Aligments for a candidate for dopDH in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Aligments for a candidate for dopDH in Sphingomonas koreensis DSMZ 15582

Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Ga0059261_0516 Ga0059261_0516 vanillin dehydrogenase (EC 1.2.1.67)

Query= reanno::Smeli:SM_b20891
         (477 letters)



>FitnessBrowser__Korea:Ga0059261_0516
          Length = 478

 Score =  257 bits (656), Expect = 7e-73
 Identities = 165/461 (35%), Positives = 239/461 (51%), Gaps = 9/461 (1%)

Query: 15  GDGVANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHAILKKTADEI 74
           G   A +NP  T +V  E    + + A  A+ AA AAFPAWS  G   R A L K A+ +
Sbjct: 10  GKTFARLNPV-TGEVATEAQAFTVDQANEAVEAAAAAFPAWSTLGPNARRAALNKAAEAL 68

Query: 75  LARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPSVRPGIGVEIT 134
            A+ ++    ++ E G T        + A  +    A  T ++ GEV+PS +PG      
Sbjct: 69  AAKAEDFVEAMNGEIGATEGWARFNLMLAVSMVREAAALTTQIGGEVIPSDKPGCIAMAI 128

Query: 135 REPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVDILHRAGLPK 194
           REP GV+  I PWN PI +    +A  L  GNT+V K +E  P     I +    A LPK
Sbjct: 129 REPVGVMLGIAPWNAPIILGVRAVAAPLACGNTVVLKASEQCPRTHSLIAEAFDEA-LPK 187

Query: 195 GVLNLVMGKGS----VVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRKYQLEMGGK 250
           G +++V         +VG A++D+P ++ I FTGSTA G+ +A  + EH +   LE+GGK
Sbjct: 188 GAVSIVTNAPEDAPEIVG-ALIDNPHIRRINFTGSTAVGRIIAKRAAEHLKPVLLELGGK 246

Query: 251 NPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERIKGLVVD 310
            P +VL+DADL  AV+AA   AF + GQ C ++ RIIV + + D FV     ++  + V 
Sbjct: 247 APMLVLEDADLDEAVKAAAFGAFMNQGQICMSTERIIVVDAVADAFVEKFAAKVGTMPVG 306

Query: 311 DALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFYLQPALFTEAT 370
           D  +  T +G VVDQ  +      I      GA    GG V+   T G  +   +    T
Sbjct: 307 DPREGKTPLGAVVDQKTVAHVKALIGDALAAGAVQVNGGGVL-EGTGGVLMPAHVIDHVT 365

Query: 371 NEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFKRNAEAGM 430
            +M++ R+E FGPV  VIR +D   A+ +ANDT +GLS+ + T          R  ++G+
Sbjct: 366 PDMKLFRDESFGPVVGVIRARDEAHAILLANDTEYGLSASVFTRDTARGLRVARQIKSGI 425

Query: 431 VMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVK 471
             VN PT   +  +PFGG KAS YG R  GK   + +T ++
Sbjct: 426 CHVNGPTVHDEAQMPFGGVKASGYG-RFGGKAGIDAFTELR 465


Lambda     K      H
   0.317    0.134    0.391 

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: 564
Number of extensions: 31
Number of successful extensions: 4
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: 477
Length of database: 478
Length adjustment: 34
Effective length of query: 443
Effective length of database: 444
Effective search space:   196692
Effective search space used:   196692
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: 51 (24.3 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)
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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