Alignments for a candidate for metX in Hydrogenovibrio marinus DSM 11271

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Hydrogenovibrio marinus DSM 11271

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_029910298.1 P166_RS0106945 homoserine O-acetyltransferase

Query= SwissProt::D7E9E0
         (489 letters)



>NCBI__GCF_000711315.1:WP_029910298.1
          Length = 384

 Score =  389 bits (999), Expect = e-112
 Identities = 191/376 (50%), Positives = 263/376 (69%), Gaps = 6/376 (1%)

Query: 4   KSIGNVETKYYQIPEELVLESGKKISDVTLAYETYGTLNWDKSNAILVCHALTGDAHAAG 63
           KS+G V ++   +   L +  G  + +  +AYETYG+L+ +KSNAIL+CHAL+G  H AG
Sbjct: 2   KSVGIVSSQTLHVSTPLNMVCGSVLPEYDIAYETYGSLDAEKSNAILICHALSGHQHVAG 61

Query: 64  WHEGDRKPGWWDIIIGPGKALDTRKYFIICSNVIGGCKGSTGPSSINPDTGESYGLDFPV 123
           +HEG++ PGWWD  IGPGK +DT ++F++CSN +GGC GS+GP+S NP+TG+ YG DFP+
Sbjct: 62  FHEGNKNPGWWDDYIGPGKVIDTNQFFVVCSNNLGGCHGSSGPASTNPETGKVYGPDFPI 121

Query: 124 VTIKDMVNAQKKLIDYLGISKLLAVIGGSMGGLQVLQWSVSYPDMVKKAIPIATAGYSTP 183
           VT KD VN+Q +L  +LGI    A+IGGSMGG+QV+QW++ +PD +K AI IA+A   + 
Sbjct: 122 VTCKDWVNSQNELRQHLGIDAWSAIIGGSMGGMQVMQWAIDFPDKIKHAIVIASAPKLSA 181

Query: 184 QQIAFNEVGRIAIVSDPNWNSGNYY-GEKEPTHGLALARMIGHITYLSDDSMHQKFGRRL 242
           Q IAFNEV R AI++DP ++ G +      P  GLALARM+GH+TYLSDD M  KFGR L
Sbjct: 182 QNIAFNEVARRAIMTDPEFHDGRFIEAGTTPKRGLALARMLGHLTYLSDDLMGTKFGREL 241

Query: 243 QDKNEYEFDFSREFEVESYLHYQGLTFT--ERFDANSYLYLTKAIDYFDLTE--NNSLAE 298
           ++  +  ++F  EF+VESYL YQG  F   + FDAN+YL +TKA+DYFD     ++ L +
Sbjct: 242 RE-GKLNYNFEVEFQVESYLRYQGEKFATKQNFDANTYLLMTKALDYFDPASEFDDDLTK 300

Query: 299 GLKNVEAKFLVISFTSDWLYPPYQLREIVMALSANNADVTYREIESNYGHDSFLLESGQL 358
            L +  AKFLVI+FT+DW + P +  EIV AL  N+ADV+Y EIES++GHD+FLL +   
Sbjct: 301 ALSSATAKFLVIAFTTDWRFSPERSHEIVKALLDNDADVSYAEIESSHGHDAFLLPNEHY 360

Query: 359 NYVLNNFLSHTYVSDI 374
             V   +LS     D+
Sbjct: 361 EEVFRTYLSQVVQKDL 376


Lambda     K      H
   0.316    0.134    0.392 

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: 603
Number of extensions: 39
Number of successful extensions: 5
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: 489
Length of database: 384
Length adjustment: 32
Effective length of query: 457
Effective length of database: 352
Effective search space:   160864
Effective search space used:   160864
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: 41 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_029910298.1 P166_RS0106945 (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.1147975.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-143  462.6   0.0   4.8e-143  462.4   0.0    1.0  1  NCBI__GCF_000711315.1:WP_029910298.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000711315.1:WP_029910298.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.4   0.0  4.8e-143  4.8e-143       3     350 ..      16     368 ..      14     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 462.4 bits;  conditional E-value: 4.8e-143
                             TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldtsryf 74 
                                           ++l++ +G+vl+e+++ay+tyG l ae++Na+l+cHal+g++hvag ++ +++ GWWd+++Gpg+ +dt+++f
  NCBI__GCF_000711315.1:WP_029910298.1  16 TPLNMVCGSVLPEYDIAYETYGSLDAEKSNAILICHALSGHQHVAGFHEGNKNpGWWDDYIGPGKVIDTNQFF 88 
                                           679999****************************************99987778******************* PP

                             TIGR01392  75 vvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewal 147
                                           vvc+N+lG+c+Gs+gP+s+npetgk yg++fP vt +D+v+ q++l ++Lg++ + a++GgS+GGmq+++wa+
  NCBI__GCF_000711315.1:WP_029910298.1  89 VVCSNNLGGCHGSSGPASTNPETGKVYGPDFPIVTCKDWVNSQNELRQHLGIDAWSAIIGGSMGGMQVMQWAI 161
                                           ************************************************************************* PP

                             TIGR01392 148 sypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesle 219
                                           + p+++k+++v+a+++++saq+iafnev+r+ai++Dpe++dG++ e + +P++GLalARml++ltY+s++ + 
  NCBI__GCF_000711315.1:WP_029910298.1 162 DFPDKIKHAIVIASAPKLSAQNIAFNEVARRAIMTDPEFHDGRFIEAGtTPKRGLALARMLGHLTYLSDDLMG 234
                                           **********************************************999************************ PP

                             TIGR01392 220 erfgreakseeslassleeefsvesylryqgkkfver..FdAnsYllltkaldthdlargrrdslkealkkik 290
                                           ++fgre ++  +l++++e ef+vesylryqg+kf+++  FdAn+Yll+tkald++d a + +d+l++al++++
  NCBI__GCF_000711315.1:WP_029910298.1 235 TKFGRELREG-KLNYNFEVEFQVESYLRYQGEKFATKqnFDANTYLLMTKALDYFDPASEFDDDLTKALSSAT 306
                                           *******999.88999******************96444********************************** PP

                             TIGR01392 291 apvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350
                                           a++lv+++++D++f++e+++e++kal +++++  yaeies++GHDaFll +e++ee+ r +l
  NCBI__GCF_000711315.1:WP_029910298.1 307 AKFLVIAFTTDWRFSPERSHEIVKALLDNDADvsYAEIESSHGHDAFLLPNEHYEEVFRTYL 368
                                           **************************98888778*********************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (384 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: 00:00:00.00
# Mc/sec: 23.54
//
[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