Alignments for a candidate for metX in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Pseudomonas stutzeri RCH2

Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate GFF279 Psest_0280 homoserine O-acetyltransferase

Query= curated2:Q1QQD3
         (399 letters)



>FitnessBrowser__psRCH2:GFF279
          Length = 379

 Score =  375 bits (964), Expect = e-109
 Identities = 185/361 (51%), Positives = 245/361 (67%), Gaps = 3/361 (0%)

Query: 26  QVAMFAGDQPLPLDCGIDLAPFQIAYQTYGELNAGKSNAILVCHALTGDQHVANVHPVTG 85
           Q+A FA  +PL L CG  LA +Q+ Y+TYGELNA +SNA+L+CHAL+G  H A  H    
Sbjct: 16  QIAHFA--EPLTLACGRTLADYQLIYETYGELNAARSNAVLICHALSGHHHAAGYHSEDD 73

Query: 86  -KPGWWVTLVGPGKPLDTDKYFVICSNVIGGCMGSTGPASTNPATGTVWGLDFPVITIPD 144
            KPGWW + +GPGK +DT+++FV+  N +GGC GSTGP+STNPA+G  +G DFPV+T+ D
Sbjct: 74  RKPGWWDSCIGPGKAIDTNRFFVVSLNNLGGCNGSTGPSSTNPASGKPYGADFPVVTVED 133

Query: 145 MVRAQAMLIDRLGIDTLFSVVGGSMGGMQVLQWCVAYPQRVFSALPIACSTRHSAQNIAF 204
            V +QA L DRLGI    +VVGGS+GGMQ LQW ++YP+RV   L IA + + SAQNIAF
Sbjct: 134 WVHSQARLADRLGIAQWAAVVGGSLGGMQALQWTISYPERVRHCLAIASAPKLSAQNIAF 193

Query: 205 HELGRQAVMADPDWRDGRYVEQGTYPHRGLGVARMAAHITYLSDAALHRKFGRRMQDRDL 264
           +E+ RQA+++DP++  G + E G  P RGL +ARM  HITYLSD A+  KFGR ++   L
Sbjct: 194 NEVARQAILSDPEFHGGHFQEMGVIPKRGLMLARMVGHITYLSDDAMGTKFGRGLKSEKL 253

Query: 265 PTFSFDADFQVESYLRHQGSSFVERFDANSYLYLTRAMDYFDIAADHNGVLAAAFRDTRT 324
                  +FQVESYLR+QG  F  RFDAN+YL +T+A+DYFD AA ++  LA  F   + 
Sbjct: 254 NYDFNSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAAANDDDLAKTFEVAKA 313

Query: 325 RFCVVSFTSDWLFPTSESRATVHALNAGGARVSFAEIETDRGHDAFLLDLPEFFDIAHAF 384
            FCV+SFT+DW F    SR  V AL A    V + EI+  +GHDAFL+  P +      +
Sbjct: 314 DFCVMSFTTDWRFSPERSREIVDALLAARKNVCYLEIDAPQGHDAFLIPNPRYLQAFRGY 373

Query: 385 L 385
           +
Sbjct: 374 M 374


Lambda     K      H
   0.323    0.136    0.427 

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: 431
Number of extensions: 16
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: 399
Length of database: 379
Length adjustment: 30
Effective length of query: 369
Effective length of database: 349
Effective search space:   128781
Effective search space used:   128781
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)

Align candidate GFF279 Psest_0280 (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.6417.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.8e-144  467.1   0.0   2.1e-144  466.9   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF279  Psest_0280 homoserine O-acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF279  Psest_0280 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.9   0.0  2.1e-144  2.1e-144       3     350 ..      22     374 ..      20     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 466.9 bits;  conditional E-value: 2.1e-144
                          TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldtsryfvv 76 
                                        e+ltl +G +l ++++ y+tyG+lna+r+Navl+cHal+g++h+ag+++e+d+  GWWd+ +Gpg+a+dt+r+fvv
  lcl|FitnessBrowser__psRCH2:GFF279  22 EPLTLACGRTLADYQLIYETYGELNAARSNAVLICHALSGHHHAAGYHSEDDRkpGWWDSCIGPGKAIDTNRFFVV 97 
                                        79**********************************************9988889********************* PP

                          TIGR01392  77 clNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewalsyper 152
                                        +lN+lG+c+GstgP+s+np++gkpyga+fP+vt++D+v+ q++l+d+Lg+ ++aavvGgSlGGmqal+w++syper
  lcl|FitnessBrowser__psRCH2:GFF279  98 SLNNLGGCNGSTGPSSTNPASGKPYGADFPVVTVEDWVHSQARLADRLGIAQWAAVVGGSLGGMQALQWTISYPER 173
                                        **************************************************************************** PP

                          TIGR01392 153 vkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesleerfgreak 227
                                        v++++++a+++++saq+iafnev+rqailsDpe+++G+++e +  P++GL lARm++++tY+s++++ ++fgr  k
  lcl|FitnessBrowser__psRCH2:GFF279 174 VRHCLAIASAPKLSAQNIAFNEVARQAILSDPEFHGGHFQEMGvIPKRGLMLARMVGHITYLSDDAMGTKFGRGLK 249
                                        *******************************************9*******************************9 PP

                          TIGR01392 228 seeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikapvlvvgiesDll 303
                                        se+      + ef+vesylryqg++f  rFdAn+Yll+tkald++d a+ ++d+l+++++ +ka+++v+++++D++
  lcl|FitnessBrowser__psRCH2:GFF279 250 SEKLNYDFNSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAAANDDDLAKTFEVAKADFCVMSFTTDWR 325
                                        99666665699***************************************************************** PP

                          TIGR01392 304 ftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350
                                        f++e+++e+++al aa+++  y ei+ ++GHDaFl+ + ++ ++ r ++
  lcl|FitnessBrowser__psRCH2:GFF279 326 FSPERSREIVDALLAARKNvcYLEIDAPQGHDAFLIPNPRYLQAFRGYM 374
                                        ****************99999***************9999888877665 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.27
//
[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