GapMind for catabolism of small carbon sources

 

Alignments 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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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