GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Desulfovibrio vulgaris Hildenborough

Align Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized)
to candidate 207835 DVU2347 acetylornithine aminotransferase

Query= curated2:Q4A0N2
         (394 letters)



>MicrobesOnline__882:207835
          Length = 399

 Score =  247 bits (630), Expect = 5e-70
 Identities = 124/384 (32%), Positives = 217/384 (56%), Gaps = 6/384 (1%)

Query: 14  KNYSPLKLALAKGRGAKVWDIEDNCYIDCISGFSVVNQGHCHPKIIKALQEQSQRITMVS 73
           + Y    +++ +  G+++WD E   YID +SG +V + GHCHP++ + +  Q++++  VS
Sbjct: 18  RTYGRYPISVQRAEGSRMWDHEGREYIDLLSGIAVTSLGHCHPELAEVMARQARKLVHVS 77

Query: 74  RALYSDNLGKWEEKICKLANKENVLPMNTGTEAVETAIKMARKWGADIKNIDESSSEIIA 133
              Y +      EK+    +       N+G EA E AIK+AR++   ++ +D  + E++ 
Sbjct: 78  NLFYQEEQLDLAEKLLSTLHCTKAFFCNSGAEANEAAIKLARRYMQRVRGVD--AHEVVT 135

Query: 134 MNGNFHGRTLGSLSLSSQDSYKKGFGPLLNNIHYADFGDIEQLKKLINNQTTAIILEPIQ 193
           + G FHGRTL +++ + Q+ ++ GF P+      A++GDI+ L+  I   T  +++E +Q
Sbjct: 136 LTGAFHGRTLATVAATGQERFQDGFAPMPAGFRQAEWGDIDALRAAITPATAGVLVEMVQ 195

Query: 194 GEGGVNIPPTHFIQEVRQLCNEYNVLLIADEIQVGLGRTGKMFAMEWENTEPDIYLLGKS 253
           GEGGV      + + V  LC E  VLL+ DEIQ GL RTG+ +A +    EPDI    K+
Sbjct: 196 GEGGVRPMTQDYARAVADLCREKGVLLMVDEIQTGLCRTGRFWAHQHYGVEPDIVTSAKA 255

Query: 254 LGGGLYPISAVLANQDVMSVLTPGTHGSTFGGNPLACAVSMAALDVLNEEHLVQNALDLG 313
           L  GL P+ A++   +V      G+H +TFG   L  +V+ A LD++  + L + A  +G
Sbjct: 256 LANGL-PMGAMMTTDEVAQGFVAGSHATTFGAGALVSSVAAATLDIMKRDRLDERATAVG 314

Query: 314 DRLLKHLQQIESEL---IVEVRGRGLFIGIELNVAAQDYCEQMINKGVLCKETQGNIIRI 370
            R ++  + I ++L   I EVRG GL IGI L  + ++  ++++ +G +C  TQ  ++R+
Sbjct: 315 GRAMERFRAIGAKLPGTIEEVRGYGLMIGIVLTFSGKEVWKELVARGFVCNNTQEKVLRL 374

Query: 371 APPLVIDKDEIDEVIRVITEVLEK 394
            P L ID+ ++      + ++L +
Sbjct: 375 VPALTIDEADLTAFADTLEDILAR 398


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: 339
Number of extensions: 16
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: 394
Length of database: 399
Length adjustment: 31
Effective length of query: 363
Effective length of database: 368
Effective search space:   133584
Effective search space used:   133584
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