Alignments for a candidate for metX in Stenotrophomonas chelatiphaga DSM 21508

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Stenotrophomonas chelatiphaga DSM 21508

Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate WP_057687234.1 ABB28_RS15260 homoserine O-acetyltransferase

Query= SwissProt::D2Z028
         (374 letters)



>NCBI__GCF_001431535.1:WP_057687234.1
          Length = 370

 Score =  471 bits (1213), Expect = e-137
 Identities = 235/370 (63%), Positives = 281/370 (75%), Gaps = 3/370 (0%)

Query: 1   MREFIPPASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAA 60
           M EFIPP + F  LP  F  +RGGAL   R+AYET+G+L+A   NA+L++TGLSPDAHAA
Sbjct: 1   MTEFIPPGTLFHALPSPFPFKRGGALTAGRVAYETWGTLDADAGNAILIVTGLSPDAHAA 60

Query: 61  SRPDDPTPGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPE 120
           S   +P  GWWE MVGPGKP+DTD W VICVNSLGSCKGSTGPAS D  TG+PYRLSFPE
Sbjct: 61  SNAANPATGWWEGMVGPGKPIDTDRWFVICVNSLGSCKGSTGPASIDAATGKPYRLSFPE 120

Query: 121 LSIEDIADAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALP 180
           LS+ED A A+   VRALGI++LAC+VG SMGGM+ALALL  HP +AR+HI++SG+  ALP
Sbjct: 121 LSVEDGARASVEVVRALGITQLACLVGNSMGGMTALALLLLHPGIARSHINISGSAQALP 180

Query: 181 FSIAVRSLQREAIRSDPGWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRI 240
           FSIA+RSLQREAIR DP W  G YD+   P  GM  ARKLG++TYRSA EWD RFGR R+
Sbjct: 181 FSIAIRSLQREAIRLDPQWNGGQYDDANYPESGMRMARKLGVITYRSALEWDGRFGRVRL 240

Query: 241 GERRRADQGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAP 300
            +  +AD   FG EF+VESYL+ HA+RF   FDPN YLYLS +MD FDL +   G G   
Sbjct: 241 -DSDQADDDPFGLEFQVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAE--HGNGDVM 297

Query: 301 GALSRMRVERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIE 360
             L+ ++VE+AL +GA TDILFP+ QQQ+IADGL AGGA+  F+ +D+P GHDAFLVD E
Sbjct: 298 AGLATIKVEKALAIGANTDILFPVQQQQQIADGLRAGGAEAHFIGLDSPQGHDAFLVDFE 357

Query: 361 RFGPPVAKFL 370
           RFGP V  FL
Sbjct: 358 RFGPAVRGFL 367


Lambda     K      H
   0.321    0.138    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: 498
Number of extensions: 13
Number of successful extensions: 3
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: 374
Length of database: 370
Length adjustment: 30
Effective length of query: 344
Effective length of database: 340
Effective search space:   116960
Effective search space used:   116960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_057687234.1 ABB28_RS15260 (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.14093.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-113  364.4   0.0   3.8e-113  364.1   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057687234.1  ABB28_RS15260 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057687234.1  ABB28_RS15260 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.1   0.0  3.8e-113  3.8e-113       4     350 ..      17     367 ..      15     368 .. 0.96

  Alignments for each domain:
  == domain 1  score: 364.1 bits;  conditional E-value: 3.8e-113
                                 TIGR01392   4 eltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedkGWWdellGpgraldtsr 72 
                                               ++ ++ G+ l+  +vay+t+Gtl a+  Na+l++  l+ +ah+a++a + ++GWW+ ++Gpg+++dt+r
  lcl|NCBI__GCF_001431535.1:WP_057687234.1  17 PFPFKRGGALTAGRVAYETWGTLDADAGNAILIVTGLSPDAHAASNAANPATGWWEGMVGPGKPIDTDR 85 
                                               78899***************************************99999999***************** PP

                                 TIGR01392  73 yfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmq 141
                                               +fv+c+N+lGsckGstgP+si+ +tgkpy+ +fP ++++D ++a+ +++++Lg+++la+ vG S+GGm+
  lcl|NCBI__GCF_001431535.1:WP_057687234.1  86 WFVICVNSLGSCKGSTGPASIDAATGKPYRLSFPELSVEDGARASVEVVRALGITQLACLVGNSMGGMT 154
                                               ********************************************************************* PP

                                 TIGR01392 142 alewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlall 210
                                               al + l  p ++++ ++++ sa+a +  ia++++qr+ai+ Dp++n+G+y++ + Pe+G+++AR+l+ +
  lcl|NCBI__GCF_001431535.1:WP_057687234.1 155 ALALLLLHPGIARSHINISGSAQALPFSIAIRSLQREAIRLDPQWNGGQYDDANYPESGMRMARKLGVI 223
                                               ********************************************************************* PP

                                 TIGR01392 211 tYrseesleerfgreakseeslass.leeefsvesylryqgkkfverFdAnsYllltkaldthdlargr 278
                                               tYrs  + + rfgr + ++++ +   +  ef+vesyl+ ++++fv+ Fd n+Yl+l++++d +dla+  
  lcl|NCBI__GCF_001431535.1:WP_057687234.1 224 TYRSALEWDGRFGRVRLDSDQADDDpFGLEFQVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAEHG 292
                                               *************98777655544327****************************************99 PP

                                 TIGR01392 279 rdslkealkkikap.vlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekvee 344
                                               ++++++ l++ik++ +l +g ++D+lf++++q+++a+ l+a ++e  +  ++s++GHDaFl+++e++  
  lcl|NCBI__GCF_001431535.1:WP_057687234.1 293 NGDVMAGLATIKVEkALAIGANTDILFPVQQQQQIADGLRAGGAEahFIGLDSPQGHDAFLVDFERFGP 361
                                               ************986899**********************998888899******************** PP

                                 TIGR01392 345 lirefl 350
                                               ++r fl
  lcl|NCBI__GCF_001431535.1:WP_057687234.1 362 AVRGFL 367
                                               **9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (370 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.87
//
[ok]

This GapMind analysis is from Apr 10 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