GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davT in Phaeobacter inhibens BS107

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III

Query= BRENDA::Q9I6M4
         (426 letters)



>lcl|FitnessBrowser__Phaeo:GFF2829 PGA1_c28750 aminotransferase
           class-III
          Length = 440

 Score =  183 bits (464), Expect = 1e-50
 Identities = 134/373 (35%), Positives = 184/373 (49%), Gaps = 26/373 (6%)

Query: 38  DVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKR 97
           D  G+ Y+D +GG AV   GH   +VIAAVQEQ+GKL+      L  EP   LA+ +  +
Sbjct: 26  DANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGFLTSEPAEALADLLISQ 85

Query: 98  VPGDFPKKTLLVTSGSEAVENAVKIAR------AATGRAGVIAFTGAYHGRTMMTLGLTG 151
            PGD   +   V+ GSEA E A+K+AR        T R  VIA   +YHG T+  L   G
Sbjct: 86  APGDL-HRVYFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGNTLGALAAGG 144

Query: 152 KVVPYSAGMGLMPGGIFRALAPC-ELHGVSEDDSIASIERIFKNDAQ-------PQDIAA 203
                     L+       +APC E     + +S     +   N+ +       P+ + A
Sbjct: 145 NAWRRQQFAPLLID--ISHIAPCYEYVDRGDGESRYDYGQRVANELEAEILRLGPETVMA 202

Query: 204 IIIEPVQGE-GGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVP 262
            + EPV G   G     + + +R+R +CDQ+G+LLI DEV  G GRTG  FA E  G+ P
Sbjct: 203 FMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGHLFACEADGVAP 262

Query: 263 DLTTFAKSVGGGF-PISGVAGKAEIMDAIAPGG----LGGTYAGSPIACAAALAVLKVFE 317
           D+   AK +G G+ PI  +    +I DAI  G      G TY G P+A AA LAV++   
Sbjct: 263 DILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATAAGLAVVRALL 322

Query: 318 EEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELF---EGGDTHKPAAELV 374
           +  L++RS  +GE L A L     +H  +GD+RG G    IEL    E      P   + 
Sbjct: 323 DRGLVQRSAEMGETLHAALVARFGQHPHVGDLRGRGLFRGIELVADRESKTPFDPGLGIA 382

Query: 375 SKIVVRAREKGLI 387
            K+   A E GLI
Sbjct: 383 GKLKKAAFEAGLI 395


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: 513
Number of extensions: 30
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: 426
Length of database: 440
Length adjustment: 32
Effective length of query: 394
Effective length of database: 408
Effective search space:   160752
Effective search space used:   160752
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: 51 (24.3 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