Alignments for a candidate for metX in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Marinobacter adhaerens HP15

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate GFF285 HP15_284 homoserine O-acetyltransferase

Query= SwissProt::K2QXP6
         (493 letters)



>FitnessBrowser__Marino:GFF285
          Length = 382

 Score =  378 bits (971), Expect = e-109
 Identities = 187/366 (51%), Positives = 253/366 (69%), Gaps = 3/366 (0%)

Query: 4   ESVGVVETKHYNLSEELILDGGDSLKDVTIAYETYGTLNKQKSNAILVCHALSGNAHVAG 63
           +SVG+V  + Y+    + L  G SL++  +  ETYGTLN   SNA+L+CHALSG+ H AG
Sbjct: 8   DSVGIVSPQTYHFDAPIDLACGQSLENYDLVVETYGTLNADASNAVLICHALSGHHHAAG 67

Query: 64  WHEG-DRKPGWWDNIIGPGKCLDTDRYFIICSNVLGGCQGSTGPSSLNPETGKQYALEFP 122
           +H   DRKPGWWD+ IGPGK +DTDR+F++  N LGGC GSTGP+S+NPETGK +  EFP
Sbjct: 68  YHSAEDRKPGWWDSCIGPGKPIDTDRFFVVSLNNLGGCHGSTGPNSINPETGKPFGPEFP 127

Query: 123 IITIKDMVKAQKKLIDHLQIKQLFSVVGGSMGGMQVLQWCVSYPDMVRSAIPIATTSYSS 182
           +IT+ D VK+Q  L D L I+   +VVGGS+GGMQ LQW + YPD +R A+ IA+T   +
Sbjct: 128 VITVGDWVKSQALLADRLGIQCWAAVVGGSLGGMQALQWSLDYPDRLRHAVVIASTPRLT 187

Query: 183 PQQIAFNEVGRRAIISDPHWNEGNYYEGE-FPDSGLALARMIGHITYLSNESMYEKFGRR 241
            Q IAFNEV R+AI SD  +++G YY+ +  P  GL LARM+GHITYLS+ SM EKFGR 
Sbjct: 188 AQNIAFNEVARQAITSDREFHDGRYYDFDTVPRRGLMLARMVGHITYLSDASMGEKFGRE 247

Query: 242 LQDKEEYSFDFSTDFEVESYLHYQGDTFTKRFDANSYLYISKAIDYFDLTENGTVSLSEA 301
           L+D + Y F +  +F+VESYL YQG+ F++ FDAN+YL +++A+DYFD        LS+A
Sbjct: 248 LRD-QAYKFGYDAEFQVESYLRYQGERFSESFDANTYLLMTRALDYFDPAYEFGGDLSKA 306

Query: 302 LKNVKARVLVISVDSDWLYTPAESKEIVMAMTANEVDVSYCQIKSSYGHDAFLLEAGQLS 361
           L       LV+S  +DW +TPA S+E+V AM      VSY ++ + +GHDAFL+   + +
Sbjct: 307 LAAASCEYLVLSFSTDWRFTPARSEEMVNAMIGARRKVSYAEVDAPWGHDAFLIPTPRYT 366

Query: 362 YIINGF 367
            I N +
Sbjct: 367 DIFNAY 372


Lambda     K      H
   0.317    0.134    0.391 

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: 494
Number of extensions: 24
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: 493
Length of database: 382
Length adjustment: 32
Effective length of query: 461
Effective length of database: 350
Effective search space:   161350
Effective search space used:   161350
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 GFF285 HP15_284 (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.19398.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.5e-142  459.2   0.0   5.2e-142  459.0   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF285  HP15_284 homoserine O-acetyltran


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF285  HP15_284 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.0   0.0  5.2e-142  5.2e-142       3     350 ..      22     373 ..      20     374 .. 0.97

  Alignments for each domain:
  == domain 1  score: 459.0 bits;  conditional E-value: 5.2e-142
                          TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldtsryfvv 76 
                                         ++ l +G+ l++++++++tyGtlna+ +Navl+cHal+g++h+ag++++ed+  GWWd+ +Gpg+++dt+r+fvv
  lcl|FitnessBrowser__Marino:GFF285  22 APIDLACGQSLENYDLVVETYGTLNADASNAVLICHALSGHHHAAGYHSAEDRkpGWWDSCIGPGKPIDTDRFFVV 97 
                                        57889******************************************99888789********************* PP

                          TIGR01392  77 clNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewalsyper 152
                                        +lN+lG+c+GstgP sinpetgkp+g+efP++t+ D+vk q+ l+d+Lg++ +aavvGgSlGGmqal+w+l+yp+r
  lcl|FitnessBrowser__Marino:GFF285  98 SLNNLGGCHGSTGPNSINPETGKPFGPEFPVITVGDWVKSQALLADRLGIQCWAAVVGGSLGGMQALQWSLDYPDR 173
                                        **************************************************************************** PP

                          TIGR01392 153 vkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesleerfgreak 227
                                        ++++vv+a+++r++aq+iafnev+rqai+sD e++dG+y++ +  P++GL lARm++++tY+s++s+ e+fgre +
  lcl|FitnessBrowser__Marino:GFF285 174 LRHAVVIASTPRLTAQNIAFNEVARQAITSDREFHDGRYYDFDtVPRRGLMLARMVGHITYLSDASMGEKFGRELR 249
                                        ***************************************99888*******************************9 PP

                          TIGR01392 228 seeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikapvlvvgiesDll 303
                                        ++ ++++ +++ef+vesylryqg++f e FdAn+Yll+t+ald++d a +  ++l++al+++++++lv+++++D++
  lcl|FitnessBrowser__Marino:GFF285 250 DQ-AYKFGYDAEFQVESYLRYQGERFSESFDANTYLLMTRALDYFDPAYEFGGDLSKALAAASCEYLVLSFSTDWR 324
                                        99.778999******************************************************************* PP

                          TIGR01392 304 ftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350
                                        ft++++ee+++a+  a+ +  yae++ + GHDaFl+ + +++++ ++++
  lcl|FitnessBrowser__Marino:GFF285 325 FTPARSEEMVNAMIGARRKvsYAEVDAPWGHDAFLIPTPRYTDIFNAYM 373
                                        ************999988888*****************99999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (382 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: 11.29
//
[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