Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate 206067 DVU0648 iron compound ABC transporter, ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >MicrobesOnline__882:206067 Length = 271 Score = 148 bits (373), Expect = 1e-40 Identities = 82/243 (33%), Positives = 125/243 (51%) Query: 8 LTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLGDNPIN 67 L Y +VL+ + L + ++ L+GPNG GK+TLL S +L + G V L P+ Sbjct: 7 LHAGYAQTEVLHGIDLRIAQDELVGLLGPNGSGKTTLLLALSGVLPARGGDVLLDGTPLA 66 Query: 68 MLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVAMNQTR 127 ++ R+ ARR++ +PQ + LV GR P +A D+ A+ T Sbjct: 67 AMAPRERARRIATVPQRPEVIPDVDAFSLVLMGRYPHTGPLRGYTAVDHDAAAAALAATG 126 Query: 128 INHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMGELRTQ 187 HLA R LSGG+ QR +A LAQ+T +LLDE T LD+ V++ L+ + Sbjct: 127 TAHLARRSAATLSGGELQRVLVARALAQDTDTLLLDEVTAGLDVARMVEVFDLLAQRHRH 186 Query: 188 GKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEIHPEPVS 247 G +VA +HD+N A+ YC +LV + +G V+ G +V L ++ +HP PV+ Sbjct: 187 GLRIVAAIHDINLAALYCTRLVFLKSGRVVLDGPVAQVFDEQALSAIYETRITVHPHPVT 246 Query: 248 GRP 250 G P Sbjct: 247 GTP 249 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: 159 Number of extensions: 7 Number of successful extensions: 1 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: 271 Length adjustment: 25 Effective length of query: 230 Effective length of database: 246 Effective search space: 56580 Effective search space used: 56580 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: 47 (22.7 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