Alignments for a candidate for hisC in Thauera aminoaromatica S2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Thauera aminoaromatica S2

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_004299041.1 C665_RS02140 histidinol-phosphate transaminase

Query= metacyc::BSU22620-MONOMER
         (360 letters)



>NCBI__GCF_000310185.1:WP_004299041.1
          Length = 365

 Score =  260 bits (665), Expect = 4e-74
 Identities = 153/358 (42%), Positives = 211/358 (58%), Gaps = 4/358 (1%)

Query: 5   EHLKQLKPYQPGKPIEAVKSEYGL--DKVVKLASNENPYGCSEAAKEALHHEIQQLALYP 62
           ++++ +  YQPGKPI  +  E G+  + +VKLASNENP G S  A++A    I +++ YP
Sbjct: 9   DYIRAIMAYQPGKPISELAREMGIPEESIVKLASNENPLGMSARARDAAIAAIGEVSRYP 68

Query: 63  DGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNA 122
           DG + AL+  L +   V    L+ GNGS++I+++  +AFL    + V +   F  Y    
Sbjct: 69  DGGAFALKKALCERFGVKPEQLVIGNGSNDILELASQAFLAPGLSAVYSRHAFAVYPLAT 128

Query: 123 VIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVP 182
              GA   E+A +  G HDLDAM  AI+ QT+VV+I +PNNPTGT+    EL AFL +VP
Sbjct: 129 NARGARGIEVAAKNFG-HDLDAMAAAIEPQTRVVFIANPNNPTGTFVPGAELEAFLAKVP 187

Query: 183 SRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLI 242
             VLVVLDEAY EY+  E   +++  L+++ NL++ RTFSKAYGLA LRVGYGIA   + 
Sbjct: 188 RHVLVVLDEAYTEYLAPEQRYDSIAWLARFPNLLVSRTFSKAYGLAGLRVGYGIAHPEVA 247

Query: 243 RQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQT 302
             +   R+PFN S +  AAA AAL D  F+A   E N  G+ Q     +  GL+  PS  
Sbjct: 248 DLMNRVRQPFNVSSVALAAAEAALGDDEFLARSAELNRRGMTQLVAAFRELGLEWIPSAG 307

Query: 303 NFVLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360
           NFV       A  + QALL +G IVR   A G P  LR++IG  E+N   +  L + L
Sbjct: 308 NFVTFKV-GDAIGVNQALLRQGVIVRPIAAYGMPHWLRVSIGLPEENARFIEALRQAL 364


Lambda     K      H
   0.317    0.134    0.382 

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: 308
Number of extensions: 18
Number of successful extensions: 4
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: 360
Length of database: 365
Length adjustment: 29
Effective length of query: 331
Effective length of database: 336
Effective search space:   111216
Effective search space used:   111216
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_004299041.1 C665_RS02140 (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.2399379.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-110  355.7   0.0   1.3e-110  355.5   0.0    1.0  1  NCBI__GCF_000310185.1:WP_004299041.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000310185.1:WP_004299041.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.5   0.0  1.3e-110  1.3e-110       3     348 ..      10     362 ..       8     363 .. 0.97

  Alignments for each domain:
  == domain 1  score: 355.5 bits;  conditional E-value: 1.3e-110
                             TIGR01141   3 kikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealaky 67 
                                            i+++ +Yqpg      are+g+    +vkL+snEnP+g+s ++++a+ +++ ++ rYpd  a++lk+al ++
  NCBI__GCF_000310185.1:WP_004299041.1  10 YIRAIMAYQPGkpiselAREMGIPeeSIVKLASNENPLGMSARARDAAIAAIGEVSRYPDGGAFALKKALCER 82 
                                           5999*************9998876669********************************************** PP

                             TIGR01141  68 lgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaa 140
                                           +gv++e++++gnGs++++el  +afl pg +++++ +++++Y++ ++++ga+ +ev++k+   +dl+a+++a+
  NCBI__GCF_000310185.1:WP_004299041.1  83 FGVKPEQLVIGNGSNDILELASQAFLAPGLSAVYSRHAFAVYPLATNARGARGIEVAAKNF-GHDLDAMAAAI 154
                                           ********************************************************99887.69********* PP

                             TIGR01141 141 kekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlrTlS 209
                                           + ++++vf+a+PnnPtG+++  +e+e++l++v +++lVV+DeAY+e+      ++ + +la++pnl+v+rT+S
  NCBI__GCF_000310185.1:WP_004299041.1 155 EPQTRVVFIANPNNPTGTFVPGAELEAFLAKVpRHVLVVLDEAYTEYLAPeqrYDSIAWLARFPNLLVSRTFS 227
                                           ********************************88*************86657899****************** PP

                             TIGR01141 210 KafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleg 282
                                           Ka+gLAglRvGy+ia++e+++ +++vr+p+nvss+al+aa aal d+++++++ e +++++++l +++++l g
  NCBI__GCF_000310185.1:WP_004299041.1 228 KAYGLAGLRVGYGIAHPEVADLMNRVRQPFNVSSVALAAAEAALGDDEFLARSAELNRRGMTQLVAAFREL-G 299
                                           ***********************************************************************.8 PP

                             TIGR01141 283 levyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                           le+++S +NFv++kv  da  + +all++g+ivR ++++ g+ +++lR+++G +een r++eal++
  NCBI__GCF_000310185.1:WP_004299041.1 300 LEWIPSAGNFVTFKVG-DAIGVNQALLRQGVIVRPIAAY-GM-PHWLRVSIGLPEENARFIEALRQ 362
                                           ***************9.********************99.96.********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (365 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: 00:00:00.01
# Mc/sec: 9.11
//
[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