Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate 5211369 Shew_3781 ABC transporter-related protein (RefSeq)
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__PV4:5211369 Length = 244 Score = 102 bits (253), Expect = 1e-26 Identities = 68/224 (30%), Positives = 112/224 (50%), Gaps = 7/224 (3%) Query: 3 LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62 ++ NL+ G + LND+S G+IT L+GPNG GK+T L LL P G + Sbjct: 2 IKVSNLSKRIGEVQALNDLSFEALDGQITGLLGPNGAGKTTCLRTVFGLLKPDLGIAEI- 60 Query: 63 DNPINMLSSRQLARR-LSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNV 121 + I++ A++ L L P E +T +E + Y + L G + A Sbjct: 61 -DGIDVAKQPVAAKQQLGLFPDPFGLYERLTPREYIRY----FAELNGLSREQAKAASAK 115 Query: 122 AMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLM 181 +++ ++ +A RR S GQR + LA + ++LDEPT LD+ L L+ Sbjct: 116 VLSKLHMDDIADRRCKGFSQGQRMKTALAQAIVHEPTNIILDEPTRGLDVMSTRVLRDLL 175 Query: 182 GELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEV 225 +L+ G V+ H + + + CD+++VMA G V+A G+P+E+ Sbjct: 176 RDLKQAGHCVLFSSHVMQEVAALCDRVIVMAEGRVVAVGSPQEL 219 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: 140 Number of extensions: 5 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: 244 Length adjustment: 24 Effective length of query: 231 Effective length of database: 220 Effective search space: 50820 Effective search space used: 50820 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