Alignments for a candidate for ilvI in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudomonas fluorescens FW300-N2C3

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate AO356_17755 AO356_17755 hypothetical protein

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17755
          Length = 543

 Score =  214 bits (544), Expect = 9e-60
 Identities = 168/551 (30%), Positives = 258/551 (46%), Gaps = 44/551 (7%)

Query: 3   MLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLA 62
           M +  E++V+ L   GV+QVFG PG   +++Y  L     I HV  RHEQ A  MADG A
Sbjct: 1   MATCGEVLVKLLEGYGVEQVFGIPGVHTVELYRGLAR-SSIRHVTPRHEQGAGFMADGYA 59

Query: 63  RATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIG------YDAFQEC 116
           R +G+ GV  + +GPG TN  T +  AY DSIP++V+S   + S +G      ++   + 
Sbjct: 60  RVSGKPGVCFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRSQLGGGRGKLHELLNQS 119

Query: 117 DMVGISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDIL-NPANKLPYV 175
            +VG    V   S  +    ++P VL +AF +  +GRP PV +++P D+L   A+ L   
Sbjct: 120 ALVG---GVAAFSHTLMSAAELPGVLARAFAVFQAGRPRPVHIEIPLDVLVEDADALLAS 176

Query: 176 WPESVSMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNL 235
            P ++S     P      G +K+    L  A++P++ VGGGAI A    +L E  E L  
Sbjct: 177 VPVNISRAGAAP------GAVKQMADLLATARRPLILVGGGAIDA--RAELTELAERLGA 228

Query: 236 PVVCSLMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRF--DDRTTNNLAK 293
           PV  ++   G  PA H   +G             +  ADV+ A+G      D        
Sbjct: 229 PVALTINAKGLLPARHPLLIG--STQSLVVTRALVAEADVVLAIGTELAETDYDITFAGG 286

Query: 294 YCPNATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQ 353
           +     +L IDIDP    +     + +V DA      +L+ L Q    +PL E +  W  
Sbjct: 287 FEIPGALLRIDIDPDQTVRNYPPHLALVADAGVAARALLDELDQ----RPLAERQADWGP 342

Query: 354 IEQWRARQCLKYD----THSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFD 409
               R R  L+      T ++ +    V++TL      +A    D  Q      L +  +
Sbjct: 343 ARAARLRAELQGSWDAATRAQTVFLDTVLQTL-----PEAVFVGDSTQPVYTGNLTFNPE 397

Query: 410 KPRRWINSG-GLGTMGFGLPAALGV-----KMALPEETVVCVTGDGSIQMNIQELSTALQ 463
           +PRRW NS  G GT+G+ LPAA+G       +      VVC+ GDG +Q  + EL++A++
Sbjct: 398 QPRRWFNSSTGYGTLGYALPAAIGAWLGGKDLGHGRPAVVCLIGDGGLQFTLPELASAVE 457

Query: 464 YELPVLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHE 523
              PV+V+  NN+    +K++  M+             PDF+ +A+A G     I     
Sbjct: 458 ASTPVIVLLWNNQGYEEIKKY--MLNRAIEPVGVDIYTPDFIGVAKALGCFAQAIDDVPS 515

Query: 524 LESKLSEALEQ 534
           L + L  A E+
Sbjct: 516 LRAALLAARER 526


Lambda     K      H
   0.319    0.135    0.403 

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: 751
Number of extensions: 42
Number of successful extensions: 9
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: 574
Length of database: 543
Length adjustment: 36
Effective length of query: 538
Effective length of database: 507
Effective search space:   272766
Effective search space used:   272766
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 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)
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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