GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisA in Pseudomonas fluorescens FW300-N1B4

Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate Pf1N1B4_1623 Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.3.-)

Query= curated2:Q8TU55
         (245 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1623 Imidazole glycerol
           phosphate synthase cyclase subunit (EC 4.1.3.-)
          Length = 256

 Score =  130 bits (326), Expect = 3e-35
 Identities = 77/248 (31%), Positives = 135/248 (54%), Gaps = 16/248 (6%)

Query: 1   MAFEVIPAVDMRGGKCVQLVQGVPGSEIVSLNDPLAVALDWIGKGAKTLHLVDLDGAIEG 60
           +A  +IP +D+  G+   +V+GV    I    DP+ +A  +  +GA  +  +D+  +++G
Sbjct: 3   LAKRIIPCLDVDNGR---VVKGVKFENIRDAGDPVEIARRYDEQGADEITFLDITASVDG 59

Query: 61  ERKNAPIIEKIVQACREKGVSIQVGGGIRSFEDAASLLELGVSRIILGTAALQNPELVKQ 120
                  +E++     +  + + VGGG+R+ +D  +LL  G  ++ + TAA+ NPE V +
Sbjct: 60  RDTTLHTVERMAS---QVFIPLTVGGGVRTVQDIRNLLNAGADKVSINTAAVFNPEFVGE 116

Query: 121 LSDAFGSSCVNVALDAK---------NGKISIKGWTEECAQTPVEMGREFEELGAGSLLF 171
            +  FGS C+ VA+DAK           +I   G  +      VE  ++ E LGAG +L 
Sbjct: 117 AAQHFGSQCIVVAIDAKKVSGPGETPRWEIFTHGGRKPTGLDAVEWAKKMEGLGAGEILL 176

Query: 172 TNIDTEGLMQGVNPGPTRELVESVSIPVIASGGVSSLEDL-KVLKQTGASGVVVGSALYT 230
           T++D +G+  G + G TR + +++ IPVIASGGV +L+ L   + +  AS V+  S  + 
Sbjct: 177 TSMDQDGMKNGFDLGVTRAISDALGIPVIASGGVGNLQHLADGILEGHASAVLAASIFHF 236

Query: 231 GRFTLEAA 238
           G +T++ A
Sbjct: 237 GEYTVQEA 244


Lambda     K      H
   0.315    0.135    0.378 

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: 155
Number of extensions: 10
Number of successful extensions: 4
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: 245
Length of database: 256
Length adjustment: 24
Effective length of query: 221
Effective length of database: 232
Effective search space:    51272
Effective search space used:    51272
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: 42 (22.0 bits)
S2: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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, 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