Alignments for a candidate for hisF in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisF in Kyrpidia tusciae DSM 2912

Align Imidazole glycerol phosphate synthase subunit HisF; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF; EC 4.3.2.10 (characterized)
to candidate WP_013076129.1 BTUS_RS10910 imidazole glycerol phosphate synthase subunit HisF

Query= SwissProt::Q7SIB9
         (252 letters)



>NCBI__GCF_000092905.1:WP_013076129.1
          Length = 253

 Score =  294 bits (753), Expect = 1e-84
 Identities = 157/253 (62%), Positives = 194/253 (76%), Gaps = 6/253 (2%)

Query: 3   LAKRIVPCLDVHAGRVVKGVNFV-NLRDAGDPVEAARAYDEAGADELVFLDISATHEERA 61
           L +RIVPC DV  GRVVK V+F+ N RDAGDPVE AR YDE+GADELV LDISA+ E RA
Sbjct: 2   LTRRIVPCFDVKNGRVVKNVSFLTNERDAGDPVELARYYDESGADELVLLDISASVEGRA 61

Query: 62  ILLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHF 121
            ++DVVAR A  VFIPLTVGGG+ S++D R LL +GADKVS+N+ AV+ P+L+ E A  +
Sbjct: 62  TMVDVVARTAAEVFIPLTVGGGITSVDDIRVLLKAGADKVSINTGAVKHPQLVLEAAKRY 121

Query: 122 GAQAVVLAIDARW---RGDFPEVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDRDG 178
           G Q +V+AID ++   +GD+ EV + GGR  TGL AVEWA K   LGAGEILLTS D+DG
Sbjct: 122 GQQCIVVAIDGKYDGQKGDW-EVLINGGRTRTGLSAVEWAKKMENLGAGEILLTSFDQDG 180

Query: 179 TKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAG-AEAALAASVFHFGEIPIPK 237
            K+GYDL  TR+++E+V +PVIASGGAG+ EHF E F  G A+AALAAS+FHF E  I +
Sbjct: 181 RKDGYDLTFTRVISESVNIPVIASGGAGKKEHFYEVFTKGKADAALAASIFHFKETTIQE 240

Query: 238 LKRYLAEKGVHVR 250
           +KRYL +KGV VR
Sbjct: 241 VKRYLRQKGVPVR 253


Lambda     K      H
   0.321    0.138    0.398 

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: 223
Number of extensions: 11
Number of successful extensions: 6
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: 252
Length of database: 253
Length adjustment: 24
Effective length of query: 228
Effective length of database: 229
Effective search space:    52212
Effective search space used:    52212
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 (21.9 bits)
S2: 46 (22.3 bits)

Align candidate WP_013076129.1 BTUS_RS10910 (imidazole glycerol phosphate synthase subunit HisF)
to HMM TIGR00735 (hisF: imidazoleglycerol phosphate synthase, cyclase subunit)

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00735.hmm
# target sequence database:        /tmp/gapView.13637.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00735  [M=254]
Accession:   TIGR00735
Description: hisF: imidazoleglycerol phosphate synthase, cyclase subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.5e-118  379.4   1.1   3.9e-118  379.3   1.1    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013076129.1  BTUS_RS10910 imidazole glycerol 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013076129.1  BTUS_RS10910 imidazole glycerol phosphate synthase subunit HisF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.3   1.1  3.9e-118  3.9e-118       1     254 []       1     253 []       1     253 [] 0.99

  Alignments for each domain:
  == domain 1  score: 379.3 bits;  conditional E-value: 3.9e-118
                                 TIGR00735   1 mlakriipCLdvkdgrvvkGvqfk.nlrdaGdpvelakkydeeGadelvflditassekretmlevver 68 
                                               ml++ri+pC+dvk+grvvk v f  n rdaGdpvela++yde Gadelv+ldi+as e+r+tm++vv r
  lcl|NCBI__GCF_000092905.1:WP_013076129.1   1 MLTRRIVPCFDVKNGRVVKNVSFLtNERDAGDPVELARYYDESGADELVLLDISASVEGRATMVDVVAR 69 
                                               8**********************62699***************************************** PP

                                 TIGR00735  69 vaekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaen 137
                                               +a +vfiPltvgGGi s++d++ ll+aGadkvsint avk+p+l+ e+a+r+G+q+ivvaid k++ ++
  lcl|NCBI__GCF_000092905.1:WP_013076129.1  70 TAAEVFIPLTVGGGITSVDDIRVLLKAGADKVSINTGAVKHPQLVLEAAKRYGQQCIVVAIDGKYDGQK 138
                                               ****************************************************************99875 PP

                                 TIGR00735 138 eeakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasg 206
                                                 + +ev i+gGr++t+l +vewak++e+lGaGeillts+d+dG k+Gydl+ ++ ++e+v+iPviasg
  lcl|NCBI__GCF_000092905.1:WP_013076129.1 139 --GDWEVLINGGRTRTGLSAVEWAKKMENLGAGEILLTSFDQDGRKDGYDLTFTRVISESVNIPVIASG 205
                                               ..9****************************************************************** PP

                                 TIGR00735 207 GaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254
                                               GaGk+eh++e+f+kgkadaaLaas+fh++e+ti+evk+yl+++gv+vr
  lcl|NCBI__GCF_000092905.1:WP_013076129.1 206 GAGKKEHFYEVFTKGKADAALAASIFHFKETTIQEVKRYLRQKGVPVR 253
                                               ***********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (253 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 10.13
//
[ok]

This GapMind analysis is from Apr 10 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