Alignments for a candidate for ilvI in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Acidovorax sp. GW101-3H11

Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate Ac3H11_1086 Glyoxylate carboligase (EC 4.1.1.47)

Query= curated2:O08353
         (599 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1086
          Length = 596

 Score =  321 bits (822), Expect = 6e-92
 Identities = 188/592 (31%), Positives = 318/592 (53%), Gaps = 39/592 (6%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALH-HSDLIHLLTRHEQAAAHAADGYAR 59
           M   EA +K +E E V + FG PG A+ P Y AL  H  + H+L RH + A+H A+GY R
Sbjct: 4   MKAIEAAVKVMEKEGVSVAFGVPGAAINPLYAALKAHGGIGHILARHVEGASHMAEGYTR 63

Query: 60  A-SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118
           A +G +GVCIGTSGP  T+++TG+ +A +DS P++ +TGQ P   +  + FQ +D   + 
Sbjct: 64  AVAGNIGVCIGTSGPAGTDMITGLYSASADSIPILCITGQAPRARLHKEDFQAVDIASIA 123

Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178
             + K    + +  Q+P  F+ AF + ++GRPGPV IDLP DVQ  E++ D     +   
Sbjct: 124 KSVTKWATTVLEPAQVPGAFQQAFHLMRSGRPGPVLIDLPIDVQLAEIEFDP---DTYEP 180

Query: 179 LIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238
           L+ Y P       QI+KA+ ++ +A+RP+I+AGGG++ + A++ L++  E+L +PV  TL
Sbjct: 181 LVPYKPAAT--RAQIEKALSMLNAAERPLIVAGGGIINADASDLLVQFAEVLGVPVIPTL 238

Query: 239 MGKGCISENHPLALGMVGMH-GTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKI 297
           MG G I ++HPL +GM G+    +  N  L  SD ++ IG R+++R TG +  +    K 
Sbjct: 239 MGWGSIPDDHPLMVGMCGLQTSQRYGNATLLASDFVLGIGNRWANRHTGSVDVYTKGRKF 298

Query: 298 IHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVN 357
           +H+DI+P +IG+    D  IV DA   LK  ++     + ++ K      + S W     
Sbjct: 299 VHVDIEPTQIGRVFAPDFGIVSDAGAALKLFVE-----VAREWKAVGQLRDRSTWAAECQ 353

Query: 358 SLKKS--SIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKT 415
             K S   +    +D +P+KPQ++ + +     +  + K+    + +G +Q+  A +   
Sbjct: 354 GRKHSVDYLRKTHFDSVPMKPQRVYQCM-----NRALGKDVCYVSTIGLSQIAGAQFLHV 408

Query: 416 QTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPV 475
             PR +++ G  G +G+  P+A+G +VA P  K++ ++GD  F    +EL   A++ +P 
Sbjct: 409 YQPRHWINCGQAGPLGWTVPAALGVRVADPARKIVALSGDYDFQFMIEELAVGAQFKLPY 468

Query: 476 VICIFDNRTLGMVYQWQNLF------------YGKRQCSVNFGGAPDFIKLAESYGIKAR 523
           +  + +N  LG++ Q Q  F                +  V  G   D +K+ E  G KA 
Sbjct: 469 LHVLVNNSYLGLIRQAQRTFSIDYCVQLAFDNVNMAEGEVARGYGVDHVKVVEGLGCKAI 528

Query: 524 RIESPNEINEALKEA----INCDEPYLLDFAIDPSSALSMVPPGAKLTNIID 571
           R+  P E   AL +A         P +++  ++  + ++M   G ++ NI++
Sbjct: 529 RVHRPEEFAPALAQAEAWMAEHRTPVVIEVILERVTNIAM---GTEIDNIVE 577


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: 801
Number of extensions: 43
Number of successful extensions: 7
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: 596
Length adjustment: 37
Effective length of query: 562
Effective length of database: 559
Effective search space:   314158
Effective search space used:   314158
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis