Aligments for a candidate for gadh1 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for gadh1 in Pseudomonas putida KT2440

Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate PP_3383 PP_3383 gluconate 2-dehydrogenase flavoprotein subunit

Query= BRENDA::C0LE03
         (594 letters)



>lcl|FitnessBrowser__Putida:PP_3383 PP_3383 gluconate
           2-dehydrogenase flavoprotein subunit
          Length = 594

 Score = 1129 bits (2921), Expect = 0.0
 Identities = 527/594 (88%), Positives = 568/594 (95%)

Query: 1   MATVMKKVDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTYS 60
           MATV+ KVDAVIVGFGW GAIMAKELTEAGL+V+ALERGPMQDTYP+G+YPQVIDELTYS
Sbjct: 1   MATVLNKVDAVIVGFGWAGAIMAKELTEAGLHVVALERGPMQDTYPEGSYPQVIDELTYS 60

Query: 61  VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM 120
           VRKKLF D+SKETVT+RHSVNDVALPNRQLGAFLPG GVGGAGLHWSGVHFRVDP+ELR+
Sbjct: 61  VRKKLFVDVSKETVTVRHSVNDVALPNRQLGAFLPGKGVGGAGLHWSGVHFRVDPVELRL 120

Query: 121 RSHYEERYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGDGKGG 180
           RSHYEERYG+ FIP+ MTIQDFGVSYEELEP+FD+AEKVFGTSGQAWTVKGQ+VG+GKGG
Sbjct: 121 RSHYEERYGRTFIPEGMTIQDFGVSYEELEPYFDFAEKVFGTSGQAWTVKGQVVGEGKGG 180

Query: 181 NPYAPDRSDHFPLESQKNTYSAQLFQKAANEVGYKPYNLPSANTSGPYTNPYGAQMGPCN 240
           NPYAPDRS+ FPL +QKN  SA+LF+KAA  +GYKPYNLPSANTSGPYTNPYGAQMGPCN
Sbjct: 181 NPYAPDRSNPFPLPAQKNVVSARLFEKAATSLGYKPYNLPSANTSGPYTNPYGAQMGPCN 240

Query: 241 FCGFCSGYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDG 300
           FCGFCSGYVCYMYSKASPNVNILPAL+ +PNFELRPN+HVLRVNLD SK RATGVTY+D 
Sbjct: 241 FCGFCSGYVCYMYSKASPNVNILPALRQVPNFELRPNAHVLRVNLDDSKRRATGVTYIDA 300

Query: 301 QGREIEQPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYFD 360
           QGRE+EQPA+LVIL AFQF+NVRLMLLSGIGKPYDP+  EGVVG+NFAYQNM T+KA+FD
Sbjct: 301 QGREVEQPAELVILAAFQFNNVRLMLLSGIGKPYDPVKNEGVVGRNFAYQNMGTVKAFFD 360

Query: 361 KDVHTNNFIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA 420
           KD +TNNFIGAGGNG+A+DDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA
Sbjct: 361 KDTYTNNFIGAGGNGIAIDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPA 420

Query: 421 WGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDIK 480
           WGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDP YRDAYG PLLRMTFDWQENDIK
Sbjct: 421 WGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPTYRDAYGQPLLRMTFDWQENDIK 480

Query: 481 MNRFMVEKMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRY 540
           MN+FMV+K+ KIA+AMNPKAIA+LGK+V +HFNT SYQTTHLNGGAIMGTDPKTSALNRY
Sbjct: 481 MNQFMVDKLSKIAQAMNPKAIAVLGKQVKDHFNTTSYQTTHLNGGAIMGTDPKTSALNRY 540

Query: 541 LQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594
           LQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA
Sbjct: 541 LQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 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: 1564
Number of extensions: 53
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources