GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Azospirillum brasilense Sp245

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__azobra:AZOBR_RS24065
          Length = 392

 Score =  222 bits (566), Expect = 1e-62
 Identities = 127/355 (35%), Positives = 199/355 (56%), Gaps = 4/355 (1%)

Query: 28  EDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYD 87
           EDVI L++G PDF TP  V+ AA  A+    T YTP  G  ELR A+   + ++     +
Sbjct: 32  EDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTHYTPIPGRPELRAALARDVARRTGLPVE 91

Query: 88  AESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTSHGF 147
            E+ +I+  GA   +  A   ++  GDEV++P P+Y  YE  +   GA  V V   +   
Sbjct: 92  PEN-VIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGATLVPVAPDAATL 150

Query: 148 KLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSELT 207
           +L    +  A+TP T+ + L  P+NPTG+ +S EEL+++A L +  +++V++DE+Y+ LT
Sbjct: 151 RLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRHDLWVVADEVYASLT 210

Query: 208 YDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCAS 265
           +DRPH  IAT   + ++T+ IN LSKSH+MTGWR G++ AP  +  H+  +    +    
Sbjct: 211 FDRPHIGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLALCMLYGLP 270

Query: 266 SISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIFPSIKSF 324
              Q+AAL AV  G +    MRE Y++R D   + L S+ GL  +KP    ++   ++  
Sbjct: 271 GFVQQAALVAVEQGDEAVAAMREGYRRRRDIALEALGSVPGLRCLKPEAGMFMLVDVRGT 330

Query: 325 GMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRLELFV 379
           G+ + +F+  L  + GV+++   +F     G VRLSFA S   L E   R+  FV
Sbjct: 331 GLPTMEFAWRLFRETGVSVLDAGAFGPAAAGCVRLSFAVSEAELAEACRRIAAFV 385


Lambda     K      H
   0.319    0.135    0.388 

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: 311
Number of extensions: 17
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: 393
Length of database: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
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 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