Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate Dsui_0724 Dsui_0724 ABC-type multidrug transport system, ATPase component
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__PS:Dsui_0724 Length = 307 Score = 117 bits (293), Expect = 3e-31 Identities = 78/247 (31%), Positives = 121/247 (48%), Gaps = 7/247 (2%) Query: 3 LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62 L E+L YG ++ VS ++ G L+GPNG GK+T L C L P+SG V L Sbjct: 9 LIVESLVKRYGDFTAVDGVSFAVEPGTCFGLLGPNGAGKTTTLRCCLGLTAPESGAVRLN 68 Query: 63 DNPINMLSSRQLARRLSLLPQH-HLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNV 121 P+ ++R+ R ++PQ +L P+ + L+ YGR +G A AR+ Sbjct: 69 GLPVPQ-AAREARLRTGVVPQFDNLDPDFTVAENLLVYGR-----YFGLSDATVLARIPE 122 Query: 122 AMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLM 181 + + L LSGG ++R LA L + +V LDEPTT LD + + + Sbjct: 123 LLEFAGLGGKEKSPLKSLSGGMKRRLTLARALVNDPDIVFLDEPTTGLDPQARHLIWERL 182 Query: 182 GELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEI 241 L +GKT++ H +++A R C QL V+ +G ++ QG+P E++ + V V E Sbjct: 183 KALTARGKTLILTTHFMDEAERLCHQLAVLDHGRLITQGSPRELIASHIEPQVVEVYGEN 242 Query: 242 HPEPVSG 248 P G Sbjct: 243 APAWAEG 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: 199 Number of extensions: 8 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: 307 Length adjustment: 26 Effective length of query: 229 Effective length of database: 281 Effective search space: 64349 Effective search space used: 64349 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 Apr 09 2024. 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