GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Azospirillum brasilense Sp245

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate AZOBR_RS19590 AZOBR_RS19590 ornithine-oxoacid aminotransferase

Query= uniprot:A1S8Y2
         (425 letters)



>FitnessBrowser__azobra:AZOBR_RS19590
          Length = 405

 Score =  197 bits (501), Expect = 5e-55
 Identities = 137/419 (32%), Positives = 206/419 (49%), Gaps = 65/419 (15%)

Query: 26  VFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCF------ 79
           V   R E   VWD EG  Y+D     + +N GH HPK+  A+ +Q  K + T        
Sbjct: 25  VVLARGEGVYVWDTEGNRYLDCLSAYSAVNQGHCHPKILEAMVQQASKLTLTSRAFRNDQ 84

Query: 80  MVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVARAY--------TKRAG 131
           + L YE   A+    ++++P           SG+EAVE+AIK  R +          +A 
Sbjct: 85  LALFYEELAALTGS-HKILP---------MNSGAEAVESAIKTVRKWGYEVRGVPENQAE 134

Query: 132 VIAFTSGYHGRTMAALALT------GKVAPYSKGMGLMQANVFRAEFPCALHGVSEDDAM 185
           +I  +  +HGRT++ ++ +      G   P++ G        FR         V   DA 
Sbjct: 135 IIVCSDNFHGRTISIVSFSTDPDARGGFGPFTPG--------FRT--------VPFGDAA 178

Query: 186 ASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTG 245
           A    +  N        A++LEP+QGE G      G+++R+R+LC    +++I DE+QTG
Sbjct: 179 ALEAALTPNTV------AVLLEPIQGEAGVVIPPAGYLRRVRDLCTERNVVMILDEIQTG 232

Query: 246 AGRTGTFFAMEQMGVAADITTFAKSIAGGF-PLSGITGRAEVMDAIGPGGLGGTYGGSPL 304
            GRTG   A E  GV AD+T   K+++GGF P+S +   +EV+  + PG  G T+GG+PL
Sbjct: 233 LGRTGKLLAEEHEGVEADVTLIGKALSGGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPL 292

Query: 305 ACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELMENG 364
           ACA A A + V  EE +++ + A G      +G + S    I E RG G M+A+EL    
Sbjct: 293 ACAVARAAMRVLVEEGMIDNAAAQGAYFLEQLGAIRSNV--IREARGRGLMLAVELHPEA 350

Query: 365 KPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFEAVL 423
             A  YC  +    R RG  +L+  T+ + +RI  P+    EQ+   L    E F+AVL
Sbjct: 351 GGARRYCEAL----RARG--VLAKDTHDHTIRIAPPLVITREQVDWAL----EQFDAVL 399


Lambda     K      H
   0.319    0.136    0.391 

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: 405
Number of extensions: 23
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: 425
Length of database: 405
Length adjustment: 31
Effective length of query: 394
Effective length of database: 374
Effective search space:   147356
Effective search space used:   147356
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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