GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Thiohalospira halophila DSM 15071 HL 3

Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_093428506.1 BM272_RS09260 imidazole glycerol phosphate synthase subunit HisF

Query= BRENDA::Q5NMD6
         (255 letters)



>NCBI__GCF_900112605.1:WP_093428506.1
          Length = 253

 Score =  330 bits (847), Expect = 1e-95
 Identities = 166/252 (65%), Positives = 198/252 (78%), Gaps = 1/252 (0%)

Query: 1   MTLCTRIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGR 60
           M+L  RIIPCLDV  GRVVKGV F D+ DAGDPVE A+ YD  GADEL FLDI+ASHEGR
Sbjct: 1   MSLAKRIIPCLDVEGGRVVKGVQFVDIRDAGDPVEAAQRYDQQGADELTFLDITASHEGR 60

Query: 61  GTMLDVVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADR 120
           GT+L+VV   A   F+PLTVGGGVR VED RALL AGADKVA+N+AAV  P LV   ADR
Sbjct: 61  GTILEVVEAVAGRVFIPLTVGGGVRAVEDVRALLAAGADKVAINTAAVNDPALVRAAADR 120

Query: 121 FGAQCVVAAIDARR-NGDHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGT 179
           FG QC+V AIDAR+     WE++THGGR PTG++A++ A  +   GAGE+L+TSMD+DGT
Sbjct: 121 FGRQCIVVAIDARQVEPGRWEIFTHGGRTPTGLDAVEWAARMEEEGAGELLVTSMDRDGT 180

Query: 180 RDGYDLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHFGQYSLAEA 239
           RDG+D++LTR +AD V VPVIASGGVGNLDH+ EG+  GHA A+LAASIFHFG+Y++ EA
Sbjct: 181 RDGFDIDLTRAIADRVGVPVIASGGVGNLDHLAEGLRDGHADAVLAASIFHFGEYTIGEA 240

Query: 240 HEALAKAGLTVR 251
              L +AGL VR
Sbjct: 241 KAHLHRAGLPVR 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: 275
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: 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 WP_093428506.1 BM272_RS09260 (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.3454219.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-114  367.0   1.1   2.4e-114  366.9   1.1    1.0  1  NCBI__GCF_900112605.1:WP_093428506.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900112605.1:WP_093428506.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.9   1.1  2.4e-114  2.4e-114       2     254 .]       3     252 ..       2     252 .. 0.99

  Alignments for each domain:
  == domain 1  score: 366.9 bits;  conditional E-value: 2.4e-114
                             TIGR00735   2 lakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevvervaekvf 74 
                                           lakriipCLdv+ grvvkGvqf ++rdaGdpve a++yd++Gadel+flditas+e+r t+levve va +vf
  NCBI__GCF_900112605.1:WP_093428506.1   3 LAKRIIPCLDVEGGRVVKGVQFVDIRDAGDPVEAAQRYDQQGADELTFLDITASHEGRGTILEVVEAVAGRVF 75 
                                           9************************************************************************ PP

                             TIGR00735  75 iPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidakreaeneeakyevtik 147
                                           iPltvgGG++ +edv+ ll+aGadkv+intaav++p l++ +adrfG+q+ivvaida++++    + +e+ ++
  NCBI__GCF_900112605.1:WP_093428506.1  76 IPLTVGGGVRAVEDVRALLAAGADKVAINTAAVNDPALVRAAADRFGRQCIVVAIDARQVEP---GRWEIFTH 145
                                           *********************************************************99876...69****** PP

                             TIGR00735 148 gGrestdldvvewakeveelGaGeilltsmdkdGtksGydlellkkvkeavkiPviasgGaGkaehleeaflk 220
                                           gGr+ t+ld+vewa+++ee GaGe+l+tsmd+dGt++G+d+ l+++++++v +PviasgG+G+ +hl+e++ +
  NCBI__GCF_900112605.1:WP_093428506.1 146 GGRTPTGLDAVEWAARMEEEGAGELLVTSMDRDGTRDGFDIDLTRAIADRVGVPVIASGGVGNLDHLAEGLRD 218
                                           ************************************************************************* PP

                             TIGR00735 221 gkadaaLaasvfhkreltieevkeylaergvkvr 254
                                           g+ada+Laas+fh++e+ti+e k++l+  g++vr
  NCBI__GCF_900112605.1:WP_093428506.1 219 GHADAVLAASIFHFGEYTIGEAKAHLHRAGLPVR 252
                                           ********************************98 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: 19.89
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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