GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Azospirillum brasilense Sp245

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase

Query= curated2:Q30ZX9
         (388 letters)



>FitnessBrowser__azobra:AZOBR_RS24065
          Length = 392

 Score =  173 bits (438), Expect = 9e-48
 Identities = 120/360 (33%), Positives = 179/360 (49%), Gaps = 9/360 (2%)

Query: 31  RGVDIISLGIGDPDMPTPDFVIEALKKAAEKPANHQYPSYTGMLAFRQEVANWYKRRYAV 90
           RG D+I L +GDPD  TP  V +A   A      H Y    G    R  +A    RR  +
Sbjct: 30  RGEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTH-YTPIPGRPELRAALARDVARRTGL 88

Query: 91  ELDPKTEVLTLIGSKEGIAHFPTAFVNPGDLVLVCPPCYPVYAIASRFMGGVVQELPLLE 150
            ++P+  V+   G++ G+ +     V  GD VLV  P Y  Y    R  G  +  +P+  
Sbjct: 89  PVEPEN-VIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGATL--VPVAP 145

Query: 151 ENDFLP-DLDAVDEATWEKARCIFVNYPNNPTAAMAPRSFFEKLIGIARKHNVIVVHDAA 209
           +   L  D  A+  A   + R IF+  P NPT  +      E +  +AR+H++ VV D  
Sbjct: 146 DAATLRLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRHDLWVVADEV 205

Query: 210 YTEMYYNENNRPLSIMEIPGAMDVAIEFNSLSKPYNMTGWRIAMAVGNASLVAGLGKVKE 269
           Y  + ++  +  + I  +PG  +  +  NSLSK + MTGWR    V  A LVA +G +  
Sbjct: 206 YASLTFDRPH--IGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLAL 263

Query: 270 NMDSGAFQAVQEAAIVALRDGDAFLAEIRDIYRKRRDTVIAALNKI-GITCRVPEASLYV 328
            M  G    VQ+AA+VA+  GD  +A +R+ YR+RRD  + AL  + G+ C  PEA +++
Sbjct: 264 CMLYGLPGFVQQAALVAVEQGDEAVAAMREGYRRRRDIALEALGSVPGLRCLKPEAGMFM 323

Query: 329 WARV-PEGYTSSDFVTRVLQETGVVMTPGNGFGAAGEGYFRISLTVNDERLEEAVSRIAS 387
              V   G  + +F  R+ +ETGV +     FG A  G  R+S  V++  L EA  RIA+
Sbjct: 324 LVDVRGTGLPTMEFAWRLFRETGVSVLDAGAFGPAAAGCVRLSFAVSEAELAEACRRIAA 383


Lambda     K      H
   0.320    0.136    0.403 

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: 400
Number of extensions: 25
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: 388
Length of database: 392
Length adjustment: 31
Effective length of query: 357
Effective length of database: 361
Effective search space:   128877
Effective search space used:   128877
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