Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate GFF993 Psest_1025 ABC-type hemin transport system, ATPase component
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__psRCH2:GFF993 Length = 255 Score = 157 bits (397), Expect = 2e-43 Identities = 100/258 (38%), Positives = 140/258 (54%), Gaps = 9/258 (3%) Query: 3 LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62 L +LTV G+ L VSL L G++ ++GPNG GKSTLL S L P +G V L Sbjct: 2 LAGNDLTVRRGSITALQGVSLQLRAGQVFGVLGPNGAGKSTLLAALSGELRPSAGHVLLQ 61 Query: 63 DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVA 122 + + AR L++LPQ V ++V+ GR P + GR A A V A Sbjct: 62 GRALADWPDVERARCLAVLPQSSTLNFAFRVADVVAMGRLPHRT-GGRADA---AIVEAA 117 Query: 123 MNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTP-----VVLLDEPTTYLDINHQVDL 177 + HLA R +LSGG+RQR LA VLAQ P V+LLDEPT+ LD HQ + Sbjct: 118 LAAADAQHLAARSYLKLSGGERQRVHLARVLAQLWPGGPGRVLLLDEPTSMLDPAHQHSI 177 Query: 178 MRLMGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSV 237 ++ + QG + +LHDLN A+RYCD+L+++ NG A+G+ +EV+ L+ VF + Sbjct: 178 LQTVRGFAAQGGAALVILHDLNLAARYCDRLLLLKNGCPQAEGSVDEVLRAEQLQAVFGL 237 Query: 238 EAEIHPEPVSGRPMCLMR 255 E + P G P+ + R Sbjct: 238 EVLVQRHPERGHPLIIAR 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: 169 Number of extensions: 6 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