Align iron(III) dicitrate transport ATP-binding protein FecE (characterized)
to candidate WP_232502519.1 LFE_RS09120 ATP-binding cassette domain-containing protein
Query= CharProtDB::CH_088321 (255 letters) >NCBI__GCF_000284315.1:WP_232502519.1 Length = 588 Score = 94.7 bits (234), Expect = 4e-24 Identities = 74/235 (31%), Positives = 115/235 (48%), Gaps = 20/235 (8%) Query: 13 GTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTV-FLGDNPINMLSS 71 G L+ +S SL G IT LIGP+G GK+TL+ S LL P G + +G++P S Sbjct: 25 GIVTALDKISFSLKKGSITGLIGPDGAGKTTLMRLLSGLLWPDGGDIRIMGNDPSKAPLS 84 Query: 72 RQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVAMNQTRINHL 131 Q + L +PQ E ++VQE + N L G ++ T ++ Sbjct: 85 VQGS--LGYMPQKFGLYEDLSVQENLDLYAN----LQGVPKDRRKELYAPLLSMTGLSPF 138 Query: 132 AVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMGELRTQ-GKT 190 R +LSGG +Q+ +A L P++LLDEPT +D + +L ++ +L ++ G T Sbjct: 139 QKRLAGQLSGGMKQKLGVACSLVHQPPILLLDEPTVGVDPVSRRELWEILRKLVSESGAT 198 Query: 191 VVAVLHDLNQASRYCDQLVVMANGHVMAQGTPE-----------EVMTPGLLRTV 234 + L++A R CD+++++ NG V+ G PE T G LRTV Sbjct: 199 LFVSTSYLDEAER-CDEILILYNGKVLGSGPPESFRKEVAGRGYRAETTGSLRTV 252 Score = 88.6 bits (218), Expect = 3e-22 Identities = 55/223 (24%), Positives = 107/223 (47%), Gaps = 6/223 (2%) Query: 3 LRTENLTVSYGTDKVLNDVSLSLPTGKITALIGPNGCGKSTLLNCFSRLLMPQSGTVFLG 62 + ENL + + K +N+++ + G++ L+G NG GK+T + LL P +G + + Sbjct: 342 IEVENLDRYFDSFKAVNNLTFHVKKGEVFGLLGANGAGKTTTFRMLAGLLEPTAGKLIVA 401 Query: 63 DNPINMLSSRQLARRLSLLPQHHLTPEGITVQELVSYGRNPWLSLWGRLSAEDNARVNVA 122 + ++++ + + + L + Q L+ Y S +G ++ + Sbjct: 402 GEDVRKVAAQARGKIGYMAQKFSLYSQLTVFQNLIFYS-----SAYGLSGTLQKEKIQDS 456 Query: 123 MNQTRINHLAVRRLTELSGGQRQRAFLAMVLAQNTPVVLLDEPTTYLDINHQVDLMRLMG 182 +N + L G RQR L+ L ++ LDEPT+ +D N + + ++ Sbjct: 457 LNFFELEPYKNVSSGILPLGFRQRLALSCALIHEPSILFLDEPTSGVDPNARREFWHIIN 516 Query: 183 ELRTQGKTVVAVLHDLNQASRYCDQLVVMANGHVMAQGTPEEV 225 L T G +V+ H + +A YCD+L++MA G ++A G+P E+ Sbjct: 517 ALATVGVSVLVTTHFMEEA-EYCDRLLIMAQGALLAMGSPAEI 558 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: 314 Number of extensions: 14 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 255 Length of database: 588 Length adjustment: 30 Effective length of query: 225 Effective length of database: 558 Effective search space: 125550 Effective search space used: 125550 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: 50 (23.9 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