Alignments for a candidate for hisH in Desulfacinum hydrothermale DSM 13146

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisH in Desulfacinum hydrothermale DSM 13146

Align imidazole glycerol-phosphate synthase (EC 4.3.2.10) (characterized)
to candidate WP_084057265.1 B9A12_RS07505 imidazole glycerol phosphate synthase subunit HisH

Query= BRENDA::Q9SZ30
         (592 letters)



>NCBI__GCF_900176285.1:WP_084057265.1
          Length = 526

 Score =  607 bits (1565), Expect = e-178
 Identities = 305/523 (58%), Positives = 384/523 (73%), Gaps = 8/523 (1%)

Query: 63  VVTLLDYGAGNVRSIRNALRHLGFSIKDVQTPGDILNADRLIFPGVGAFAPAMDVLNRTG 122
           +VT+LDYGAGNVRS+ NA+R LG  ++ V+ P DI+ A+RL+FPGVGAF   M VL   G
Sbjct: 1   MVTVLDYGAGNVRSVVNAIRSLGRDVRFVERPEDIVQAERLVFPGVGAFGEMMRVLRHRG 60

Query: 123 MAEALCKYIENDRPFLGICLGLQLLFDSSEENGPVKGLGVIPGIVGRFDASAGIRVPHIG 182
             + L  Y+ + RPFLGICLGLQ LF+ SEE     GLG  PGIV RF       VPH+G
Sbjct: 61  YVDPLLAYLRSGRPFLGICLGLQALFEGSEEAPGEDGLGFFPGIVRRFRVDRA--VPHMG 118

Query: 183 WNALQVGKDSEILDDV-GNRHVYFVHSYRAIPSDENKDWISSTCNYGESFISSIRRGNVH 241
           WN ++  K S +L  + G+  +YFVHSY     D +   + +  +YG  F+S++ +G V 
Sbjct: 119 WNGIRARKPSSLLHGLKGDEKLYFVHSYYVDSGDPSV--VLTVTDYGVEFVSAVEKGQVA 176

Query: 242 AVQFHPEKSGEVGLSVLRRFLHPKLPATQKPMEGKASKLAKRVIACLDVRTNDKGDLVVT 301
           AVQFHPEKSG  GL +L  FL  +      P+    ++LA+R+IACLDVR ND+GDLVVT
Sbjct: 177 AVQFHPEKSGPAGLKILENFLGGQAAPVLPPVAASQTELARRIIACLDVRANDQGDLVVT 236

Query: 302 KGDQYDVREQSNENEVRNLGKPVDLAGQYYKDGADEISFLNITGFRDFPLGDLPMIQVLR 361
           KGDQYDVRE   E  VRNLGKPV+LA +YY++GADEI+FLNITGFRDFPL D+PM++VLR
Sbjct: 237 KGDQYDVRE---EGRVRNLGKPVELARRYYEEGADEITFLNITGFRDFPLKDMPMLEVLR 293

Query: 362 QTSKNVFVPLTVGGGIRDFTDASGRYYSSLEVAAEYFRSGADKISIGSDAVSAAEEFIKS 421
           +TS+ VFVPLT+GGGIRD+TD  G  Y +L+VA++YFRSGADK+SIGSDAV+  EE +K 
Sbjct: 294 RTSEEVFVPLTIGGGIRDYTDKDGTRYDALQVASQYFRSGADKVSIGSDAVAVVEEVLKR 353

Query: 422 GVKTGKSSLEQISRVYGNQAVVVSIDPRRVYVNHPDDVPYKVIRVTNPGPNGEEYAWYQC 481
           G  TG+S++E ISRVYG+QAVV+SIDPRRVYV  PD VP++VI    PGPNGE + WYQC
Sbjct: 354 GGPTGRSAIETISRVYGSQAVVISIDPRRVYVPSPDAVPHRVIETAFPGPNGERFCWYQC 413

Query: 482 TVSGGREGRPIGAFELAKAVEELGAGEILLNCIDCDGQGKGFDIDLVKLISDSVGIPVIA 541
           TV GGREGR + A  LA+  ++LGAGEILLNCID DG  +GFD++L+  + ++V IPVIA
Sbjct: 414 TVKGGREGRDVDAVTLARVCQQLGAGEILLNCIDRDGTNQGFDLELIHAVREAVTIPVIA 473

Query: 542 SSGAGTPDHFSEVFEKTNASAALAAGIFHRKEVPIQSVKEHLQ 584
           SSGAG   HF +VF KT A AALAAGIFHR++V I  VK  L+
Sbjct: 474 SSGAGCAQHFLDVFTKTRAEAALAAGIFHRRKVGIGEVKAFLK 516


Lambda     K      H
   0.317    0.135    0.391 

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: 886
Number of extensions: 45
Number of successful extensions: 6
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: 592
Length of database: 526
Length adjustment: 36
Effective length of query: 556
Effective length of database: 490
Effective search space:   272440
Effective search space used:   272440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_084057265.1 B9A12_RS07505 (imidazole glycerol phosphate synthase subunit HisH)
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.29341.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.8e-67  213.1   0.0    2.4e-67  212.6   0.0    1.2  1  lcl|NCBI__GCF_900176285.1:WP_084057265.1  B9A12_RS07505 imidazole glycerol


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176285.1:WP_084057265.1  B9A12_RS07505 imidazole glycerol phosphate synthase subunit HisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.6   0.0   2.4e-67   2.4e-67       1     196 [.       2     197 ..       2     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 212.6 bits;  conditional E-value: 2.4e-67
                                 TIGR01855   1 ivvidygvgNlksvkkalervgaesevvkdskelekadklvlPGVGafkeamkklrele.lellaekvv 68 
                                               ++v+dyg+gN++sv +a++++g  ++ v+  +++ +a++lv+PGVGaf e m+ lr+++ ++ l     
  lcl|NCBI__GCF_900176285.1:WP_084057265.1   2 VTVLDYGAGNVRSVVNAIRSLGRDVRFVERPEDIVQAERLVFPGVGAFGEMMRVLRHRGyVDPL-LAYL 69 
                                               689********************************************************77766.7889 PP

                                 TIGR01855  69 kkkkpvlgiClGmQllfekseEgkevkglglikgkvkkleaekkvPhiGWnevevvkesellkgleeea 137
                                               ++++p+lgiClG+Q lfe seE+  ++glg+++g v++++ +  vPh+GWn +   k s+ll+gl+ ++
  lcl|NCBI__GCF_900176285.1:WP_084057265.1  70 RSGRPFLGICLGLQALFEGSEEAPGEDGLGFFPGIVRRFRVDRAVPHMGWNGIRARKPSSLLHGLKGDE 138
                                               999****************************************************************** PP

                                 TIGR01855 138 rvYfvHsYaveleeeeavlakadygekfvaavekdnivgvQFHPEkSgktGlkllknfl 196
                                               ++YfvHsY+v   + + vl+ +dyg +fv+avek+++++vQFHPEkSg +Glk+l+nfl
  lcl|NCBI__GCF_900176285.1:WP_084057265.1 139 KLYFVHSYYVDSGDPSVVLTVTDYGVEFVSAVEKGQVAAVQFHPEKSGPAGLKILENFL 197
                                               *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (198 nodes)
Target sequences:                          1  (526 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: 17.59
//
[ok]

This GapMind analysis is from Apr 10 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