Alignments for a candidate for hisF in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisF in Dyella japonica UNC79MFTsu3.2

Align IGP synthase cyclase subunit; EC 4.1.3.- (characterized)
to candidate N515DRAFT_2932 N515DRAFT_2932 cyclase

Query= CharProtDB::CH_024847
         (258 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2932
          Length = 256

 Score =  330 bits (847), Expect = 1e-95
 Identities = 165/257 (64%), Positives = 197/257 (76%), Gaps = 1/257 (0%)

Query: 1   MLAKRIIPCLDVRDGQVVKGVQFRNHEIIGDIVPLAKRYAEEGADELVFYDITASSDGRV 60
           ML++RIIPCLDVRDG+VVKGV+FR+H ++G+IV LA RY +EGADELVFYDITAS +GR 
Sbjct: 1   MLSRRIIPCLDVRDGKVVKGVRFRDHVVMGEIVELALRYRDEGADELVFYDITASPEGRS 60

Query: 61  VDKSWVSRVAEVIDIPFCVAGGIKSLEDAAKILSFGADKISINSPALADPTLITRLADRF 120
           VD+ WV RVA  IDIPFCVAGGI+S+EDA ++L  GADKIS+NSPAL  P LI  LA  F
Sbjct: 61  VDRGWVERVARAIDIPFCVAGGIRSVEDAREVLHAGADKISVNSPALERPALIGELAAAF 120

Query: 121 GVQCIVVGIDTWYDAETGKYHVNQYTGDESRTRVTQWETLDWVQEVQKRGAGEIVLNMMN 180
           GVQC+VVG+D+  DA+ G++ V QYTGD ++T+     TLDW+ E Q+ GAGEIVLN M 
Sbjct: 121 GVQCVVVGVDSLRDAD-GEWRVRQYTGDPTKTQALARRTLDWIDEAQRLGAGEIVLNCMG 179

Query: 181 QDGVRNGYDLEQLKKVREVCHVPLIASGGAGTMEHFLEAFRDADVDGALAASVFHKQIIN 240
            DGVR GYDLEQL   R +C VPL+ASGGAG  EHF +AF  ADVDGALAASVFH   I 
Sbjct: 180 SDGVREGYDLEQLHAARALCRVPLVASGGAGAPEHFRDAFAVADVDGALAASVFHSGAIA 239

Query: 241 IGELKAYLATQGVEIRI 257
           I  LK YL   G+  R+
Sbjct: 240 IPSLKQYLRRAGIATRL 256


Lambda     K      H
   0.321    0.138    0.409 

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: 295
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: 258
Length of database: 256
Length adjustment: 24
Effective length of query: 234
Effective length of database: 232
Effective search space:    54288
Effective search space used:    54288
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 N515DRAFT_2932 N515DRAFT_2932 (cyclase)
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.24848.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.2e-101  324.4   0.1   2.5e-101  324.2   0.1    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2932  N515DRAFT_2932 cyclase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2932  N515DRAFT_2932 cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.2   0.1  2.5e-101  2.5e-101       1     254 []       1     255 [.       1     255 [. 0.96

  Alignments for each domain:
  == domain 1  score: 324.2 bits;  conditional E-value: 2.5e-101
                                    TIGR00735   1 mlakriipCLdvkdgrvvkGvqfknlrdaGdpvelakkydeeGadelvflditassekretmlevv 66 
                                                  ml++riipCLdv+dg+vvkGv+f+++  +G++vela +y +eGadelvf+ditas e+r+++  +v
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2932   1 MLSRRIIPCLDVRDGKVVKGVRFRDHVVMGEIVELALRYRDEGADELVFYDITASPEGRSVDRGWV 66 
                                                  89**************************************************************** PP

                                    TIGR00735  67 ervaekvfiPltvgGGiksiedvkkllraGadkvsintaavkapelikeladrfGsqaivvaidak 132
                                                  erva+ ++iP++v+GGi+s+ed++++l+aGadk+s+n++a+++p li ela  fG+q++vv++d+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2932  67 ERVARAIDIPFCVAGGIRSVEDAREVLHAGADKISVNSPALERPALIGELAAAFGVQCVVVGVDSL 132
                                                  ****************************************************************** PP

                                    TIGR00735 133 reaeneeakyevtikgGres....tdldvvewakeveelGaGeilltsmdkdGtksGydlellkkv 194
                                                  r+a+   ++++v +++G+ +        +++w+ e+++lGaGei+l++m +dG+++Gydle+l++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2932 133 RDAD---GEWRVRQYTGDPTktqaLARRTLDWIDEAQRLGAGEIVLNCMGSDGVREGYDLEQLHAA 195
                                                  *997...58********97633223346899*********************************** PP

                                    TIGR00735 195 keavkiPviasgGaGkaehleeaflkgkadaaLaasvfhkreltieevkeylaergvkvr 254
                                                  +  +++P++asgGaG++eh+++af+ +++d+aLaasvfh + + i  +k+yl+  g+  r
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2932 196 RALCRVPLVASGGAGAPEHFRDAFAVADVDGALAASVFHSGAIAIPSLKQYLRRAGIATR 255
                                                  ********************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (254 nodes)
Target sequences:                          1  (256 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: 6.84
//
[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