Alignments for a candidate for metX in Desulfuromonas acetexigens

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Desulfuromonas acetexigens

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_092055967.1 BQ4888_RS07655 homoserine O-acetyltransferase

Query= SwissProt::B3E278
         (367 letters)



>NCBI__GCF_900111775.1:WP_092055967.1
          Length = 370

 Score =  507 bits (1305), Expect = e-148
 Identities = 245/366 (66%), Positives = 288/366 (78%), Gaps = 2/366 (0%)

Query: 2   SIGVVHEQTITFEAGIRLESGRILAPITLVYELYGTMNADCSNVIMVEHAWTGDAHLAGK 61
           S+G+V  Q   F+  +RLESGR+L P+TL YE YG +NAD SNVI+V HAWTGDAH AGK
Sbjct: 4   SVGIVTTQFAEFDVELRLESGRLLGPLTLAYETYGELNADRSNVILVAHAWTGDAHAAGK 63

Query: 62  RREDDPKPGWWDAIVGPGRLLDTDRYCVLCSNVIGSCYGSTGPASINPRTGKRYNLSFPV 121
              DD KPGWWD ++GPG++LDTDRY VLCSNVIGSC GSTGP S NPRTGK YNL+FPV
Sbjct: 64  NTPDDRKPGWWDDMIGPGKVLDTDRYFVLCSNVIGSCKGSTGPTSTNPRTGKPYNLTFPV 123

Query: 122 ITVRDMVRAQELLLDHLGIRRLLCVMGGSMGGMQALEWATQYPERVASVVALATTPRPSP 181
           + VRDMVRAQ+LLLD LGI  LL V+GGSMG MQALEW+  YPE V S++ +A T R SP
Sbjct: 124 LMVRDMVRAQKLLLDRLGIDSLLTVIGGSMGAMQALEWSILYPEMVRSIIPIAGTGRTSP 183

Query: 182 QAISLNAVARWAIYNDPTWKKGEYK--HNPKDGLALARGIGHITFLSDESMWQKFERRFS 239
            AI+LNA+AR AI+NDP WKKG YK  H P DGLAL R +GHI+FLSD SM  KF RRFS
Sbjct: 184 MAIALNALARQAIFNDPLWKKGNYKPEHPPADGLALGRAVGHISFLSDVSMQLKFGRRFS 243

Query: 240 AKDGLFDFFGQFEVERYLNYNGYNFVDRFDANCFLYLAKALDLYDVAWGYESMTDAFSRI 299
           A+ G FDFFGQFE+ERYL+YNG +FVDRFD N FLYLAKALDLYDVAW +ES+ +A  ++
Sbjct: 244 ARHGQFDFFGQFEIERYLDYNGASFVDRFDTNAFLYLAKALDLYDVAWNFESLEEALDQL 303

Query: 300 TAPIQFFAFSSDWLYPPYQTEEMVTCLQGLGKEVEYHLIQSAYGHDAFLLEHETFTPMVR 359
             P  +FAF+SDWLY P QTEE+VT L+ LGK V YHLI+S YGHD+FL+E E FTP V 
Sbjct: 304 RCPSLWFAFTSDWLYTPSQTEEVVTVLRKLGKPVAYHLIESDYGHDSFLVEPEKFTPKVV 363

Query: 360 SLLERV 365
             L+R+
Sbjct: 364 EFLQRL 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: 468
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: 370
Length adjustment: 30
Effective length of query: 337
Effective length of database: 340
Effective search space:   114580
Effective search space used:   114580
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_092055967.1 BQ4888_RS07655 (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.22329.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-131  424.9   0.0   1.4e-131  424.7   0.0    1.0  1  lcl|NCBI__GCF_900111775.1:WP_092055967.1  BQ4888_RS07655 homoserine O-acet


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900111775.1:WP_092055967.1  BQ4888_RS07655 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.7   0.0  1.4e-131  1.4e-131       4     350 ..      18     366 ..      15     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 424.7 bits;  conditional E-value: 1.4e-131
                                 TIGR01392   4 eltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldt 70 
                                               el lesG  l  +++ay+tyG+lna+r+N++lv Ha tg+ah+agk+  +d+  GWWd+++Gpg+ ldt
  lcl|NCBI__GCF_900111775.1:WP_092055967.1  18 ELRLESGRLLGPLTLAYETYGELNADRSNVILVAHAWTGDAHAAGKNTPDDRkpGWWDDMIGPGKVLDT 86 
                                               799*****************************************9988777678*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               +ryfv+c+Nv+GsckGstgP+s+np+tgkpy   fP++ +rD+v+aqk lld+Lg+++l +v+GgS+G 
  lcl|NCBI__GCF_900111775.1:WP_092055967.1  87 DRYFVLCSNVIGSCKGSTGPTSTNPRTGKPYNLTFPVLMVRDMVRAQKLLLDRLGIDSLLTVIGGSMGA 155
                                               ********************************************************************* PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmla 208
                                               mqalew++ ype+v++i+++a + r+s++aia+n+++rqai +Dp +++G+y+ e+ P+ GLal R ++
  lcl|NCBI__GCF_900111775.1:WP_092055967.1 156 MQALEWSILYPEMVRSIIPIAGTGRTSPMAIALNALARQAIFNDPLWKKGNYKPEHPPADGLALGRAVG 224
                                               ********************************************************************* PP

                                 TIGR01392 209 lltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlarg 277
                                               +++++s+ s++ +fgr+ ++++  ++ +  +f++e yl+y+g +fv+rFd n++l+l+kald +d+a +
  lcl|NCBI__GCF_900111775.1:WP_092055967.1 225 HISFLSDVSMQLKFGRRFSARH-GQFDFFGQFEIERYLDYNGASFVDRFDTNAFLYLAKALDLYDVAWN 292
                                               ***************9999885.578899***************************************9 PP

                                 TIGR01392 278 rrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekvee 344
                                                 +sl+eal+++++p+l  +++sD+l+t++++ee+++ l++ ++   y+ ies++GHD+Fl+e ek++ 
  lcl|NCBI__GCF_900111775.1:WP_092055967.1 293 -FESLEEALDQLRCPSLWFAFTSDWLYTPSQTEEVVTVLRKLGKPvaYHLIESDYGHDSFLVEPEKFTP 360
                                               .8****************************************99999********************** PP

                                 TIGR01392 345 lirefl 350
                                                + efl
  lcl|NCBI__GCF_900111775.1:WP_092055967.1 361 KVVEFL 366
                                               **9998 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.53
//
[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