GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_0006
          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.

Links

Downloads

Related tools

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