GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Azospirillum brasilense Sp245

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate AZOBR_RS06795 AZOBR_RS06795 serine/threonine dehydratase

Query= BRENDA::A0QY48
         (316 letters)



>FitnessBrowser__azobra:AZOBR_RS06795
          Length = 331

 Score =  220 bits (560), Expect = 4e-62
 Identities = 143/318 (44%), Positives = 184/318 (57%), Gaps = 13/318 (4%)

Query: 8   DISGAAARIAADIVRTPLLAADWGDPRCP--LWLKAETLQPIGAFKIRGAFNALGRLDTH 65
           DI  AAAR+    VRTPLL     + R    + LK E LQ  G+FK RGAFN L +L   
Sbjct: 13  DIVEAAARLDGFAVRTPLLENALLNERVGGRVLLKPEVLQRSGSFKFRGAFNRLSQLTPE 72

Query: 66  TRARGVVAYSSGNHAQAVAYAAAAYGVPAHIVMPEETPAVKVEATRRRGAHVVLCG--AG 123
            R  GVVA+SSGNHAQ VA AAA  G+PA IVMP + PA+K+  TR  GA VVL      
Sbjct: 73  ERRGGVVAWSSGNHAQGVAAAAALLGMPAVIVMPSDAPALKIANTRGYGAEVVLYDRWTE 132

Query: 124 ERERTAAELVEKTGAVLIPPFDHPDIIAGQGTIGIEIAEDLPELAT----VLIPVSGGGL 179
            RE  A  + E+ GA  +PP+DHP I+AGQGT+G+EIA     +      V+ P SGGGL
Sbjct: 133 SREAIATAIAEERGAATVPPYDHPQIMAGQGTVGLEIAAQAQAIGAVPDDVIAPCSGGGL 192

Query: 180 ASGIGTAIRALRPKAKIFAVEPELAADTAESLALGSIVEWPVAKRNRTIADGLRS-TPSE 238
            SG+ TA+R   P A+++A EP    D A SLA G  VE   A   R+I D L + TP  
Sbjct: 193 MSGVATAVRHSFPDARLWAAEPAGFDDVARSLAAGERVE--NAAGQRSICDALLTPTPGA 250

Query: 239 LTFAHLRQVIDDVITVSEDEIRSAVRELALRARLVAEPSGAVSLAGYRKAALP-DGSAVA 297
           LTF  ++ ++   + V++ E+++A+       +LV EP GAV LA      LP  G  VA
Sbjct: 251 LTFPVMKDLLSGSLAVTDAEVKAAMAYAFTVLKLVVEPGGAVGLAAVLTGKLPAAGRTVA 310

Query: 298 IV-SGGNIEPAQLAAILA 314
           +V SGGN++ A     LA
Sbjct: 311 VVLSGGNVDAATFTDALA 328


Lambda     K      H
   0.318    0.134    0.384 

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: 314
Number of extensions: 18
Number of successful extensions: 5
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: 316
Length of database: 331
Length adjustment: 28
Effective length of query: 288
Effective length of database: 303
Effective search space:    87264
Effective search space used:    87264
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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