GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_1751
          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:

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