GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Dechlorosoma suillum PS

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate Dsui_3250 Dsui_3250 acetylornithine/succinylornithine aminotransferase

Query= curated2:C3P3K3
         (396 letters)



>FitnessBrowser__PS:Dsui_3250
          Length = 390

 Score =  261 bits (666), Expect = 3e-74
 Identities = 149/383 (38%), Positives = 216/383 (56%), Gaps = 8/383 (2%)

Query: 17  NNYHPLPIVISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTS 76
           N Y  LP+  S  EG  + D +G  Y+D LS  +    GH HPK++NA+  QA RV  TS
Sbjct: 6   NTYARLPVAFSHGEGNRIYDTDGKCYLDALSGIAVNTLGHNHPKLVNAIASQAARVLHTS 65

Query: 77  RAFHSDQLGPWYEKVAKLTNKEMVLPMNTGAEAVETAIKTARRWAYDVKKVEANRAEIIV 136
             +         +++A L+  E V   N+G EA E AIK AR + +  K V+A    IIV
Sbjct: 66  NLYRIPLQEELADRLAGLSRMEEVFFCNSGCEANEAAIKLARFFGHQ-KGVDA--PVIIV 122

Query: 137 CEDNFHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIPYGDLEALKAA--ITPNTAAFILEP 194
            E  FHGRT+  +S + N + + GF P++ G + +PY DL+A++AA  + PN  A +LE 
Sbjct: 123 MEKAFHGRTLATLSATGNRKAQAGFEPLVSGFVRVPYNDLDAIRAAAELNPNVVAVLLEM 182

Query: 195 IQGEAGINIPPAGFLKEALEVCKKENVLFVADEIQTGLGRTGKVFACDWDNVTPDMYILG 254
           +QGE GI++    F +    +C +++ L + DE+Q G+GRTG  F      + PD+  L 
Sbjct: 183 VQGEGGIHVADPEFQRGLRSLCDEKDWLLMCDEVQCGMGRTGTWFGFQHAGILPDVATLA 242

Query: 255 KALGGGVFPISCAAANRDILGVFEPGSHGSTFGGNPLACAVSIAALEVLEEEKLTERSLQ 314
           K LG GV PI          G+F+PG+HGSTFGGNPLACA ++  +  +EEEKL E ++ 
Sbjct: 243 KGLGSGV-PIGACMTAGKAAGLFKPGNHGSTFGGNPLACAAALTTIACIEEEKLRENAVA 301

Query: 315 LGEKLVGQLKEIDNPM--ITEVRGKGLFIGIELNEPARPYCEQLKAAGLLCKETHENVIR 372
            GE +   L E    +  + E+RGKGL +GIEL+ P      +   AGLL   T E V+R
Sbjct: 302 QGEAIRRGLSEALAGVGGLVEIRGKGLMLGIELDRPCGELVAKGLEAGLLINVTAEKVVR 361

Query: 373 IAPPLVISEEDLEWAFQKIKAVL 395
           + P L  S  D +   Q++ A++
Sbjct: 362 LLPALTFSAADTQELVQRLAALI 384


Lambda     K      H
   0.317    0.136    0.402 

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: 404
Number of extensions: 21
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: 396
Length of database: 390
Length adjustment: 31
Effective length of query: 365
Effective length of database: 359
Effective search space:   131035
Effective search space used:   131035
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.

Links

Downloads

Related tools

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