Alignments for a candidate for metX in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Dyella japonica UNC79MFTsu3.2

Align L-serine/homoserine O-acetyltransferase; Homoserine O-trans-acetylase; EC 2.3.1.30; EC 2.3.1.31 (characterized)
to candidate N515DRAFT_2885 N515DRAFT_2885 homoserine O-acetyltransferase

Query= SwissProt::D2Z028
         (374 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2885
          Length = 368

 Score =  452 bits (1163), Expect = e-132
 Identities = 225/363 (61%), Positives = 270/363 (74%), Gaps = 2/363 (0%)

Query: 8   ASRFIELPDGFAMRRGGALYGARIAYETFGSLNAARDNAVLVLTGLSPDAHAASRPDDPT 67
           A R+  LP  F M+RGG L+GAR+A+ET+G+L+ ARDNA+L+LTGLSP AHAAS   DP+
Sbjct: 5   ARRYFSLPSPFPMKRGGELHGARVAFETWGALSDARDNALLILTGLSPSAHAASNEQDPS 64

Query: 68  PGWWEAMVGPGKPVDTDLWHVICVNSLGSCKGSTGPASTDPRTGEPYRLSFPELSIEDIA 127
           PGWWEAM+GPGK +DTD W VICVNSLGS KGST PAS DP TGEPYRLSFPEL++ED+A
Sbjct: 65  PGWWEAMIGPGKAIDTDRWFVICVNSLGSDKGSTCPASIDPATGEPYRLSFPELALEDVA 124

Query: 128 DAAAHTVRALGISRLACVVGASMGGMSALALLARHPELARTHISLSGAVHALPFSIAVRS 187
           +AA   V +LGI +LAC+VG SMGGMSALA +  HP   RTHIS+  A  A PF+IA+RS
Sbjct: 125 NAAHAAVSSLGIEQLACLVGCSMGGMSALAYMLLHPGSVRTHISVDTAPQAQPFAIAIRS 184

Query: 188 LQREAIRSDPGWLQGHYDEGEGPRRGMLTARKLGMMTYRSAQEWDCRFGRTRIGERRRAD 247
           LQREAIR DP W  G YD+   P  GM  ARKLG++TYRSA EW+ RF R R+   +R D
Sbjct: 185 LQREAIRLDPQWNNGRYDDAHYPETGMSIARKLGVITYRSAMEWNGRFARIRLDAEQRDD 244

Query: 248 QGRFGPEFEVESYLDFHAQRFADRFDPNSYLYLSHAMDQFDLGDGGGGGGGAPGALSRMR 307
              FG EF+VESYL+ HAQRF   FDPNSYLYLS A D FD+ +   G G     L R+R
Sbjct: 245 DVPFGFEFQVESYLEGHAQRFVRTFDPNSYLYLSRASDWFDISE--YGEGSIQAGLKRIR 302

Query: 308 VERALVMGARTDILFPLSQQQEIADGLSAGGADVSFLPVDTPAGHDAFLVDIERFGPPVA 367
           VE+ALV+G  TDILFPL QQ++IA+GL A GA V F+ +D+P GHDAFLVDIE +   + 
Sbjct: 303 VEQALVIGVSTDILFPLEQQEQIAEGLEAAGAAVEFVALDSPQGHDAFLVDIENYSRAIG 362

Query: 368 KFL 370
            FL
Sbjct: 363 GFL 365


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: 469
Number of extensions: 15
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: 374
Length of database: 368
Length adjustment: 30
Effective length of query: 344
Effective length of database: 338
Effective search space:   116272
Effective search space used:   116272
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 N515DRAFT_2885 N515DRAFT_2885 (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.4690.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.9e-113  365.1   0.0   2.3e-113  364.8   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2885  N515DRAFT_2885 homoserine O-acet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2885  N515DRAFT_2885 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.8   0.0  2.3e-113  2.3e-113       4     350 ..      14     365 ..      12     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 364.8 bits;  conditional E-value: 2.3e-113
                                    TIGR01392   4 eltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedkGWWdellGpgrald 69 
                                                  ++ ++ G++l+ ++va++t+G l+++rdNa+l++  l+ sah+a++ ++ ++GWW+ ++Gpg+a+d
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2885  14 PFPMKRGGELHGARVAFETWGALSDARDNALLILTGLSPSAHAASNEQDPSPGWWEAMIGPGKAID 79 
                                                  78999***************************************88887888************** PP

                                    TIGR01392  70 tsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGg 135
                                                  t+r+fv+c+N+lGs kGst P+si+p+tg+py+ +fP ++++D ++a +a + sLg+e+la+ vG 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2885  80 TDRWFVICVNSLGSDKGSTCPASIDPATGEPYRLSFPELALEDVANAAHAAVSSLGIEQLACLVGC 145
                                                  ****************************************************************** PP

                                    TIGR01392 136 SlGGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGL 201
                                                  S+GGm+al + l  p +v++ + + t+++a++ aia++++qr+ai+ Dp++n+G+y++ + Pe+G+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2885 146 SMGGMSALAYMLLHPGSVRTHISVDTAPQAQPFAIAIRSLQREAIRLDPQWNNGRYDDAHYPETGM 211
                                                  ****************************************************************** PP

                                    TIGR01392 202 alARmlalltYrseesleerfgreakseeslassl..eeefsvesylryqgkkfverFdAnsYlll 265
                                                  ++AR+l+ +tYrs  + + rf+r + ++e+ +  +    ef+vesyl+ ++++fv+ Fd nsYl+l
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2885 212 SIARKLGVITYRSAMEWNGRFARIRLDAEQRDDDVpfGFEFQVESYLEGHAQRFVRTFDPNSYLYL 277
                                                  **********************9988877666554449**************************** PP

                                    TIGR01392 266 tkaldthdlargrrdslkealkkikap.vlvvgiesDllftleeqeelakalkaakle..yaeies 328
                                                  ++a d +d+++  ++s+++ lk+i+++ +lv+g+++D+lf+le+qe++a+ l+aa+++  ++ ++s
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2885 278 SRASDWFDISEYGEGSIQAGLKRIRVEqALVIGVSTDILFPLEQQEQIAEGLEAAGAAveFVALDS 343
                                                  ***********99************98699************************998888****** PP

                                    TIGR01392 329 eeGHDaFllekekveelirefl 350
                                                  ++GHDaFl++ e+++++i  fl
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2885 344 PQGHDAFLVDIENYSRAIGGFL 365
                                                  *****************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (368 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: 6.94
//
[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