Alignments for a candidate for hisC in Thiohalomonas denitrificans HLD2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Thiohalomonas denitrificans HLD2

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9 (characterized, see rationale)
to candidate WP_092992325.1 BLP65_RS02175 histidinol-phosphate transaminase

Query= uniprot:A0A975E8Y9
         (377 letters)



>NCBI__GCF_900102855.1:WP_092992325.1
          Length = 359

 Score =  303 bits (777), Expect = 4e-87
 Identities = 175/368 (47%), Positives = 232/368 (63%), Gaps = 16/368 (4%)

Query: 12  LIQRRIRQDVLSMHAYAIQDSVGMVKLDAMENPHRLPAALQEALGKRLGALALNRYPDGR 71
           LI + IR ++ +++AY + D   ++KLDAMENP+ LP  L E     L  + LNRYPD +
Sbjct: 5   LIDKWIRPEIRAINAYPVPDPGRLIKLDAMENPYTLPPELLEEWLDALRDVPLNRYPDAK 64

Query: 72  VNDLRRALAAYAQMPEGFDIMLGNGSDELISLLAMACDVPTDPVTGKRPVILAPLPGFVM 131
              L   L A   +P G D++LGNGSDE+I +LA+A       + G    +LAP PGFVM
Sbjct: 65  ARHLTDRLRATMDVPAGMDLLLGNGSDEIIQMLALA-------LGGPGRTVLAPEPGFVM 117

Query: 132 YAMSAALQGLDFVGVPLTA-DFELDEAAMLAAIAQHQPAIVYLAYPNNPTANLWNAESMA 190
           Y M A   G+D+VGVPL   DF L+  AML  I QHQPAIVYLAYPNNPT NL++ E M 
Sbjct: 118 YRMIATFTGMDYVGVPLQEEDFGLNRDAMLKGIDQHQPAIVYLAYPNNPTGNLFDPEDMV 177

Query: 191 RVIAATGAVGGLVVLDEAYQPFSSRTYLDTIRSNPAAHAHVLLMRTMSKFGLAGVRIGYM 250
            +I A     GLVV+DEAY  F+ ++++  +        ++L+MRT+SK GLAG+R+G++
Sbjct: 178 AIIEAAP---GLVVVDEAYHAFAEQSFMGRL----GEWDNLLVMRTVSKLGLAGLRLGFL 230

Query: 251 VGPKPLIAQVDKVRPPYNISVLNYECALFALEHADVFAGQAADLRAQRTRLLTALRAMPA 310
            GP+  I ++DKVR PYNI+VL      FAL H  V   Q A +R +R RL +AL  +  
Sbjct: 231 AGPREWIGELDKVRLPYNINVLTQVSGEFALSHMGVLDEQTARIREERGRLASALGGIEG 290

Query: 311 VKAWDSDANMILVRMA-DAQKTFDGLKARGVLVKNVSKMHPLLAQCLRLTVGTADENTRL 369
           V    S AN IL R+A DA   F GL+ARGVL+KN++     L+ CLR+TVGT +EN   
Sbjct: 291 VTPCPSAANFILFRVADDADAVFAGLQARGVLIKNLNPAGGALSGCLRVTVGTPEENEAF 350

Query: 370 LAALLESL 377
           LAAL ESL
Sbjct: 351 LAALRESL 358


Lambda     K      H
   0.322    0.135    0.389 

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: 366
Number of extensions: 14
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: 377
Length of database: 359
Length adjustment: 30
Effective length of query: 347
Effective length of database: 329
Effective search space:   114163
Effective search space used:   114163
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate WP_092992325.1 BLP65_RS02175 (histidinol-phosphate transaminase)
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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/TIGR01141.hmm
# target sequence database:        /tmp/gapView.28583.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-100  321.6   0.0   2.9e-100  321.5   0.0    1.0  1  lcl|NCBI__GCF_900102855.1:WP_092992325.1  BLP65_RS02175 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900102855.1:WP_092992325.1  BLP65_RS02175 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.5   0.0  2.9e-100  2.9e-100       1     348 [.      11     356 ..      11     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: 321.5 bits;  conditional E-value: 2.9e-100
                                 TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealaky 67 
                                               r++i+++++Y  +   +++   +kL+++EnP+  +++++e++ ++l+  +l+rYpd++a +l+ +l++ 
  lcl|NCBI__GCF_900102855.1:WP_092992325.1  11 RPEIRAINAYPVP---DPG-RLIKLDAMENPYTLPPELLEEWLDALRdvPLNRYPDAKARHLTDRLRAT 75 
                                               6789999999884...444.59*************************999******************* PP

                                 TIGR01141  68 lgvee.enillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplked.gqedle 134
                                               ++v +  ++llgnGsde+i++l+ a+  pg++vl++ep + mY+++a+++g++++ vpl+e+ +  + +
  lcl|NCBI__GCF_900102855.1:WP_092992325.1  76 MDVPAgMDLLLGNGSDEIIQMLALALGGPGRTVLAPEPGFVMYRMIATFTGMDYVGVPLQEEdFGLNRD 144
                                               **765279*****************************************************98667777 PP

                                 TIGR01141 135 avle.aakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnl 202
                                               a+l+ + ++++ +v+la+PnnPtGnl++ e++++++e++  +lVVvDeAY  F+e+ s++  l e++nl
  lcl|NCBI__GCF_900102855.1:WP_092992325.1 145 AMLKgIDQHQPAIVYLAYPNNPTGNLFDPEDMVAIIEAA-PGLVVVDEAYHAFAEQ-SFMGRLGEWDNL 211
                                               77777999******************************8.9**************7.************ PP

                                 TIGR01141 203 vvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkere 271
                                               +v+rT+SK+  LAglR+G++ +  e+i +l+kvr pyn+++l++  +  al++   + ++++++++er 
  lcl|NCBI__GCF_900102855.1:WP_092992325.1 212 LVMRTVSKLG-LAGLRLGFLAGPREWIGELDKVRLPYNINVLTQVSGEFALSHMGVLDEQTARIREERG 279
                                               ********86.********************************************************** PP

                                 TIGR01141 272 rlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreene 340
                                               rl ++l  +eg+  ++S aNF+l++v  da++++  l  +g+++++l+ a g l++clR+tvGt+eene
  lcl|NCBI__GCF_900102855.1:WP_092992325.1 280 RLASALGGIEGVTPCPSAANFILFRVADDADAVFAGLQARGVLIKNLNPAGGALSGCLRVTVGTPEENE 348
                                               ********************************************************************* PP

                                 TIGR01141 341 rllealke 348
                                               ++l+al+e
  lcl|NCBI__GCF_900102855.1:WP_092992325.1 349 AFLAALRE 356
                                               ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (359 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: 7.62
//
[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