Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate AO353_14450 AO353_14450 hemin ABC transporter ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__pseudo3_N2E3:AO353_14450 Length = 255 Score = 171 bits (434), Expect = 1e-47 Identities = 99/258 (38%), Positives = 144/258 (55%), Gaps = 9/258 (3%) Query: 3 LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62 LR ENL + G VL D+ L L G++ ++GPNG GKSTLL L P G V+L Sbjct: 2 LRVENLQICRGKKIVLADIDLELKPGEVLGVLGPNGAGKSTLLGALCGELRPDHGRVWLD 61 Query: 63 DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVA 122 ++ Q A+RL++LPQ V+E+V GR P + GR+ D+ V A Sbjct: 62 QRELSQWDGAQRAQRLAVLPQTSTLDFAFRVEEVVGMGRLPHQT--GRV--RDDEIVAAA 117 Query: 123 MNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTP-----VVLLDEPTTYLDINHQVDL 177 + + HL+ R LSGG+RQR LA VLAQ P +LLDEPT+ LD HQ Sbjct: 118 LQAADVGHLSGRSYLALSGGERQRVHLARVLAQLWPGEAGQTLLLDEPTSMLDPLHQHTT 177 Query: 178 MRLMGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSV 237 ++ + E +G V+ +LHDLN A+RYCD+++++ +G A TP++V+ P L+ VF + Sbjct: 178 LQAIREFADRGAAVLVILHDLNLAARYCDRILLLESGRPHALDTPQQVLRPEPLKAVFGL 237 Query: 238 EAEIHPEPVSGRPMCLMR 255 + + P P G P+ + R Sbjct: 238 DVLVQPHPERGHPLIIAR 255 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: 182 Number of extensions: 11 Number of successful extensions: 3 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: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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