Alignments for a candidate for metX in Sulfuritalea hydrogenivorans sk43H DSM 22779

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_041101080.1 SUTH_RS17455 homoserine O-acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>NCBI__GCF_000828635.1:WP_041101080.1
          Length = 372

 Score =  375 bits (964), Expect = e-109
 Identities = 184/355 (51%), Positives = 246/355 (69%), Gaps = 6/355 (1%)

Query: 21  EPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKP---GWW 77
           +PL L  GG++   ++ Y+TYG LNA KSNA+L+CHAL+G  HVA    T G P   GWW
Sbjct: 16  QPLALKGGGLLPAFDLVYETYGTLNAAKSNAILVCHALSGHHHVAGH--TEGNPANIGWW 73

Query: 78  QRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQA 137
             +VGPG+PLD  R FI+  N +GGC GSTGPAS NPATGK +G  FPV+T+ D V AQA
Sbjct: 74  DNIVGPGRPLDTERFFIVGVNNLGGCHGSTGPASTNPATGKPWGADFPVVTVEDWVDAQA 133

Query: 138 MLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGRQ 197
            L   LG+    AV+GGS+GGMQ  QW + +P+R+  A+V+A+A + SA+NIAF++V RQ
Sbjct: 134 RLADHLGIGAWAAVMGGSLGGMQALQWTLSFPDRVRHALVIAAAPKLSAENIAFNDVARQ 193

Query: 198 AIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQRDGLSWGFDA 257
           AI+ DPD+ GG + EHGVRP +GL +ARM  HITYLS+  +  KFGR L+    S+GFD 
Sbjct: 194 AILTDPDFHGGHFYEHGVRPVRGLRLARMLGHITYLSDDQMAEKFGRRLRTGAGSYGFDV 253

Query: 258 DFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFCVLS 317
           +F++ESYLR+QG  F   FDAN+YL +T+A+DYFD A      LA+A  RAR  +F V++
Sbjct: 254 EFEIESYLRYQGDKFAGVFDANTYLRMTKALDYFDPAQDFDDDLARALARAR-AKFLVVA 312

Query: 318 FSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFL 372
           FS+DW +    +R +V AL   G   A+AEI+S  GHD+FL+DEP   A ++ +L
Sbjct: 313 FSTDWRFSPERSREIVHALVHNGQAVAYAEIDSAHGHDSFLMDEPHYHAVVDTYL 367


Lambda     K      H
   0.321    0.135    0.417 

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: 18
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: 382
Length of database: 372
Length adjustment: 30
Effective length of query: 352
Effective length of database: 342
Effective search space:   120384
Effective search space used:   120384
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_041101080.1 SUTH_RS17455 (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.3637569.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-144  466.5   0.0   3.1e-144  466.3   0.0    1.0  1  NCBI__GCF_000828635.1:WP_041101080.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000828635.1:WP_041101080.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.3   0.0  3.1e-144  3.1e-144       2     350 ..      15     367 ..      14     368 .. 0.97

  Alignments for each domain:
  == domain 1  score: 466.3 bits;  conditional E-value: 3.1e-144
                             TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldtsr 72 
                                           +++l l+ G+ l+ ++++y+tyGtlna+++Na+lvcHal+g++hvag+++ +    GWWd+++Gpgr+ldt+r
  NCBI__GCF_000828635.1:WP_041101080.1  15 TQPLALKGGGLLPAFDLVYETYGTLNAAKSNAILVCHALSGHHHVAGHTEGNPAniGWWDNIVGPGRPLDTER 87 
                                           5899******************************************9998776689***************** PP

                             TIGR01392  73 yfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalew 145
                                           +f+v++N+lG+c+GstgP+s+np+tgkp+ga+fP+vt++D+v aq++l+d+Lg+  +aav+GgSlGGmqal+w
  NCBI__GCF_000828635.1:WP_041101080.1  88 FFIVGVNNLGGCHGSTGPASTNPATGKPWGADFPVVTVEDWVDAQARLADHLGIGAWAAVMGGSLGGMQALQW 160
                                           ************************************************************************* PP

                             TIGR01392 146 alsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrsees 217
                                           +ls p+rv++++v+a+++++sa++iafn+v+rqail+Dp++++G+++e++ +P++GL+lARml+++tY+s+++
  NCBI__GCF_000828635.1:WP_041101080.1 161 TLSFPDRVRHALVIAAAPKLSAENIAFNDVARQAILTDPDFHGGHFYEHGvRPVRGLRLARMLGHITYLSDDQ 233
                                           ************************************************************************* PP

                             TIGR01392 218 leerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkik 290
                                           ++e+fgr+ ++ +  ++ ++ ef++esylryqg+kf+  FdAn+Yl +tkald++d a++ +d+l++al++++
  NCBI__GCF_000828635.1:WP_041101080.1 234 MAEKFGRRLRTGAG-SYGFDVEFEIESYLRYQGDKFAGVFDANTYLRMTKALDYFDPAQDFDDDLARALARAR 305
                                           **********9965.6779****************************************************** PP

                             TIGR01392 291 apvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350
                                           a++lvv++++D++f++e+++e+++al +++++  yaei+s++GHD+Fl+++ +++++++ +l
  NCBI__GCF_000828635.1:WP_041101080.1 306 AKFLVVAFSTDWRFSPERSREIVHALVHNGQAvaYAEIDSAHGHDSFLMDEPHYHAVVDTYL 367
                                           *************************998887778**********************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (372 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: 00:00:00.00
# Mc/sec: 14.68
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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