Alignments for a candidate for hisF in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisF in Dechlorosoma suillum PS

Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate Dsui_1418 Dsui_1418 imidazoleglycerol phosphate synthase, cyclase subunit

Query= BRENDA::Q5NMD6
         (255 letters)



>FitnessBrowser__PS:Dsui_1418
          Length = 253

 Score =  291 bits (744), Expect = 1e-83
 Identities = 146/252 (57%), Positives = 190/252 (75%), Gaps = 1/252 (0%)

Query: 1   MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60
           M L  RIIPCLDV  GRVVKG NF +L DAGDPVE A+ YD  GADE+ FLDI+AS + R
Sbjct: 1   MALAKRIIPCLDVTAGRVVKGTNFVELRDAGDPVEIARRYDEQGADEVTFLDITASSDQR 60

Query: 61  GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120
             +L ++   A   F+PLTVGGGVR+VED R LL AGADKV++N+AAV  P+LV++ + +
Sbjct: 61  DIILHIIEACASQVFIPLTVGGGVRKVEDVRRLLNAGADKVSMNTAAVQNPDLVSDASAK 120

Query: 121 FGAQCVVAAIDARRNG-DHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGT 179
            G+QC+V AIDA++     W V+THGGR  TGI+ +  A ++   GAGEILLTSMD+DGT
Sbjct: 121 VGSQCIVVAIDAKQTAPGQWCVFTHGGRNNTGIDVVTWAKDVATRGAGEILLTSMDRDGT 180

Query: 180 RDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEA 239
           ++G+DL LTR V+D+V +PVIASGGVGNL H+ +GVT+G A A+LAASIFHFG+Y++ +A
Sbjct: 181 KNGFDLALTRAVSDAVAIPVIASGGVGNLQHLADGVTQGGADAVLAASIFHFGEYTVRQA 240

Query: 240 HEALAKAGLTVR 251
            E +   G+ VR
Sbjct: 241 KEYMRDRGIEVR 252


Lambda     K      H
   0.320    0.136    0.400 

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: 242
Number of extensions: 11
Number of successful extensions: 3
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: 255
Length of database: 253
Length adjustment: 24
Effective length of query: 231
Effective length of database: 229
Effective search space:    52899
Effective search space used:    52899
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 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate Dsui_1418 Dsui_1418 (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.1915.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.9e-118  378.9   3.6   5.7e-118  378.7   3.6    1.0  1  lcl|FitnessBrowser__PS:Dsui_1418  Dsui_1418 imidazoleglycerol phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1418  Dsui_1418 imidazoleglycerol phosphate synthase, cyclase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.7   3.6  5.7e-118  5.7e-118       2     254 .]       3     252 ..       2     252 .. 0.99

  Alignments for each domain:
  == domain 1  score: 378.7 bits;  conditional E-value: 5.7e-118
                         TIGR00735   2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiPlt 78 
                                       lakriipCLdv++grvvkG++f +lrdaGdpve+a++yde+Gade++flditass++r+++l+++e  a +vfiPlt
  lcl|FitnessBrowser__PS:Dsui_1418   3 LAKRIIPCLDVTAGRVVKGTNFVELRDAGDPVEIARRYDEQGADEVTFLDITASSDQRDIILHIIEACASQVFIPLT 79 
                                       9**************************************************************************** PP

                         TIGR00735  79 vgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevtikgGrestdl 155
                                       vgGG++++edv++ll+aGadkvs+ntaav++p+l+++++ ++Gsq+ivvaidak++a    +++ v ++gGr++t++
  lcl|FitnessBrowser__PS:Dsui_1418  80 VGGGVRKVEDVRRLLNAGADKVSMNTAAVQNPDLVSDASAKVGSQCIVVAIDAKQTAP---GQWCVFTHGGRNNTGI 153
                                       ******************************************************9987...58************** PP

                         TIGR00735 156 dvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflkgkadaaLaasvf 232
                                       dvv+wak+v+++GaGeilltsmd+dGtk+G+dl+l+++v++av iPviasgG+G+ +hl++++++g ada+Laas+f
  lcl|FitnessBrowser__PS:Dsui_1418 154 DVVTWAKDVATRGAGEILLTSMDRDGTKNGFDLALTRAVSDAVAIPVIASGGVGNLQHLADGVTQGGADAVLAASIF 230
                                       ***************************************************************************** PP

                         TIGR00735 233 hkreltieevkeylaergvkvr 254
                                       h++e+t+++ key+++rg++vr
  lcl|FitnessBrowser__PS:Dsui_1418 231 HFGEYTVRQAKEYMRDRGIEVR 252
                                       *********************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.31
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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