Alignments for a candidate for hisH in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisH in Desulfovibrio vulgaris Miyazaki F

Align IGP synthase, amidotransferase subunit (EC 4.3.2.10) (characterized)
to candidate 8501586 DvMF_2305 imidazole glycerol phosphate synthase subunit HisH (RefSeq)

Query= reanno::Miya:8501586
         (212 letters)



>FitnessBrowser__Miya:8501586
          Length = 212

 Score =  444 bits (1143), Expect = e-130
 Identities = 212/212 (100%), Positives = 212/212 (100%)

Query: 1   MLAILDYKAGNQTSVRRALDHLGIPCVITADPAVIAGAHGVIFPGVGAAGQAMNELLTTG 60
           MLAILDYKAGNQTSVRRALDHLGIPCVITADPAVIAGAHGVIFPGVGAAGQAMNELLTTG
Sbjct: 1   MLAILDYKAGNQTSVRRALDHLGIPCVITADPAVIAGAHGVIFPGVGAAGQAMNELLTTG 60

Query: 61  LDKVLKDQVQAGKPLLGICVGCQIMLDYSQENDTKALGIVPGECRLFNAAWTEEDGTPIR 120
           LDKVLKDQVQAGKPLLGICVGCQIMLDYSQENDTKALGIVPGECRLFNAAWTEEDGTPIR
Sbjct: 61  LDKVLKDQVQAGKPLLGICVGCQIMLDYSQENDTKALGIVPGECRLFNAAWTEEDGTPIR 120

Query: 121 VPHMGWNSIVQKRPCELLKGIEPEAEFYFVHSYYPAPPESYVIATCTYGEEFCAIHGGPG 180
           VPHMGWNSIVQKRPCELLKGIEPEAEFYFVHSYYPAPPESYVIATCTYGEEFCAIHGGPG
Sbjct: 121 VPHMGWNSIVQKRPCELLKGIEPEAEFYFVHSYYPAPPESYVIATCTYGEEFCAIHGGPG 180

Query: 181 LWAVQFHPEKSGRPGLALLRNFYAYCKEASRA 212
           LWAVQFHPEKSGRPGLALLRNFYAYCKEASRA
Sbjct: 181 LWAVQFHPEKSGRPGLALLRNFYAYCKEASRA 212


Lambda     K      H
   0.321    0.139    0.445 

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: 332
Number of extensions: 13
Number of successful extensions: 1
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: 212
Length of database: 212
Length adjustment: 21
Effective length of query: 191
Effective length of database: 191
Effective search space:    36481
Effective search space used:    36481
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: 45 (21.9 bits)

Align candidate 8501586 DvMF_2305 (imidazole glycerol phosphate synthase subunit HisH (RefSeq))
to HMM TIGR01855 (hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (EC 2.4.2.-))

# 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/TIGR01855.hmm
# target sequence database:        /tmp/gapView.28943.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01855  [M=198]
Accession:   TIGR01855
Description: IMP_synth_hisH: imidazole glycerol phosphate synthase, glutamine amidotransferase 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    2.3e-60  189.8   0.0    2.7e-60  189.6   0.0    1.0  1  lcl|FitnessBrowser__Miya:8501586  DvMF_2305 imidazole glycerol pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501586  DvMF_2305 imidazole glycerol phosphate synthase subunit HisH (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.6   0.0   2.7e-60   2.7e-60       2     196 ..       3     203 ..       2     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 189.6 bits;  conditional E-value: 2.7e-60
                         TIGR01855   2 vvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrelelellaekvvkkkkpvlgiC 78 
                                       +++dy++gN +sv++al+++g   ++++d   +  a  +++PGVGa+ +am++l  ++l+++ +++v+++kp+lgiC
  lcl|FitnessBrowser__Miya:8501586   3 AILDYKAGNQTSVRRALDHLGIPCVITADPAVIAGAHGVIFPGVGAAGQAMNELLTTGLDKVLKDQVQAGKPLLGIC 79 
                                       79********************************************************99999************** PP

                         TIGR01855  79 lGmQllfekseEgkevkglglikgkvkkleaek........kvPhiGWnevevvkesellkgleeearvYfvHsYav 147
                                       +G Q++++ s+E +++k+lg+++g+ + ++a+         +vPh+GWn++  ++ +ellkg+e ea++YfvHsY+ 
  lcl|FitnessBrowser__Miya:8501586  80 VGCQIMLDYSQE-NDTKALGIVPGECRLFNAAWteedgtpiRVPHMGWNSIVQKRPCELLKGIEPEAEFYFVHSYYP 155
                                       ************.579*************987777889999***********************************9 PP

                         TIGR01855 148 eleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfl 196
                                        + e ++v+a+++yge+f a+     + +vQFHPEkSg+ Gl+ll+nf 
  lcl|FitnessBrowser__Miya:8501586 156 APPE-SYVIATCTYGEEFCAIHGGPGLWAVQFHPEKSGRPGLALLRNFY 203
                                       9987.8*****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (212 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.38
//
[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