Alignments for a candidate for hisC in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Marinobacter adhaerens HP15

Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate GFF1396 HP15_1363 histidinol-phosphate aminotransferase

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



>FitnessBrowser__Marino:GFF1396
          Length = 374

 Score =  273 bits (699), Expect = 4e-78
 Identities = 149/356 (41%), Positives = 214/356 (60%), Gaps = 3/356 (0%)

Query: 7   LKQLKPYQPGKPIEAVKSEYGLD--KVVKLASNENPYGCSEAAKEALHHEIQQLALYPDG 64
           ++ L PYQPGKPIE +  E GL+  +++KLASNENP G SE A  A    + +L LYPDG
Sbjct: 13  VQALSPYQPGKPIEELARELGLNPAEIIKLASNENPLGPSEKALSAARRALSELCLYPDG 72

Query: 65  YSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVI 124
               L+  LS  LNV    +  GNGS++++++I R F +  +  V +   F  Y      
Sbjct: 73  NGFNLKQALSTRLNVGMDQITLGNGSNDVLEVITRCFADADSEVVFSQYAFAVYPLVTQA 132

Query: 125 EGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVPSR 184
            GA    +  R  G HDLDAM  A+ ++T++V++ +PNNPTGT  +   + AFL+++P  
Sbjct: 133 IGARGVSVPAREWG-HDLDAMAAAVTDRTRLVFVANPNNPTGTVHTAEAIEAFLKKIPEN 191

Query: 185 VLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQ 244
           VLVVLDEAY EY+T + YP+ V LL+++ NL++ RTFSKA+GLAALRVGY I+   +   
Sbjct: 192 VLVVLDEAYCEYLTGDQYPDGVELLARFPNLIVCRTFSKAWGLAALRVGYSISSPAIADI 251

Query: 245 IEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQTNF 304
           +   R+PFN   +  +AA A LDD+ ++    + N AGL+Q  +     GL   PS  NF
Sbjct: 252 LNRVRQPFNVDTVALSAATAVLDDEDYLQRSRDVNTAGLRQLQEAFDRMGLGYIPSAGNF 311

Query: 305 VLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360
           V ++    A  ++QALL  G IVR     G P  LR+++G  E+NE  +  LA+ L
Sbjct: 312 VAVEVGEQAMGVYQALLAHGVIVRPIAGYGMPRHLRVSVGLPEENERFIEALAQAL 367


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: 357
Number of extensions: 13
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: 360
Length of database: 374
Length adjustment: 30
Effective length of query: 330
Effective length of database: 344
Effective search space:   113520
Effective search space used:   113520
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 GFF1396 HP15_1363 (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.16755.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.3e-112  362.1   0.0   1.4e-112  361.9   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF1396  HP15_1363 histidinol-phosphate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1396  HP15_1363 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.9   0.0  1.4e-112  1.4e-112       3     348 ..      12     365 ..      10     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 361.9 bits;  conditional E-value: 1.4e-112
                           TIGR01141   3 kikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 
                                          +++l+pYqpg      arelg +  e++kL+snEnP+gpsek++ a++++l++l +Ypd ++++lk+al+ +l+
  lcl|FitnessBrowser__Marino:GFF1396  12 GVQALSPYQPGkpieelARELGLNpaEIIKLASNENPLGPSEKALSAARRALSELCLYPDGNGFNLKQALSTRLN 86 
                                         699************************************************************************ PP

                           TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekv 144
                                         v++++i+lgnGs++++e+++r f++   +v+++++++++Y++++++ ga+ ++vp++e+g +dl+a+++a+++++
  lcl|FitnessBrowser__Marino:GFF1396  87 VGMDQITLGNGSNDVLEVITRCFADADSEVVFSQYAFAVYPLVTQAIGARGVSVPAREWG-HDLDAMAAAVTDRT 160
                                         **********************************************************95.9************* PP

                           TIGR01141 145 klvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlrTlSKafgLA 215
                                         +lvf+a+PnnPtG++ ++e ie++l++  e++lVV+DeAY e+ +    ++ +ella++pnl+v rT+SKa gLA
  lcl|FitnessBrowser__Marino:GFF1396 161 RLVFVANPNNPTGTVHTAEAIEAFLKKIpENVLVVLDEAYCEYLTGdqyPDGVELLARFPNLIVCRTFSKAWGLA 235
                                         ****************************99*************9877899************************* PP

                           TIGR01141 216 glRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSka 290
                                         +lRvGy i++++i+++l++vr+p+nv+++al+aa+a l+d+d+++++ + + ++ ++l+e++  + gl +++S +
  lcl|FitnessBrowser__Marino:GFF1396 236 ALRVGYSISSPAIADILNRVRQPFNVDTVALSAATAVLDDEDYLQRSRDVNTAGLRQLQEAFDRM-GLGYIPSAG 309
                                         *****************************************************************.8******** PP

                           TIGR01141 291 NFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                         NFv ++v e+a  +++all +g+ivR ++ + g+ + +lR++vG +eener++eal++
  lcl|FitnessBrowser__Marino:GFF1396 310 NFVAVEVGEQAMGVYQALLAHGVIVRPIAGY-GM-PRHLRVSVGLPEENERFIEALAQ 365
                                         *******************************.96.********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (374 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: 7.79
//
[ok]

This GapMind analysis is from Apr 09 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