Align Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale)
to candidate GFF1051 PGA1_c10670 putative putrescine transport ATP-binding protein
Query= uniprot:P40735 (281 letters) >FitnessBrowser__Phaeo:GFF1051 Length = 375 Score = 129 bits (323), Expect = 1e-34 Identities = 83/224 (37%), Positives = 139/224 (62%), Gaps = 11/224 (4%) Query: 22 RRALDGVSLQVYEGEWLAIVGHNGSGKSTLARALNGLILPESGDIEVAGIQLTEESVWEV 81 R +D VSLQ+ G+ ++G +G GKST R + G+ + +SG+I V G +L ++V+ V Sbjct: 34 RAVVDDVSLQIQAGQVTCLLGPSGCGKSTTLRMIAGVEMQDSGEIYVDG-KLICDTVFRV 92 Query: 82 ---RKKIGMVFQNPDNQFVGTTVRDDVAFGLENNGVPREEMIERVDWAVKQVNMQDFLDQ 138 R++IG++FQ+ F +V D+VAFGL+ + ++E RV+ +++V++ ++D+ Sbjct: 93 PPERREIGLMFQD-FALFPHLSVADNVAFGLKGS---KDEKRARVEELLRKVSLSQYIDE 148 Query: 139 EPHHLSGGQKQRVAIAGVIAARPDIIILDEATSMLDPIGREEVL-ETVRHLKEQGMATVI 197 PH LSGG++QRVA+A +A RP I+++DE S LD R+ + ET+ LKE+G A V+ Sbjct: 149 FPHQLSGGEQQRVALARALAPRPRIMLMDEPFSGLDNRLRDGIRDETLTLLKEEG-AAVL 207 Query: 198 SITHDLNEAAK-ADRIIVMNGGKKYAEGPPEEIFKLNKELVRIG 240 +TH+ EA + AD I +M GK +G P ++ + +G Sbjct: 208 LVTHEPEEAMRMADEIALMRSGKIVQQGAPYNVYTRPADRAAVG 251 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: 264 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 281 Length of database: 375 Length adjustment: 28 Effective length of query: 253 Effective length of database: 347 Effective search space: 87791 Effective search space used: 87791 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: 48 (23.1 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