Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate GFF2182 PGA1_c22140 glutathione import ATP-binding protein GsiA
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Phaeo:GFF2182 Length = 545 Score = 126 bits (316), Expect = 1e-33 Identities = 86/235 (36%), Positives = 132/235 (56%), Gaps = 16/235 (6%) Query: 6 LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGD 65 ++SV +I RY K + L V++ ++ G+ LA+VG +GSGKSTLAR + GL+ P G+ Sbjct: 278 VLSVRNITARY-KGTKFDVLHNVNVDLHPGQTLAVVGESGSGKSTLARVITGLLPPREGE 336 Query: 66 IEVAGIQLTEESVWEVR---KKIGMVFQNPD-----NQFVGTTVRDDVAFGLENNGVP-R 116 IE AG L+ + R +++ M++Q D Q VGT + + F G R Sbjct: 337 IEFAGRTLSSDLAGRSREDLRELQMIYQMADVAMNPRQTVGTIIGRPLEFYFGMKGAEKR 396 Query: 117 EEMIERVDWAVKQVNM-QDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDP 175 + +IE +D ++ + + F+D+ P LSGGQKQRV IA +AA+P +II DE TS LDP Sbjct: 397 KRIIELLD----EIELGESFMDRYPAELSGGQKQRVCIARALAAKPKMIICDEVTSALDP 452 Query: 176 IGREEVLETVRHLKEQGMATVISITHDL-NEAAKADRIIVMNGGKKYAEGPPEEI 229 + + +L+ + L++ + ITHDL A +D I VM G+ G E+ Sbjct: 453 LVADGILKLLLELQKIENVAFLFITHDLATVRAISDNIAVMYQGRVQRYGGKTEV 507 Score = 74.7 bits (182), Expect = 4e-18 Identities = 58/224 (25%), Positives = 109/224 (48%), Gaps = 16/224 (7%) Query: 27 GVSLQVYEGEWLAIVGHNGSGKSTLARAL----NGLILPESGDIEVAGIQLTEESVWEVR 82 GVS + G+ L ++G +G+GKST+ A G + G++ V G + + + ++R Sbjct: 32 GVSFDLQPGKVLGLIGESGAGKSTIGLASMAYGRGGVKITGGEVWVNGRDILQSKLRDIR 91 Query: 83 K----KIGMVFQNPDNQF--VGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQD-- 134 + ++ V Q+ F + + +E +++ R ++ + D Sbjct: 92 RLRGGEVTYVSQSAAASFNPAKKIMEQVIEAAVEQGKFSKKDAEARARALFAKLGLPDPD 151 Query: 135 -FLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRH-LKEQG 192 ++ PH +SGGQ QR A + PD+++ DE T+ LD + EVL ++ +++ G Sbjct: 152 NIGERYPHQVSGGQLQRCMTALALCPEPDLVVFDEPTTALDVTTQIEVLMAIKEAIRDTG 211 Query: 193 MATVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIFKLNKE 235 +A + ITHDL A+ +D I+V+ G GP ++I +E Sbjct: 212 VA-ALYITHDLAVVAQVSDDIMVLRHGNMVEYGPVDQIINAPQE 254 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: 335 Number of extensions: 22 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: 281 Length of database: 545 Length adjustment: 30 Effective length of query: 251 Effective length of database: 515 Effective search space: 129265 Effective search space used: 129265 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