GapMind for Amino acid biosynthesis

 

Alignments 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)



>MicrobesOnline__882:208820
          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.

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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