Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate Synpcc7942_2574 Synpcc7942_2574 ATPase
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__SynE:Synpcc7942_2574 Length = 251 Score = 124 bits (311), Expect = 2e-33 Identities = 88/242 (36%), Positives = 125/242 (51%), Gaps = 9/242 (3%) Query: 2 TLRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFL 61 TL+ +L+ SY +VL DV+L L G++ ++GPNG GKST L L+ P G VF Sbjct: 11 TLQAHHLSASYRDREVLQDVNLQLRAGQVVGIVGPNGAGKSTFLKALLGLV-PHQGEVFW 69 Query: 62 GDNPINMLSSRQLARRLSLLPQHHLTPEGI--TVQELVSYGRNPWLSLWGRLSAEDNARV 119 P L+SR ++ +PQ TV ++V GR R SA V Sbjct: 70 RGLP---LASR--LPHVAYVPQRAQVDFDYPATVWDVVLMGRVAQTGWLRRFSAASQQAV 124 Query: 120 NVAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMR 179 A+++ + L R + ELSGGQ+QR F+A LAQ + LLDEP +D + L Sbjct: 125 KAALDRVELWDLRSRPIGELSGGQQQRVFIARSLAQEAELFLLDEPFAGIDRRSEGLLYE 184 Query: 180 LMGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEA 239 ++ +L QG VV V HDL QA + D+LV++ N V+AQG P V+ P L + Sbjct: 185 ILRDLAQQGHGVVVVHHDLGQAIQQFDELVLL-NQRVIAQGHPRLVLQPDHLARAYGARL 243 Query: 240 EI 241 +I Sbjct: 244 DI 245 Lambda K H 0.320 0.134 0.393 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: 173 Number of extensions: 10 Number of successful extensions: 2 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: 255 Length of database: 251 Length adjustment: 24 Effective length of query: 231 Effective length of database: 227 Effective search space: 52437 Effective search space used: 52437 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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