Alignments for a candidate for metX in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Pseudomonas fluorescens FW300-N2E2

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate Pf6N2E2_4597 Homoserine O-acetyltransferase (EC 2.3.1.31)

Query= SwissProt::D7E9E0
         (489 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4597
          Length = 363

 Score =  374 bits (959), Expect = e-108
 Identities = 189/355 (53%), Positives = 251/355 (70%), Gaps = 6/355 (1%)

Query: 18  EELVLESGKKISDVTLAYETYGTLNWDKSNAILVCHALTGDAHAAGWHE-GDRKPGWWDI 76
           E L L  G+ +    L YETYGTLN   SNA+L+CHAL+G  HAAG+H   DRKPGWWD 
Sbjct: 6   EPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGYHSVDDRKPGWWDS 65

Query: 77  IIGPGKALDTRKYFIICSNVIGGCKGSTGPSSINPDTGESYGLDFPVVTIKDMVNAQKKL 136
            IGPGK +DT K+F++  N +GGC GSTGPSS+NPDTG+ +G DFPV+T++D V++Q +L
Sbjct: 66  CIGPGKPIDTSKFFVVSLNNLGGCNGSTGPSSLNPDTGKPFGADFPVLTVEDWVHSQARL 125

Query: 137 IDYLGISKLLAVIGGSMGGLQVLQWSVSYPDMVKKAIPIATAGYSTPQQIAFNEVGRIAI 196
            D LGI +  AVIGGS+GG+Q LQW+++YPD V+  + IA+A   + Q IAFNEV R AI
Sbjct: 126 ADRLGIGQWAAVIGGSLGGMQALQWTITYPDRVRHCLAIASAPKLSAQNIAFNEVARQAI 185

Query: 197 VSDPNWNSGNYYGEKE-PTHGLALARMIGHITYLSDDSMHQKFGRRLQ-DKNEYEFDFSR 254
           ++DP ++ G++      P  GL LARM+GHITYLSDDSM +KFGR L+ +K  Y+F  S 
Sbjct: 186 LTDPEFHGGSFQEHGVIPKRGLMLARMVGHITYLSDDSMGEKFGRGLKSEKLNYDF-HSV 244

Query: 255 EFEVESYLHYQGLTFTERFDANSYLYLTKAIDYFDLTEN--NSLAEGLKNVEAKFLVISF 312
           EF+VESYL YQG  F+ RFDAN+YL +TKA+DYFD   N  ++LA+   N  AKF V+SF
Sbjct: 245 EFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANFDDNLAKTFANATAKFCVMSF 304

Query: 313 TSDWLYPPYQLREIVMALSANNADVTYREIESNYGHDSFLLESGQLNYVLNNFLS 367
           T+DW + P + RE+V AL A   DV Y EI++  GHD+FL+   +      N+++
Sbjct: 305 TTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFLIPIPRYLQAFGNYMN 359


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: 473
Number of extensions: 20
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: 363
Length adjustment: 32
Effective length of query: 457
Effective length of database: 331
Effective search space:   151267
Effective search space used:   151267
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: 50 (23.9 bits)

Align candidate Pf6N2E2_4597 (Homoserine O-acetyltransferase (EC 2.3.1.31))
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.1179481.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-142  459.7   0.0   3.5e-142  459.6   0.0    1.0  1  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4597  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4597  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.6   0.0  3.5e-142  3.5e-142       3     345 ..       6     353 ..       4     359 .. 0.97

  Alignments for each domain:
  == domain 1  score: 459.6 bits;  conditional E-value: 3.5e-142
                                  TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgral 68 
                                                e+l l +G  l+ +++ y+tyGtlna  +Navl+cHal+g++h+ag+++ +d+  GWWd+ +Gpg+++
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4597   6 EPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGYHSVDDRkpGWWDSCIGPGKPI 73 
                                                789********************************************99887778************* PP

                                  TIGR01392  69 dtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgS 136
                                                dts++fvv+lN+lG+c+GstgP+s+np+tgkp+ga+fP++t++D+v+ q++l+d+Lg+ ++aav+GgS
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4597  74 DTSKFFVVSLNNLGGCNGSTGPSSLNPDTGKPFGADFPVLTVEDWVHSQARLADRLGIGQWAAVIGGS 141
                                                ******************************************************************** PP

                                  TIGR01392 137 lGGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLal 203
                                                lGGmqal+w+++yp+rv++++++a+++++saq+iafnev+rqail+Dpe+++G+++e++  P++GL l
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4597 142 LGGMQALQWTITYPDRVRHCLAIASAPKLSAQNIAFNEVARQAILTDPEFHGGSFQEHGvIPKRGLML 209
                                                ***********************************************************9******** PP

                                  TIGR01392 204 ARmlalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldt 271
                                                ARm++++tY+s++s+ e+fgr  kse+     ++ ef+vesylryqg++f  rFdAn+Yll+tkald+
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4597 210 ARMVGHITYLSDDSMGEKFGRGLKSEKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDY 277
                                                ************************9977777779********************************** PP

                                  TIGR01392 272 hdlargrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFll 337
                                                +d a++ +d+l++++++++a+++v+++++D++f++++++el++al aa+++  y ei+ ++GHDaFl+
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4597 278 FDPAANFDDNLAKTFANATAKFCVMSFTTDWRFSPARSRELVDALMAARKDvcYLEIDAPQGHDAFLI 345
                                                ***********************************************999999**************9 PP

                                  TIGR01392 338 ekekveel 345
                                                   ++ ++
  FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4597 346 PIPRYLQA 353
                                                88776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (363 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: 00:00:00.00
# Mc/sec: 13.92
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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