+KP G+I L V + R Sbjct: 305 DLSLTIHQGETVGLVGESGSGKSTLGRSIVGLIKPDSGRI-LFEGVDLLSLSRPAFRPYR 363 Query: 72 KKVGIVFQFPEHQLFEETVLKDI-SFGPMNFGVKKEDAEQKAREMLQLVGLSEELLDRSP 130 + V +VFQ P L + DI + GP+ FG + A +KA+ +L+LVGL +R P Sbjct: 364 RHVQMVFQAPYASLNPRHTVGDIITQGPVAFGEDRHKALEKAKALLKLVGLDASAAERFP 423 Query: 131 FELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELHQRGNLTTILVT 190 E SGGQ +R++IA LA++P++L+ DEP + LD + +++D+ +L R NL+ + +T Sbjct: 424 HEFSGGQRQRISIARALALEPKLLIADEPVSALDVSVQAQVLDLLEDLRHRLNLSMLFIT 483 Query: 191 HSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221 H + AA D + VM KG I G +++F Sbjct: 484 HDLRIAAQICDTIAVMQKGRIVEIGPAKEVF 514 Score = 95.9 bits (237), Expect = 2e-24 Identities = 69/221 (31%), Positives = 115/221 (52%), Gaps = 10/221 (4%) Query: 9 ALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPTKGQISLGSTVIQAGK----KN 64 A+ D+ +++ G + V+G +GSGKS + GLL P +S G Q Sbjct: 25 AVQDLTFTLEHGEILCVVGESGSGKSMTAHAVMGLL-PKAVTVSSGEIRHQGTNVFSLPE 83 Query: 65 KDLKKLRK-KVGIVFQFPEHQLFEETVLKDISFGPMNFGVKKEDAEQKAR--EMLQLVGL 121 +D + LR ++ ++FQ P L + D + + + A ++AR E+L VGL Sbjct: 84 RDQRALRGGRIAMIFQEPMTALNPLMRVGDQIDEVLRYHTTLDRAARRARVVELLASVGL 143 Query: 122 SE-ELLDRS-PFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMFYELH 179 E + L RS PF LSGGQ +RV IA LA++P++L+ DEPT LD +K+I+++ ++ Sbjct: 144 PEPDHLRRSYPFRLSGGQRQRVMIAMALAVEPDILIADEPTTALDVTTQKQILELIQDIQ 203 Query: 180 QRGNLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDL 220 + + + +TH A A + VM +G I G+ ++ Sbjct: 204 AKRRMGVMFITHDFGVVAEIAHRVAVMQRGQIVEIGTAEEV 244 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: 372 Number of extensions: 21 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: 554 Length adjustment: 30 Effective length of query: 246 Effective length of database: 524 Effective search space: 128904 Effective search space used: 128904 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