Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate Synpcc7942_1317 Synpcc7942_1317 ATPase
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__SynE:Synpcc7942_1317 Length = 245 Score = 126 bits (317), Expect = 4e-34 Identities = 82/235 (34%), Positives = 125/235 (53%), Gaps = 10/235 (4%) Query: 3 LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62 L ++L+V Y +VL D+ L + G+ ALIGPNG GKSTL+ LL P +G V Sbjct: 2 LEIQHLSVCYRQQRVLEDICLQVQAGEQLALIGPNGAGKSTLVRAILGLLTPYAGEVRWR 61 Query: 63 DNPINMLSSRQLARRLSLLPQHHLTP--EGITVQELVSYGRNPWLSLWGRLSAEDNARVN 120 P+ R+ R ++ +PQ ITV+ +V G S WGR S + +R+ Sbjct: 62 GRPL-----RRGQRSIAYVPQRSQIDWQYPITVETVVRLGAEV-RSWWGR-SPQTGSRIA 114 Query: 121 VAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRL 180 A+ Q ++ L R L ELSGGQ+QR FLA +AQ ++LLDEP T +D + + L Sbjct: 115 AALEQVQLTELRHRPLAELSGGQQQRVFLARAIAQGADLLLLDEPFTGIDHPTERLMQNL 174 Query: 181 MGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVF 235 + QGKT++ H+ A + D+L+++ N ++ P+ +TP L+ F Sbjct: 175 FQQFAQQGKTLIVCSHEWGDALQRYDRLILL-NRRIICHDIPDRALTPQNLQQTF 228 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: 156 Number of extensions: 7 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: 245 Length adjustment: 24 Effective length of query: 231 Effective length of database: 221 Effective search space: 51051 Effective search space used: 51051 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