GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Acidovorax sp. GW101-3H11

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1332
          Length = 398

 Score =  210 bits (534), Expect = 7e-59
 Identities = 137/400 (34%), Positives = 207/400 (51%), Gaps = 37/400 (9%)

Query: 25  PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84
           P+  ER +   VWDV G+EYID  GGIAV   GH H K++ A+Q+Q+ KL HT       
Sbjct: 20  PIALERGQGCRVWDVNGKEYIDGLGGIAVNTLGHNHGKLVPALQDQIAKLIHTSNYY--- 76

Query: 85  EPYIELAEEIA-KRVPGDFPKKTLLVTSGSEAVENAVKIARA-----ATGRAGVIAFTGA 138
             ++ L E++A K V     +      SG EA E A+KIAR         +  ++ +  A
Sbjct: 77  --HVPLQEKLATKLVELSGMQNVFFCNSGLEANEAALKIARKFGVDKGIAKPEIVVYEKA 134

Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQP 198
           +HGR++ T+  TG    ++ G G +  G  R               +  IE I +     
Sbjct: 135 FHGRSIATMSATGNPKIHN-GFGPLVEGFVRV-------------PMNDIEAIKQATEGN 180

Query: 199 QDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQL 258
            ++ A+  E +QGEGG       ++Q+LR LCD+ G L++ DEVQ G GRTG +FA +  
Sbjct: 181 PNVVAVFFETIQGEGGINGMRIEYLQQLRKLCDERGWLMMIDEVQCGMGRTGKWFAHQWA 240

Query: 259 GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEE 318
           GIVPD+   AK +G G PI  V    +  + + PG  G T+ G+P+A  A +  +++ EE
Sbjct: 241 GIVPDVMPLAKGLGSGVPIGAVVAGPKAANVLQPGNHGTTFGGNPLAMRAGVETIRIMEE 300

Query: 319 EKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIV 378
           + LL  +  VG+ L+A L+        + ++RG G M+ IEL      +KP   L+    
Sbjct: 301 DGLLHNAAQVGDHLRAALQRELGSLPGVKEIRGQGLMLGIEL------NKPCGALIG--- 351

Query: 379 VRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAIL 418
            RA E GL+L    T  +VIR + P+ +  A+ +  +AIL
Sbjct: 352 -RAAEAGLLL--SVTADSVIRLVPPLILTTAEADAIVAIL 388


Lambda     K      H
   0.319    0.137    0.393 

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: 402
Number of extensions: 22
Number of successful extensions: 3
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: 426
Length of database: 398
Length adjustment: 31
Effective length of query: 395
Effective length of database: 367
Effective search space:   144965
Effective search space used:   144965
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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