Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_011428578.1 RHE_RS27840 ABC transporter ATP-binding protein
Query= CharProtDB::CH_088321 (255 letters) >NCBI__GCF_000092045.1:WP_011428578.1 Length = 253 Score = 191 bits (486), Expect = 1e-53 Identities = 102/250 (40%), Positives = 147/250 (58%), Gaps = 3/250 (1%) Query: 1 MTLRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVF 60 M+++ +NLT G +L+ VS+ P G++ L+GPNG GK++LL + L P SG V Sbjct: 1 MSIKADNLTWKIGRKTILDGVSMEAPPGRMLGLLGPNGSGKTSLLRLLAGLKRPHSGRVT 60 Query: 61 LGDNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVN 120 L + I +S R +ARR++ + QH T + V ++V GR P S++ + D V Sbjct: 61 LDRSDIGKISRRSIARRIAFVEQHATTNANLKVLDVVKLGRFPHRSMFSGWTKADEEAVE 120 Query: 121 VAMNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRL 180 A+ + + R LSGG++QR +A LAQ+ ++LDEPT +LDI HQ+ LMRL Sbjct: 121 AALARAGMAEKRDERWQSLSGGEKQRTHIARALAQSPQELILDEPTNHLDIQHQIGLMRL 180 Query: 181 MGELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEVMTPGLLRTVFSVEAE 240 + L T + LHDLN A+ +CDQL++M G V+A G PEEV++ LLR VFSVEA Sbjct: 181 VSGLPI---TSIVALHDLNHAAMFCDQLIIMQQGRVVASGAPEEVLSETLLREVFSVEAR 237 Query: 241 IHPEPVSGRP 250 I P RP Sbjct: 238 IEASPYHSRP 247 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: 163 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: 253 Length adjustment: 24 Effective length of query: 231 Effective length of database: 229 Effective search space: 52899 Effective search space used: 52899 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