GapMind for catabolism of small carbon sources

 

Alignments 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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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