GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ptransferase in Pseudomonas fluorescens FW300-N2C3

Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AO356_06055 AO356_06055 succinyldiaminopimelate transaminase

Query= BRENDA::Q82IK5
         (364 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 AO356_06055
           succinyldiaminopimelate transaminase
          Length = 399

 Score =  153 bits (386), Expect = 9e-42
 Identities = 128/401 (31%), Positives = 187/401 (46%), Gaps = 43/401 (10%)

Query: 1   MSAVSDRLPTFPWDKLEPYKARAAAHPDGI-VDLSVGTPVDPVPELIQKALVAAADSPG- 58
           M+   ++L  +P++KL         +PD   + LS+G P    P  + +AL +  +    
Sbjct: 1   MNNALNQLQPYPFEKLRALLGSVTPNPDKRPIALSIGEPKHRSPSFVAEALASNLEKMAV 60

Query: 59  YPTVWGTPELRDALTGWVERRLGARGV---THHHVLPIVGSKE-LVAWLPTQLGLGPGDK 114
           YPT  G PELR+A+TGW ERR            HVLP+ G++E L A+  T +  G    
Sbjct: 61  YPTTLGIPELREAITGWCERRFNVPTGWLDPARHVLPVNGTREALFAFTQTVVNRGDDAL 120

Query: 115 VAHPRLAYPTYEVGARLARAD--HVVYDDPTELDPT----------GLKLLWLNSPSNPT 162
           V  P   Y  YE  A LA A   ++   D    +P             ++L+L SP NPT
Sbjct: 121 VVSPNPFYQIYEGAAFLAGAKPHYLPCLDANGFNPDFDAVSPDIWKRCQILFLCSPGNPT 180

Query: 163 GKVLSKAELTRIVAWAREHGILVFSDECYLELGWEAD--PVSVLHPDVCGG--SYEGIVS 218
           G ++    L +++A A EH  ++ +DECY EL ++    P  +L   V  G   ++  V 
Sbjct: 181 GALIPVDVLKKLIALADEHDFVIAADECYSELYFDEQTPPPGLLSACVELGRKDFKRCVV 240

Query: 219 VHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQ 278
            HSLSKRSNL G R+ F+AGD  +L   L  R + G      TQ A +AA  D+ HVR  
Sbjct: 241 FHSLSKRSNLPGLRSGFVAGDADILKGFLLYRTYHGCAMPVQTQLASIAAWNDEVHVRAN 300

Query: 279 RERYAARRTALRDALLSHGFRIEHSEASLYLWATRGESCWDTVAHLADL----GILVAPG 334
           R  Y  +  A+ + +LS    ++  + S YLW        D  A   DL     + V PG
Sbjct: 301 RALYREKFDAVLE-ILSPVLDVQRPDGSFYLWP---NVAGDDAAFCRDLFEQEHVTVVPG 356

Query: 335 DFYG------SAGEQFVRVALTA-------TDERVAAAVRR 362
            +        + G   VR+AL A         ER+ A ++R
Sbjct: 357 SYLSRDVDGVNPGAGRVRMALVAPLAECVEAAERIRAFIQR 397


Lambda     K      H
   0.319    0.135    0.420 

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: 446
Number of extensions: 33
Number of successful extensions: 3
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: 364
Length of database: 399
Length adjustment: 30
Effective length of query: 334
Effective length of database: 369
Effective search space:   123246
Effective search space used:   123246
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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