Alignments for a candidate for metX in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Pseudomonas fluorescens FW300-N2E3

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate AO353_08180 AO353_08180 homoserine O-acetyltransferase

Query= SwissProt::D7E9E0
         (489 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_08180
          Length = 379

 Score =  374 bits (960), Expect = e-108
 Identities = 189/368 (51%), Positives = 257/368 (69%), Gaps = 6/368 (1%)

Query: 5   SIGNVETKYYQIPEELVLESGKKISDVTLAYETYGTLNWDKSNAILVCHALTGDAHAAGW 64
           S+G V  +     E L L  G+ +    L YETYGTLN   SNA+L+CHAL+G  HAAG+
Sbjct: 9   SVGLVTPQVAHFSEPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGY 68

Query: 65  HEG-DRKPGWWDIIIGPGKALDTRKYFIICSNVIGGCKGSTGPSSINPDTGESYGLDFPV 123
           H   DRKPGWWD  IGPGK +DT K+F++  N +GGC GSTGPSS NPDTG+ +G DFPV
Sbjct: 69  HSTEDRKPGWWDSCIGPGKPIDTNKFFVVSLNNLGGCNGSTGPSSTNPDTGKPFGADFPV 128

Query: 124 VTIKDMVNAQKKLIDYLGISKLLAVIGGSMGGLQVLQWSVSYPDMVKKAIPIATAGYSTP 183
           +T++D V++Q +L D +GI++  AVIGGS+GG+Q +QWS++YPD ++  + IA+A   + 
Sbjct: 129 LTVEDWVHSQARLADRIGINQWAAVIGGSLGGMQAIQWSITYPDRIRHCLAIASAPKLSA 188

Query: 184 QQIAFNEVGRIAIVSDPNWNSGNYY-GEKEPTHGLALARMIGHITYLSDDSMHQKFGRRL 242
           Q IAFNEV R AI++DP+++ G++      P  GL LARM+GHITYLSDDSM +KFGR L
Sbjct: 189 QNIAFNEVARQAILTDPDFHGGSFQEAGVIPKRGLMLARMVGHITYLSDDSMGEKFGRGL 248

Query: 243 Q-DKNEYEFDFSREFEVESYLHYQGLTFTERFDANSYLYLTKAIDYFDLTEN--NSLAEG 299
           + +K  Y+F  S EF+VESYL YQG  F+ RFDAN+YL +TKA+DYFD   N  ++LA+ 
Sbjct: 249 KSEKLNYDF-HSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANFDDNLAKT 307

Query: 300 LKNVEAKFLVISFTSDWLYPPYQLREIVMALSANNADVTYREIESNYGHDSFLLESGQLN 359
               +AKF V+SFT+DW + P + RE+V AL A   DV Y EI++  GHD+FL+   +  
Sbjct: 308 FAGAKAKFCVMSFTTDWRFSPARSRELVDALMAAKKDVCYLEIDAPQGHDAFLIPIPRYL 367

Query: 360 YVLNNFLS 367
               N+++
Sbjct: 368 QAFRNYMN 375


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: 506
Number of extensions: 21
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: 489
Length of database: 379
Length adjustment: 32
Effective length of query: 457
Effective length of database: 347
Effective search space:   158579
Effective search space used:   158579
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 AO353_08180 AO353_08180 (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.1439.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.6e-141  456.7   0.0   2.9e-141  456.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08180  AO353_08180 homoserine O-acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_08180  AO353_08180 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  456.5   0.0  2.9e-141  2.9e-141       3     350 ..      22     374 ..      20     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 456.5 bits;  conditional E-value: 2.9e-141
                                     TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpg 65 
                                                   e+l l +G  l+ +++ y+tyGtlna  +Navl+cHal+g++h+ag++++ed+  GWWd+ +Gpg
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08180  22 EPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGYHSTEDRkpGWWDSCIGPG 86 
                                                   789********************************************99888789********** PP

                                     TIGR01392  66 raldtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgvekla 130
                                                   +++dt+++fvv+lN+lG+c+GstgP+s+np+tgkp+ga+fP++t++D+v+ q++l+d++g++++a
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08180  87 KPIDTNKFFVVSLNNLGGCNGSTGPSSTNPDTGKPFGADFPVLTVEDWVHSQARLADRIGINQWA 151
                                                   ***************************************************************** PP

                                     TIGR01392 131 avvGgSlGGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee 195
                                                   av+GgSlGGmqa++w+++yp+r+++++++a+++++saq+iafnev+rqail+Dp++++G+++e +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08180 152 AVIGGSLGGMQAIQWSITYPDRIRHCLAIASAPKLSAQNIAFNEVARQAILTDPDFHGGSFQEAG 216
                                                   ***************************************************************** PP

                                     TIGR01392 196 .qPekGLalARmlalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdA 259
                                                     P++GL lARm++++tY+s++s+ e+fgr  kse+     ++ ef+vesylryqg++f  rFdA
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08180 217 vIPKRGLMLARMVGHITYLSDDSMGEKFGRGLKSEKLNYDFHSVEFQVESYLRYQGEEFSGRFDA 281
                                                   9********************************9977777779********************** PP

                                     TIGR01392 260 nsYllltkaldthdlargrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle.. 322
                                                   n+Yll+tkald++d a++ +d+l+++++ +ka+++v+++++D++f++++++el++al aak++  
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08180 282 NTYLLMTKALDYFDPAANFDDNLAKTFAGAKAKFCVMSFTTDWRFSPARSRELVDALMAAKKDvc 346
                                                   ***********************************************************999999 PP

                                     TIGR01392 323 yaeieseeGHDaFllekekveelirefl 350
                                                   y ei+ ++GHDaFl+   ++ ++ r+++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08180 347 YLEIDAPQGHDAFLIPIPRYLQAFRNYM 374
                                                   ***************9999888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (379 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: 10.48
//
[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