Alignments for a candidate for metX in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Pseudomonas simiae WCS417

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate GFF5222 PS417_26740 homoserine acetyltransferase

Query= SwissProt::F7XKY8
         (492 letters)



>FitnessBrowser__WCS417:GFF5222
          Length = 379

 Score =  372 bits (955), Expect = e-107
 Identities = 188/372 (50%), Positives = 257/372 (69%), Gaps = 6/372 (1%)

Query: 5   SLGIVETKYYHLEEELKLESGRKISDVTIAYEAYGTLNRDKNNVILVCHALTGDAHAAGW 64
           S+G+V  +  H  E L L  GR +    + YE YG LN   +N +L+CHAL+G  HAAG+
Sbjct: 9   SVGLVVPQVAHFSEPLALACGRALPAYDLIYETYGQLNATASNAVLICHALSGHHHAAGF 68

Query: 65  HKGDN-KPGWWDILIGPGKCLDTDKYFIVCSNVIGGCRGSTGPSSIDPETGKPYGLSFPV 123
           H  D  KPGWWD  IGPGK +DT+K+F+V  N +GGC GSTGPSSI+PETGKP+G  FPV
Sbjct: 69  HSVDERKPGWWDSCIGPGKPIDTNKFFVVSLNNLGGCNGSTGPSSINPETGKPFGADFPV 128

Query: 124 ITIKDMVNAQKKLLDHLGISSIYAVIGGSMGGLQVLQWSVSYPDYINKAIALAASAYSSP 183
           +T++D V++Q +L D LGI+   AVIGGS+GG+Q LQW+++YPD +   +A+A++   S 
Sbjct: 129 LTVEDWVHSQARLADLLGINQWAAVIGGSLGGMQALQWTITYPDRVRHCLAIASAPKLSA 188

Query: 184 QQIAFNEVARIAIISDPEWNKGNYYYSRQ-PSHGLALARMIGHITYLSDESMREKFGREL 242
           Q IAFNEVAR AI++DPE++ G++  +   P  GL LARM+GHITYLSD+SM EKFGR L
Sbjct: 189 QNIAFNEVARQAILTDPEFHGGSFQEAGVIPKRGLMLARMVGHITYLSDDSMGEKFGRGL 248

Query: 243 QDRDRYNYDL-SMDFQVESYLHYKGRSFTERFDANSYLYITKAVDYFDLTEN--GSLIDG 299
           +  ++ NYD  S++FQVESYL Y+G  F+ RFDAN+YL +TKA+DYFD   N    L   
Sbjct: 249 KS-EKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANFDDDLAKT 307

Query: 300 LKDIKAKCLIIAVTSDWLYPPYQSKDIVMALNANNVDVTYREIESNYGHDAFLLEAGQLN 359
            +   AK  +++ T+DW + P +S+++V AL A   DV Y EI++  GHDAFL+   +  
Sbjct: 308 FEGATAKFCVMSFTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFLIPIPRYL 367

Query: 360 YVIGGFLNNITV 371
              G ++N ITV
Sbjct: 368 QAFGNYMNRITV 379


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: 510
Number of extensions: 24
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: 379
Length adjustment: 32
Effective length of query: 460
Effective length of database: 347
Effective search space:   159620
Effective search space used:   159620
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 GFF5222 PS417_26740 (homoserine 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.13902.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.3e-141  455.2   0.0   8.4e-141  455.0   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF5222  PS417_26740 homoserine acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5222  PS417_26740 homoserine acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.0   0.0  8.4e-141  8.4e-141       3     345 ..      22     369 ..      20     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 455.0 bits;  conditional E-value: 8.4e-141
                           TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldtsryfv 75 
                                         e+l l +G  l+ +++ y+tyG+lna  +Navl+cHal+g++h+ag ++ +++  GWWd+ +Gpg+++dt+++fv
  lcl|FitnessBrowser__WCS417:GFF5222  22 EPLALACGRALPAYDLIYETYGQLNATASNAVLICHALSGHHHAAGFHSVDERkpGWWDSCIGPGKPIDTNKFFV 96 
                                         789*******************************************998777678******************** PP

                           TIGR01392  76 vclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewalsyp 150
                                         v+lN+lG+c+GstgP+sinpetgkp+ga+fP++t++D+v+ q++l+d Lg++++aav+GgSlGGmqal+w+++yp
  lcl|FitnessBrowser__WCS417:GFF5222  97 VSLNNLGGCNGSTGPSSINPETGKPFGADFPVLTVEDWVHSQARLADLLGINQWAAVIGGSLGGMQALQWTITYP 171
                                         *************************************************************************** PP

                           TIGR01392 151 ervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesleerfgr 224
                                         +rv++++++a+++++saq+iafnev+rqail+Dpe+++G+++e +  P++GL lARm++++tY+s++s+ e+fgr
  lcl|FitnessBrowser__WCS417:GFF5222 172 DRVRHCLAIASAPKLSAQNIAFNEVARQAILTDPEFHGGSFQEAGvIPKRGLMLARMVGHITYLSDDSMGEKFGR 246
                                         *********************************************9***************************** PP

                           TIGR01392 225 eakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikapvlvvgie 299
                                           kse+     ++ ef+vesylryqg++f  rFdAn+Yll+tkald++d a++ +d+l+++++ ++a+++v++++
  lcl|FitnessBrowser__WCS417:GFF5222 247 GLKSEKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANFDDDLAKTFEGATAKFCVMSFT 321
                                         ***9977777779************************************************************** PP

                           TIGR01392 300 sDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveel 345
                                         +D++f++++++el++al aa+++  y ei+ ++GHDaFl+   ++ ++
  lcl|FitnessBrowser__WCS417:GFF5222 322 TDWRFSPARSRELVDALMAARKDvcYLEIDAPQGHDAFLIPIPRYLQA 369
                                         *******************999999**************988776665 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.64
//
[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