Alignments for a candidate for ilvI in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudomonas fluorescens GW456-L13

Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate PfGW456L13_1794 Acetolactate synthase, large subunit (EC 2.2.1.6)

Query= SwissProt::P0DP90
         (548 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1794
          Length = 545

 Score =  197 bits (501), Expect = 9e-55
 Identities = 164/544 (30%), Positives = 248/544 (45%), Gaps = 45/544 (8%)

Query: 7   VVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATGKTGV 66
           +V  L   GV  VFG PG   + +Y  L    + H+  RHEQGA   A GYAR +GK GV
Sbjct: 8   LVKLLENYGVEQVFGIPGVHTVELYRGLARSSINHVTPRHEQGAGFMADGYARTSGKPGV 67

Query: 67  CIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFI--GTDAFQEVDVLG-LSLACTK 123
           C   +GPG TN+ T +  A  DSIP++ I+   S   +  G     E+   G L      
Sbjct: 68  CFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRSQLGGGRGKLHELPNQGALCAGVAA 127

Query: 124 HSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGD--LEPWFTTVENEVTF 181
            S  + S  ELP ++A AF +  +GRP PV ++IP D+ +   D  L      ++     
Sbjct: 128 FSHTLMSASELPGVLARAFALFQAGRPRPVHIEIPLDVLVEEADDLLASLPVNIDRAGAS 187

Query: 182 PHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEADY 241
           P A V +  ++LA A++P++  GGG     A   L E       P   T+   G + + +
Sbjct: 188 PSA-VSRMAELLAGAKRPLILAGGGA--IDAAVELTELAELLDAPVALTINAKGMLASGH 244

Query: 242 PYYLGMLGMHGTKAANFAVQECDLLIAVG---ARFDDRVTGKLNTFAPHASVIHMDIDPA 298
           P  +G        A    V E D+++A+G   A  D  VT     F     ++ +DIDP 
Sbjct: 245 PLLIG--STQSLVATRALVAEADVVLAIGTELAETDYDVT-FAGGFEIPGKLLRVDIDPD 301

Query: 299 EMNKLRQAHVALQGD----LNALLPALQQPL---NQYDW-QQHCAQLRDEHSWRYDHP-- 348
           +  +    HVAL  D      ALL AL        + DW Q   A+LR++ +  +D P  
Sbjct: 302 QTVRNYPPHVALVADSRNAAQALLSALSHKSLAERRNDWGQVRAARLREDLAATWDAPTL 361

Query: 349 GDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPEN-FITSSGLGTMGFGL 407
               +   +L++L      D V   D  Q            RP   F +S+G GT+G+ L
Sbjct: 362 AQTRFLETVLQEL-----PDAVFVGDSTQPVYTGNLTFNPERPRRWFNSSTGYGTLGYAL 416

Query: 408 PAAVGAQV-------ARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGM 460
           PAA+GA +       ARP   VVC+ GDG     + EL +    + P+ ++L +NQ    
Sbjct: 417 PAAIGAWLGGRIEGGARP--PVVCLIGDGGLQFTLPELASAVEARTPVIVLLWNNQGYEE 474

Query: 461 VRQWQQLFFQERYSETTLTD--NPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPY 518
           +++    +   R  E    D   PDF+ +A A G   + ++  +Q+  AL    +  GP 
Sbjct: 475 IKK----YMVNRAIEPVGVDIYTPDFIGVAKALGCAAEAVSSVEQLRGALRVATDRQGPT 530

Query: 519 LLHV 522
           L+ +
Sbjct: 531 LIEI 534


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: 662
Number of extensions: 38
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: 548
Length of database: 545
Length adjustment: 36
Effective length of query: 512
Effective length of database: 509
Effective search space:   260608
Effective search space used:   260608
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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