GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Pseudomonas putida KT2440

Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate PP_1588 PP_1588 N-succinyl-L,L-diaminopimelate aminotransferase alternative

Query= BRENDA::Q82IK5
         (364 letters)



>FitnessBrowser__Putida:PP_1588
          Length = 398

 Score =  149 bits (377), Expect = 1e-40
 Identities = 119/392 (30%), Positives = 181/392 (46%), Gaps = 30/392 (7%)

Query: 1   MSAVSDRLPTFPWDKLEPYKARAAAHPDG-IVDLSVGTPVDPVPELIQKALVAAADSPG- 58
           M+    +L  +P++KL           D   + LS+G P    P  + +A+    D    
Sbjct: 1   MNHALTQLQPYPFEKLRALLGSVKPAADKRAIALSIGEPKHESPAFVAQAMADNLDKLAV 60

Query: 59  YPTVWGTPELRDALTGWVERRLGARGV---THHHVLPIVGSKE-LVAWLPTQLGLGPGDK 114
           YP+  G P LR A+  W ERR G          H+LP+ G++E L A+    +       
Sbjct: 61  YPSTLGLPALRQAIGQWCERRFGVPAGWLDADRHILPVNGTREALFAFTQAVVNRADDGL 120

Query: 115 VAHPRLAYPTYEVGARLARA--------DHVVYDDPTELDPTGL----KLLWLNSPSNPT 162
           V  P   Y  YE  A LA A        ++  ++   +  P  +    ++L+L SP NPT
Sbjct: 121 VISPNPFYQIYEGAALLAGATPHYLPCLENNGFNPDFDAVPAEVWKRCQILFLCSPGNPT 180

Query: 163 GKVLSKAELTRIVAWAREHGILVFSDECYLELGWEAD--PVSVLHP--DVCGGSYEGIVS 218
           G ++    L +++A A EH  ++ +DECY EL ++ D  P  +L    ++    +   V 
Sbjct: 181 GALVPMNTLKKLIALADEHDFVIAADECYSELYFDEDAPPPGLLSACAELGRSDFARCVV 240

Query: 219 VHSLSKRSNLAGYRAAFLAGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQ 278
            HSLSKRSNL G R+ F+AGD  ++ P L  R + G      TQ A +AA  D+AHVRE 
Sbjct: 241 FHSLSKRSNLPGLRSGFVAGDAQIIKPFLLYRTYHGCAMPVQTQLASIAAWQDEAHVREN 300

Query: 279 RERYAARRTALRDALLSHGFRIEHSEASLYLWA-TRGESCWDTVAHLADLGILVAPGDFY 337
           R++Y A+  A+ D +L     ++  + S YLWA   G+    T        + V PG + 
Sbjct: 301 RDQYRAKYDAVLD-ILQPVLDVQRPDGSFYLWAKVPGDDAEFTRDLFEAQHVTVVPGSYL 359

Query: 338 G------SAGEQFVRVALTATDERVAAAVRRL 363
                  + G   VR+AL A       A  R+
Sbjct: 360 SREVDGVNPGAGRVRMALVAPLAECIEAAERI 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: 409
Number of extensions: 33
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: 364
Length of database: 398
Length adjustment: 30
Effective length of query: 334
Effective length of database: 368
Effective search space:   122912
Effective search space used:   122912
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