GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF2829
          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 (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