GapMind for Amino acid biosynthesis

 

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

Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate H281DRAFT_05659 H281DRAFT_05659 imidazole glycerol phosphate synthase subunit hisF

Query= BRENDA::Q5NMD6
         (255 letters)



>FitnessBrowser__Burk376:H281DRAFT_05659
          Length = 257

 Score =  311 bits (797), Expect = 8e-90
 Identities = 153/256 (59%), Positives = 199/256 (77%), Gaps = 5/256 (1%)

Query: 1   MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60
           M L  RIIPCLDV  GRVVKGVNF +L DAGDPVE A+ YD  GADEL FLDI+A+ + R
Sbjct: 1   MALAKRIIPCLDVTAGRVVKGVNFVELRDAGDPVEIARRYDDQGADELTFLDITATSDQR 60

Query: 61  GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120
             +L ++   A   F+PLTVGGGVR VED R LL AGADK+++NS+AVA P+LV +  D+
Sbjct: 61  DLILPIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKISMNSSAVANPQLVKDATDK 120

Query: 121 FGAQCVVAAIDARR---NGD--HWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMD 175
           +G+QC+V AIDA+R   +G+   WEV+THGGR+ TG+ A++ A  +  LGAGEILLTSMD
Sbjct: 121 YGSQCIVVAIDAKRVSADGETPRWEVFTHGGRKATGLEAVEWARKMAELGAGEILLTSMD 180

Query: 176 KDGTRDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYS 235
           +DGT+ G+DL LTR V+D+VPVPVIASGGVGNL H+ +G+T GHA A+LAASIFH+G+++
Sbjct: 181 RDGTKSGFDLALTRAVSDAVPVPVIASGGVGNLQHLADGITSGHADAVLAASIFHYGEHT 240

Query: 236 LAEAHEALAKAGLTVR 251
           + EA   +A+ G++VR
Sbjct: 241 VGEAKRFMAEQGISVR 256


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: 238
Number of extensions: 8
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: 257
Length adjustment: 24
Effective length of query: 231
Effective length of database: 233
Effective search space:    53823
Effective search space used:    53823
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 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.9348.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.02
//
[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:

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:

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