Alignments for a candidate for hisC in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Thermomonospora curvata DSM 43183

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_012853225.1 TCUR_RS27540 histidinol-phosphate transaminase

Query= curated2:Q2J8K9
         (397 letters)



>NCBI__GCF_000024385.1:WP_012853225.1
          Length = 366

 Score =  446 bits (1146), Expect = e-130
 Identities = 234/360 (65%), Positives = 267/360 (74%), Gaps = 5/360 (1%)

Query: 23  LPLRDSLRGLSPYGAPQLDVPVRLNTNENPHPPSVGLVDAIGKAAALAATEANRYPDRDA 82
           LPLR+ LRG  PYGAPQLDVPVRLNTNENP+PPS  LV+A+ KA A AA   NRYPDRDA
Sbjct: 7   LPLREDLRGREPYGAPQLDVPVRLNTNENPYPPSERLVEALAKAVAAAAASLNRYPDRDA 66

Query: 83  EALRADLAYYLTPDA-GFGVHTSQVWAANGSNEILQQLLQAFGGPGRVALGFEPSYSMHR 141
            ALRA+LA +L  D  G  +   +VWAANGSNEI+QQ+LQAFGGPGR ALGFEPSYSMH 
Sbjct: 67  LALRAELADFLNHDTPGAELTAERVWAANGSNEIIQQILQAFGGPGRCALGFEPSYSMHP 126

Query: 142 LIALATATEWVAGQRAEDFTLSPAVVTDAIARHRPALVFLCSPNNPTGTALPPEVVAAAC 201
           +I   T T W+   R EDF L       AI  HRP +VFL SPNNPTGT+LP EV+    
Sbjct: 127 IITHVTGTRWINAHRDEDFGLDVDRALAAIDEHRPDVVFLTSPNNPTGTSLPLEVI---- 182

Query: 202 EAVEATGSGMVVVDEAYAEFRRAGVPSTLTLLPRHPRLVVTRTMSKAFALAGARVGYLAA 261
           EA+ A   GMVVVDEAYAEFRR    S L LL  HPRL+VTRTMSKAFA+AG R+GYLAA
Sbjct: 183 EAIAAAAPGMVVVDEAYAEFRREDTLSALELLAEHPRLIVTRTMSKAFAMAGVRLGYLAA 242

Query: 262 HPAVVDSLYLVRLPYHLSSFTQAVARTALAHADELLGTVEAVKAQRDRIVRELPALGLRL 321
           HPAV+++L LVRLPYHLSS TQA ARTALAHADELLG+V  ++ +RD IV  L   GLR+
Sbjct: 243 HPAVIEALLLVRLPYHLSSITQAAARTALAHADELLGSVAQLRTERDLIVGWLRGQGLRV 302

Query: 322 APSDANFVFFGRFADQRAVWQSLLDAGVLVRDVGLTGWLRVTAGLPNEVDAFLGALGRTL 381
           A SDANFV FG F D+R VWQ++LD GVL+R+VG   WLRVT G P E+ AF  AL   L
Sbjct: 303 ADSDANFVLFGTFPDRRRVWQAMLDQGVLIREVGPPQWLRVTVGTPAEMAAFRSALTTAL 362


Lambda     K      H
   0.320    0.135    0.403 

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: 466
Number of extensions: 17
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: 397
Length of database: 366
Length adjustment: 30
Effective length of query: 367
Effective length of database: 336
Effective search space:   123312
Effective search space used:   123312
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: 50 (23.9 bits)

Align candidate WP_012853225.1 TCUR_RS27540 (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.677513.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.1e-100  320.7   0.0     6e-100  320.4   0.0    1.0  1  NCBI__GCF_000024385.1:WP_012853225.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000024385.1:WP_012853225.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.4   0.0    6e-100    6e-100       1     346 [.      10     358 ..      10     361 .. 0.95

  Alignments for each domain:
  == domain 1  score: 320.4 bits;  conditional E-value: 6e-100
                             TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk....klhrYpdpqalelkealakylg 69 
                                           re+++  epY ++      +  v+Ln+nEnP++pse+++eal ++++    +l+rYpd++al+l+++la++l+
  NCBI__GCF_000024385.1:WP_012853225.1  10 REDLRGREPYGAP----QLDVPVRLNTNENPYPPSERLVEALAKAVAaaaaSLNRYPDRDALALRAELADFLN 78 
                                           6788888899885....45579*******************9999988888********************** PP

                             TIGR01141  70 .......veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedlea 135
                                                  +++e ++++nGs+e+i+ +++af  pg+ +l +ep+ysm++++++++g+++++++ +ed+  d++ 
  NCBI__GCF_000024385.1:WP_012853225.1  79 hdtpgaeLTAERVWAANGSNEIIQQILQAFGGPGRCALGFEPSYSMHPIITHVTGTRWINAHRDEDFGLDVDR 151
                                           ******************************************************************7777777 PP

                             TIGR01141 136 vle.aakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFsee..asvlellaeypnlvvl 205
                                           +l+ + ++++++vfl+sPnnPtG++l  e ie++++++  ++VVvDeAY eF +e   s+lellae+p l+v+
  NCBI__GCF_000024385.1:WP_012853225.1 152 ALAaIDEHRPDVVFLTSPNNPTGTSLPLEVIEAIAAAA-PGMVVVDEAYAEFRREdtLSALELLAEHPRLIVT 223
                                           766477899****************************8.9*************998899************** PP

                             TIGR01141 206 rTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelk 278
                                           rT+SKaf++Ag+R+Gy+ a++++ieal  vr py++ss++++aa +al ++d++  +v++++ er+ +   l+
  NCBI__GCF_000024385.1:WP_012853225.1 224 RTMSKAFAMAGVRLGYLAAHPAVIEALLLVRLPYHLSSITQAAARTALAHADELLGSVAQLRTERDLIVGWLR 296
                                           ************************************************************************9 PP

                             TIGR01141 279 kleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerlleal 346
                                              gl+v +S+aNFvl+ +  d +++++a+l++g+++R+++  +   +++lR+tvGt+ e+ ++  al
  NCBI__GCF_000024385.1:WP_012853225.1 297 GQ-GLRVADSDANFVLFGTFPDRRRVWQAMLDQGVLIREVG--P---PQWLRVTVGTPAEMAAFRSAL 358
                                           87.8*************9999*******************8..3...78************9997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (366 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.68
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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