GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Burkholderia phytofirmans PsJN

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate BPHYT_RS01595 BPHYT_RS01595 homoserine O-acetyltransferase

Query= SwissProt::Q12XS2
         (488 letters)



>FitnessBrowser__BFirm:BPHYT_RS01595
          Length = 381

 Score =  360 bits (924), Expect = e-104
 Identities = 179/369 (48%), Positives = 243/369 (65%), Gaps = 7/369 (1%)

Query: 5   SVGIVATNYHTIEGEFQLEGGHTLKNIRLAYETYGNLNKEKSNAILVCHALTGDAHAAGR 64
           S+GIVA +        QL+ G +L    L  ETYG LN  +SNA+LVCHAL    H AG 
Sbjct: 3   SIGIVAPHKMHFTEPLQLQNGSSLAGYDLMVETYGTLNAARSNAVLVCHALNASHHVAGV 62

Query: 65  HSDDDKKPGWWDDIIGPGKALDTDRYFVLCSNVLGGCKGTTGPASLDPDTGRQYGITFPV 124
           ++D+ K  GWWD+++GPGK LDTD++FV+  N LG C G+TGP S+DP TG  YG  FPV
Sbjct: 63  YADNPKDIGWWDNMVGPGKPLDTDKFFVIGVNNLGSCFGSTGPMSIDPATGNPYGAAFPV 122

Query: 125 ITIRDMVNVQKRLIDHMGITTLFAVVGGSMGGMQTLQWCVAYPELVKKAVVIASTAVSSP 184
           +T+ D VN Q R+ D  GIT   AV+GGS+GGMQ L W + YPE V   +V+AST   S 
Sbjct: 123 VTVEDWVNAQARVADQFGITRFAAVMGGSLGGMQALAWSMMYPERVGHCIVVASTPKLSA 182

Query: 185 QQIAFNEVGRNAIISDPDWNGGDYY-EGEPPVNGLSTARMIAHITYLSDASMHEKFGRRL 243
           Q IAFNEV R+AI+SDPD++GG+YY     P  GL  ARMI HITYLSD  M EKFGR L
Sbjct: 183 QNIAFNEVARSAILSDPDFHGGNYYAHNVKPKRGLRVARMIGHITYLSDDDMAEKFGRSL 242

Query: 244 QQGE----SYKFDMSNDFQVGSYLKYQGDTFTGRFDANSYLYATKAVDYFD--LSMNGSL 297
           ++ E    +Y F+   +F+V SYL+YQGD F   FDAN+YL  T+A+DYFD   + +G L
Sbjct: 243 RRAEGAVDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFDGDL 302

Query: 298 AEGLKYVQAKMLVISITSDWLYSPYHSKKIVEGLTVKEHDVSYREIESSYGHDAFLLESG 357
              + +  AK L+ S ++DW ++P  S+++V+ L   +  V+Y EI++ +GHDAFLL+  
Sbjct: 303 TAAVAHTTAKYLIASFSTDWRFAPARSRELVKALLDHKRTVTYAEIDAPHGHDAFLLDDA 362

Query: 358 QINYVIHNF 366
           + + ++  +
Sbjct: 363 RYHNLMRAY 371


Lambda     K      H
   0.318    0.134    0.397 

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: 528
Number of extensions: 28
Number of successful extensions: 4
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: 488
Length of database: 381
Length adjustment: 32
Effective length of query: 456
Effective length of database: 349
Effective search space:   159144
Effective search space used:   159144
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 BPHYT_RS01595 BPHYT_RS01595 (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.6934.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.1e-143  463.0   0.1   3.5e-143  462.8   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS01595  BPHYT_RS01595 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS01595  BPHYT_RS01595 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.8   0.1  3.5e-143  3.5e-143       2     349 ..      15     371 ..      14     373 .. 0.96

  Alignments for each domain:
  == domain 1  score: 462.8 bits;  conditional E-value: 3.5e-143
                                TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgrald 69 
                                              +e+l+l++G+ l  ++++++tyGtlna+r+NavlvcHal +s+hvag + ++ k  GWWd+++Gpg++ld
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595  15 TEPLQLQNGSSLAGYDLMVETYGTLNAARSNAVLVCHALNASHHVAGVYADNPKdiGWWDNMVGPGKPLD 84 
                                              579**********************************************9888899************** PP

                                TIGR01392  70 tsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139
                                              t+++fv+++N+lGsc GstgP+si+p+tg+pyga fP+vt++D+v+aq++++d++g++++aav+GgSlGG
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595  85 TDKFFVIGVNNLGSCFGSTGPMSIDPATGNPYGAAFPVVTVEDWVNAQARVADQFGITRFAAVMGGSLGG 154
                                              ********************************************************************** PP

                                TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmla 208
                                              mqal w+++yperv +++v+a+++++saq+iafnev+r ailsDp++++G+y+ ++ +P++GL++ARm++
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595 155 MQALAWSMMYPERVGHCIVVASTPKLSAQNIAFNEVARSAILSDPDFHGGNYYAHNvKPKRGLRVARMIG 224
                                              *******************************************************99************* PP

                                TIGR01392 209 lltYrseesleerfgreaksee....slassleeefsvesylryqgkkfverFdAnsYllltkaldthdl 274
                                              ++tY+s+++++e+fgr+ +++e    +++++++ ef+vesylryqg+kf++ FdAn+Yll+t+ald++d 
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595 225 HITYLSDDDMAEKFGRSLRRAEgavdAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDP 294
                                              *****************999984444444556************************************** PP

                                TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekv 342
                                              a+  +++l++a+++++a++l++++++D++f++++++el+kal + k +  yaei+ ++GHDaFll+++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595 295 AKAFDGDLTAAVAHTTAKYLIASFSTDWRFAPARSRELVKALLDHKRTvtYAEIDAPHGHDAFLLDDARY 364
                                              ******************************************98888778******************** PP

                                TIGR01392 343 eeliref 349
                                              ++l+r++
  lcl|FitnessBrowser__BFirm:BPHYT_RS01595 365 HNLMRAY 371
                                              *999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (381 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.61
//
[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:

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:

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:

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:

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