Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate Synpcc7942_1305 Synpcc7942_1305 ATPase
Query= uniprot:P40735 (281 letters) >FitnessBrowser__SynE:Synpcc7942_1305 Length = 536 Score = 124 bits (310), Expect = 6e-33 Identities = 77/216 (35%), Positives = 125/216 (57%), Gaps = 9/216 (4%) Query: 23 RALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAG---IQLTEESVW 79 RA+DG+SL+V+ GE L ++G +G GKSTL R + L+ P G + G QL + + Sbjct: 298 RAVDGLSLEVWPGETLGLIGESGCGKSTLLRTILQLLRPSQGKVLFQGQDLTQLPDRRLR 357 Query: 80 EVRKKIGMVFQNPDNQF-VGTTVRDDVAFGLENNGVPREEMIERVDWAV-KQVNMQD--- 134 +R+++ ++FQ+P T+ D +A L+ G+ R ++ A+ +QV + Sbjct: 358 SLRRELQLIFQDPAACLNPRLTIGDAIADPLKIQGLARGAAAKQQVLAILEQVGLTPAPT 417 Query: 135 FLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVLETVRHLKEQGMA 194 ++D+ PH LSGGQ+QRVAIA + RP +++ DE SMLD + +VL ++ LK+Q Sbjct: 418 WIDRYPHQLSGGQQQRVAIARALITRPKLVLCDEPVSMLDATVQAQVLALMQELKQQLNL 477 Query: 195 TVISITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEI 229 T + +THDL A + DR+ V+ GK GP ++ Sbjct: 478 TYLFVTHDLRVAREFCDRVAVLQRGKIVEIGPAAQV 513 Score = 99.4 bits (246), Expect = 2e-25 Identities = 80/235 (34%), Positives = 123/235 (52%), Gaps = 19/235 (8%) Query: 6 LISVEDIVFRYRKDAERRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPES-- 63 L+S++ + Y +E+ AL +SL++ GE L +VG +G GKSTL RA+ L+ P S Sbjct: 3 LLSIDQLSVTY-PGSEQPALQQLSLELAAGERLGLVGESGCGKSTLGRAILRLLPPGSHQ 61 Query: 64 -GDIEVAGI---QLTEESVWEVRK-KIGMVFQNPDNQFVGT-TVRDDVAFGLENNGVPRE 117 GDI +AG QL S+ R ++G+VFQ+P + T+ D + LE V R Sbjct: 62 QGDIRLAGQALGQLQGRSLQRFRGGQVGLVFQDPMTRLDPLQTIGDHL---LETLQVHRP 118 Query: 118 EMIER------VDWAVKQVNMQDFLDQEPHHLSGGQKQRVAIAGVIAARPDIIILDEATS 171 + R + W + + Q PH SGG +QRVAIA + +P +++ DE T+ Sbjct: 119 HLSRRQAKQQALSWLERVRIPANRWSQYPHQFSGGMRQRVAIALALLLQPRLVVADEPTT 178 Query: 172 MLDPIGREEVLETVRHLKEQGMATVISITHDL-NEAAKADRIIVMNGGKKYAEGP 225 LD E+L+ + L + +++ I+HDL AA DRI V+ G+ GP Sbjct: 179 SLDVTVAAEILQELTRLCSEENTSLLLISHDLPMVAAYCDRIAVLYQGQLVETGP 233 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: 329 Number of extensions: 24 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: 536 Length adjustment: 30 Effective length of query: 251 Effective length of database: 506 Effective search space: 127006 Effective search space used: 127006 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