GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Pseudomonas simiae WCS417

Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate GFF1219 PS417_06195 succinyldiaminopimelate aminotransferase

Query= BRENDA::Q82IK5
         (364 letters)



>FitnessBrowser__WCS417:GFF1219
          Length = 399

 Score =  139 bits (350), Expect = 1e-37
 Identities = 119/392 (30%), Positives = 180/392 (45%), Gaps = 30/392 (7%)

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

Query: 59  YPTVWGTPELRDALTGWVERRLGA-RGVTH--HHVLPIVGSKE-LVAWLPTQLGLGPGDK 114
           YPT  G P LR+A+  W ERR    +G      ++LP+ G++E L A+  T +  G    
Sbjct: 61  YPTTLGIPALREAIGAWCERRFNVPKGWLDPARNILPVNGTREALFAFTQTVVNRGDDAL 120

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

Query: 163 GKVLSKAELTRIVAWAREHGILVFSDECYLELGWE--ADPVSVLHPDVCGG--SYEGIVS 218
           G ++    L +++A A E+  ++ +DECY EL ++  + P  +L   V  G   ++  V 
Sbjct: 181 GALIPVDTLKKLIALADEYDFVIAADECYSELYFDEQSPPPGLLSACVELGRQDFKRCVV 240

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

Query: 279 RERYAARRTALRDALLSHGFRIEHSEASLYLWA-TRGESCWDTVAHLADLGILVAPGDFY 337
           R+ Y  +  A+  A+L     +E  +   YLW    G+          +  + V PG + 
Sbjct: 301 RDLYREKFDAVL-AILKPVLDVESPDGGFYLWPNVNGDDAGFCRDLFVEEHVTVVPGSYL 359

Query: 338 GSAGEQF------VRVALTATDERVAAAVRRL 363
               + F      VR+AL A       A  R+
Sbjct: 360 SREVDGFNPGAGRVRLALVAPLAECVEAAERI 391


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: 417
Number of extensions: 31
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:

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