Alignments for a candidate for hisF in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisF in Acidovorax sp. GW101-3H11

Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate Ac3H11_4733 Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.3.-)

Query= BRENDA::Q5NMD6
         (255 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4733
          Length = 250

 Score =  278 bits (711), Expect = 8e-80
 Identities = 139/249 (55%), Positives = 183/249 (73%), Gaps = 15/249 (6%)

Query: 18  VVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGTMLDVVARTAEVCFMP 77
           VVKGVNF +L DAGDPVE A  Y+A GADEL FLDI+A+ +GR  +L ++   A   F+P
Sbjct: 1   VVKGVNFVELRDAGDPVEIAARYNAQGADELTFLDITATSDGRDLILHIIEAVASQVFIP 60

Query: 78  LTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFGAQCVVAAIDARRN-- 135
           LTVGGGVR VED R LL AGADK + NSAA+A P+L+  ++ ++GAQC+V AIDA+R   
Sbjct: 61  LTVGGGVRTVEDVRRLLNAGADKTSFNSAAIANPDLINAVSAKYGAQCIVVAIDAKRRSA 120

Query: 136 -------------GDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGTRDG 182
                        G+ W+VY+HGGR+ TG++A+  A  + R GAGEILLTSMD+DGT+ G
Sbjct: 121 EDALRIGANGQPVGEGWDVYSHGGRKNTGLDAIAWATEMARRGAGEILLTSMDRDGTKSG 180

Query: 183 YDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEAHEA 242
           +DL LTR V+D+V VPVIASGGVGNLDH+ +GV +G A A+LAASIFH+G+Y++ +A   
Sbjct: 181 FDLALTRAVSDAVSVPVIASGGVGNLDHLADGVQQGGADAVLAASIFHYGEYTVGQAKAR 240

Query: 243 LAKAGLTVR 251
           +A+ G+ VR
Sbjct: 241 MAERGIPVR 249


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: 251
Number of extensions: 9
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: 250
Length adjustment: 24
Effective length of query: 231
Effective length of database: 226
Effective search space:    52206
Effective search space used:    52206
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: 46 (22.3 bits)

Align candidate Ac3H11_4733 (Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.3.-))
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.5454.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.4e-105  337.4   1.9   2.7e-105  337.2   1.9    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4733  Imidazole glycerol phosphate syn


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4733  Imidazole glycerol phosphate synthase cyclase subunit (EC 4.1.3.-)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.2   1.9  2.7e-105  2.7e-105      17     254 .]       1     249 [.       1     249 [. 0.99

  Alignments for each domain:
  == domain 1  score: 337.2 bits;  conditional E-value: 2.7e-105
                                        TIGR00735  17 vvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvfiPlt 78 
                                                      vvkGv+f +lrdaGdpve+a++y+++Gadel+fldita+s++r+ +l+++e va +vfiPlt
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4733   1 VVKGVNFVELRDAGDPVEIAARYNAQGADELTFLDITATSDGRDLILHIIEAVASQVFIPLT 62 
                                                      8************************************************************* PP

                                        TIGR00735  79 vgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaenee. 139
                                                      vgGG++++edv++ll+aGadk s n+aa+++p+li+ ++ ++G+q+ivvaidakr+  +++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4733  63 VGGGVRTVEDVRRLLNAGADKTSFNSAAIANPDLINAVSAKYGAQCIVVAIDAKRRSAEDAl 124
                                                      *********************************************************9988* PP

                                        TIGR00735 140 ..........akyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlell 191
                                                                  ++v+ +gGr++t+ld+++wa+e++++GaGeilltsmd+dGtksG+dl+l+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4733 125 rigangqpvgEGWDVYSHGGRKNTGLDAIAWATEMARRGAGEILLTSMDRDGTKSGFDLALT 186
                                                      *********999************************************************** PP

                                        TIGR00735 192 kkvkeavkiPviasgGaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkv 253
                                                      ++v++av++PviasgG+G+ +hl++++++g ada+Laas+fh++e+t+++ k+ +aerg++v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4733 187 RAVSDAVSVPVIASGGVGNLDHLADGVQQGGADAVLAASIFHYGEYTVGQAKARMAERGIPV 248
                                                      ************************************************************** PP

                                        TIGR00735 254 r 254
                                                      r
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4733 249 R 249
                                                      9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (250 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: 8.79
//
[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