GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvH in Acidovorax sp. GW101-3H11

Align acetolactate synthase isozyme 2 large subunit; EC 2.2.1.6 (characterized)
to candidate Ac3H11_1601 Acetolactate synthase large subunit (EC 2.2.1.6)

Query= CharProtDB::CH_003896
         (548 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1601 Acetolactate
           synthase large subunit (EC 2.2.1.6)
          Length = 561

 Score =  242 bits (618), Expect = 2e-68
 Identities = 165/532 (31%), Positives = 246/532 (46%), Gaps = 11/532 (2%)

Query: 3   GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATG 62
           G Q +V  L   GV  +F  PG + + V DAL+D  +   +CR E GAAM A    + TG
Sbjct: 11  GGQILVQQLITHGVKQLFCVPGESYLAVLDALHDADIGVTVCRQEGGAAMMAEAQGKLTG 70

Query: 63  KTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLACT 122
           + G+C  T GPGATN   G+  A  DS P++   GQV+   +G +AFQE+D   +     
Sbjct: 71  QPGICFVTRGPGATNASAGVHIAHQDSTPMILFVGQVARGAMGREAFQELDYSAVFGTMA 130

Query: 123 KHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVTFP 182
           K    +     +P +++ AF VA SGRPGPV+V +P+D+   +  +         E    
Sbjct: 131 KWVVQIDDPARVPELISRAFHVATSGRPGPVVVALPEDMLTEAATVADALPYQVTETHPG 190

Query: 183 HAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEADYP 242
            A++ +  Q L  A+ P+  +GG     +AV     F  A  +P  C+ +      A + 
Sbjct: 191 AAQLAELAQRLQAAKNPVAILGGSRWSEEAVREFTAFAEAWSIPVYCSFRRQMLFPATHA 250

Query: 243 YYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTF---APHASVIHMDIDPAE 299
            Y G LG+         ++  DL++ VG R  +  +     F    P  S +H+  D  E
Sbjct: 251 CYGGDLGLGVNPKLLARIKASDLVLVVGGRLSEVPSQGYELFDIPTPAQSFVHVHADADE 310

Query: 300 MNKLRQAHVALQGDLNALLPALQ--QPLNQYDWQQHCAQLRDEH-SWRYDHP---GDAIY 353
           + KL +   A+     A   AL   +P     W+ H      E+ +W    P      + 
Sbjct: 311 LGKLYRPTQAIHATPQAFTAALNAVRPTASVAWKAHTEAAHAEYLAWSDPAPIRIPGNLQ 370

Query: 354 APLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAAVGA 413
              +++ L    PAD +     G    W  +    T   + +  +  G+MG+GLPA VG 
Sbjct: 371 MGEVMQHLKSVLPADTIFCNGAGNFATWVHRFWPFTTYASQLAPTS-GSMGYGLPAGVGG 429

Query: 414 QVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERY 473
           +   P   VV  +GDG F+M+ QE  T  +  LP+ +VLLDN   G +R  Q+  +  R 
Sbjct: 430 KRLWPQREVVVFAGDGDFLMHGQEFATAVQYGLPILVVLLDNAMYGTIRMHQEREYPGRI 489

Query: 474 SETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525
           S T L  NPDF   A AFG HG+ + R +    AL     S  P +LH  ID
Sbjct: 490 SATQL-KNPDFKAYAQAFGGHGERVERTEDFAPALARARASGLPSVLHCLID 540


Lambda     K      H
   0.320    0.135    0.410 

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: 767
Number of extensions: 51
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: 548
Length of database: 561
Length adjustment: 36
Effective length of query: 512
Effective length of database: 525
Effective search space:   268800
Effective search space used:   268800
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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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