GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__ANA3:7023380
          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 (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