GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Phaeobacter inhibens BS107

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate GFF3422 PGA1_c34750 putative aminotransferase class 3

Query= SwissProt::P50457
         (421 letters)



>FitnessBrowser__Phaeo:GFF3422
          Length = 1009

 Score =  144 bits (364), Expect = 9e-39
 Identities = 121/399 (30%), Positives = 179/399 (44%), Gaps = 19/399 (4%)

Query: 34   LKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYVTLAEKIN 93
            L D  G  Y+D  A   V + GH HP + A    QL++       + P ++    AEKI 
Sbjct: 615  LFDEWGRPYLD--AYNNVPHVGHAHPRIQAIAADQLKRMNSNTRYLHPAQN--AFAEKI- 669

Query: 94   ALAPVSGQAKTAFFT-TGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMTMALTGKVA 152
             L+ +    +  FF  +G EA E A+++ARAHTG  G++    G+HG T   + ++    
Sbjct: 670  -LSKMPDHLEVCFFVNSGTEANELALRLARAHTGAKGMVTPDHGYHGNTTGAIDISAYKF 728

Query: 153  PYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIER--------LFKSDIEAKQVAAIIF 204
              K G GP    V  V    D  G   +D     ++        + K       VA  I 
Sbjct: 729  NAKGGVGPSDW-VELVEVADDYRGTYGRDDPQRAQKYADLVDPAIAKLQASGHGVAGFIA 787

Query: 205  EPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKL-FAMDHYADKPDLM 263
            E     GG  + PK  + A+       G + IADEVQ+G  R G+  F  +H    PD++
Sbjct: 788  ETFPSVGGQIIPPKGYLPAVYEKIRAAGGICIADEVQTGLGRLGEYYFGFEHQGASPDIV 847

Query: 264  TMAKSLAGGMPLSGVVGNANIMDAPAPGG-LGGTYAGNPLAVAAAHAVLNIIDKESLCER 322
             + K +  G PL  +V    I D+ A G     T+ G+ L+      VLNI+D+E L E 
Sbjct: 848  VLGKPIGNGHPLGVLVTTRAIADSFAQGPEFFSTFGGSTLSCRIGTEVLNIVDEEGLQEN 907

Query: 323  ANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQRALAQG 382
            A Q G  L N L D +    AI  VRG+G  I VE      G  ++ I   ++ R     
Sbjct: 908  ARQRGADLLNGLRDLQSRHQAIGDVRGMGLFIGVELIRTD-GSEASEICAYVKNRMRDHR 966

Query: 383  LLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALSD 421
            +L+ + G   N+++   PLTI     +  +K L   LS+
Sbjct: 967  ILIGSEGPKDNILKIRPPLTIDAEGIEMILKTLDSILSE 1005


Lambda     K      H
   0.319    0.134    0.388 

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: 991
Number of extensions: 49
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: 421
Length of database: 1009
Length adjustment: 38
Effective length of query: 383
Effective length of database: 971
Effective search space:   371893
Effective search space used:   371893
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: 54 (25.4 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