Alignments for a candidate for metX in Hydrogenovibrio halophilus DSM 15072

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Hydrogenovibrio halophilus DSM 15072

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_028485384.1 A377_RS0108115 homoserine O-acetyltransferase

Query= SwissProt::D7E9E0
         (489 letters)



>NCBI__GCF_000384235.1:WP_028485384.1
          Length = 380

 Score =  380 bits (977), Expect = e-110
 Identities = 191/368 (51%), Positives = 255/368 (69%), Gaps = 6/368 (1%)

Query: 4   KSIGNVETKYYQIPEELVLESGKKISDVTLAYETYGTLNWDKSNAILVCHALTGDAHAAG 63
           +SIG V  +   +   L +  G ++    L YETYG LN D SNA+L+CHAL+G+ H AG
Sbjct: 3   ESIGLVAPETLHVTTPLDMVCGARLPQYDLTYETYGQLNADASNAVLICHALSGNHHVAG 62

Query: 64  WHEGDRKPGWWDIIIGPGKALDTRKYFIICSNVIGGCKGSTGPSSINPDTGESYGLDFPV 123
            ++ ++  GWWD  IGPGK +DT ++F++CSN +GGC GS+GP+SINP+TG+ +G DFP+
Sbjct: 63  HYDEEKSQGWWDQYIGPGKPIDTNRFFVVCSNNLGGCHGSSGPASINPETGDVFGPDFPI 122

Query: 124 VTIKDMVNAQKKLIDYLGISKLLAVIGGSMGGLQVLQWSVSYPDMVKKAIPIATAGYSTP 183
           VT KD VN+Q  L DYLGI    AVIGGSMGG+QV+QW++ YPD ++ A+ IA A   + 
Sbjct: 123 VTCKDWVNSQNVLRDYLGIDAWAAVIGGSMGGMQVMQWAMDYPDRLRHALVIAAAPKLSA 182

Query: 184 QQIAFNEVGRIAIVSDPNWNSGNYY-GEKEPTHGLALARMIGHITYLSDDSMHQKFGRRL 242
           Q IAFNEV R AI++DP ++ G +      P  GLALARM+GH+TYLSDD M  KFGR L
Sbjct: 183 QNIAFNEVARRAIMTDPEFHHGRFIEAGTTPKRGLALARMLGHLTYLSDDMMGSKFGREL 242

Query: 243 QDKNEYEFDFSREFEVESYLHYQGLTFT--ERFDANSYLYLTKAIDYFDLTE--NNSLAE 298
           ++  + +++F  EF+VESYL YQG  F   + FDAN+YL +TKA+DYFD     +NSLA+
Sbjct: 243 RE-GKLKYNFDVEFQVESYLRYQGEKFATKQNFDANTYLLMTKALDYFDPAAEFDNSLAK 301

Query: 299 GLKNVEAKFLVISFTSDWLYPPYQLREIVMALSANNADVTYREIESNYGHDSFLLESGQL 358
            L    AKFLVISFTSDW + P + +EIV AL  N+ADVTY EI S +GHD+FLL +   
Sbjct: 302 ALAQTTAKFLVISFTSDWRFSPKRSQEIVKALLDNDADVTYAEINSKHGHDAFLLPNAHY 361

Query: 359 NYVLNNFL 366
             V   ++
Sbjct: 362 EGVFRAYM 369


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: 558
Number of extensions: 34
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: 380
Length adjustment: 32
Effective length of query: 457
Effective length of database: 348
Effective search space:   159036
Effective search space used:   159036
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_028485384.1 A377_RS0108115 (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.13524.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-144  465.4   0.0   6.7e-144  465.2   0.0    1.0  1  lcl|NCBI__GCF_000384235.1:WP_028485384.1  A377_RS0108115 homoserine O-acet


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384235.1:WP_028485384.1  A377_RS0108115 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.2   0.0  6.7e-144  6.7e-144       3     350 ..      17     369 ..      15     370 .. 0.97

  Alignments for each domain:
  == domain 1  score: 465.2 bits;  conditional E-value: 6.7e-144
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldt 70 
                                               ++l + +G+ l++++++y+tyG+lna+ +Navl+cHal+g++hvag++dee++ GWWd+++Gpg+++dt
  lcl|NCBI__GCF_000384235.1:WP_028485384.1  17 TPLDMVCGARLPQYDLTYETYGQLNADASNAVLICHALSGNHHVAGHYDEEKSqGWWDQYIGPGKPIDT 85 
                                               678999*******************************************88877*************** PP

                                 TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                               +r+fvvc+N+lG+c+Gs+gP+sinpetg+ +g++fP vt +D+v+ q+ l d Lg++ +aav+GgS+GG
  lcl|NCBI__GCF_000384235.1:WP_028485384.1  86 NRFFVVCSNNLGGCHGSSGPASINPETGDVFGPDFPIVTCKDWVNSQNVLRDYLGIDAWAAVIGGSMGG 154
                                               ********************************************************************* PP

                                 TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARml 207
                                               mq+++wa++yp+r+++++v+a+++++saq+iafnev+r+ai++Dpe+++G++ e + +P++GLalARml
  lcl|NCBI__GCF_000384235.1:WP_028485384.1 155 MQVMQWAMDYPDRLRHALVIAAAPKLSAQNIAFNEVARRAIMTDPEFHHGRFIEAGtTPKRGLALARML 223
                                               ******************************************************999************ PP

                                 TIGR01392 208 alltYrseesleerfgreakseeslassleeefsvesylryqgkkfver..FdAnsYllltkaldthdl 274
                                               ++ltY+s++ + ++fgre ++  +l+++++ ef+vesylryqg+kf+++  FdAn+Yll+tkald++d 
  lcl|NCBI__GCF_000384235.1:WP_028485384.1 224 GHLTYLSDDMMGSKFGRELREG-KLKYNFDVEFQVESYLRYQGEKFATKqnFDANTYLLMTKALDYFDP 291
                                               *******************999.88999******************96444****************** PP

                                 TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekek 341
                                               a++ ++sl++al++++a++lv++++sD++f++++++e++kal +++++  yaei+s++GHDaFll +++
  lcl|NCBI__GCF_000384235.1:WP_028485384.1 292 AAEFDNSLAKALAQTTAKFLVISFTSDWRFSPKRSQEIVKALLDNDADvtYAEINSKHGHDAFLLPNAH 360
                                               ******************************************99888888****************999 PP

                                 TIGR01392 342 veelirefl 350
                                               +e + r+++
  lcl|NCBI__GCF_000384235.1:WP_028485384.1 361 YEGVFRAYM 369
                                               998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (380 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: 10.58
//
[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