Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate AZOBR_RS04895 AZOBR_RS04895 putative ABC transporter (ATP-binding protein); putative dipeptide/oligopeptide/nickel transporter
Query= uniprot:P40735 (281 letters) >FitnessBrowser__azobra:AZOBR_RS04895 Length = 557 Score = 134 bits (338), Expect = 3e-36 Identities = 86/240 (35%), Positives = 140/240 (58%), Gaps = 16/240 (6%) Query: 2 NQNQLISVEDIVFRYRKDAER-RALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLIL 60 ++ L+ V D+ Y +AL G SL + GE +A+VG +GSGKST+ARA+ GL+ Sbjct: 282 DRTPLLEVRDLAVCYDTGGFAVKALSGASLTLNGGEMMAVVGESGSGKSTMARAIAGLVQ 341 Query: 61 PESGDIEVAGIQLTEESVWE----VRKKIGMVFQNPDNQF-----VGTTVRDDVAFGLEN 111 P GD+ V G +L E V + +R+ + + FQ+ D VG + + F E Sbjct: 342 PSHGDVLVNG-RLMERDVLKRPLPMRRAVQITFQSADTSLNRHHTVGRILGQVLTFFGER 400 Query: 112 NGVPREEMIERVDWAVKQVNMQ-DFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEAT 170 + +E ER+ ++QV++ D++D++P +SGG+KQRV +A +AARPD++I DE T Sbjct: 401 S---KERRAERIRELLEQVHLPADYVDRKPSQMSGGEKQRVNLARSLAARPDVLICDEIT 457 Query: 171 SMLDPIGREEVLETVRHLKEQGMATVISITHDLNE-AAKADRIIVMNGGKKYAEGPPEEI 229 S LD I VL+ + LK + ++ I+HDL+ AA +D+I+V+ G+ +GP ++ Sbjct: 458 SALDNIVAASVLDLINELKRELNIGILFISHDLSAVAAMSDKIMVLRNGEVVEQGPTAQV 517 Score = 69.3 bits (168), Expect = 2e-16 Identities = 64/230 (27%), Positives = 110/230 (47%), Gaps = 24/230 (10%) Query: 19 DAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPE----SGDIEVAG---I 71 D+ + L VSL + G+ LA++G +GSGK+TLA G + P SG + G + Sbjct: 14 DSGKPILRDVSLTLEHGQILALIGASGSGKTTLALTALGHMRPGVRHVSGQVLFQGQDLL 73 Query: 72 QLTEESVWEVR-KKIGMVFQNPDNQF---------VGTTVRDDVAFGLENNGVPREEMIE 121 +++ ++ +R +K+ + Q+ F V + R + E+ Sbjct: 74 RMSRRALARLRGRKLAYIAQSAAVSFNPRIRLDRQVTESSRIHHTMSPDAAHARAREVYR 133 Query: 122 RVDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEV 181 +D + F ++ PH +SGGQ QR IA + P+I+I DE TS LD + EV Sbjct: 134 TLDLPTGEA----FYNRFPHEVSGGQLQRFMIAMGLHEMPEILICDEPTSALDATTQVEV 189 Query: 182 LETV-RHLKEQGMATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEI 229 L+ + ++ G A ++ + HD+ + + A I+VM G+ G E+I Sbjct: 190 LKALDTGIRASGTAAIL-VGHDIAQVVQVATHILVMRNGEVVERGTVEQI 238 Lambda K H 0.316 0.135 0.383 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: 332 Number of extensions: 16 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 281 Length of database: 557 Length adjustment: 31 Effective length of query: 250 Effective length of database: 526 Effective search space: 131500 Effective search space used: 131500 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 (21.6 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