Aligments for a candidate for gadh1 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for gadh1 in Herbaspirillum seropedicae SmR1

Align D-gluconate dehydrogenase dehydrogenase subunit (EC 1.1.99.3) (characterized)
to candidate HSERO_RS16740 HSERO_RS16740 GMC family oxidoreductase

Query= metacyc::MONOMER-12745
         (594 letters)



>FitnessBrowser__HerbieS:HSERO_RS16740
          Length = 593

 Score =  732 bits (1890), Expect = 0.0
 Identities = 356/596 (59%), Positives = 436/596 (73%), Gaps = 5/596 (0%)

Query: 1   MATVMKKVDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTYS 60
           MA    KVD V+VG GWTG+IM  ELTEAGL+VLALERG M+DT  D  YP+ +DEL YS
Sbjct: 1   MAIKKDKVDVVMVGLGWTGSIMGMELTEAGLSVLALERGDMRDTNTDTPYPKAVDELKYS 60

Query: 61  VRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRM 120
           VR  LFQD+S+ETVTIRH+++DVA+P RQ G+FL G+GVGGAG HW+G+ +R  P EL M
Sbjct: 61  VRGALFQDLSRETVTIRHTLSDVAVPYRQHGSFLLGDGVGGAGFHWNGMMYRNLPEELEM 120

Query: 121 RSHYEERYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVRGQLVGDGKGG 180
           R+H+E++YGK FIP+DMTIQD GV+Y+ELEPF+D++EKV   SG+A  ++GQ+V    GG
Sbjct: 121 RTHHEQKYGKKFIPEDMTIQDHGVTYKELEPFYDFSEKVMAVSGKAGNLKGQIV---PGG 177

Query: 181 NPYAPDRSDHFPLESQKNTYSAQLFQKAANDVGYKPYNLPSANTSGPYTNPYGAQMGPCN 240
           NP   +RSD FP    +  YSA L +KA  DVGY PY  P+AN S P+TNPYG ++GPCN
Sbjct: 178 NPLEGERSDEFPTPPLQYQYSASLVEKAMRDVGYHPYPAPAANASQPFTNPYGVRIGPCN 237

Query: 241 FCGFCSGYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDG 300
           +CGFC  Y CYMYSKASP   ILP L    NFE+R  + V++VNLD+S  RATGVTY+D 
Sbjct: 238 YCGFCENYGCYMYSKASPQTTILPVLLKRKNFEVRTKAQVIKVNLDASGKRATGVTYIDA 297

Query: 301 QGREIEQPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYFD 360
           QGRE+EQPADLV+L AFQ HNVRL+LLSGIGKPYDP+TGEGVVGKNFAYQ    I     
Sbjct: 298 QGREVEQPADLVLLTAFQTHNVRLLLLSGIGKPYDPVTGEGVVGKNFAYQYNGGINVIMP 357

Query: 361 KDVHTNNFIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPG--T 418
           K    N FIG G  GV +DD NAD FDHGP GF+GG+ +   + G RPI      PG   
Sbjct: 358 KGTQFNPFIGTGAGGVGMDDLNADQFDHGPLGFIGGASIRHVRYGGRPIKQAGTMPGEKV 417

Query: 419 PAWGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQEND 478
           P+WGS WK +  D Y   +++   G+  +YR  YL LDP YRDA G PLLR+T +W+EN+
Sbjct: 418 PSWGSEWKASVQDAYQRTLTIGMSGSVMAYRDCYLSLDPTYRDANGQPLLRLTLNWKENE 477

Query: 479 IKMNRFMVEKMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALN 538
            KM  ++  +M K+ +AMNP+ +    +K G  ++T  YQ+THL GGAIMGT PK S +N
Sbjct: 478 GKMLTYIASQMEKVGQAMNPEKVVKAVRKTGSSWDTRVYQSTHLTGGAIMGTTPKNSVVN 537

Query: 539 RYLQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594
           +YLQSWDV NVFV GA AFPQ +GYNPTGLV AL Y SA+AIREQYLKNPGPLVQA
Sbjct: 538 KYLQSWDVPNVFVYGACAFPQNMGYNPTGLVTALAYHSAKAIREQYLKNPGPLVQA 593


Lambda     K      H
   0.318    0.136    0.423 

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: 1271
Number of extensions: 57
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: 594
Length of database: 593
Length adjustment: 37
Effective length of query: 557
Effective length of database: 556
Effective search space:   309692
Effective search space used:   309692
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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Protein sequences (fasta format)
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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 paper from 2022 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