GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Dyella japonica UNC79MFTsu3.2

Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Query= SwissProt::Q84P52
         (520 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1751 N515DRAFT_1751
           adenosylmethionine-8-amino-7-oxononanoate
           aminotransferase
          Length = 467

 Score =  222 bits (566), Expect = 2e-62
 Identities = 126/420 (30%), Positives = 224/420 (53%), Gaps = 9/420 (2%)

Query: 78  HSTDLEPLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELAFYH 137
           H+  +  L I + EG ++ D +G++YLD ++  W    G   PR+ AA  +QL+ L  + 
Sbjct: 41  HAGTVPMLPIVRGEGPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLE-HV 99

Query: 138 SFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPDKKK 197
            F   + +P+++LA+ L  +  A  + + F  ++GS A +  +K+ ++Y    G   K +
Sbjct: 100 IFAGFTHEPAIELAERLAQITPAG-LERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTR 158

Query: 198 FIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLH---TDCPHFWRFHQPGETEEEFS 254
           FIA T SYHG TL + S+S +    + +   AP +L       P  +   +PGE+ E  +
Sbjct: 159 FIALTGSYHGETLGALSVSDVALYRKTY---APLLLTPVLAPSPDAYEA-EPGESAEACA 214

Query: 255 TRLANNLENLILKEGPETIAAFIAEPVMGAGGVIPPPATYFEKVQAILKKYDILFIADEV 314
            R    L  L+ +   ET A  +   V  AGG+     +Y   ++A+  ++ + FIADE+
Sbjct: 215 ARRLGELRVLLEQHAHETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEI 274

Query: 315 ICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFS 374
             GFGR GT+F CE+  + PD + ++K L+ G++P+ AVL +  V +  Y++ N    F 
Sbjct: 275 AVGFGRTGTLFACEQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFL 334

Query: 375 HGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEIRGTGLL 434
           H  +Y+G+P++C  AL TL I+++  ++E+   ++      L    + P + ++R TG++
Sbjct: 335 HSHSYTGNPLACRAALATLDIFRDEPVLERNRELAAHLARRLAPLREHPQVADVRQTGMI 394

Query: 435 HGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLEEIDELI 494
              E   +K+   P+P E   G        +HG L+R  G+ +   PPY++S +E+D L+
Sbjct: 395 AAVELVRDKATRAPYPSEERRGLRVYLHGLEHGALLRPLGNVVYFMPPYVVSTDELDHLV 454


Lambda     K      H
   0.317    0.135    0.401 

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: 519
Number of extensions: 22
Number of successful extensions: 4
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: 520
Length of database: 467
Length adjustment: 34
Effective length of query: 486
Effective length of database: 433
Effective search space:   210438
Effective search space used:   210438
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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