GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Azospirillum brasilense Sp245

Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase

Query= SwissProt::P18335
         (406 letters)



>FitnessBrowser__azobra:AZOBR_RS19630
          Length = 428

 Score =  238 bits (607), Expect = 3e-67
 Identities = 143/419 (34%), Positives = 220/419 (52%), Gaps = 42/419 (10%)

Query: 18  LPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHI 77
           +P+Y        + + + +WD +G  ++DFAGGIAV   GH HP ++ A+K Q +   H 
Sbjct: 22  MPVYVD------RAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRFTHT 75

Query: 78  SNVFTN-EPALRLGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTK 133
             + T  E  + L  +L   +  +  ++  F  +G EA E A K+AR +        +  
Sbjct: 76  CAMVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIARAHTG------RPG 129

Query: 134 IIAFHNAFHGRSLFTVSVGGQP-KYSDGFGPKPADIIHVPFNDLHAVKAVMDD------- 185
           +IAF  AFHGR+L  +++ G+   Y  GFGP PA++ H PF + +   +V D        
Sbjct: 130 VIAFSGAFHGRTLLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQDSLKALEQL 189

Query: 186 --------HTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGD 237
                      A++VEP+QGEGG   A PEFLQ LR++CD++  LL+ DE+Q G  RTG 
Sbjct: 190 FKSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTGK 249

Query: 238 LFAYMHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGA 297
           +FA  H GV PD++T AK+L GGFP+SA+   AEI  A  PG  G TY G+PLA   A A
Sbjct: 250 MFAIEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGSPLATTAALA 309

Query: 298 AFDIINTPEVLEGIQAKRQRFVDHLQKIDQQ--YDVFSDIRGMGLLIGAEL------KPQ 349
             D+I   ++++      +R     + + Q+    V  D+R +G +I  EL      K  
Sbjct: 310 VLDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMELVKDRGTKEP 369

Query: 350 YKGRARDFLYAGAEAGVMVLNAGP--DVMRFAPSLVVEDADIDEGMQRFAHAVAKVVGA 406
                +  +   AE G+++L+ G   +V+R    L   DA +DEG+     ++ ++V A
Sbjct: 370 AAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIERSLEELVSA 428


Lambda     K      H
   0.322    0.138    0.415 

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: 437
Number of extensions: 20
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: 406
Length of database: 428
Length adjustment: 31
Effective length of query: 375
Effective length of database: 397
Effective search space:   148875
Effective search space used:   148875
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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