Alignments for a candidate for metX in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Pseudomonas putida KT2440

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate PP_5097 PP_5097 homoserine O-acetyltransferase

Query= SwissProt::D7E9E0
         (489 letters)



>FitnessBrowser__Putida:PP_5097
          Length = 379

 Score =  377 bits (969), Expect = e-109
 Identities = 190/368 (51%), Positives = 259/368 (70%), Gaps = 6/368 (1%)

Query: 5   SIGNVETKYYQIPEELVLESGKKISDVTLAYETYGTLNWDKSNAILVCHALTGDAHAAGW 64
           S+G V  +  +  E L L  G+ ++   L YETYGTLN   SNA+L+CHAL+G  HAAG+
Sbjct: 9   SVGLVVPQTARFDEPLALACGRSLASYELVYETYGTLNASASNAVLICHALSGHHHAAGY 68

Query: 65  HEG-DRKPGWWDIIIGPGKALDTRKYFIICSNVIGGCKGSTGPSSINPDTGESYGLDFPV 123
           H   DRKPGWWD  IGPGK +DT ++F++  N +GGC GSTGPSS+NP TG+ YG DFPV
Sbjct: 69  HAATDRKPGWWDSCIGPGKPIDTNRFFVVSLNNLGGCNGSTGPSSVNPATGKPYGADFPV 128

Query: 124 VTIKDMVNAQKKLIDYLGISKLLAVIGGSMGGLQVLQWSVSYPDMVKKAIPIATAGYSTP 183
           +T++D V++Q +L + LGI +  AV+GGS+GG+Q LQW++SYP+ V+  + IA+A   + 
Sbjct: 129 LTVEDWVHSQVRLGERLGIQQWAAVVGGSLGGMQALQWTISYPERVRHCVDIASAPKLSA 188

Query: 184 QQIAFNEVGRIAIVSDPNWNSGNYYGEKE-PTHGLALARMIGHITYLSDDSMHQKFGRRL 242
           Q IAFNEV R AI++DP ++ G++  +   P  GL LARM+GHITYLSDDSM +KFGR L
Sbjct: 189 QNIAFNEVARQAILTDPEFHGGSFQDQGVIPKRGLMLARMVGHITYLSDDSMGEKFGREL 248

Query: 243 Q-DKNEYEFDFSREFEVESYLHYQGLTFTERFDANSYLYLTKAIDYFD--LTENNSLAEG 299
           + DK  Y+F  S EF+VESYL YQG  F+ RFDAN+YL +TKA+DYFD   T    LA  
Sbjct: 249 KSDKLNYDF-HSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAATHGGDLAAT 307

Query: 300 LKNVEAKFLVISFTSDWLYPPYQLREIVMALSANNADVTYREIESNYGHDSFLLESGQLN 359
           L +V A + ++SFT+DW + P + REIV AL A   +V Y EI+S YGHD+FL+ + +  
Sbjct: 308 LAHVTADYCIMSFTTDWRFSPARSREIVDALMAARKNVCYLEIDSPYGHDAFLIPTPRYM 367

Query: 360 YVLNNFLS 367
              +N+++
Sbjct: 368 QGFSNYMN 375


Lambda     K      H
   0.316    0.134    0.392 

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: 510
Number of extensions: 23
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: 489
Length of database: 379
Length adjustment: 32
Effective length of query: 457
Effective length of database: 347
Effective search space:   158579
Effective search space used:   158579
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: 51 (24.3 bits)

Align candidate PP_5097 PP_5097 (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.20072.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-143  464.6   0.0   1.2e-143  464.4   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_5097  PP_5097 homoserine O-acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5097  PP_5097 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.4   0.0  1.2e-143  1.2e-143       2     349 ..      21     373 ..      20     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 464.4 bits;  conditional E-value: 1.2e-143
                           TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldtsryf 74 
                                         +e+l l +G  l ++e++y+tyGtlna+ +Navl+cHal+g++h+ag++ ++d+  GWWd+ +Gpg+++dt+r+f
  lcl|FitnessBrowser__Putida:PP_5097  21 DEPLALACGRSLASYELVYETYGTLNASASNAVLICHALSGHHHAAGYHAATDRkpGWWDSCIGPGKPIDTNRFF 95 
                                         5799*******************************************998777678******************* PP

                           TIGR01392  75 vvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewalsy 149
                                         vv+lN+lG+c+GstgP+s+np+tgkpyga+fP++t++D+v+ q +l ++Lg++++aavvGgSlGGmqal+w++sy
  lcl|FitnessBrowser__Putida:PP_5097  96 VVSLNNLGGCNGSTGPSSVNPATGKPYGADFPVLTVEDWVHSQVRLGERLGIQQWAAVVGGSLGGMQALQWTISY 170
                                         *************************************************************************** PP

                           TIGR01392 150 pervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesleerfg 223
                                         perv+++v +a+++++saq+iafnev+rqail+Dpe+++G++++++  P++GL lARm++++tY+s++s+ e+fg
  lcl|FitnessBrowser__Putida:PP_5097 171 PERVRHCVDIASAPKLSAQNIAFNEVARQAILTDPEFHGGSFQDQGvIPKRGLMLARMVGHITYLSDDSMGEKFG 245
                                         **********************************************9**************************** PP

                           TIGR01392 224 reakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikapvlvvgi 298
                                         re ks++     ++ ef+vesylryqg++f  rFdAn+Yll+tkald++d a+ + ++l+++l++++a+++++++
  lcl|FitnessBrowser__Putida:PP_5097 246 RELKSDKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAATHGGDLAATLAHVTADYCIMSF 320
                                         *****977777779************************************************************* PP

                           TIGR01392 299 esDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveeliref 349
                                         ++D++f++++++e+++al aa+++  y ei+s++GHDaFl+ + ++++  +++
  lcl|FitnessBrowser__Putida:PP_5097 321 TTDWRFSPARSREIVDALMAARKNvcYLEIDSPYGHDAFLIPTPRYMQGFSNY 373
                                         *********************99999***************999888766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (379 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: 10.30
//
[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