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 Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate Pf1N1B4_3661 Glyoxylate carboligase (EC 4.1.1.47)

Query= curated2:O08353
         (599 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3661
          Length = 591

 Score =  330 bits (847), Expect = 8e-95
 Identities = 193/581 (33%), Positives = 318/581 (54%), Gaps = 43/581 (7%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHH-SDLIHLLTRHEQAAAHAADGYAR 59
           M   EA +  +  E V+  FG PG A+ P Y AL     + H+L RH + A+H A+GY R
Sbjct: 4   MRAIEAAVLVMRREGVDTAFGIPGAAINPLYSALQKVGGIDHVLARHVEGASHMAEGYTR 63

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

Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQ--ELELDIDKHPIPSK 176
            P+ K +  + +  Q+P  F+ AF   ++GRPGPV IDLP DVQ  E+E DID       
Sbjct: 124 KPVTKWSTTVMEPGQVPYAFQKAFYEMRSGRPGPVLIDLPFDVQMAEIEFDID------- 176

Query: 177 VKLIGYNPTTIGHPR----QIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNI 232
                Y P  +  P     QI+KA+ ++  A+RP+++AGGG++ + A+E L++  EL  I
Sbjct: 177 ----AYEPLPLAKPTANRVQIEKALAMLDQAERPLLVAGGGIINADASELLVEFAELTGI 232

Query: 233 PVCTTLMGKGCISENHPLALGMVGMHGT-KPANYCLSESDVLISIGCRFSDRITGDIKSF 291
           PV  TLMG G I ++HPL +GMVG+  + +  N  + +SDV++ +G R+++R TG +  +
Sbjct: 233 PVIPTLMGWGTIPDDHPLMVGMVGLQTSHRYGNATMLKSDVVLGVGNRWANRHTGSVDVY 292

Query: 292 ATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQ 351
               K IH+DI+P +IG+    D+ IV DA   L   I+     + ++ +     +N S 
Sbjct: 293 TEGRKFIHVDIEPTQIGRVFTPDLGIVSDAAAALTVFIE-----VAREWQAAGKLKNRSA 347

Query: 352 WIENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAH 411
           W+++    K S      +D++P+KPQ++ +E+  V       K+T   + +G +Q+  A 
Sbjct: 348 WLQDCQQRKASLQRKTHFDNVPVKPQRVYEEMNQV-----FGKDTCYVSTIGLSQIAGAQ 402

Query: 412 YFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEY 471
           +     PR +++ G  G +G+  P+A+G   A P  KV+ ++GD  F    +EL   A++
Sbjct: 403 FLHVYKPRHWINCGQAGPLGWTIPAALGVVKADPTRKVVALSGDYDFQFMIEELAVGAQF 462

Query: 472 NIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNF---------GGAPDFIKLAESYGIKA 522
            +P +  + +N  LG++ Q Q  F       ++F         G   D + +AE  G KA
Sbjct: 463 KLPYIHVVVNNSYLGLIRQAQRGFDMDYCVQLSFDNLNAPELNGYGVDHVAVAEGLGCKA 522

Query: 523 RRIESPNEINEALKEAINCDE----PYLLDFAIDPSSALSM 559
            R+  P +I  AL++A    E    P +++  ++  + +SM
Sbjct: 523 LRVFEPAQIQPALRKAQELIEEFKVPVIVEIILERVTNISM 563


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: 804
Number of extensions: 39
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: 591
Length adjustment: 37
Effective length of query: 562
Effective length of database: 554
Effective search space:   311348
Effective search space used:   311348
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Candidates (tab-delimited)
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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