Alignments for a candidate for hisC in Methylovulum miyakonense HT12

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Methylovulum miyakonense HT12

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_019866295.1 METMI_RS0110735 histidinol-phosphate transaminase

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



>NCBI__GCF_000384075.1:WP_019866295.1
          Length = 367

 Score =  254 bits (650), Expect = 2e-72
 Identities = 142/354 (40%), Positives = 208/354 (58%), Gaps = 1/354 (0%)

Query: 7   LKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYPDGYS 66
           +++L PY+ GKPIE ++ E GL +++KLASNENP G  + A  A+   + +LALYPDG  
Sbjct: 14  VQKLIPYKAGKPIEELERELGLTQIIKLASNENPLGPGKQAIAAIQKALPELALYPDGSG 73

Query: 67  AALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVIEG 126
             L+  L+    +  + +  GNGS+E+++++ RAFL  +   V +   F  Y       G
Sbjct: 74  FHLKQALATKYALDASQITLGNGSNELLELVARAFLIPELEVVFSQHAFAVYPLVTQAVG 133

Query: 127 AEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVPSRVL 186
           A    +  +  G HDL  M +A+  +T++V+I +PNNPTGT  ++ EL  F+  +P  V+
Sbjct: 134 ATAVVVPAKEYG-HDLAGMAQAVTAKTRLVFIANPNNPTGTLLAQAELEQFIGALPDTVI 192

Query: 187 VVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQIE 246
            VLDEAY+E+V+      ++  L K+ NL+I RTFSKAYGLA LRVGY ++   +   + 
Sbjct: 193 CVLDEAYFEFVSQSAAINSIDWLKKFPNLIITRTFSKAYGLAGLRVGYSLSCPEIADILN 252

Query: 247 PAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQTNFVL 306
             R+PFN + L  AAA AAL D+  + + +  N  G+QQ  D  K  GL   PS  NFV 
Sbjct: 253 RVRQPFNNNSLALAAAEAALADEEHLHNTISNNRLGMQQLTDGFKALGLPWIPSAGNFVS 312

Query: 307 IDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360
           +D KR    +++ALL KG IVR       P  LRI+IGT  +N   L  L+E+L
Sbjct: 313 VDVKREGMPVYEALLRKGVIVRPVANYEMPGFLRISIGTPAENTLFLQALSEVL 366


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: 341
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: 360
Length of database: 367
Length adjustment: 29
Effective length of query: 331
Effective length of database: 338
Effective search space:   111878
Effective search space used:   111878
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_019866295.1 METMI_RS0110735 (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.28803.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-114  366.9   0.0   5.6e-114  366.6   0.0    1.0  1  lcl|NCBI__GCF_000384075.1:WP_019866295.1  METMI_RS0110735 histidinol-phosp


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384075.1:WP_019866295.1  METMI_RS0110735 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.6   0.0  5.6e-114  5.6e-114       4     349 .]      14     365 ..      12     365 .. 0.98

  Alignments for each domain:
  == domain 1  score: 366.6 bits;  conditional E-value: 5.6e-114
                                 TIGR01141   4 ikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealak 66 
                                               ++kl pY++g      +relg ++++kL+snEnP+gp +++++a++++l +l +Ypd ++++lk+ala 
  lcl|NCBI__GCF_000384075.1:WP_019866295.1  14 VQKLIPYKAGkpieelERELGLTQIIKLASNENPLGPGKQAIAAIQKALPELALYPDGSGFHLKQALAT 82 
                                               89******************************************************************* PP

                                 TIGR01141  67 ylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedlea 135
                                               ++ +++ +i+lgnGs+el+el++rafl p+ +v+++++++++Y++++++ ga  + vp+ke g +dl+ 
  lcl|NCBI__GCF_000384075.1:WP_019866295.1  83 KYALDASQITLGNGSNELLELVARAFLIPELEVVFSQHAFAVYPLVTQAVGATAVVVPAKEYG-HDLAG 150
                                               **************************************************************6.9**** PP

                                 TIGR01141 136 vleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeyp 200
                                               +++a++ k++lvf+a+PnnPtG+ll ++e+e+++ +   ++++V+DeAY eF ++    + +++l+++p
  lcl|NCBI__GCF_000384075.1:WP_019866295.1 151 MAQAVTAKTRLVFIANPNNPTGTLLAQAELEQFIGALpDTVICVLDEAYFEFVSQsaaINSIDWLKKFP 219
                                               *************************************77***************98888999******* PP

                                 TIGR01141 201 nlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkke 269
                                               nl+++rT+SKa+gLAglRvGy ++++ei+++l++vr+p+n +slal+aa aal d++++++t+ +++ +
  lcl|NCBI__GCF_000384075.1:WP_019866295.1 220 NLIITRTFSKAYGLAGLRVGYSLSCPEIADILNRVRQPFNNNSLALAAAEAALADEEHLHNTISNNRLG 288
                                               ********************************************************************* PP

                                 TIGR01141 270 rerlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtree 338
                                               +++l++++k+l gl +++S +NFv ++vk++   ++eall+kg+ivR ++++e  ++++lRi++Gt+ e
  lcl|NCBI__GCF_000384075.1:WP_019866295.1 289 MQQLTDGFKAL-GLPWIPSAGNFVSVDVKREGMPVYEALLRKGVIVRPVANYE--MPGFLRISIGTPAE 354
                                               ***********.8***************************************5..5************* PP

                                 TIGR01141 339 nerllealkei 349
                                               n+ +l+al+e+
  lcl|NCBI__GCF_000384075.1:WP_019866295.1 355 NTLFLQALSEV 365
                                               ********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (367 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.78
//
[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