Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate H281DRAFT_04927 H281DRAFT_04927 iron complex transport system ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >FitnessBrowser__Burk376:H281DRAFT_04927 Length = 272 Score = 185 bits (469), Expect = 1e-51 Identities = 96/247 (38%), Positives = 151/247 (61%), Gaps = 1/247 (0%) Query: 6 ENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLGDNP 65 ++++ G +L+ ++L+LP G++ LIG NG GKSTLL +R P++GT+ P Sbjct: 22 DDVSFRIGERVLLHPLALTLPRGRVCGLIGHNGSGKSTLLKLLARQQSPKAGTLRFAGRP 81 Query: 66 INMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVAMNQ 125 + +R+ AR+++ LPQ G+TV+ELV+ GR PW GR + D +V+ AM Sbjct: 82 LREWENREFARQVAYLPQQQPAASGMTVRELVALGRYPWHGALGRFTGVDAEKVHEAMEL 141 Query: 126 TRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMGELR 185 T I R + LSGG+RQRA++AM++AQ++ +LLDEP + LDI HQ++++ L+ L Sbjct: 142 TDITRFGDRAVDSLSGGERQRAWIAMLVAQDSQCLLLDEPISALDIAHQIEVLDLVRTLS 201 Query: 186 TQ-GKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAEIHPE 244 Q G VV VLHD+N A+R+CD L+ + NG ++A GT E++ +L ++ V Sbjct: 202 QQRGLGVVVVLHDINMAARFCDDLIALKNGRLLASGTAPELIEEKMLGAIYGVPMGTVAH 261 Query: 245 PVSGRPM 251 P G P+ Sbjct: 262 PRGGMPI 268 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: 4 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: 272 Length adjustment: 25 Effective length of query: 230 Effective length of database: 247 Effective search space: 56810 Effective search space used: 56810 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