GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabT in Marinobacter adhaerens HP15

Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate GFF2981 HP15_2925 adenosylmethionine-8-amino-7-oxononanoate transaminase

Query= SwissProt::Q84P52
         (520 letters)



>lcl|FitnessBrowser__Marino:GFF2981 HP15_2925
           adenosylmethionine-8-amino-7-oxononanoate transaminase
          Length = 450

 Score =  222 bits (566), Expect = 2e-62
 Identities = 133/413 (32%), Positives = 220/413 (53%), Gaps = 8/413 (1%)

Query: 84  PLV-IQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELAFYHSFWNR 142
           PLV I++ EG ++ D  G +++DA++  W    G   PR+ AA  KQ+ EL   H     
Sbjct: 29  PLVPIKRGEGVWLEDFEGNRFIDAVSSWWVNLFGHANPRINAAIQKQIGELE--HVILAG 86

Query: 143 ST-KPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPDKKKFIAR 201
            T +P ++L++ L+++ T   + K F+ ++GS A +  +K+ ++Y     +P KK F+  
Sbjct: 87  FTHEPVVNLSERLIEV-TPPGLNKVFYADNGSSAIEAALKMSFHYWKNHDKPGKKNFVNL 145

Query: 202 TKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEEEFSTRLANNL 261
           + SYHG TL + +L  +      +      VL    P  +   +PGET+E+++ R    +
Sbjct: 146 SNSYHGETLGALALGDVSLYKDTYQPLLMEVLTAPSPDAFN-KEPGETDEDYALRQFEAM 204

Query: 262 ENLILKEGPETIAAFIAEPVMG-AGGVIPPPATYFEKVQAILKKYDILFIADEVICGFGR 320
           E L L E  E I A + EP++  AGG+      Y  K++    +Y +  IADE+  GFGR
Sbjct: 205 EKL-LAEKHEEICAVVVEPLIQCAGGMRMHHPIYHTKLREACDRYGVHLIADEIAVGFGR 263

Query: 321 LGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFSHGFTYS 380
            GT+F CE+  I PD + ++K L++GY+P+  VL + +V +  Y     L  F H  +Y+
Sbjct: 264 TGTLFACEQSGITPDFMCLSKGLTAGYLPLSVVLTTDDVYNAFYDDYETLKAFLHSHSYT 323

Query: 381 GHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEIRGTGLLHGTEFT 440
           G+P+ CAVAL TL I+++ N+IE    +S    E +   +D P +G+IR  G+    E  
Sbjct: 324 GNPIGCAVALATLDIFRDDNVIESNRALSTCMAESVAHLADHPNVGDIRQHGMTLAVEMV 383

Query: 441 DNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLEEIDEL 493
            +K+   PFP +   G            L+R  G+ +   PPY+++ E+I  L
Sbjct: 384 KDKASKTPFPWQERRGIRVYQHALTRQALLRPLGNVVYFMPPYVITEEQIRHL 436


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: 512
Number of extensions: 24
Number of successful extensions: 3
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: 450
Length adjustment: 34
Effective length of query: 486
Effective length of database: 416
Effective search space:   202176
Effective search space used:   202176
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