Alignments for a candidate for hisC in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Mycolicibacterium vanbaalenii PYR-1

Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate WP_011782728.1 MVAN_RS28225 aminotransferase

Query= curated2:Q5QZ49
         (367 letters)



>NCBI__GCF_000015305.1:WP_011782728.1
          Length = 351

 Score =  212 bits (540), Expect = 1e-59
 Identities = 123/322 (38%), Positives = 183/322 (56%), Gaps = 6/322 (1%)

Query: 39  VKLASNENPLGLSEKVKTALEAELTDLVRYPDANGYY-LKSRLAELNEVGTQQITLGNGS 97
           +K+ASNE   G    V+ A+E  +  + RYPD NGY  L+ RLA+      + I++G GS
Sbjct: 25  IKIASNETVHGPLPSVRAAIEKAIDGINRYPD-NGYVELRERLAKHVNFAPEYISVGCGS 83

Query: 98  NDVLEILARTFVSDKDEVIFSQHAFVVYPLVTQAIGAKPVAVPAVDYGHDLDGMAKAVTD 157
             + + L +   +  DEV+F   +F +YPL  +  GA PV VP  D+  DLD M  A+TD
Sbjct: 84  VSLCQQLIQITSTVGDEVLFGWRSFEIYPLQVRTAGATPVQVPLTDHTFDLDAMLAAITD 143

Query: 158 KTKMIFIANPNNPTGTFLSTSALKSFLDKIPQHIIVVLDEAYYEYVPEDQRAPSVEWIKE 217
           +T++IF+ NPNNPT T +   AL  F++ +P HI+VV+DEAY EY+ +     S   ++ 
Sbjct: 144 RTRLIFVCNPNNPTSTVVDPDALARFVEAVPPHIMVVVDEAYVEYIRDGLAPDSFGLVRA 203

Query: 218 YPNLVVSRTFSKAYGLAGLRAGYAVSHESVADVLNRIRQPFNMNSLSLKAAEVVLDDHAY 277
           + N+VV RTFSKAYGLAGLR GYAV+   +   L+++  PF   S+S  AA   LD    
Sbjct: 204 HSNVVVLRTFSKAYGLAGLRIGYAVADPDIIAALSKVYVPFTATSVSQAAAIACLDAADE 263

Query: 278 LQKAVELNAQGMQLLTEFCEESGLNYIPSYGNFLTIEVGPGAEKLYDELLHEGVIVRPVG 337
           L +  +        ++    E+G +  PS  NF+ + +   A++   +  +  VIVRP G
Sbjct: 264 LLERTDAVVAERTRVSAALREAGYDLPPSQANFVWLPLVGRAQQFAADAANSRVIVRPYG 323

Query: 338 GYELPNHLRVSIGLPEENQAFI 359
                + +RV+I  P EN AF+
Sbjct: 324 ----EDGVRVTIAAPHENDAFL 341


Lambda     K      H
   0.316    0.135    0.380 

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: 293
Number of extensions: 11
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: 367
Length of database: 351
Length adjustment: 29
Effective length of query: 338
Effective length of database: 322
Effective search space:   108836
Effective search space used:   108836
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: 49 (23.5 bits)

Align candidate WP_011782728.1 MVAN_RS28225 (aminotransferase)
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.25202.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    9.3e-88  280.4   0.0    1.1e-87  280.1   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011782728.1  MVAN_RS28225 aminotransferase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011782728.1  MVAN_RS28225 aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.1   0.0   1.1e-87   1.1e-87       1     344 [.       6     342 ..       6     346 .. 0.96

  Alignments for each domain:
  == domain 1  score: 280.1 bits;  conditional E-value: 1.1e-87
                                 TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 
                                               r+++ +l +Y pg   ++  + +k +snE  +gp ++v++a++++++ ++rYpd+  +el+e+lak+++
  lcl|NCBI__GCF_000015305.1:WP_011782728.1   6 RPELADLPAYAPG---KTVPGAIKIASNETVHGPLPSVRAAIEKAIDGINRYPDNGYVELRERLAKHVN 71 
                                               6789999*****8...333468*********************************************** PP

                                 TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavle 138
                                               + +e i +g+Gs  l + li+ + + gd+vl+   ++++Y++ +++aga  ++vpl+++ + dl+a+l+
  lcl|NCBI__GCF_000015305.1:WP_011782728.1  72 FAPEYISVGCGSVSLCQQLIQITSTVGDEVLFGWRSFEIYPLQVRTAGATPVQVPLTDH-TFDLDAMLA 139
                                               ***********************************************************.479999999 PP

                                 TIGR01141 139 aakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlv 203
                                               a++++++l+f+++PnnPt ++++ + + +++e+v  + +VVvDeAY+e+ ++   ++ + l++ ++n+v
  lcl|NCBI__GCF_000015305.1:WP_011782728.1 140 AITDRTRLIFVCNPNNPTSTVVDPDALARFVEAVpPHIMVVVDEAYVEYIRDglaPDSFGLVRAHSNVV 208
                                               **********************************66****************999************** PP

                                 TIGR01141 204 vlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkerer 272
                                               vlrT+SKa+gLAglR+Gya+a+++ii al+kv  p+  +s++++aa+a l+ +d++ +++++v +er+r
  lcl|NCBI__GCF_000015305.1:WP_011782728.1 209 VLRTFSKAYGLAGLRIGYAVADPDIIAALSKVYVPFTATSVSQAAAIACLDAADELLERTDAVVAERTR 277
                                               ********************************************************************* PP

                                 TIGR01141 273 lleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreener 341
                                               + ++l++  g +  +S+aNFv + +   a++++  + ++++ivR  ++      + +R+t+  ++en++
  lcl|NCBI__GCF_000015305.1:WP_011782728.1 278 VSAALREA-GYDLPPSQANFVWLPLVGRAQQFAADAANSRVIVRPYGE------DGVRVTIAAPHENDA 339
                                               ********.8***************99******************983......458************ PP

                                 TIGR01141 342 lle 344
                                               +l 
  lcl|NCBI__GCF_000015305.1:WP_011782728.1 340 FLG 342
                                               996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (351 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.50
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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