GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1601
          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:

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