GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh1 in Pseudomonas simiae WCS417

Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate GFF52 PS417_00265 GMC family oxidoreductase

Query= BRENDA::C0LE03
         (594 letters)



>FitnessBrowser__WCS417:GFF52
          Length = 594

 Score = 1189 bits (3076), Expect = 0.0
 Identities = 564/594 (94%), Positives = 584/594 (98%)

Query: 1   MATVMKKVDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTYS 60
           MAT+MKKVDAVIVGFGWTGAIMAKELTEAGLNV+ALERGPMQDTYPDGNYPQVIDELTYS
Sbjct: 1   MATIMKKVDAVIVGFGWTGAIMAKELTEAGLNVVALERGPMQDTYPDGNYPQVIDELTYS 60

Query: 61  VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM 120
           VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM
Sbjct: 61  VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM 120

Query: 121 RSHYEERYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGDGKGG 180
           RSHYEERYGK+FIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVG+G+GG
Sbjct: 121 RSHYEERYGKHFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGEGRGG 180

Query: 181 NPYAPDRSDHFPLESQKNTYSAQLFQKAANEVGYKPYNLPSANTSGPYTNPYGAQMGPCN 240
           NPYAPDRS+ FPLESQKNT SAQLFQKAA EVGYKPYNLPSANTSGPYTNPYGAQMGPCN
Sbjct: 181 NPYAPDRSNPFPLESQKNTVSAQLFQKAAAEVGYKPYNLPSANTSGPYTNPYGAQMGPCN 240

Query: 241 FCGFCSGYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDG 300
           FCGFCSGYVCYMYSKASPNVNILPAL+ +PNFELRPNSHVL+VNLDS+K++ATGVTY+D 
Sbjct: 241 FCGFCSGYVCYMYSKASPNVNILPALRQVPNFELRPNSHVLKVNLDSTKSKATGVTYIDA 300

Query: 301 QGREIEQPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYFD 360
           QGRE EQPA+LVILGAFQFHNVRLMLLSGIGKPYDPIT EGVVG+NFAYQNMATIKA+FD
Sbjct: 301 QGRECEQPAELVILGAFQFHNVRLMLLSGIGKPYDPITNEGVVGRNFAYQNMATIKAFFD 360

Query: 361 KDVHTNNFIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA 420
           KD HTNNFIGAGGNGVA+DDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA
Sbjct: 361 KDTHTNNFIGAGGNGVAIDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA 420

Query: 421 WGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDIK 480
           WGSAWK+ATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYG PLLRMTFDWQENDIK
Sbjct: 421 WGSAWKRATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGQPLLRMTFDWQENDIK 480

Query: 481 MNRFMVEKMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRY 540
           MNRFMVEKMGK+AEAMNPKAIA+LGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRY
Sbjct: 481 MNRFMVEKMGKVAEAMNPKAIAVLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRY 540

Query: 541 LQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594
           LQ WDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA
Sbjct: 541 LQCWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594


Lambda     K      H
   0.317    0.136    0.422 

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: 1593
Number of extensions: 50
Number of successful extensions: 1
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: 594
Length of database: 594
Length adjustment: 37
Effective length of query: 557
Effective length of database: 557
Effective search space:   310249
Effective search space used:   310249
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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