Alignments for a candidate for metX in Desulfuromusa kysingii DSM 7343

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Desulfuromusa kysingii DSM 7343

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_092345255.1 BLU87_RS04830 homoserine O-acetyltransferase

Query= SwissProt::B3E278
         (367 letters)



>NCBI__GCF_900107645.1:WP_092345255.1
          Length = 370

 Score =  489 bits (1258), Expect = e-143
 Identities = 228/366 (62%), Positives = 288/366 (78%), Gaps = 2/366 (0%)

Query: 2   SIGVVHEQTITFEAGIRLESGRILAPITLVYELYGTMNADCSNVIMVEHAWTGDAHLAGK 61
           S+G+V  +   F+  +RLESGR+L P+TL YE YG +NAD SNVI+V HAWTG+AH AG+
Sbjct: 4   SVGIVTTKYAEFDVELRLESGRLLGPLTLAYETYGELNADASNVILVTHAWTGNAHAAGR 63

Query: 62  RREDDPKPGWWDAIVGPGRLLDTDRYCVLCSNVIGSCYGSTGPASINPRTGKRYNLSFPV 121
             E+D KPGWWD ++GPG++LDT+RY +L SN IGSC GSTGP SINPRT K Y LSFPV
Sbjct: 64  HSEEDRKPGWWDNMIGPGKVLDTNRYFILSSNTIGSCKGSTGPTSINPRTRKPYRLSFPV 123

Query: 122 ITVRDMVRAQELLLDHLGIRRLLCVMGGSMGGMQALEWATQYPERVASVVALATTPRPSP 181
           I +RDMVRAQ+LLLDHLGI  L  ++GGSMG MQA+EWA  YP+ V ++V +A T + +P
Sbjct: 124 IMIRDMVRAQKLLLDHLGITSLAAIVGGSMGAMQAIEWAIHYPDMVRAIVPIAGTGKTAP 183

Query: 182 QAISLNAVARWAIYNDPTWKKGEY--KHNPKDGLALARGIGHITFLSDESMWQKFERRFS 239
            AI+LNA+AR AI+NDP WKKG Y  +H P DG +LAR +GHI+FLSD SM  KFERRFS
Sbjct: 184 MAIALNALARQAIFNDPLWKKGNYQPEHPPADGFSLARAVGHISFLSDISMQLKFERRFS 243

Query: 240 AKDGLFDFFGQFEVERYLNYNGYNFVDRFDANCFLYLAKALDLYDVAWGYESMTDAFSRI 299
            +DG+FDFFG+FEVERYL+YNG NFVD+FD N FLYLAKALDLYDVAW ++S+++A  R+
Sbjct: 244 VRDGMFDFFGKFEVERYLDYNGKNFVDQFDPNSFLYLAKALDLYDVAWNFDSLSEALERV 303

Query: 300 TAPIQFFAFSSDWLYPPYQTEEMVTCLQGLGKEVEYHLIQSAYGHDAFLLEHETFTPMVR 359
             P  +FAF+SDWLYP  QTEE+V  LQ L K V+YHLI S YGHD+FL+E E + P+++
Sbjct: 304 QCPSIWFAFNSDWLYPAQQTEELVEELQRLNKTVDYHLIDSDYGHDSFLVEPEKYIPLLK 363

Query: 360 SLLERV 365
             L+++
Sbjct: 364 EFLDQL 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: 452
Number of extensions: 12
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_092345255.1 BLU87_RS04830 (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.3725071.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-131  424.4   0.0   1.9e-131  424.2   0.0    1.0  1  NCBI__GCF_900107645.1:WP_092345255.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900107645.1:WP_092345255.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.2   0.0  1.9e-131  1.9e-131       4     350 ..      18     366 ..      15     367 .. 0.98

  Alignments for each domain:
  == domain 1  score: 424.2 bits;  conditional E-value: 1.9e-131
                             TIGR01392   4 eltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldtsryf 74 
                                           el lesG  l  +++ay+tyG+lna+ +N++lv Ha tg+ah+ag+++eed+  GWWd+++Gpg+ ldt+ryf
  NCBI__GCF_900107645.1:WP_092345255.1  18 ELRLESGRLLGPLTLAYETYGELNADASNVILVTHAWTGNAHAAGRHSEEDRkpGWWDNMIGPGKVLDTNRYF 90 
                                           799********************************************9998889******************* PP

                             TIGR01392  75 vvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewal 147
                                           ++++N++GsckGstgP+sinp+t kpy+ +fP++ irD+v+aqk lld+Lg+++laa+vGgS+G mqa+ewa+
  NCBI__GCF_900107645.1:WP_092345255.1  91 ILSSNTIGSCKGSTGPTSINPRTRKPYRLSFPVIMIRDMVRAQKLLLDHLGITSLAAIVGGSMGAMQAIEWAI 163
                                           ************************************************************************* PP

                             TIGR01392 148 sypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlalltYrseeslee 220
                                           +yp++v++iv++a + ++ ++aia+n+++rqai +Dp +++G+y+ e+ P+ G++lAR +++++++s+ s++ 
  NCBI__GCF_900107645.1:WP_092345255.1 164 HYPDMVRAIVPIAGTGKTAPMAIALNALARQAIFNDPLWKKGNYQPEHPPADGFSLARAVGHISFLSDISMQL 236
                                           ************************************************************************* PP

                             TIGR01392 221 rfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikapv 293
                                           +f+r+ + ++  ++ +  +f+ve yl+y+gk+fv++Fd ns+l+l+kald +d+a +  dsl+eal+++++p+
  NCBI__GCF_900107645.1:WP_092345255.1 237 KFERRFSVRD-GMFDFFGKFEVERYLDYNGKNFVDQFDPNSFLYLAKALDLYDVAWN-FDSLSEALERVQCPS 307
                                           ***9998885.577799***************************************9.8************** PP

                             TIGR01392 294 lvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350
                                           +  +++sD+l++++++eel+++l++ +++  y+ i+s++GHD+Fl+e ek+  l++efl
  NCBI__GCF_900107645.1:WP_092345255.1 308 IWFAFNSDWLYPAQQTEELVEELQRLNKTvdYHLIDSDYGHDSFLVEPEKYIPLLKEFL 366
                                           ************************9999889*************************998 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 21.38
//
[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