Alignments for a candidate for metX in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Hydrogenophaga taeniospiralis NBRC 102512

Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_068170716.1 HTA01S_RS10920 homoserine O-acetyltransferase

Query= curated2:Q1QQD3
         (399 letters)



>NCBI__GCF_001592305.1:WP_068170716.1
          Length = 391

 Score =  371 bits (953), Expect = e-107
 Identities = 185/372 (49%), Positives = 242/372 (65%), Gaps = 17/372 (4%)

Query: 30  FAGDQPLPLDCGIDLAPFQIAYQTYGELNAGKSNAILVCHALTGDQHVANVH------PV 83
           F  D PLPL  G  L  +++  +TYG LNA +SNA+LVCHAL    HVA  H      P+
Sbjct: 8   FRFDTPLPLKSGATLPAYELVVETYGTLNADRSNAVLVCHALNASHHVAGWHADANGQPL 67

Query: 84  TGKPGWWVTLVGPGKPLDTDKYFVICSNVIGGCMGSTGPASTNPATGTVWGLDFPVITIP 143
               GWW +++GP K +DTDK+FVI  N +G C GSTGP  TNPATG  WG DFPV+T+ 
Sbjct: 68  PRSEGWWHSMIGPSKAVDTDKWFVIGVNNLGSCFGSTGPTHTNPATGQPWGADFPVVTVE 127

Query: 144 DMVRAQAMLIDRLGIDTLFSVVGGSMGGMQVLQWCVAYPQRVFSALPIACSTRHSAQNIA 203
           D V AQA L+D +GI+ L +V+GGS+GGMQ L W + YP+RV  A+ +A +   +A+NIA
Sbjct: 128 DWVNAQARLLDVMGIEQLAAVMGGSLGGMQTLSWTLQYPERVRHAIVVASAPNLTAENIA 187

Query: 204 FHELGRQAVMADPDWRDGRYVEQGTYPHRGLGVARMAAHITYLSDAALHRKFGR--RMQD 261
           F+E+ R+A++ DPD+  G Y+ +GT P RGL +ARM  HITYLSD  ++ KFGR  R  +
Sbjct: 188 FNEVARRAIVTDPDFHGGHYLREGTLPRRGLRIARMIGHITYLSDDVMNEKFGRSLRTAN 247

Query: 262 RDLPT---------FSFDADFQVESYLRHQGSSFVERFDANSYLYLTRAMDYFDIAADHN 312
            D P           + D +FQ+ESYLR+QG  F E FDAN+YL +TRA+DYFD A +H 
Sbjct: 248 GDDPADTAELAYRYTTQDVEFQIESYLRYQGDKFSEYFDANTYLLITRALDYFDPAREHG 307

Query: 313 GVLAAAFRDTRTRFCVVSFTSDWLFPTSESRATVHALNAGGARVSFAEIETDRGHDAFLL 372
           G L+AA    + RF +VSFT+DW F  + SR  V AL   G  VS+AEI+   GHDAFLL
Sbjct: 308 GSLSAALARAKARFLLVSFTTDWRFSPARSREMVKALLENGRDVSYAEIDAPHGHDAFLL 367

Query: 373 DLPEFFDIAHAF 384
           D P +     A+
Sbjct: 368 DDPRYHQAVRAY 379


Lambda     K      H
   0.323    0.136    0.427 

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: 486
Number of extensions: 18
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: 399
Length of database: 391
Length adjustment: 31
Effective length of query: 368
Effective length of database: 360
Effective search space:   132480
Effective search space used:   132480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)

Align candidate WP_068170716.1 HTA01S_RS10920 (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.9077.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-139  450.7   0.0     2e-139  450.5   0.0    1.0  1  lcl|NCBI__GCF_001592305.1:WP_068170716.1  HTA01S_RS10920 homoserine O-acet


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001592305.1:WP_068170716.1  HTA01S_RS10920 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.5   0.0    2e-139    2e-139       3     350 ..      12     380 ..      10     381 .. 0.95

  Alignments for each domain:
  == domain 1  score: 450.5 bits;  conditional E-value: 2e-139
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.......GWWdellGp 64 
                                               ++l l+sG++l+ +e++++tyGtlna+r+NavlvcHal +s+hvag + + +        GWW++++Gp
  lcl|NCBI__GCF_001592305.1:WP_068170716.1  12 TPLPLKSGATLPAYELVVETYGTLNADRSNAVLVCHALNASHHVAGWHADANGqplprseGWWHSMIGP 80 
                                               6899*****************************************9887554468999*********** PP

                                 TIGR01392  65 graldtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavv 133
                                                +a+dt+++fv+++N+lGsc GstgP+ +np+tg+p+ga+fP+vt++D+v+aq++lld +g+e+laav+
  lcl|NCBI__GCF_001592305.1:WP_068170716.1  81 SKAVDTDKWFVIGVNNLGSCFGSTGPTHTNPATGQPWGADFPVVTVEDWVNAQARLLDVMGIEQLAAVM 149
                                               ********************************************************************* PP

                                 TIGR01392 134 GgSlGGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGL 201
                                               GgSlGGmq+l w+l+yperv++++v+a++++++a++iafnev+r+ai +Dp++++G+y +e+  P++GL
  lcl|NCBI__GCF_001592305.1:WP_068170716.1 150 GGSLGGMQTLSWTLQYPERVRHAIVVASAPNLTAENIAFNEVARRAIVTDPDFHGGHYLREGtLPRRGL 218
                                               ************************************************************9999***** PP

                                 TIGR01392 202 alARmlalltYrseesleerfgreaksee...........slass...leeefsvesylryqgkkfver 256
                                               ++ARm++++tY+s++ ++e+fgr+ ++++                   ++ ef++esylryqg+kf e 
  lcl|NCBI__GCF_001592305.1:WP_068170716.1 219 RIARMIGHITYLSDDVMNEKFGRSLRTANgddpadtaelaY---RyttQDVEFQIESYLRYQGDKFSEY 284
                                               ***********************999988776666654431...1333599****************** PP

                                 TIGR01392 257 FdAnsYllltkaldthdlargrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..y 323
                                               FdAn+Yll+t+ald++d ar++ +sl++al+++ka++l+v++++D++f++++++e++kal +++ +  y
  lcl|NCBI__GCF_001592305.1:WP_068170716.1 285 FDANTYLLITRALDYFDPAREHGGSLSAALARAKARFLLVSFTTDWRFSPARSREMVKALLENGRDvsY 353
                                               ***********************************************************998877778* PP

                                 TIGR01392 324 aeieseeGHDaFllekekveelirefl 350
                                               aei+ ++GHDaFll++ ++++++r+++
  lcl|NCBI__GCF_001592305.1:WP_068170716.1 354 AEIDAPHGHDAFLLDDPRYHQAVRAYF 380
                                               ***********************9876 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.97
//
[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