GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Shewanella sp. ANA-3

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate 7023380 Shewana3_0610 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)

Query= curated2:Q4A0N2
         (394 letters)



>lcl|FitnessBrowser__ANA3:7023380 Shewana3_0610 bifunctional
           N-succinyldiaminopimelate-
           aminotransferase/acetylornithine transaminase protein
           (RefSeq)
          Length = 405

 Score =  254 bits (648), Expect = 4e-72
 Identities = 138/375 (36%), Positives = 220/375 (58%), Gaps = 9/375 (2%)

Query: 15  NYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVSR 74
           NY+P  +   +G G++VWD E N +ID   G +V   GHCHP ++ AL+ Q +++  +S 
Sbjct: 19  NYAPAAVIPVRGEGSRVWDQEGNEFIDFAGGIAVNCLGHCHPALVNALKTQGEKLWHLSN 78

Query: 75  ALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIAM 134
            + ++   +   K+      E V   N+G EA E A+K+AR++  +   +++   EIIA 
Sbjct: 79  VMTNEPALELATKLVNSTFAERVYFANSGAEANEAALKLARRYALEKFGVEKD--EIIAF 136

Query: 135 NGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQG 194
           +  FHGRT  ++S+  Q +Y  GFGP   +I +  + D+  L+  ++++T AI+LEP+QG
Sbjct: 137 DKAFHGRTFFTVSVGGQAAYSDGFGPKPQSITHLPYNDVAALEAAVSDKTCAIMLEPLQG 196

Query: 195 EGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKSL 254
           EGG+      F++ VR+L N++N L+I DE+Q G+GRTG+++A    +  PDI    K+L
Sbjct: 197 EGGIIDADPAFLKAVRELANKHNALVIFDEVQTGVGRTGELYAYMGTDIVPDILTTAKAL 256

Query: 255 GGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLGD 314
           GGG +PI+A+L   ++   L  GTHGST+GGNPLACA+  A LDV+N   ++        
Sbjct: 257 GGG-FPIAAMLTTAEIAEHLKVGTHGSTYGGNPLACAIGNAVLDVVNTPEVLNGVKHREQ 315

Query: 315 RLLKHLQQIESELIV--EVRGRGLFIGIELNVAAQ----DYCEQMINKGVLCKETQGNII 368
            L   L +I  +  V  E+RG+GL +G  LN   Q    D+    + +G++      N++
Sbjct: 316 LLRDGLNKINEKYHVFSEIRGKGLLLGAVLNEQYQGRSRDFLVASVAEGLMSLMAGANVV 375

Query: 369 RIAPPLVIDKDEIDE 383
           R AP LVI + +I E
Sbjct: 376 RFAPSLVIPEADIAE 390


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: 375
Number of extensions: 18
Number of successful extensions: 5
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: 405
Length adjustment: 31
Effective length of query: 363
Effective length of database: 374
Effective search space:   135762
Effective search space used:   135762
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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