Alignments for a candidate for metX in Heliobacterium modesticaldum Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Heliobacterium modesticaldum Ice1; ATCC 51547

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_012281269.1 HM1_RS00420 homoserine O-acetyltransferase

Query= SwissProt::D3P9D1
         (377 letters)



>NCBI__GCF_000019165.1:WP_012281269.1
          Length = 391

 Score =  409 bits (1051), Expect = e-119
 Identities = 201/373 (53%), Positives = 258/373 (69%), Gaps = 5/373 (1%)

Query: 3   ENSVGLVKTKYVTF---KDDFYFESGRILSPITVAYETYGKLNEKKDNAILICHALTGSA 59
           E+  G+V+ +  TF    D F  ESG  L PITV YETYG LN ++ NAILI HALTG  
Sbjct: 13  ESREGIVQPQTFTFAEGSDAFVLESGSRLGPITVVYETYGVLNRERSNAILIAHALTGDH 72

Query: 60  HAAGYNSPDDQKPGWWDDMIGPGKAFDTDKYFIICSNFLGSCYGTTGPASIDPSTGKPYG 119
           HAAG N P ++ PGWWDD+IGPGK FDT+++FIICSN LG C GTTGPASI+P+TG+PYG
Sbjct: 73  HAAGKNHPSEKTPGWWDDLIGPGKPFDTNRFFIICSNVLGGCRGTTGPASINPATGRPYG 132

Query: 120 LKFPVFTVKDMVKLQKKLIDYLGIEKLLCVAGGSMGGMQALEWAVTFPEKTYSIIPIATA 179
           + FPV+T++DMV++QK LID+LGIE+LL VAGGSMGGMQ LEW VT+P+    ++PIATA
Sbjct: 133 MNFPVYTIRDMVRVQKALIDHLGIERLLLVAGGSMGGMQVLEWGVTYPDMMDGLLPIATA 192

Query: 180 GRITPMAIAFNTIGRFAIMKDPNWMNGDYYGKTFPRDGLAIARMAGHITYMSDKSFHKKF 239
           GR+T M IAFN I R  IM DP W  GDY     P  GLAIARM G +TY SD+ F  +F
Sbjct: 193 GRMTAMGIAFNEIMRQTIMLDPAWNGGDYAPGKGPAQGLAIARMLGMVTYRSDELFTARF 252

Query: 240 GRRYATF--GGIYDFFGYFEVENYLRYNGYKFTERFDANSYLYIIKAMDIFDLSYGYGSY 297
           GRR         +DF   FE+E+YL Y G K   RFDAN+Y+Y+ KAMD+ D+  G G Y
Sbjct: 253 GRRMTNNQPKAYFDFNNRFEIESYLHYQGDKLVRRFDANTYIYLCKAMDLLDVGRGRGGY 312

Query: 298 EEAIGRIEADSLFITFTSDFLFPSYQTEEIVNIMKNHGKNPEWVNIESDYGHDAFLLEFD 357
           E+A+  I A +LFI   SD+L+P     E+  IMK  G +  +  ++S +GHDAFL+EF+
Sbjct: 313 EKALASITARTLFIGVDSDWLYPPVYMIEMAEIMKKAGCDARYWELKSPHGHDAFLIEFE 372

Query: 358 TQTSCIKEFLSKI 370
                +  F++++
Sbjct: 373 RMRPLVASFVNEL 385


Lambda     K      H
   0.321    0.140    0.432 

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: 507
Number of extensions: 25
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: 377
Length of database: 391
Length adjustment: 30
Effective length of query: 347
Effective length of database: 361
Effective search space:   125267
Effective search space used:   125267
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_012281269.1 HM1_RS00420 (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.31491.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-145  470.5   0.0     2e-145  470.2   0.0    1.0  1  lcl|NCBI__GCF_000019165.1:WP_012281269.1  HM1_RS00420 homoserine O-acetylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019165.1:WP_012281269.1  HM1_RS00420 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.2   0.0    2e-145    2e-145       3     350 ..      31     382 ..      29     383 .. 0.96

  Alignments for each domain:
  == domain 1  score: 470.2 bits;  conditional E-value: 2e-145
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgrald 69 
                                               + ++lesG+ l  ++v+y+tyG ln+er+Na+l+ Haltg++h+agk++ ++k  GWWd+l+Gpg+++d
  lcl|NCBI__GCF_000019165.1:WP_012281269.1  31 DAFVLESGSRLGPITVVYETYGVLNRERSNAILIAHALTGDHHAAGKNHPSEKtpGWWDDLIGPGKPFD 99 
                                               5799*****************************************9988777778************** PP

                                 TIGR01392  70 tsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlG 138
                                               t+r+f++c+NvlG+c+G+tgP+sinp+tg+pyg +fP+ tirD+v++qkal+d+Lg+e+l +v GgS+G
  lcl|NCBI__GCF_000019165.1:WP_012281269.1 100 TNRFFIICSNVLGGCRGTTGPASINPATGRPYGMNFPVYTIRDMVRVQKALIDHLGIERLLLVAGGSMG 168
                                               ********************************************************************* PP

                                 TIGR01392 139 GmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARml 207
                                               Gmq+lew ++yp++++ ++++at+ r++a+ iafne++rq+i+ Dp +n+G+ya  + P++GLa+ARml
  lcl|NCBI__GCF_000019165.1:WP_012281269.1 169 GMQVLEWGVTYPDMMDGLLPIATAGRMTAMGIAFNEIMRQTIMLDPAWNGGDYAPGKGPAQGLAIARML 237
                                               *******************************************************9************* PP

                                 TIGR01392 208 alltYrseesleerfgreakseeslas.sleeefsvesylryqgkkfverFdAnsYllltkaldthdla 275
                                               +++tYrs+e + +rfgr++++++  a+  ++++f++esyl+yqg+k+v+rFdAn+Y++l ka+d  d++
  lcl|NCBI__GCF_000019165.1:WP_012281269.1 238 GMVTYRSDELFTARFGRRMTNNQPKAYfDFNNRFEIESYLHYQGDKLVRRFDANTYIYLCKAMDLLDVG 306
                                               ****************99998865544146*************************************** PP

                                 TIGR01392 276 rgrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekv 342
                                               rg r+++++al++i+a++l++g++sD+l+++    e+a+ +k+a+ +  y e++s++GHDaFl+e+e++
  lcl|NCBI__GCF_000019165.1:WP_012281269.1 307 RG-RGGYEKALASITARTLFIGVDSDWLYPPVYMIEMAEIMKKAGCDarYWELKSPHGHDAFLIEFERM 374
                                               **.8**************************************9987777******************** PP

                                 TIGR01392 343 eelirefl 350
                                               + l+++f+
  lcl|NCBI__GCF_000019165.1:WP_012281269.1 375 RPLVASFV 382
                                               ****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (391 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: 11.48
//
[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