Alignments for a candidate for metX in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Dechlorosoma suillum PS

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate Dsui_0741 Dsui_0741 homoserine O-acetyltransferase

Query= SwissProt::F7XKY8
         (492 letters)



>FitnessBrowser__PS:Dsui_0741
          Length = 375

 Score =  381 bits (979), Expect = e-110
 Identities = 191/375 (50%), Positives = 263/375 (70%), Gaps = 9/375 (2%)

Query: 3   KGSLGIVETKYYHLEEELKLESGRKISDVTIAYEAYGTLNRDKNNVILVCHALTGDAHAA 62
           K S+G+V  +  H  E ++L SG  ++   + YE YG LN D++N +LVCHAL+G  H A
Sbjct: 4   KHSVGVVSPQRAHFAEPIQLASGATLAAYDLVYETYGRLNADRSNAVLVCHALSGSHHVA 63

Query: 63  GWHKGDNKP--GWWDILIGPGKCLDTDKYFIVCSNVIGGCRGSTGPSSIDPETGKPYGLS 120
           G H  DN    GWWD L+GPGK LDTDK+F+V  N +GGC GSTGP SI+P TGKPYG  
Sbjct: 64  G-HYADNPKNVGWWDNLVGPGKPLDTDKFFVVGVNNLGGCYGSTGPGSINPATGKPYGAD 122

Query: 121 FPVITIKDMVNAQKKLLDHLGISSIYAVIGGSMGGLQVLQWSVSYPDYINKAIALAASAY 180
           FPV+T++D V +Q +L D LGI+   A+IGGS+GG+Q LQWS+ YP+ +  A+ +A++  
Sbjct: 123 FPVVTVEDWVESQARLADRLGINQWAAIIGGSLGGMQALQWSLEYPERVRHALVIASAPK 182

Query: 181 SSPQQIAFNEVARIAIISDPEWNKGNYY-YSRQPSHGLALARMIGHITYLSDESMREKFG 239
            + Q IAFNEVAR AI++DP+++ GNYY +   P+ GL LARM+GHITYLSD+ M EKFG
Sbjct: 183 LTAQNIAFNEVARQAILTDPDFHGGNYYEHGVVPARGLRLARMVGHITYLSDDQMGEKFG 242

Query: 240 RELQDRD-RYNYDLSMDFQVESYLHYKGRSFTERFDANSYLYITKAVDYFDLTEN--GSL 296
           R+L++   +YNYD  +DF++ESYL Y+G  F   FDAN+YL  TKA+DYFD   +  G L
Sbjct: 243 RQLREGVLKYNYD--VDFEIESYLRYQGDKFAGFFDANTYLITTKALDYFDPARDFGGDL 300

Query: 297 IDGLKDIKAKCLIIAVTSDWLYPPYQSKDIVMALNANNVDVTYREIESNYGHDAFLLEAG 356
              L    AK L+++ T+DW + P +S+++V AL  NN +V+Y EI+ N GHD+FLL+  
Sbjct: 301 KAALARASAKFLLVSFTTDWRFAPERSREMVYALLHNNREVSYAEIDCNAGHDSFLLDDA 360

Query: 357 QLNYVIGGFLNNITV 371
           Q + V+G +L+NI V
Sbjct: 361 QYHAVMGAYLHNIAV 375


Lambda     K      H
   0.318    0.136    0.405 

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: 570
Number of extensions: 27
Number of successful extensions: 5
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: 492
Length of database: 375
Length adjustment: 32
Effective length of query: 460
Effective length of database: 343
Effective search space:   157780
Effective search space used:   157780
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate Dsui_0741 Dsui_0741 (homoserine O-acetyltransferase)
to HMM TIGR01392 (metX: homoserine O-acetyltransferase (EC 2.3.1.31))

# 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/TIGR01392.hmm
# target sequence database:        /tmp/gapView.21676.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01392  [M=351]
Accession:   TIGR01392
Description: homoserO_Ac_trn: homoserine O-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.7e-146  472.6   0.0   4.3e-146  472.4   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0741  Dsui_0741 homoserine O-acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0741  Dsui_0741 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.4   0.0  4.3e-146  4.3e-146       3     349 ..      19     369 ..      17     371 .. 0.97

  Alignments for each domain:
  == domain 1  score: 472.4 bits;  conditional E-value: 4.3e-146
                         TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldtsryfvvc 77 
                                       e+++l sG++l  ++++y+tyG+lna+r+NavlvcHal+gs+hvag++ ++ k  GWWd+l+Gpg++ldt+++fvv+
  lcl|FitnessBrowser__PS:Dsui_0741  19 EPIQLASGATLAAYDLVYETYGRLNADRSNAVLVCHALSGSHHVAGHYADNPKnvGWWDNLVGPGKPLDTDKFFVVG 95 
                                       7899********************************************9888899********************** PP

                         TIGR01392  78 lNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewalsypervk 154
                                       +N+lG+c+GstgP sinp+tgkpyga+fP+vt++D+v+ q++l+d+Lg++++aa++GgSlGGmqal+w+l+yperv+
  lcl|FitnessBrowser__PS:Dsui_0741  96 VNNLGGCYGSTGPGSINPATGKPYGADFPVVTVEDWVESQARLADRLGINQWAAIIGGSLGGMQALQWSLEYPERVR 172
                                       ***************************************************************************** PP

                         TIGR01392 155 kivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesleerfgreaksee 230
                                       +++v+a++++++aq+iafnev+rqail+Dp++++G+y+e++  P++GL+lARm++++tY+s++++ e+fgr+ ++  
  lcl|FitnessBrowser__PS:Dsui_0741 173 HALVIASAPKLTAQNIAFNEVARQAILTDPDFHGGNYYEHGvVPARGLRLARMVGHITYLSDDQMGEKFGRQLREG- 248
                                       *****************************************9******************************9999. PP

                         TIGR01392 231 slassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikapvlvvgiesDllftle 307
                                        l+++++ +f++esylryqg+kf+  FdAn+Yl+ tkald++d ar+  ++lk+al++++a++l+v++++D++f++e
  lcl|FitnessBrowser__PS:Dsui_0741 249 VLKYNYDVDFEIESYLRYQGDKFAGFFDANTYLITTKALDYFDPARDFGGDLKAALARASAKFLLVSFTTDWRFAPE 325
                                       789999*********************************************************************** PP

                         TIGR01392 308 eqeelakalkaakle..yaeieseeGHDaFllekekveeliref 349
                                       +++e++ al +++ e  yaei+ ++GHD+Fll+++++++++ ++
  lcl|FitnessBrowser__PS:Dsui_0741 326 RSREMVYALLHNNREvsYAEIDCNAGHDSFLLDDAQYHAVMGAY 369
                                       *****999877776668********************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (375 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.76
//
[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