GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Algiphilus aromaticivorans DG1253

Align Ornithine aminotransferase; OAT; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase (uncharacterized)
to candidate WP_043768728.1 U743_RS12545 adenosylmethionine--8-amino-7-oxononanoate transaminase

Query= curated2:C3P3K3
         (396 letters)



>NCBI__GCF_000733765.1:WP_043768728.1
          Length = 456

 Score =  173 bits (439), Expect = 8e-48
 Identities = 122/417 (29%), Positives = 193/417 (46%), Gaps = 56/417 (13%)

Query: 22  LPIV-ISKAEGVWVEDPEGNRYMDLLSAYSAVNQGHRHPKIINALIDQANRVTLTSRA-F 79
           LP+V + +AEG W+  P G RY+D +S++     GHRHP I+  L  Q + +     A F
Sbjct: 29  LPLVPVERAEGAWLYGPNGERYLDAVSSWWTNIFGHRHPHIVERLKTQLDTLDHAMLAGF 88

Query: 80  HSDQLGPWYEKVAKLTNKEMVLPM--NTGAEAVETAIKTARRWAYDVKKVEANRAEIIVC 137
               +    E++A +T   +   M  + G+ A+E A+K +    Y V   +  R   I  
Sbjct: 89  THPPVVELSERLAAITPGGLSRCMYADNGSSAIEVALKMSHH--YWVNSGQPQRTRFIAL 146

Query: 138 EDNFHGRTMGAVSMSSNEEYKRGFGPMLPGIIVIP------------------------- 172
             ++HG TMGA+++SS   Y+  +  +L   IV+                          
Sbjct: 147 SGSYHGETMGALAVSSTGLYRDAYKALLMEPIVVQAPDCGVMDPGTRAPGVSWEDHARRT 206

Query: 173 YGDLEALKAAITPNTAAFILEP-IQGEAGINIPPAGFLKEALEVCKKENVLFVADEIQTG 231
           + ++EA   A    TAA I+EP +Q   G+ + P  +LK   E C +  V  +ADEI TG
Sbjct: 207 FKEMEAALEAHAHETAAVIVEPMLQCAGGMRMWPPIYLKLLREACDRHGVHLIADEIATG 266

Query: 232 LGRTGKVFACDWDNVTPDMYILGKALGGGVFPISCAAANRDILGVF-------EPGSHGS 284
             RTGK+FAC+W ++ PD   L K L GG  P++    N  +   F       +   H  
Sbjct: 267 FCRTGKLFACEWADIEPDFLCLSKGLTGGTLPLAVCMTNEQVYRAFYDDYSSGKAFLHSH 326

Query: 285 TFGGNPLACAVSIAALEVLEEEKLTERSLQLGEKLVGQLKEID-NPMITEVRGKGLFIGI 343
           ++ GNPL C  ++A L++LEE        +LG+ L  Q+ E+  +P + +VR +G  + I
Sbjct: 327 SYTGNPLTCTAALATLDILEERDWPAHVRKLGQHLWNQVSELTRHPHVADVRQQGFVLAI 386

Query: 344 EL--------------NEPARPYCEQLKAAGLLCKETHENVIRIAPPLVISEEDLEW 386
           +L                  R Y   L    LL      N +   PP  ++EE+++W
Sbjct: 387 DLAADGPGRVPYPAGERRGLRVYQHGLSQGALL--RPLGNTVYFMPPYCVTEEEIDW 441


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: 495
Number of extensions: 31
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: 456
Length adjustment: 32
Effective length of query: 364
Effective length of database: 424
Effective search space:   154336
Effective search space used:   154336
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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