GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvH in Desulfovibrio vulgaris Hildenborough

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate 208820 DVU3293 thiamine pyrophosphate-requiring enzyme

Query= curated2:O08353
         (599 letters)



>lcl|MicrobesOnline__882:208820 DVU3293 thiamine
           pyrophosphate-requiring enzyme
          Length = 547

 Score =  269 bits (688), Expect = 2e-76
 Identities = 167/559 (29%), Positives = 273/559 (48%), Gaps = 34/559 (6%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           MN A   ++ LEAE V+ +FG PG   L F +AL  S +  +LTRHEQAA   A  Y R 
Sbjct: 1   MNAATLFVRCLEAEGVDHIFGIPGEENLAFLEALRTSSIRLVLTRHEQAAGFMAATYGRL 60

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           +G+ GVC+ T GPGATNLVT VA A     P++ +TGQ P K      FQ +D + +  P
Sbjct: 61  TGRPGVCLSTLGPGATNLVTAVAYARLGGMPLIVITGQKPIKHSKQGRFQILDVVRMMEP 120

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
           I K   Q+     IP + R AF +A   +PGPVHI+LP+D+   E+    H  PS V+  
Sbjct: 121 ITKSTRQVASGSAIPSLVREAFRLAAKEKPGPVHIELPEDIAAEEVATTPH-TPSLVRPA 179

Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240
             +P  +G      +A + I  AKRP++L   G         L + ++   +   +T MG
Sbjct: 180 QADPELVG------EAARRIRKAKRPLLLMAAGANRHDVCGHLRRFIDTTGMFFFSTQMG 233

Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300
           KG + + HP +LG   +      +  +  +D ++++G    ++             +IH+
Sbjct: 234 KGAVDQRHPRSLGTAALSDHDYLHCAIERADCIVNVGHDVVEK-PPFFMHRDDGRTVIHV 292

Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENND-----KENISQWIEN 355
           ++ PA++       + +VGD    + E ++ +  I+ +    ++D     KE+I   +  
Sbjct: 293 NVFPAQVDDVYFPQLEVVGD----IGESLQLMADIVGRCPGADDDYLRRIKEHIDAHVYA 348

Query: 356 VNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKT 415
                         +  P  PQ IV E+   + +     N ++  D G  ++W A  ++ 
Sbjct: 349 TGLT----------NSFPPTPQSIVSEVREAMPE-----NGVLALDNGMYKLWFARNYRA 393

Query: 416 QTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPV 475
             P + L    L TMG G PSA+   + +P + V  + GDGGFMMN QEL T     + +
Sbjct: 394 YAPNTLLLDNALATMGAGLPSALAVALLRPGTPVAALCGDGGFMMNSQELETAVRLGVDL 453

Query: 476 VICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEAL 535
            + +  +   GM+ +W+          ++FG  PDF++ AESYG    R+ +P+ + + L
Sbjct: 454 TVMVLRDDGYGMI-KWKQAGMELPVHGLDFGN-PDFVRYAESYGATGHRVSAPDGLRQTL 511

Query: 536 KEAINCDEPYLLDFAIDPS 554
           +  +     +L++  +D S
Sbjct: 512 RRCLATPGVHLIEVPVDYS 530


Lambda     K      H
   0.319    0.137    0.405 

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: 704
Number of extensions: 28
Number of successful extensions: 5
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: 599
Length of database: 547
Length adjustment: 36
Effective length of query: 563
Effective length of database: 511
Effective search space:   287693
Effective search space used:   287693
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: 53 (25.0 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 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