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 transaminase (EC 2.6.1.9) (characterized)
to candidate WP_011780020.1 MVAN_RS14090 histidinol-phosphate aminotransferase

Query= BRENDA::P9WML7
         (380 letters)



>NCBI__GCF_000015305.1:WP_011780020.1
          Length = 373

 Score =  579 bits (1492), Expect = e-170
 Identities = 289/365 (79%), Positives = 317/365 (86%), Gaps = 4/365 (1%)

Query: 5   GHPVTLDDLPLRADLRGKAPYGAPQLAVPVRLNTNENPHPPTRALVDDVVRSVREAAIDL 64
           G  +TLDDLPLR DLRGK+PYGAPQL+VPVRLNTNENPHPPTRAL+DDV +SVRE A +L
Sbjct: 6   GSSITLDDLPLRDDLRGKSPYGAPQLSVPVRLNTNENPHPPTRALIDDVAQSVREVAGEL 65

Query: 65  HRYPDRDAVALRADLAGYLTAQTGIQLGVENIWAANGSNEILQQLLQAFGGPGRSAIGFV 124
           HRYPDRDAVALR DLA YL+AQTG  +GVEN+WAANGSNEILQQLLQAFGGPGRSA+GFV
Sbjct: 66  HRYPDRDAVALRTDLAAYLSAQTGTAVGVENVWAANGSNEILQQLLQAFGGPGRSALGFV 125

Query: 125 PSYSMHPIISDGTHTEWIEASRANDFGLDVDVAVAAVVDRKPDVVFIASPNNPSGQSVSL 184
           PSYSMHPIISDGT T W+ A+R +DFGLD  VA  A+ +  PDVVF+ SPNNPSGQSVSL
Sbjct: 126 PSYSMHPIISDGTQTRWLVANRGDDFGLDAAVAATAIKEHTPDVVFVTSPNNPSGQSVSL 185

Query: 185 PDLCKLLDVA----PGIAIVDEAYGEFSSQPSAVSLVEEYPSKLVVTRTMSKAFAFAGGR 240
            DL  LLD       G+ IVDEAYGEFSSQPSA+ L+E YP KLVVTRTMSKAFAFAGGR
Sbjct: 186 DDLRLLLDALCLQDGGVMIVDEAYGEFSSQPSAIGLIESYPGKLVVTRTMSKAFAFAGGR 245

Query: 241 LGYLIATPAVIDAMLLVRLPYHLSSVTQAAARAALRHSDDTLSSVAALIAERERVTTSLN 300
           +GYL+A PAVIDAMLLVRLPYHLSSVTQAAARAALRH+DDTL SVA LIAERERV+ +L 
Sbjct: 246 VGYLVAAPAVIDAMLLVRLPYHLSSVTQAAARAALRHADDTLGSVATLIAERERVSQALT 305

Query: 301 DMGFRVIPSDANFVLFGEFADAPAAWRRYLEAGILIRDVGIPGYLRATTGLAEENDAFLR 360
            MGFRVIPSDANF+LFGEFADAPA W+RYL+ G+LIRDVGIPGYLR T GLAEENDA L 
Sbjct: 306 GMGFRVIPSDANFILFGEFADAPATWQRYLDEGVLIRDVGIPGYLRTTIGLAEENDALLA 365

Query: 361 ASARI 365
           ASARI
Sbjct: 366 ASARI 370


Lambda     K      H
   0.319    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: 534
Number of extensions: 14
Number of successful extensions: 2
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: 380
Length of database: 373
Length adjustment: 30
Effective length of query: 350
Effective length of database: 343
Effective search space:   120050
Effective search space used:   120050
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_011780020.1 MVAN_RS14090 (histidinol-phosphate 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.20067.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.6e-102  326.4   0.0   1.1e-101  326.2   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011780020.1  MVAN_RS14090 histidinol-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011780020.1  MVAN_RS14090 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.2   0.0  1.1e-101  1.1e-101       1     348 [.      17     369 ..      17     370 .. 0.95

  Alignments for each domain:
  == domain 1  score: 326.2 bits;  conditional E-value: 1.1e-101
                                 TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk....klhrYpdpqalelkeala 65 
                                               r++++  +pY ++      +  v+Ln+nEnP++p++++++++ ++++    +lhrYpd++a++l+++la
  lcl|NCBI__GCF_000015305.1:WP_011780020.1  17 RDDLRGKSPYGAP----QLSVPVRLNTNENPHPPTRALIDDVAQSVRevagELHRYPDRDAVALRTDLA 81 
                                               6788889999995....44568**********************99999999***************** PP

                                 TIGR01141  66 kylg......veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplked 128
                                               +yl+      v++en++++nGs+e+++ l++af  pg+++l + p+ysm++++++ +++++  ++  +d
  lcl|NCBI__GCF_000015305.1:WP_011780020.1  82 AYLSaqtgtaVGVENVWAANGSNEILQQLLQAFGGPGRSALGFVPSYSMHPIISDGTQTRWLVANRGDD 150
                                               ********************************************************************* PP

                                 TIGR01141 129 gqedleavle.aakekvklvflasPnnPtGnllkreeiekvleev..e.dalVVvDeAYieFseeasvl 193
                                               +  d + +++ ++++ +++vf++sPnnP+G++++ ++++ +l++   +  ++ +vDeAY+eFs+++s++
  lcl|NCBI__GCF_000015305.1:WP_011780020.1 151 FGLDAAVAATaIKEHTPDVVFVTSPNNPSGQSVSLDDLRLLLDALclQdGGVMIVDEAYGEFSSQPSAI 219
                                               55555555443888999**************************9986678999**************** PP

                                 TIGR01141 194 ellaeyp.nlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiek 261
                                                l++ yp +lvv+rT+SKaf++Ag RvGy++a +++i+a+  vr py++ss++++aa aalr++d++  
  lcl|NCBI__GCF_000015305.1:WP_011780020.1 220 GLIESYPgKLVVTRTMSKAFAFAGGRVGYLVAAPAVIDAMLLVRLPYHLSSVTQAAARAALRHADDTLG 288
                                               *******9************************************************************* PP

                                 TIGR01141 262 tveevkkererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclR 330
                                               +v+ +++erer+ ++l+ + g++v++S+aNF+l+   +da + ++++l++g+++Rd++     ++++lR
  lcl|NCBI__GCF_000015305.1:WP_011780020.1 289 SVATLIAERERVSQALTGM-GFRVIPSDANFILFGEFADAPATWQRYLDEGVLIRDVG-----IPGYLR 351
                                               *******************.8**************999*******************7.....689*** PP

                                 TIGR01141 331 itvGtreenerllealke 348
                                                t+G +een++ll+a ++
  lcl|NCBI__GCF_000015305.1:WP_011780020.1 352 TTIGLAEENDALLAASAR 369
                                               *************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (373 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: 8.32
//
[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