GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Brucella inopinata BO1

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_002968535.1 BIBO1_RS18510 aspartate aminotransferase family protein

Query= BRENDA::O30508
         (406 letters)



>NCBI__GCF_000182725.1:WP_002968535.1
          Length = 484

 Score =  181 bits (460), Expect = 3e-50
 Identities = 126/415 (30%), Positives = 207/415 (49%), Gaps = 44/415 (10%)

Query: 30  RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWH-VSNVFTNEPALR 88
           R EG   +DQ+GR ++DF GG    + GH HP ++ A  +  + + H ++  F ++ A  
Sbjct: 67  RAEGMYYYDQNGRRILDFFGGFGSLAFGHNHPRIIAARRKFQEELRHEIAIAFMSQYAAA 126

Query: 89  LARKLVDATFAE--RVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTL 146
           LA  L   +  +   VFL +SG+EA EAA K+A R A    GP+K +I+ A NSFHG+T 
Sbjct: 127 LAYDLAACSPGDLDMVFLGSSGSEAMEAAIKVAERAA----GPKKPKIVYAENSFHGKTK 182

Query: 147 FTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISD--KTCAVVLEPIQGEGGVLPA 204
             +++     Y   F    +    VP+ D+ A++ A     +   +VLE +QG GG++ A
Sbjct: 183 GVLSITDGGLYRGEF-KLVDNTVRVPFGDITAIENAFRSDPEIGTIVLETVQGGGGIIQA 241

Query: 205 QQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGGFPIG 264
              + +  R+LCD +  + V DEVQ G GR G+ +A+ HYGV+PD+ + AKSLGGG    
Sbjct: 242 DAEFWQKLRQLCDRYGVIWVADEVQCGFGRTGKFYAFEHYGVIPDVTALAKSLGGGKAAM 301

Query: 265 AMLTTGEIAKHLSVGTHGT-------TYGGNPLASAVAEAALDVINTPEVLDGVKAKHER 317
           A +         + GT  T       T+GG   A   A  A++++   +++D      + 
Sbjct: 302 AAMIARRDIYMKAYGTPKTAMIHAMATFGGIGEACITAIEAVNILYDEQLIDNSAEVGDY 361

Query: 318 FKSRLQKIGQEY-GIFDEIRGMGLLIG------------------AALTDEWKGKARDVL 358
              RL+++   Y G+  ++RG G+++G                  A L D+ KG     +
Sbjct: 362 LLERLKELQVRYPGLLKDVRGKGMMVGLEFHDFSQAMPMVLRPMLAMLDDKLKGSLPGFI 421

Query: 359 NA--AEKEAVMV--LQASPDVVRFAPSLVIDDAEIDEGL----ERFERAVAKLVR 405
            +       V+V   + + +V+R  P L+   A +DE +    E   R + K+V+
Sbjct: 422 GSHLLRDHGVLVAFTEYNRNVIRLEPPLICQRAHVDEFIKALDEVLSRGIVKIVK 476


Lambda     K      H
   0.318    0.135    0.394 

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: 483
Number of extensions: 20
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: 406
Length of database: 484
Length adjustment: 32
Effective length of query: 374
Effective length of database: 452
Effective search space:   169048
Effective search space used:   169048
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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