Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate GFF2551 PGA1_c25920 ferric enterobactin transport ATP-binding protein FepC
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__Phaeo:GFF2551 Length = 260 Score = 220 bits (561), Expect = 2e-62 Identities = 115/249 (46%), Positives = 165/249 (66%), Gaps = 1/249 (0%) Query: 3 LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62 LR E+L+VSY VLN +S LP G +T ++GPN CGKSTLL +RL G V L Sbjct: 7 LRAEDLSVSYSRTPVLNSLSTDLPDGALTVIVGPNACGKSTLLRALARLQPAGKGQVLLD 66 Query: 63 DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVA 122 I+ SR +A+RL++LPQ PEG+TV++L + GR P S + S +D V A Sbjct: 67 GKAIHRQGSRAVAQRLAILPQTPTAPEGLTVRDLATRGRTPHQSPLRQWSRQDAEAVTRA 126 Query: 123 MNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMG 182 ++ T + A R L LSGGQRQRA++AM LAQ+T ++LLDEPTTYLD+ HQ++L++L+ Sbjct: 127 LDLTHMAPHADRPLEALSGGQRQRAWIAMALAQDTDILLLDEPTTYLDLPHQIELLKLVQ 186 Query: 183 EL-RTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEI 241 +L R G+TVV VLHD+N A+R+ ++ + +G V +G P+EV+T G+L++VF++ I Sbjct: 187 QLNRDTGRTVVMVLHDINLAARFASHMIALKDGQVFCEGPPDEVITEGVLQSVFALPCRI 246 Query: 242 HPEPVSGRP 250 +PV G P Sbjct: 247 IADPVHGSP 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: 185 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: 260 Length adjustment: 24 Effective length of query: 231 Effective length of database: 236 Effective search space: 54516 Effective search space used: 54516 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