Alignments for a candidate for metX in Methanosarcina barkeri Fusaro

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Methanosarcina barkeri Fusaro

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_011307393.1 MBAR_RS12890 homoserine O-acetyltransferase

Query= SwissProt::Q8TME4
         (540 letters)



>NCBI__GCF_000195895.1:WP_011307393.1
          Length = 579

 Score =  850 bits (2197), Expect = 0.0
 Identities = 434/575 (75%), Positives = 488/575 (84%), Gaps = 42/575 (7%)

Query: 7   NSSVNSSKKLFSGKKGQSIGIVRSMNYKIPGTFGLESGKTLSGVRVEYEMYGKMNADKSN 66
           ++ V S K LFSGKKGQ++G+VRSMNY+IPG F LESGKTLS VR+EYEMYGKMNADKSN
Sbjct: 4   STQVPSFKNLFSGKKGQNLGLVRSMNYEIPGIFRLESGKTLSHVRIEYEMYGKMNADKSN 63

Query: 67  VILICHALTGDAHAAGFHEGDKKPGWWEIVIGPNKAFDTEKYCVICSNILGGCKGSTGPS 126
           VIL+CHALTGDAHAAGFH GDKKPGWW IVIGPNKAFDTE+YC++CSNI+GGCKGSTGPS
Sbjct: 64  VILVCHALTGDAHAAGFHTGDKKPGWWNIVIGPNKAFDTERYCIVCSNIIGGCKGSTGPS 123

Query: 127 SIDPETGKHYGISFPVITVKDMVNAQKKLIEHLGVKQLFAVAGGSMGGMQVLQWTVSYPE 186
           SI+PETGK YGISFP++T+ DMVNAQKKL+EHLGVKQLFAVAGGSMGGMQVLQWTVSYPE
Sbjct: 124 SINPETGKPYGISFPILTIADMVNAQKKLVEHLGVKQLFAVAGGSMGGMQVLQWTVSYPE 183

Query: 187 MVRKAIAIATTASTTPQQIAFGAIGRKAITDDPKWNGGDYYGKEIPSQGLALARMIGHIT 246
           MV+KAIAIATTASTTPQQIAFGAIGRKAITDDPKWNGG+YYGK+ P+QGLALARMIGHIT
Sbjct: 184 MVKKAIAIATTASTTPQQIAFGAIGRKAITDDPKWNGGNYYGKKTPAQGLALARMIGHIT 243

Query: 247 YLSDASMQNKFGRLQQD---------------------------------TDKSGIKGTT 273
           YLSDASMQ KFGR +Q+                                 + K+  K ++
Sbjct: 244 YLSDASMQKKFGRDKQEKVGPDMPKISSKVSSEVSPAASSKTSSETSPETSSKTSSKTSS 303

Query: 274 GTEGKNSSEISSEISS-ISSEISSELSY--------DFTPNFQVESYLNYKGDNFTKRFD 324
            T  K SS+ SS+ SS  SSE SSE S         D + +FQVESYLN++GD FTKRFD
Sbjct: 304 ETSSKTSSKTSSKTSSKTSSETSSETSSKTFSETFPDRSSHFQVESYLNHQGDTFTKRFD 363

Query: 325 ANSYLYITKAVDYFDLAKNGSLIEGFSGVTAKYLVISISSDWLYPPYQSQEIVSALTANG 384
           ANSYLYITKAVD+FDL+KNGSLIEG S VTAKYLVISI+SDWLYPPYQSQEIVSALTANG
Sbjct: 364 ANSYLYITKAVDFFDLSKNGSLIEGLSVVTAKYLVISITSDWLYPPYQSQEIVSALTANG 423

Query: 385 VDARYEEIRSQHGHDAFLLEEGQLSYLLRSFLSHILVSDVMNRNFYTVSRDETIEHSSKL 444
           VDA+YEEIRSQ+GHDAFLLEEGQL+YL+R FLS ILVSD+M RNFY+VSR+ETIE++S L
Sbjct: 424 VDAKYEEIRSQYGHDAFLLEEGQLNYLIRGFLSQILVSDIMYRNFYSVSRNETIENASTL 483

Query: 445 MVKECVSHLPVISEDGKLEGIVTSWDITKAVACKINELDEIITRDVKYVYEDEKIEHASS 504
           MVK+ V+HLPV+SEDGKLEGIVTSWDITKAVACKI ELDEIITRDVKYV+  +KIE ASS
Sbjct: 484 MVKKKVNHLPVVSEDGKLEGIVTSWDITKAVACKITELDEIITRDVKYVFSGDKIETASS 543

Query: 505 IMEKHSISALPVIDSEHRIIGIVTSESISALFGKY 539
           IME  SISALPVIDSE+R+IG+VTSESISAL GK+
Sbjct: 544 IMEDFSISALPVIDSENRVIGMVTSESISALIGKF 578


Lambda     K      H
   0.315    0.132    0.379 

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: 1016
Number of extensions: 35
Number of successful extensions: 4
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: 540
Length of database: 579
Length adjustment: 36
Effective length of query: 504
Effective length of database: 543
Effective search space:   273672
Effective search space used:   273672
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: 42 (22.0 bits)
S2: 53 (25.0 bits)

Align candidate WP_011307393.1 MBAR_RS12890 (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.20464.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-145  469.1   0.1   6.5e-145  468.5   0.1    1.2  1  lcl|NCBI__GCF_000195895.1:WP_011307393.1  MBAR_RS12890 homoserine O-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195895.1:WP_011307393.1  MBAR_RS12890 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.5   0.1  6.5e-145  6.5e-145       5     350 ..      36     455 ..      33     456 .. 0.94

  Alignments for each domain:
  == domain 1  score: 468.5 bits;  conditional E-value: 6.5e-145
                                 TIGR01392   5 ltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldtsr 72 
                                               + lesG++ls+v++ y+ yG++na+++N++lvcHaltg+ah+ag +  ++k GWW+ ++Gp++a+dt+r
  lcl|NCBI__GCF_000195895.1:WP_011307393.1  36 FRLESGKTLSHVRIEYEMYGKMNADKSNVILVCHALTGDAHAAGFHTGDKKpGWWNIVIGPNKAFDTER 104
                                               789*****************************************99988878***************** PP

                                 TIGR01392  73 yfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmq 141
                                               y++vc+N +G+ckGstgP+sinpetgkpyg +fP +ti D+v+aqk+l+++Lgv++l+av GgS+GGmq
  lcl|NCBI__GCF_000195895.1:WP_011307393.1 105 YCIVCSNIIGGCKGSTGPSSINPETGKPYGISFPILTIADMVNAQKKLVEHLGVKQLFAVAGGSMGGMQ 173
                                               ********************************************************************* PP

                                 TIGR01392 142 alewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlall 210
                                               +l+w++sype+vkk++++at+a +++q+iaf ++ r+ai++Dp++n+G+y+ +++P++GLalARm++++
  lcl|NCBI__GCF_000195895.1:WP_011307393.1 174 VLQWTVSYPEMVKKAIAIATTASTTPQQIAFGAIGRKAITDDPKWNGGNYYGKKTPAQGLALARMIGHI 242
                                               ********************************************************************* PP

                                 TIGR01392 211 tYrseesleerfgreaksee................................................. 230
                                               tY+s++s++++fgr+++++                                                  
  lcl|NCBI__GCF_000195895.1:WP_011307393.1 243 TYLSDASMQKKFGRDKQEKVgpdmpkisskvssevspaassktssetspetssktssktssetssktss 311
                                               **************99999899**************999999999999999999999888888888877 PP

                                 TIGR01392 231 ..............slass.............leeefsvesylryqgkkfverFdAnsYllltkaldth 272
                                                             s   s             ++++f+vesyl++qg++f +rFdAnsYl++tka+d +
  lcl|NCBI__GCF_000195895.1:WP_011307393.1 312 ktssktssktssetS---SetssktfsetfpdRSSHFQVESYLNHQGDTFTKRFDANSYLYITKAVDFF 377
                                               777766666655550...0555566666655569*********************************** PP

                                 TIGR01392 273 dlargrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllek 339
                                               dl+++  +sl e l+ ++a++lv++i+sD+l+++ +++e+++al+a++++  y+ei+s++GHDaFlle+
  lcl|NCBI__GCF_000195895.1:WP_011307393.1 378 DLSKN--GSLIEGLSVVTAKYLVISITSDWLYPPYQSQEIVSALTANGVDakYEEIRSQYGHDAFLLEE 444
                                               ****7..9************************************99988777***************** PP

                                 TIGR01392 340 ekveelirefl 350
                                                +++ lir fl
  lcl|NCBI__GCF_000195895.1:WP_011307393.1 445 GQLNYLIRGFL 455
                                               ********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (579 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: 00:00:00.01
# Mc/sec: 13.48
//
[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