Alignments for a candidate for metX in Methylocella silvestris BL2

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Methylocella silvestris BL2

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_012590062.1 MSIL_RS21000 homoserine O-acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>NCBI__GCF_000021745.1:WP_012590062.1
          Length = 394

 Score =  515 bits (1326), Expect = e-151
 Identities = 246/366 (67%), Positives = 298/366 (81%), Gaps = 2/366 (0%)

Query: 17  FPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGW 76
           F  +  L++DSGG +    IAYQTYG+LNA KSNA+L+CHALTGDQHVA+ HP TGKPGW
Sbjct: 25  FGPDHALQMDSGGRLNQWTIAYQTYGELNAAKSNAILVCHALTGDQHVANAHPVTGKPGW 84

Query: 77  WQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQ 136
           W  +VGPG+P+D  R+F+ICSNVIGGCMG+TGPAS+NP TG+ YGL  P++TI DMVRAQ
Sbjct: 85  WSTMVGPGRPIDTDRYFVICSNVIGGCMGTTGPASLNPQTGRPYGLELPIVTIRDMVRAQ 144

Query: 137 AMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGR 196
           AML+  LGV+TLF VVGGSMGGMQV QW   +PER+FSA+ +A+A++HS+QNIAFHEVGR
Sbjct: 145 AMLIDHLGVDTLFCVVGGSMGGMQVLQWVASFPERVFSAMPIATAAKHSSQNIAFHEVGR 204

Query: 197 QAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-RDGLSWGF 255
           QA+MADPDWR G Y E GV P KGLAVARMAAHITYLS+ ALQ KFGR+LQ RD  ++ F
Sbjct: 205 QAVMADPDWRKGRYLEEGVIPTKGLAVARMAAHITYLSDEALQSKFGRKLQDRDAPTFSF 264

Query: 256 DADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFCV 315
           DA+FQ+E+YLR+QGSSFVDRFD NSYLY+TRA DYFD+AA + G LA+AF   +  RFCV
Sbjct: 265 DAEFQIENYLRYQGSSFVDRFDPNSYLYVTRACDYFDLAADYDGSLARAFQGVK-ARFCV 323

Query: 316 LSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLASA 375
           +SF+SDWLYPTA +R +V AL A GA  +F +IE+D+GHDAFLLD P   A  +GFL SA
Sbjct: 324 VSFNSDWLYPTAASRAIVHALNAGGASVSFVDIETDRGHDAFLLDLPEFIATSQGFLDSA 383

Query: 376 ERDRGL 381
            + RGL
Sbjct: 384 AKARGL 389


Lambda     K      H
   0.321    0.135    0.417 

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: 496
Number of extensions: 20
Number of successful extensions: 3
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: 382
Length of database: 394
Length adjustment: 30
Effective length of query: 352
Effective length of database: 364
Effective search space:   128128
Effective search space used:   128128
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: 50 (23.9 bits)

Align candidate WP_012590062.1 MSIL_RS21000 (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.8712.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-146  472.8   0.0   4.1e-146  472.5   0.0    1.1  1  lcl|NCBI__GCF_000021745.1:WP_012590062.1  MSIL_RS21000 homoserine O-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021745.1:WP_012590062.1  MSIL_RS21000 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.5   0.0  4.1e-146  4.1e-146       3     347 ..      29     377 ..      27     381 .. 0.97

  Alignments for each domain:
  == domain 1  score: 472.5 bits;  conditional E-value: 4.1e-146
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldt 70 
                                               + l+++sG+ l++ ++ay+tyG+lna+++Na+lvcHaltg++hva+ +  + k GWW++++Gpgr++dt
  lcl|NCBI__GCF_000021745.1:WP_012590062.1  29 HALQMDSGGRLNQWTIAYQTYGELNAAKSNAILVCHALTGDQHVANAHPVTGKpGWWSTMVGPGRPIDT 97 
                                               5799*****************************************999877667*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               +ryfv+c+Nv+G+c G+tgP+s+np+tg+pyg e+P vtirD+v+aq++l+d+Lgv++l++vvGgS+GG
  lcl|NCBI__GCF_000021745.1:WP_012590062.1  98 DRYFVICSNVIGGCMGTTGPASLNPQTGRPYGLELPIVTIRDMVRAQAMLIDHLGVDTLFCVVGGSMGG 166
                                               ********************************************************************* PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARml 207
                                               mq+l+w++s perv +++++at+a++s+q+iaf+ev rqa+++Dp++++G+y ee+  P+kGLa+ARm 
  lcl|NCBI__GCF_000021745.1:WP_012590062.1 167 MQVLQWVASFPERVFSAMPIATAAKHSSQNIAFHEVGRQAVMADPDWRKGRYLEEGvIPTKGLAVARMA 235
                                               ********************************************************9************ PP

                                 TIGR01392 208 alltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlar 276
                                               a++tY+s+e+l+++fgr+ ++++++++s+++ef++e ylryqg++fv+rFd nsYl++t+a d++dla+
  lcl|NCBI__GCF_000021745.1:WP_012590062.1 236 AHITYLSDEALQSKFGRKLQDRDAPTFSFDAEFQIENYLRYQGSSFVDRFDPNSYLYVTRACDYFDLAA 304
                                               ********************************************************************* PP

                                 TIGR01392 277 grrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekve 343
                                               ++++sl++a++ +ka+++vv+++sD+l++++ ++ +++al+a +++  ++ ie+++GHDaFll+  ++ 
  lcl|NCBI__GCF_000021745.1:WP_012590062.1 305 DYDGSLARAFQGVKARFCVVSFNSDWLYPTAASRAIVHALNAGGASvsFVDIETDRGHDAFLLDLPEFI 373
                                               *****************************************9998888****************98877 PP

                                 TIGR01392 344 elir 347
                                               ++ +
  lcl|NCBI__GCF_000021745.1:WP_012590062.1 374 ATSQ 377
                                               6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (394 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.06
//
[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