GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF2981
          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:

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