GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Azospirillum brasilense Sp245

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate AZOBR_RS20195 AZOBR_RS20195 aminotransferase

Query= BRENDA::Q8TQ40
         (389 letters)



>FitnessBrowser__azobra:AZOBR_RS20195
          Length = 369

 Score =  156 bits (395), Expect = 8e-43
 Identities = 108/355 (30%), Positives = 171/355 (48%), Gaps = 7/355 (1%)

Query: 36  IDLGVGDPDLPTHPHIVEAMREAVCDPKTHQYPSYAGMPEFREAAAEWCKKYKGIELDPA 95
           I+LG G PD      +++   +A+ +   +QYP   G P+ R+A A   +++ G+++D  
Sbjct: 11  INLGQGFPDERGPADVLDVAAKAILEG-WNQYPPMMGTPDLRQALAAHGRRFYGLDIDWK 69

Query: 96  TEVLSLIGSKEAVAHIPLAFVNPGDVVLYTDPGYPVYKIGTLFAGGEPYSLPLKAENSFL 155
           TEVL   G+ EA+    L  + PGD V+   P Y  Y      AGG P  + LKA +   
Sbjct: 70  TEVLVTSGATEALTASLLGLIEPGDEVVLFQPMYDSYLPIVRLAGGVPRFVSLKAPDWSF 129

Query: 156 PDLDSIPADILKRAKLFFFNYPNNPTSATADMKFFEKVVEFCKKNDIIAVHDNAYSQMVY 215
              D + A    + KL   N P NP +        E + EF ++ D  AV D  Y  +V+
Sbjct: 130 TRAD-LEAAFSPKTKLVLINDPLNPAAKVFSRAELELLAEFVQRFDAFAVCDEVYEHIVF 188

Query: 216 DGYDAPSFLAAEGAMDIGIELYSHSKTYNMTGWRLGFAVGSKALIKGLGKVKSNVDSGVF 275
           DG      +   G  D  +++ S  KT+++TGW++G+  G+  L++ + K    +     
Sbjct: 189 DGRQHIPLMTLPGMRDRCLKIGSAGKTFSLTGWKVGYVTGAPHLLQPVAKAHQYITFTTP 248

Query: 276 DAIQIAGIAALSSSQACVDDTNKIYEERRNVLIEGLTAMGLEVKPPKATFYVWAPV-PTG 334
             +Q A    L    A     +   + +R+ L +GL A+G EV P   T++V A V P G
Sbjct: 249 PNLQTAVAYGLGKDDAYFAGLSSGLQAKRDRLADGLRAVGFEVLPSAGTYFVVADVSPFG 308

Query: 335 FTSIE--FAKLLLEEAGIVATPGVGF--GDAGEGYVRFALTKPVERIKEAVERMK 385
           F   +  F + L  EAG+ A P   F   DA   ++RF  +K  E +  AVER++
Sbjct: 309 FDGNDEAFCRRLTAEAGVTAIPVGAFFVQDAPRSFIRFCFSKRDEILDGAVERLR 363


Lambda     K      H
   0.319    0.137    0.409 

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: 359
Number of extensions: 15
Number of successful extensions: 4
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: 389
Length of database: 369
Length adjustment: 30
Effective length of query: 359
Effective length of database: 339
Effective search space:   121701
Effective search space used:   121701
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 (21.7 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