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

GapMind for Amino acid biosynthesis

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

Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate AO356_28690 AO356_28690 acetolactate synthase

Query= BRENDA::O53554
         (515 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28690
          Length = 513

 Score =  394 bits (1011), Expect = e-114
 Identities = 241/518 (46%), Positives = 306/518 (59%), Gaps = 13/518 (2%)

Query: 1   MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60
           MNGAQ ++   V  G++ CFANPGT+E+  VAA+ + P ++ +L+LFEGV TGAADGY R
Sbjct: 1   MNGAQLIVKAAVASGIEYCFANPGTTEIPLVAAMASAPALKPVLSLFEGVCTGAADGYGR 60

Query: 61  IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120
           IAG+PA  L HLGPG  NG+ANLHNARRA  P+V V+GDHA++H  YD PL SDI A+AG
Sbjct: 61  IAGKPAMTLTHLGPGFANGIANLHNARRANTPIVNVIGDHASWHVNYDPPLASDIQALAG 120

Query: 121 TVSGWVRRTEAAADVGADAEAAI-AASRSGSQIATLILPADVCWSDGAHAAAGVPAQAAA 179
           +VS WVR +  A+ VG D + A+ AA ++  QIA+LILP D+  +   H  A    QA  
Sbjct: 121 SVSKWVRTSRTASGVGEDFQEAVRAAWQANGQIASLILPMDLQANTVQHEKAFTALQAPV 180

Query: 180 ---APVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLER 236
              A   V  VA  LR G   + ++G       GL AA R+ Q  G R   ETFP    R
Sbjct: 181 RRFAGDRVEAVAQALRDGRRLVFIVGDQGLSVAGLEAAGRLAQLPGVRLFAETFPRLSYR 240

Query: 237 GAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAE 296
           G G+P ++RL YF E A   LD    +V AG   P+S+F Y G+ S L      +  LAE
Sbjct: 241 GGGLPDLDRLPYFPEVAIEILDQYDAVVCAGVPEPISYFGYEGIASRLAERE-RLLCLAE 299

Query: 297 PG-GAADALAALADEV-APGTVAPVAGASRPQLPTGD--LTSVSAADVVGALLPERAIVV 352
            G   A AL ALAD + AP  V    G    +LP G+  LT  S   V+ A LP+  IV 
Sbjct: 300 VGDDVAGALTALADALEAPAYVPTPTGI---ELPPGEATLTPQSVGQVLAASLPDDCIVS 356

Query: 353 DESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMY 412
            E  TCG     A+A A  H  LT TGGAIG GIP   GAA+A     V CL+SDGSA Y
Sbjct: 357 VEGGTCGYPFFTASAHAARHRVLTNTGGAIGQGIPVGFGAAMAERGNKVFCLQSDGSAQY 416

Query: 413 TISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVK 472
           TI  LWS ARE L V  +I  N  Y IL+ EL+R G  ++ GP+AL L  + RP +D+  
Sbjct: 417 TIQTLWSIAREQLPVVILIAANHRYAILQNELRRFGM-TELGPEALSLTVLDRPRIDWKA 475

Query: 473 IAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510
           +A+G G+PA  V T  E   AL  A A+ GP LI++ +
Sbjct: 476 LAKGYGLPASTVHTNGELQRALANAKADGGPCLIEMAL 513


Lambda     K      H
   0.318    0.134    0.402 

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: 585
Number of extensions: 31
Number of successful extensions: 5
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: 515
Length of database: 513
Length adjustment: 35
Effective length of query: 480
Effective length of database: 478
Effective search space:   229440
Effective search space used:   229440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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