Alignments for a candidate for metX in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Malonomonas rubra DSM 5091

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_072906806.1 BUB13_RS06080 homoserine O-acetyltransferase

Query= SwissProt::B3E278
         (367 letters)



>NCBI__GCF_900142125.1:WP_072906806.1
          Length = 373

 Score =  487 bits (1253), Expect = e-142
 Identities = 226/366 (61%), Positives = 286/366 (78%), Gaps = 2/366 (0%)

Query: 2   SIGVVHEQTITFEAGIRLESGRILAPITLVYELYGTMNADCSNVIMVEHAWTGDAHLAGK 61
           S+G+V  +   F+  +RLESGR+L P+T+ +E YG +NA   NVI+V HAWTGDAH AG 
Sbjct: 4   SVGLVKTEYADFDVELRLESGRLLGPLTIAFERYGQLNAAKDNVILVTHAWTGDAHAAGV 63

Query: 62  RREDDPKPGWWDAIVGPGRLLDTDRYCVLCSNVIGSCYGSTGPASINPRTGKRYNLSFPV 121
             E+D KPGWWD ++GPG++ DTD+Y VLCSNVIGSC GSTGP SI+P+TG+ Y L FP 
Sbjct: 64  HDEEDRKPGWWDNMIGPGKVFDTDKYFVLCSNVIGSCKGSTGPTSIDPKTGRPYRLKFPS 123

Query: 122 ITVRDMVRAQELLLDHLGIRRLLCVMGGSMGGMQALEWATQYPERVASVVALATTPRPSP 181
           + VRDMVRAQ+LL+DHLGI  +  V+GGSMG MQA+EWA  YPE + ++V +A T R SP
Sbjct: 124 LMVRDMVRAQKLLIDHLGITSIHAVVGGSMGAMQAIEWAIHYPEMIRAIVPIAGTGRTSP 183

Query: 182 QAISLNAVARWAIYNDPTWKKGEYK--HNPKDGLALARGIGHITFLSDESMWQKFERRFS 239
            AI+LNA+AR AI+NDP WKKG Y+  H P DGLALAR +GHI+FLSD SMW KF RRFS
Sbjct: 184 MAIALNALARQAIFNDPLWKKGNYRPEHPPADGLALARAVGHISFLSDASMWLKFGRRFS 243

Query: 240 AKDGLFDFFGQFEVERYLNYNGYNFVDRFDANCFLYLAKALDLYDVAWGYESMTDAFSRI 299
            +DG+FDFFG+FE+ERYL+YNG NFVDRFD N FLYLAKALDLYDVAW ++S+++A  R+
Sbjct: 244 VRDGMFDFFGKFEIERYLDYNGGNFVDRFDTNSFLYLAKALDLYDVAWNFDSLSEALDRL 303

Query: 300 TAPIQFFAFSSDWLYPPYQTEEMVTCLQGLGKEVEYHLIQSAYGHDAFLLEHETFTPMVR 359
             P  +FAF+SDWLY P QT+E+V  L+ L K V+YHLI+S YGHD+FL+E E F P+++
Sbjct: 304 NCPSLWFAFTSDWLYTPQQTQEVVDELRRLNKPVDYHLIESDYGHDSFLVEPEKFIPILQ 363

Query: 360 SLLERV 365
           + L  V
Sbjct: 364 TFLAEV 369


Lambda     K      H
   0.323    0.138    0.439 

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: 472
Number of extensions: 17
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: 367
Length of database: 373
Length adjustment: 30
Effective length of query: 337
Effective length of database: 343
Effective search space:   115591
Effective search space used:   115591
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: 49 (23.5 bits)

Align candidate WP_072906806.1 BUB13_RS06080 (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.20705.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.9e-134  431.9   0.0     1e-133  431.7   0.0    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072906806.1  BUB13_RS06080 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072906806.1  BUB13_RS06080 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.7   0.0    1e-133    1e-133       4     350 ..      18     366 ..      15     367 .. 0.98

  Alignments for each domain:
  == domain 1  score: 431.7 bits;  conditional E-value: 1e-133
                                 TIGR01392   4 eltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldt 70 
                                               el lesG  l  +++a+++yG+lna++dN++lv Ha tg+ah+ag +deed+  GWWd+++Gpg+ +dt
  lcl|NCBI__GCF_900142125.1:WP_072906806.1  18 ELRLESGRLLGPLTIAFERYGQLNAAKDNVILVTHAWTGDAHAAGVHDEEDRkpGWWDNMIGPGKVFDT 86 
                                               799*********************************************998889*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               ++yfv+c+Nv+GsckGstgP+si+p+tg+py+ +fP + +rD+v+aqk l+d+Lg+++++avvGgS+G 
  lcl|NCBI__GCF_900142125.1:WP_072906806.1  87 DKYFVLCSNVIGSCKGSTGPTSIDPKTGRPYRLKFPSLMVRDMVRAQKLLIDHLGITSIHAVVGGSMGA 155
                                               ********************************************************************* PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmla 208
                                               mqa+ewa++ype++++iv++a + r+s++aia+n+++rqai +Dp +++G+y+ e+ P+ GLalAR ++
  lcl|NCBI__GCF_900142125.1:WP_072906806.1 156 MQAIEWAIHYPEMIRAIVPIAGTGRTSPMAIALNALARQAIFNDPLWKKGNYRPEHPPADGLALARAVG 224
                                               ********************************************************************* PP

                                 TIGR01392 209 lltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlarg 277
                                               +++++s++s+  +fgr+ + ++  ++ +  +f++e yl+y+g +fv+rFd ns+l+l+kald +d+a +
  lcl|NCBI__GCF_900142125.1:WP_072906806.1 225 HISFLSDASMWLKFGRRFSVRD-GMFDFFGKFEIERYLDYNGGNFVDRFDTNSFLYLAKALDLYDVAWN 292
                                               ***************9998885.577799***************************************9 PP

                                 TIGR01392 278 rrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekvee 344
                                                 dsl+eal+++++p+l  +++sD+l+t+++++e++++l++ ++   y+ ies++GHD+Fl+e ek+  
  lcl|NCBI__GCF_900142125.1:WP_072906806.1 293 -FDSLSEALDRLNCPSLWFAFTSDWLYTPQQTQEVVDELRRLNKPvdYHLIESDYGHDSFLVEPEKFIP 360
                                               .8***************************************999889********************** PP

                                 TIGR01392 345 lirefl 350
                                               +++ fl
  lcl|NCBI__GCF_900142125.1:WP_072906806.1 361 ILQTFL 366
                                               *99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (373 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: 9.46
//
[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