GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Acidovorax sp. GW101-3H11

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate Ac3H11_4277 Homoserine O-acetyltransferase (EC 2.3.1.31)

Query= SwissProt::Q8TME4
         (540 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4277
          Length = 401

 Score =  342 bits (877), Expect = 2e-98
 Identities = 175/388 (45%), Positives = 242/388 (62%), Gaps = 9/388 (2%)

Query: 36  PGTFGLESGKTLSGVRVEYEMYGKMNADKSNVILICHALTGDAHAAGFHEG-DKKPGWWE 94
           P    L+SG +L    + YE YG +NAD+SN +L+CHAL    H AG + G DK  GWW+
Sbjct: 13  PEVLPLQSGASLRDYHLAYETYGTLNADRSNAVLVCHALNASHHVAGVYAGQDKSEGWWD 72

Query: 95  IVIGPNKAFDTEKYCVICSNILGGCKGSTGPSSIDPETGKHYGISFPVITVKDMVNAQKK 154
            +IGP K  DT+++ VI  N LG C GSTGP    P+TG+ YG  FPV+TV+D VNAQ +
Sbjct: 73  NMIGPGKPVDTDRFFVIGVNNLGSCFGSTGPMHNHPDTGEVYGADFPVVTVEDWVNAQAR 132

Query: 155 LIEHLGVKQLFAVAGGSMGGMQVLQWTVSYPEMVRKAIAIATTASTTPQQIAFGAIGRKA 214
           L++ LG+ QL AV GGS+GGMQ L WT+ YPE +R A+ +A+  + T + IAF  + R+A
Sbjct: 133 LLDRLGITQLAAVLGGSLGGMQALSWTLQYPERMRHAVVVASAPNLTAENIAFNEVARRA 192

Query: 215 ITDDPKWNGGDYYGK-EIPSQGLALARMIGHITYLSDASMQNKFGRLQQDTDKSGIKGTT 273
           I  DP ++GG +Y    IP +GL +ARMIGHITYLSD  M  KFGR  +       +G+ 
Sbjct: 193 IVTDPDFHGGHFYRHGVIPKRGLRIARMIGHITYLSDDVMNEKFGRSLRAPTLPAARGSL 252

Query: 274 GTEGKNSSEISSEISSISSEISSELSYDFTPNFQVESYLNYKGDNFTKRFDANSYLYITK 333
             EG   +         + ++   L       FQ+ESYL Y+GD F+  FDAN+YL IT+
Sbjct: 253 PPEGAGPAR-----GGPAPDLRDYLYSTQDIEFQIESYLRYQGDKFSDYFDANTYLLITR 307

Query: 334 AVDYFDLAK--NGSLIEGFSGVTAKYLVISISSDWLYPPYQSQEIVSALTANGVDARYEE 391
           A+DYFD A+   G+L    +  TAK+L++S ++DW + P +S+EIV AL  N     Y E
Sbjct: 308 ALDYFDPARAHGGNLTRALARATAKFLLVSFTTDWRFSPQRSREIVKALLDNRRRVSYAE 367

Query: 392 IRSQHGHDAFLLEEGQLSYLLRSFLSHI 419
           I + HGHDAFLL++ +   ++RS+   I
Sbjct: 368 IDAPHGHDAFLLDDARYMGVMRSYFDSI 395


Lambda     K      H
   0.315    0.132    0.379 

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: 545
Number of extensions: 25
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: 540
Length of database: 401
Length adjustment: 33
Effective length of query: 507
Effective length of database: 368
Effective search space:   186576
Effective search space used:   186576
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: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate Ac3H11_4277 (Homoserine O-acetyltransferase (EC 2.3.1.31))
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.3930009.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   3.1e-141  456.4   0.0   3.6e-141  456.2   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4277  Homoserine O-acetyltransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4277  Homoserine O-acetyltransferase (EC 2.3.1.31)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.2   0.0  3.6e-141  3.6e-141       4     349 ..      15     391 ..      12     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: 456.2 bits;  conditional E-value: 3.6e-141
                                        TIGR01392   4 eltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellG 63 
                                                       l l+sG+ l+++++ay+tyGtlna+r+NavlvcHal +s+hvag +  +dk  GWWd+++G
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4277  15 VLPLQSGASLRDYHLAYETYGTLNADRSNAVLVCHALNASHHVAGVYAGQDKseGWWDNMIG 76 
                                                      5889******************************************99888788******** PP

                                        TIGR01392  64 pgraldtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLg 125
                                                      pg+++dt+r+fv+++N+lGsc GstgP+  +p+tg+ yga+fP+vt++D+v+aq++lld+Lg
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4277  77 PGKPVDTDRFFVIGVNNLGSCFGSTGPMHNHPDTGEVYGADFPVVTVEDWVNAQARLLDRLG 138
                                                      ************************************************************** PP

                                        TIGR01392 126 veklaavvGgSlGGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyn 187
                                                      +++laav+GgSlGGmqal w+l+yper++++vv+a++++++a++iafnev+r+ai +Dp+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4277 139 ITQLAAVLGGSLGGMQALSWTLQYPERMRHAVVVASAPNLTAENIAFNEVARRAIVTDPDFH 200
                                                      ************************************************************** PP

                                        TIGR01392 188 dGeyaeee.qPekGLalARmlalltYrseesleerfgreaksee.................. 230
                                                      +G++++++  P++GL++ARm++++tY+s++ ++e+fgr+ ++ +                  
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4277 201 GGHFYRHGvIPKRGLRIARMIGHITYLSDDVMNEKFGRSLRAPTlpaargslppegagparg 262
                                                      *******99********************************999555555555555555555 PP

                                        TIGR01392 231 ..slass.........leeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrds 281
                                                        +             ++ ef++esylryqg+kf + FdAn+Yll+t+ald++d ar + ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4277 263 gpA---PdlrdylystQDIEFQIESYLRYQGDKFSDYFDANTYLLITRALDYFDPARAHGGN 321
                                                      550...0555555443699******************************************* PP

                                        TIGR01392 282 lkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekek 341
                                                      l++al++++a++l+v++++D++f++++++e++kal +++ +  yaei+ ++GHDaFll++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4277 322 LTRALARATAKFLLVSFTTDWRFSPQRSREIVKALLDNRRRvsYAEIDAPHGHDAFLLDDAR 383
                                                      ***********************************99988888*****************99 PP

                                        TIGR01392 342 veeliref 349
                                                      ++ ++r++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4277 384 YMGVMRSY 391
                                                      98887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (401 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: 15.31
//
[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:

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:

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:

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:

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