GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Sphingomonas koreensis DSMZ 15582

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate Ga0059261_4131 Ga0059261_4131 Ornithine/acetylornithine aminotransferase

Query= curated2:Q4A0N2
         (394 letters)



>FitnessBrowser__Korea:Ga0059261_4131
          Length = 398

 Score =  221 bits (562), Expect = 4e-62
 Identities = 124/376 (32%), Positives = 206/376 (54%), Gaps = 9/376 (2%)

Query: 16  YSPLKLALAKGRGAKVWDIEDN-CYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSR 74
           Y+   +A  +G GA ++ ++    Y+DC++G +    GHCHP ++ AL+ Q+ ++  +S 
Sbjct: 9   YARAPIAFDRGEGAWLYPVDGGEPYLDCVAGVATNALGHCHPVLVAALEAQAAKLWHISN 68

Query: 75  ALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAM 134
                      E++   +  + V   N+GTEAVE AIK+AR++ A     +     +I  
Sbjct: 69  MFEMPGQNALAERLTTASFADTVFFTNSGTEAVECAIKVARRYHA--ARGEPQRQTVIGF 126

Query: 135 NGNFHGRTLGSLSLSSQDSYKKGFGPLLNN-IHYADFGDIEQLKKLINNQTTAIILEPIQ 193
           +G FHGRT G+++ +   ++  GFG  L   +H+A          + ++ T A+++EP+Q
Sbjct: 127 SGAFHGRTYGAMNAAGNPAHLDGFGDRLPGFVHFAVDNWPALALAIADSATAAVVVEPVQ 186

Query: 194 GEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEW-ENTEPDIYLLGK 252
           GEGG       F+ ++R  C  + VLLI DE+Q G+GRTGK+FA +W  +  PDI  L K
Sbjct: 187 GEGGARAMTEPFLDKLRAACTAHGVLLIYDEVQTGMGRTGKLFAHQWYPDATPDIMALAK 246

Query: 253 SLGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDL 312
           +LG G +P+ A LA  +  S + PG HG+T GGNPLA AV++AA D + +   + +A ++
Sbjct: 247 ALGSG-FPVGACLATAEAASGMVPGVHGTTAGGNPLAMAVAIAAFDEIAKPETLTHAREV 305

Query: 313 GDRL---LKHLQQIESELIVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIR 369
              L   L  L      +I E+RG+GL +G+ L    + +      + +L      N +R
Sbjct: 306 AQHLRAGLDRLAATHPGVISEIRGKGLLVGVRLVPNNRAFMAAAREQRLLVAGGGDNCVR 365

Query: 370 IAPPLVIDKDEIDEVI 385
           + PPL +   E D+++
Sbjct: 366 LLPPLTLTVAEADQIL 381


Lambda     K      H
   0.317    0.136    0.396 

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: 342
Number of extensions: 13
Number of successful extensions: 6
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: 394
Length of database: 398
Length adjustment: 31
Effective length of query: 363
Effective length of database: 367
Effective search space:   133221
Effective search space used:   133221
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 (21.6 bits)
S2: 50 (23.9 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