GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisF in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_05659 H281DRAFT_05659 imidazole glycerol phosphate synthase subunit hisF

Query= SwissProt::Q7SIB9
         (252 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05659 H281DRAFT_05659
           imidazole glycerol phosphate synthase subunit hisF
          Length = 257

 Score =  309 bits (791), Expect = 4e-89
 Identities = 158/257 (61%), Positives = 202/257 (78%), Gaps = 6/257 (2%)

Query: 1   MSLAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEER 60
           M+LAKRI+PCLDV AGRVVKGVNFV LRDAGDPVE AR YD+ GADEL FLDI+AT ++R
Sbjct: 1   MALAKRIIPCLDVTAGRVVKGVNFVELRDAGDPVEIARRYDDQGADELTFLDITATSDQR 60

Query: 61  AILLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADH 120
            ++L ++  VA +VFIPLTVGGGVR++ED R+LL +GADK+S+NS+AV  P+L+++  D 
Sbjct: 61  DLILPIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKISMNSSAVANPQLVKDATDK 120

Query: 121 FGAQAVVLAIDAR---WRGDFP--EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMD 175
           +G+Q +V+AIDA+     G+ P  EV   GGR  TGL AVEWA K  ELGAGEILLTSMD
Sbjct: 121 YGSQCIVVAIDAKRVSADGETPRWEVFTHGGRKATGLEAVEWARKMAELGAGEILLTSMD 180

Query: 176 RDGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAG-AEAALAASVFHFGEIP 234
           RDGTK G+DL LTR V++AV VPVIASGG G ++H  +   +G A+A LAAS+FH+GE  
Sbjct: 181 RDGTKSGFDLALTRAVSDAVPVPVIASGGVGNLQHLADGITSGHADAVLAASIFHYGEHT 240

Query: 235 IPKLKRYLAEKGVHVRL 251
           + + KR++AE+G+ VRL
Sbjct: 241 VGEAKRFMAEQGISVRL 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: 242
Number of extensions: 10
Number of successful extensions: 5
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: 257
Length adjustment: 24
Effective length of query: 228
Effective length of database: 233
Effective search space:    53124
Effective search space used:    53124
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 H281DRAFT_05659 H281DRAFT_05659 (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.31990.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     1e-118  381.1   0.9   1.2e-118  381.0   0.9    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05659  H281DRAFT_05659 imidazole glycer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05659  H281DRAFT_05659 imidazole glycerol phosphate synthase subunit hisF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.0   0.9  1.2e-118  1.2e-118       2     254 .]       3     256 ..       2     256 .. 0.98

  Alignments for each domain:
  == domain 1  score: 381.0 bits;  conditional E-value: 1.2e-118
                                    TIGR00735   2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevve 67 
                                                  lakriipCLdv++grvvkGv+f +lrdaGdpve+a++yd++Gadel+fldita+s++r+ +l ++e
  lcl|FitnessBrowser__Burk376:H281DRAFT_05659   3 LAKRIIPCLDVTAGRVVKGVNFVELRDAGDPVEIARRYDDQGADELTFLDITATSDQRDLILPIIE 68 
                                                  9***************************************************************** PP

                                    TIGR00735  68 rvaekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakr 133
                                                   va +vfiPltvgGG++ +edv++ll+aGadk+s+n++av++p+l+k+++d++Gsq+ivvaidakr
  lcl|FitnessBrowser__Burk376:H281DRAFT_05659  69 AVASQVFIPLTVGGGVRAVEDVRRLLNAGADKISMNSSAVANPQLVKDATDKYGSQCIVVAIDAKR 134
                                                  *****************************************************************9 PP

                                    TIGR00735 134 eae.neeakyevtikgGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeav 198
                                                  +    e   +ev ++gGr+ t+l++vewa++++elGaGeilltsmd+dGtksG+dl+l+++v++av
  lcl|FitnessBrowser__Burk376:H281DRAFT_05659 135 VSAdGETPRWEVFTHGGRKATGLEAVEWARKMAELGAGEILLTSMDRDGTKSGFDLALTRAVSDAV 200
                                                  86515679********************************************************** PP

                                    TIGR00735 199 kiPviasgGaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254
                                                   +PviasgG+G+ +hl++++++g+ada+Laas+fh++e t++e k+++ae+g++vr
  lcl|FitnessBrowser__Burk376:H281DRAFT_05659 201 PVPVIASGGVGNLQHLADGITSGHADAVLAASIFHYGEHTVGEAKRFMAEQGISVR 256
                                                  ******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (257 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: 7.55
//
[ok]

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 (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:

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. 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:

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 preprint on GapMind for carbon sources, 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