GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutB in Cupriavidus basilensis 4G11

Align Putative L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF (characterized, see rationale)
to candidate RR42_RS21285 RR42_RS21285 (Fe-S)-binding protein

Query= uniprot:A0A0C4Y8G6
         (489 letters)



>FitnessBrowser__Cup4G11:RR42_RS21285
          Length = 476

 Score =  958 bits (2476), Expect = 0.0
 Identities = 475/476 (99%), Positives = 476/476 (100%)

Query: 14  LHFVPAADFKARSRAALDDPKLRSSFRGAMDFLQAKRAVQFPDGDELEQLRDLGEAIRQH 73
           +HFVPAADFKARSRAALDDPKLRSSFRGAMDFLQAKRAVQFPDGDELEQLRDLGEAIRQH
Sbjct: 1   MHFVPAADFKARSRAALDDPKLRSSFRGAMDFLQAKRAVQFPDGDELEQLRDLGEAIRQH 60

Query: 74  ALSQLPDLLVQLEDKLTAAGVQVHWAETADEANAIVHGIAQARQASRVIKGKSMASEEIE 133
           ALSQLPDLLVQLEDKLTAAGVQVHWAETADEANAIVHGIAQARQASRVIKGKSMASEEIE
Sbjct: 61  ALSQLPDLLVQLEDKLTAAGVQVHWAETADEANAIVHGIAQARQASRVIKGKSMASEEIE 120

Query: 134 LNHYLAERGIDCIESDMGEYIVQLAGEKPSHIVMPAIHKTRGDIAELFEQHIPGTPYTED 193
           LNHYLAERGIDCIESDMGEYIVQLAGEKPSHIVMPAIHKTRGDIAELFEQHIPGTPYTED
Sbjct: 121 LNHYLAERGIDCIESDMGEYIVQLAGEKPSHIVMPAIHKTRGDIAELFEQHIPGTPYTED 180

Query: 194 VDELIQTGRRALRQEFVNADIGLSGVNFAAADTGTLWLVENEGNGRLSTTVPDVHIAIMG 253
           VDELIQTGRRALRQEFVNADIGLSGVNFAAADTGTLWLVENEGNGRLSTTVPDVHIAIMG
Sbjct: 181 VDELIQTGRRALRQEFVNADIGLSGVNFAAADTGTLWLVENEGNGRLSTTVPDVHIAIMG 240

Query: 254 MEKVVARLEHIVPLASLLTRSATGQAITTYFNLISGPRRAGERDGPREVHLVLLDNGRSQ 313
           MEKVVARLEHIVPLASLLTRSATGQAITTYFNLISGPRRAGERDGPREVHLVLLDNGRSQ
Sbjct: 241 MEKVVARLEHIVPLASLLTRSATGQAITTYFNLISGPRRAGERDGPREVHLVLLDNGRSQ 300

Query: 314 AYADEQLRATLQCIRCGACMNHCPVYTRIGGHAYGTTYPGPIGKIISPHLLGLDATADLA 373
           AYADEQLRATLQCIRCGACMNHCPVYTRIGGHAYGTTYPGPIGKIISPHLLGLDATADLA
Sbjct: 301 AYADEQLRATLQCIRCGACMNHCPVYTRIGGHAYGTTYPGPIGKIISPHLLGLDATADLA 360

Query: 374 TASSLCGACGEVCPVRIPIPQLLIRLRTEANRDPSEQVAHPLRGQGTKFSRGEHLVWRFW 433
           TASSLCGACGEVCPVRIPIPQLLIRLRTEANRDPSEQVAHPLRGQGTKFSRGEHLVWRFW
Sbjct: 361 TASSLCGACGEVCPVRIPIPQLLIRLRTEANRDPSEQVAHPLRGQGTKFSRGEHLVWRFW 420

Query: 434 SGAFAHPLAYRLFRWAATRLRVLTPKHQLGWTRHRAPLTPAPRSLSDLLRERGQAE 489
           SGAFAHPLAYRLFRWAATRLRVLTPKHQLGWTRHRAPLTPAPRSLSDLLRERGQAE
Sbjct: 421 SGAFAHPLAYRLFRWAATRLRVLTPKHQLGWTRHRAPLTPAPRSLSDLLRERGQAE 476


Lambda     K      H
   0.320    0.135    0.406 

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: 897
Number of extensions: 17
Number of successful extensions: 3
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: 489
Length of database: 476
Length adjustment: 34
Effective length of query: 455
Effective length of database: 442
Effective search space:   201110
Effective search space used:   201110
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. 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