Alignments for a candidate for metX in Thiomicrorhabdus arctica DSM 13458

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Thiomicrorhabdus arctica DSM 13458

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_019557573.1 F612_RS0109700 homoserine O-acetyltransferase

Query= SwissProt::F7XKY8
         (492 letters)



>NCBI__GCF_000381085.1:WP_019557573.1
          Length = 390

 Score =  370 bits (950), Expect = e-107
 Identities = 188/378 (49%), Positives = 257/378 (67%), Gaps = 8/378 (2%)

Query: 6   LGIVETKYYHLEEELKLESGRKISDVTIAYEAYGTLNRDKNNVILVCHALTGDAHAAGWH 65
           LG++  +  H+E+ L L SG  +    + YE YG LN   +N IL+CHAL+GD H AG  
Sbjct: 5   LGVITPQTLHIEQPLTLSSGSILPRYDLIYETYGQLNASASNGILICHALSGDHHVAGLD 64

Query: 66  KGDNKPGWWDILIGPGKCLDTDKYFIVCSNVIGGCRGSTGPSSIDPETGKPYGLSFPVIT 125
             +NKPGWW+  IGPGK +DTD +F+VCSN +GGC GSTGP++++PETGK YG  FP++T
Sbjct: 65  -ANNKPGWWNDYIGPGKPIDTDHFFVVCSNNLGGCHGSTGPTTLNPETGKVYGPDFPIVT 123

Query: 126 IKDMVNAQKKLLDHLGISSIYAVIGGSMGGLQVLQWSVSYPDYINKAIALAASAYSSPQQ 185
            +D VN+Q +L  HLGI+   A+IGGSMGG+QVLQW++ YPD +  AI +AA+   S Q 
Sbjct: 124 CRDWVNSQNELRKHLGINQWAALIGGSMGGMQVLQWAIDYPDKLQHAIVIAAAPKLSAQN 183

Query: 186 IAFNEVARIAIISDPEWNKGNYY-YSRQPSHGLALARMIGHITYLSDESMREKFGRELQD 244
           IAFNEVAR AI++DP++++G +  +   P  GLA ARM+GH+TYLSD+ M  KFGRE + 
Sbjct: 184 IAFNEVARRAIMTDPDFHEGRFLEHKTVPKQGLAQARMLGHLTYLSDDMMGAKFGRE-RR 242

Query: 245 RDRYNYDLSMDFQVESYLHYKGRSF--TERFDANSYLYITKAVDYFDLTE--NGSLIDGL 300
           +D   Y+  ++FQVESYL Y+G  F  T+ FDAN+YL +TKA+DYFD     +  L   L
Sbjct: 243 KDELQYNYEVEFQVESYLRYQGEKFATTQNFDANTYLLMTKALDYFDPASEFDHDLSKTL 302

Query: 301 KDIKAKCLIIAVTSDWLYPPYQSKDIVMALNANNVDVTYREIESNYGHDAFLLEAGQLNY 360
               AK L+IA T+DW + P +S +IV AL  N+ DV+Y E+ES +GHDAFLL       
Sbjct: 303 AQTTAKFLVIAFTTDWRFAPARSHEIVKALLDNDTDVSYAEVESEHGHDAFLLRNEHYEG 362

Query: 361 VIGGFLNNITVSDIMKLD 378
           +   ++  I +S+I  LD
Sbjct: 363 LFRAYMQRI-ISEITPLD 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: 532
Number of extensions: 23
Number of successful extensions: 6
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: 390
Length adjustment: 32
Effective length of query: 460
Effective length of database: 358
Effective search space:   164680
Effective search space used:   164680
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 WP_019557573.1 F612_RS0109700 (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.24577.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.3e-143  461.5   0.0   1.1e-142  461.3   0.0    1.0  1  lcl|NCBI__GCF_000381085.1:WP_019557573.1  F612_RS0109700 homoserine O-acet


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000381085.1:WP_019557573.1  F612_RS0109700 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.3   0.0  1.1e-142  1.1e-142       2     350 ..      16     368 ..      15     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 461.3 bits;  conditional E-value: 1.1e-142
                                 TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedkGWWdellGpgraldt 70 
                                               e++ltl sG++l+++++ y+tyG+lna+ +N +l+cHal+g++hvag   ++++GWW++++Gpg+++dt
  lcl|NCBI__GCF_000381085.1:WP_019557573.1  16 EQPLTLSSGSILPRYDLIYETYGQLNASASNGILICHALSGDHHVAGLDANNKPGWWNDYIGPGKPIDT 84 
                                               589*******************************************99999999*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               +++fvvc+N+lG+c+GstgP+++npetgk yg++fP vt rD+v+ q++l ++Lg++++aa +GgS+GG
  lcl|NCBI__GCF_000381085.1:WP_019557573.1  85 DHFFVVCSNNLGGCHGSTGPTTLNPETGKVYGPDFPIVTCRDWVNSQNELRKHLGINQWAALIGGSMGG 153
                                               ********************************************************************* PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARml 207
                                               mq+l+wa++yp+++++++v+a+++++saq+iafnev+r+ai++Dp++++G++ e++  P++GLa ARml
  lcl|NCBI__GCF_000381085.1:WP_019557573.1 154 MQVLQWAIDYPDKLQHAIVIAAAPKLSAQNIAFNEVARRAIMTDPDFHEGRFLEHKtVPKQGLAQARML 222
                                               ******************************************************999************ PP

                                 TIGR01392 208 alltYrseesleerfgreakseeslassleeefsvesylryqgkkfv..erFdAnsYllltkaldthdl 274
                                               ++ltY+s++ + ++fgre++++ +l++++e ef+vesylryqg+kf+  + FdAn+Yll+tkald++d 
  lcl|NCBI__GCF_000381085.1:WP_019557573.1 223 GHLTYLSDDMMGAKFGRERRKD-ELQYNYEVEFQVESYLRYQGEKFAttQNFDANTYLLMTKALDYFDP 290
                                               ****************999888.78999******************73368****************** PP

                                 TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekek 341
                                               a + +++l+++l++++a++lv+++++D++f++++++e++kal +++++  yae+ese+GHDaFll +e+
  lcl|NCBI__GCF_000381085.1:WP_019557573.1 291 ASEFDHDLSKTLAQTTAKFLVIAFTTDWRFAPARSHEIVKALLDNDTDvsYAEVESEHGHDAFLLRNEH 359
                                               ******************************************98888778******************* PP

                                 TIGR01392 342 veelirefl 350
                                               +e l r+++
  lcl|NCBI__GCF_000381085.1:WP_019557573.1 360 YEGLFRAYM 368
                                               999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (390 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.28
//
[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