GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE in Dyella japonica UNC79MFTsu3.2

Align Aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate N515DRAFT_0006 N515DRAFT_0006 aspartate aminotransferase

Query= curated2:O86459
         (400 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0006 N515DRAFT_0006
           aspartate aminotransferase
          Length = 399

 Score =  276 bits (705), Expect = 1e-78
 Identities = 150/395 (37%), Positives = 211/395 (53%), Gaps = 1/395 (0%)

Query: 1   MAFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAINRG 60
           M  LA  + R KPSA + +++KAR+LKA GRD+I    G P+F   D++ +AA +A+   
Sbjct: 1   MPQLAQRVGRAKPSAIMVIAEKARQLKAAGRDIISFSIGVPNFLPGDHVYEAAREALKHD 60

Query: 61  ETKYTPVSGIPELRKAIAAKFKRENGLDYSWEQTIVGTGGKQILFNAFMATLNPGDEVSI 120
             +Y    G   L  A     +      Y      +G G KQ+L+N   A L+ GDE+  
Sbjct: 61  SGQYGSNRGAEPLLDAFLRHIEALGFSGYGRMNLSIGIGAKQVLYNLAEAMLDEGDEICF 120

Query: 121 PAPYWVSYPEMVALCGGTRFFVSATQEHNFKLQAADLEKAITPKTKWFIFNSPSNPTGAA 180
            APYW +Y ++  + G     +    E N+KL  A LE A+  K K F+FN+PSNPTG  
Sbjct: 121 AAPYWTTYHDIADIVGAKANVLHCGPEQNYKLVPAQLEAALQRKPKVFLFNNPSNPTGMV 180

Query: 181 YTHDELKALTDVLMKNPQVWVLTDDMYEHLTYGDFKFVTPVEVEPQLYDRTLTMNGVSKA 240
           YT +E+ AL DVL+K P  W++TDD+Y  + +    +   V  +P+L +R + ++ VSK 
Sbjct: 181 YTREEIAALADVLVKYPDTWIVTDDIYNSMVFDGIGYHNFVFAQPELRERLVFVDSVSKT 240

Query: 241 YAMTGWRIGYAAGPIQLIKAMDMIQGQQTSGATSIAQWAAVEALNGTQDFIPENKKIFEG 300
           Y M GWR+G  AGP  + KA+  +     +    +   AAV A  G QD      + F G
Sbjct: 241 YGMPGWRVGLIAGPESVAKAVTTLNSNHITSVPEVITAAAVAAFGGPQDVPRAKCEEFAG 300

Query: 301 RRDLVVSMLNQAKGIVCPVPEGAFYVYPSCKGLIGKTAPSGKVIETDEDFVSELLESEGV 360
           +RD+V   L    G+VCP P+GAFY +P      GK +  G  I  D +F + LLE+ GV
Sbjct: 301 KRDVVFEALTAIPGVVCPRPQGAFYAFPDISVAFGK-SHQGTKISNDVEFCAALLEATGV 359

Query: 361 AVVHGSAFGLGPNFRISYATSEEQLEEACRRIQRF 395
           A V GSAFG     RISY     QL+    RIQ F
Sbjct: 360 ACVPGSAFGEPRAMRISYTCPTAQLKPGLERIQAF 394


Lambda     K      H
   0.317    0.134    0.399 

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: 401
Number of extensions: 13
Number of successful extensions: 2
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: 400
Length of database: 399
Length adjustment: 31
Effective length of query: 369
Effective length of database: 368
Effective search space:   135792
Effective search space used:   135792
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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