Alignments for a candidate for hisF in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisF in Desulfovibrio vulgaris Hildenborough

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 209220 DVU0286 imidazoleglycerol phosphate synthase, cyclase subunit

Query= SwissProt::Q7SIB9
         (252 letters)



>MicrobesOnline__882:209220
          Length = 259

 Score =  255 bits (652), Expect = 5e-73
 Identities = 132/256 (51%), Positives = 179/256 (69%), Gaps = 7/256 (2%)

Query: 3   LAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAI 62
           L+KRI+PCLDV AGR+ KGV F    D GDPV  AR Y E GADE+VF DI+A+HE+R I
Sbjct: 2   LSKRIIPCLDVRAGRLTKGVKFEGNVDIGDPVATARRYYEEGADEIVFYDITASHEDRGI 61

Query: 63  LLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFG 122
            LDVV RVA  +FIP +VGGG+ +++D R +L++GA+KVSVNS AV+ P++I + A  FG
Sbjct: 62  FLDVVERVASEIFIPFSVGGGINTVDDMRAVLMAGAEKVSVNSGAVKTPDIISQGAAAFG 121

Query: 123 AQAVVLAIDARW---RGDFP---EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDR 176
           +QA+V+ +D +        P   E+ + GGR   G+ A+EWA     LGAGE+ + S+D 
Sbjct: 122 SQAIVVGMDVKQVEKSATIPSGYEIVIHGGRKYMGMDAIEWAKTCESLGAGELCVNSIDA 181

Query: 177 DGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAF-QAGAEAALAASVFHFGEIPI 235
           DGTK+GY+L LTRM+++AV +PVIASGGAG  EH  +A  + GA AAL AS+ H+G   I
Sbjct: 182 DGTKDGYELTLTRMISDAVTIPVIASGGAGSPEHMYDALTRGGASAALIASIVHYGTYTI 241

Query: 236 PKLKRYLAEKGVHVRL 251
           P LKR ++  G  +R+
Sbjct: 242 PDLKRRISGMGAKMRM 257


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: 239
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: 252
Length of database: 259
Length adjustment: 24
Effective length of query: 228
Effective length of database: 235
Effective search space:    53580
Effective search space used:    53580
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: 47 (22.7 bits)

Align candidate 209220 DVU0286 (imidazoleglycerol phosphate synthase, cyclase subunit)
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.32553.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.6e-106  340.1   1.4     4e-106  339.9   1.4    1.0  1  lcl|MicrobesOnline__882:209220  DVU0286 imidazoleglycerol phosph


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209220  DVU0286 imidazoleglycerol phosphate synthase, cyclase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.9   1.4    4e-106    4e-106       1     254 []       1     256 [.       1     256 [. 0.98

  Alignments for each domain:
  == domain 1  score: 339.9 bits;  conditional E-value: 4e-106
                       TIGR00735   1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiPltv 79 
                                     ml+kriipCLdv++gr++kGv+f+   d+Gdpv  a++y+eeGade+vf+ditas+e+r + l+vverva ++fiP++v
  lcl|MicrobesOnline__882:209220   1 MLSKRIIPCLDVRAGRLTKGVKFEGNVDIGDPVATARRYYEEGADEIVFYDITASHEDRGIFLDVVERVASEIFIPFSV 79 
                                     89***************************************************************************** PP

                       TIGR00735  80 gGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaenee..akyevtikgGrestdld 156
                                     gGGi++++d++ +l aGa+kvs+n+ avk+p++i++ a  fGsqaivv++d k+++++    + ye++i+gGr+  ++d
  lcl|MicrobesOnline__882:209220  80 GGGINTVDDMRAVLMAGAEKVSVNSGAVKTPDIISQGAAAFGSQAIVVGMDVKQVEKSATipSGYEIVIHGGRKYMGMD 158
                                     *****************************************************9998766889**************** PP

                       TIGR00735 157 vvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkadaaLaasvfhkr 235
                                     ++ewak +e+lGaGe+ ++s+d+dGtk+Gy+l+l++ +++av+iPviasgGaG++eh+++a+++g a aaL as++h++
  lcl|MicrobesOnline__882:209220 159 AIEWAKTCESLGAGELCVNSIDADGTKDGYELTLTRMISDAVTIPVIASGGAGSPEHMYDALTRGGASAALIASIVHYG 237
                                     ******************************************************************************* PP

                       TIGR00735 236 eltieevkeylaergvkvr 254
                                      +ti ++k+ +   g k+r
  lcl|MicrobesOnline__882:209220 238 TYTIPDLKRRISGMGAKMR 256
                                     *********9998888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (259 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.42
//
[ok]

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