Alignments for a candidate for ilvI in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudomonas fluorescens FW300-N1B4

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Pf1N1B4_696 Acetolactate synthase, large subunit (EC 2.2.1.6)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_696
          Length = 545

 Score =  220 bits (560), Expect = 1e-61
 Identities = 168/559 (30%), Positives = 264/559 (47%), Gaps = 37/559 (6%)

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

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

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

Query: 176 WPESVSMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNL 235
            P ++     +P+       I R    L  AK+P++  GGGAI A    +L E  E L+ 
Sbjct: 177 VPVNIDRAGASPSA------ISRMTDWLAGAKRPLILAGGGAIDAAA--ELTELAELLDA 228

Query: 236 PVVCSLMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRF--DDRTTNNLAK 293
           PV  ++   G   + H   +G             +  ADV+ A+G      D        
Sbjct: 229 PVALTINAKGMLESRHPLLIG--STQSLVATRALVAEADVVLAIGTELAETDYDITFAGG 286

Query: 294 YCPNATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQ 353
           +     +L +DIDP    +     + +V D+R   + +L  LS    H+ L E R+ W Q
Sbjct: 287 FEIPGVLLRVDIDPDQTVRNYPPKVALVADSRNAAQALLSALS----HKSLAERRNDWGQ 342

Query: 354 IEQWRARQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRR 413
           +     R  L     +  +     +ET+        +V  D  Q      L +  ++PRR
Sbjct: 343 VRAAHLRDELAASWDAPTLAQTRFLETVLHELPNAVFV-GDSTQPVYTGNLTFNPERPRR 401

Query: 414 WINSG-GLGTMGFGLPAALGVKMALPEE-----TVVCVTGDGSIQMNIQELSTALQYELP 467
           W NS  G GT+G+ LPAA+G  +    E      VVC+ GDG +Q  + EL++A++   P
Sbjct: 402 WFNSSTGYGTLGYALPAAIGAWLGGRVEGGARPPVVCLIGDGGLQFTLPELASAVEARTP 461

Query: 468 VLVVNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESK 527
           V+V+  NN+    +K++  M+             PDF+ +A+A G     +S    L   
Sbjct: 462 VIVLLWNNQGYEEIKKY--MVNRAIEPVGVDIYTPDFIGVAKALGCAAEAVSSVDGLRDA 519

Query: 528 LSEALEQVRNNRLVFVDVT 546
           L  A ++ +   L+ +D T
Sbjct: 520 LRLATDR-QGPTLIEIDQT 537


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: 776
Number of extensions: 44
Number of successful extensions: 8
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: 545
Length adjustment: 36
Effective length of query: 538
Effective length of database: 509
Effective search space:   273842
Effective search space used:   273842
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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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