GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecE in Leptospirillum ferrooxidans C2-3

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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