Alignments for a candidate for metX in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Cupriavidus basilensis 4G11

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate RR42_RS01160 RR42_RS01160 homoserine O-acetyltransferase

Query= SwissProt::F7XKY8
         (492 letters)



>FitnessBrowser__Cup4G11:RR42_RS01160
          Length = 390

 Score =  360 bits (924), Expect = e-104
 Identities = 180/370 (48%), Positives = 253/370 (68%), Gaps = 7/370 (1%)

Query: 5   SLGIVETKYYHLEEELKLESGRKISDVTIAYEAYGTLNRDKNNVILVCHALTGDAHAAGW 64
           S+GIV  +  H  E LKL +G  ++D  +  E YGTLN  ++N +LVCHAL    H AG 
Sbjct: 17  SVGIVAPQCMHFTEPLKLRNGTSLADYDLMVETYGTLNAARSNAVLVCHALNASHHVAGV 76

Query: 65  HKGDNKP-GWWDILIGPGKCLDTDKYFIVCSNVIGGCRGSTGPSSIDPETGKPYGLSFPV 123
           ++ D +  GWWD ++GPGK LDTD++F++  N +G C GSTGP S +P TG+PYG +FPV
Sbjct: 77  YEHDPRDVGWWDNMVGPGKPLDTDRFFVIGVNNLGSCFGSTGPMSANPATGQPYGATFPV 136

Query: 124 ITIKDMVNAQKKLLDHLGISSIYAVIGGSMGGLQVLQWSVSYPDYINKAIALAASAYSSP 183
           +T++D VNAQ ++ D  GI+   AV+GGS+GG+Q L WS+ YPD +   I +A++   S 
Sbjct: 137 VTVEDWVNAQARVADRFGITQFAAVMGGSLGGMQALAWSLMYPDRLRHCIVVASTPKLSA 196

Query: 184 QQIAFNEVARIAIISDPEWNKGNYY-YSRQPSHGLALARMIGHITYLSDESMREKFGREL 242
           Q IAFNEVAR AI+SDP+++ GNYY +  +P  GL +ARMIGHITYLSDE M EKFGREL
Sbjct: 197 QNIAFNEVARSAILSDPDFHGGNYYAHGVKPKRGLRVARMIGHITYLSDEDMAEKFGREL 256

Query: 243 QDRD-RYNYDLSMDFQVESYLHYKGRSFTERFDANSYLYITKAVDYFD--LTENGSLIDG 299
           +  D R+++D  ++FQVESYL Y+G  F E FDAN+YL IT+A+DYFD  L   G L   
Sbjct: 257 KTDDIRFSFD--VEFQVESYLRYQGDKFAEYFDANTYLLITRALDYFDPALAFGGDLTRA 314

Query: 300 LKDIKAKCLIIAVTSDWLYPPYQSKDIVMALNANNVDVTYREIESNYGHDAFLLEAGQLN 359
           +   +A  L+ + T+DW + P +S+++V AL  N   V+Y EI++ +GHDAFLL+  + +
Sbjct: 315 VSQTQASFLVASFTTDWRFAPNRSRELVKALLDNKRPVSYAEIDAPHGHDAFLLDDPRYH 374

Query: 360 YVIGGFLNNI 369
            ++  +   I
Sbjct: 375 NLMRAYYERI 384


Lambda     K      H
   0.318    0.136    0.405 

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: 539
Number of extensions: 27
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: 492
Length of database: 390
Length adjustment: 32
Effective length of query: 460
Effective length of database: 358
Effective search space:   164680
Effective search space used:   164680
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate RR42_RS01160 RR42_RS01160 (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.1251.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-143  464.6   0.0   1.2e-143  464.4   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS01160  RR42_RS01160 homoserine O-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS01160  RR42_RS01160 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.4   0.0  1.2e-143  1.2e-143       2     349 ..      29     380 ..      28     382 .. 0.98

  Alignments for each domain:
  == domain 1  score: 464.4 bits;  conditional E-value: 1.2e-143
                                 TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgral 68 
                                               +e+l+l +G+ l +++++++tyGtlna+r+NavlvcHal +s+hvag ++++ +  GWWd+++Gpg++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS01160  29 TEPLKLRNGTSLADYDLMVETYGTLNAARSNAVLVCHALNASHHVAGVYEHDPRdvGWWDNMVGPGKPL 97 
                                               5799*******************************************999887788************* PP

                                 TIGR01392  69 dtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSl 137
                                               dt+r+fv+++N+lGsc GstgP+s+np+tg+pyga fP+vt++D+v+aq++++d++g++++aav+GgSl
  lcl|FitnessBrowser__Cup4G11:RR42_RS01160  98 DTDRFFVIGVNNLGSCFGSTGPMSANPATGQPYGATFPVVTVEDWVNAQARVADRFGITQFAAVMGGSL 166
                                               ********************************************************************* PP

                                 TIGR01392 138 GGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalAR 205
                                               GGmqal w+l+yp+r+++++v+a+++++saq+iafnev+r ailsDp++++G+y+ ++ +P++GL++AR
  lcl|FitnessBrowser__Cup4G11:RR42_RS01160 167 GGMQALAWSLMYPDRLRHCIVVASTPKLSAQNIAFNEVARSAILSDPDFHGGNYYAHGvKPKRGLRVAR 235
                                               ********************************************************************* PP

                                 TIGR01392 206 mlalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdl 274
                                               m++++tY+s+e+++e+fgre k++ ++ +s++ ef+vesylryqg+kf+e FdAn+Yll+t+ald++d 
  lcl|FitnessBrowser__Cup4G11:RR42_RS01160 236 MIGHITYLSDEDMAEKFGRELKTD-DIRFSFDVEFQVESYLRYQGDKFAEYFDANTYLLITRALDYFDP 303
                                               *******************99998.78999*************************************** PP

                                 TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekek 341
                                               a    ++l++a+++++a++lv+++++D++f++++++el+kal ++k    yaei+ ++GHDaFll++ +
  lcl|FitnessBrowser__Cup4G11:RR42_RS01160 304 ALAFGGDLTRAVSQTQASFLVASFTTDWRFAPNRSRELVKALLDNKRPvsYAEIDAPHGHDAFLLDDPR 372
                                               ******************************************99888778******************* PP

                                 TIGR01392 342 veeliref 349
                                               +++l+r++
  lcl|FitnessBrowser__Cup4G11:RR42_RS01160 373 YHNLMRAY 380
                                               **999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (390 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 0.00s 00:00:00.00 Elapsed: 00:00:00.02
# Mc/sec: 4.91
//
[ok]

This GapMind analysis is from Apr 09 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