GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Pseudomonas fluorescens FW300-N2C3

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate AO356_13410 AO356_13410 homoserine O-acetyltransferase

Query= SwissProt::D7E9E0
         (489 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_13410
          Length = 379

 Score =  377 bits (967), Expect = e-109
 Identities = 192/368 (52%), Positives = 256/368 (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   SVGLVTPQTAHFSEPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGY 68

Query: 65  HE-GDRKPGWWDIIIGPGKALDTRKYFIICSNVIGGCKGSTGPSSINPDTGESYGLDFPV 123
           H   DRKPGWWD  IGPGK +DT K+F++  N +GGC GSTGPSS+NPDTG+ +G DFPV
Sbjct: 69  HSIDDRKPGWWDSCIGPGKPIDTSKFFVVSLNNLGGCNGSTGPSSLNPDTGKPFGADFPV 128

Query: 124 VTIKDMVNAQKKLIDYLGISKLLAVIGGSMGGLQVLQWSVSYPDMVKKAIPIATAGYSTP 183
           +T++D V++Q +L D LGI +  AVIGGS+GG+Q LQW+++YPD V+  + IA+A   + 
Sbjct: 129 LTVEDWVHSQARLADRLGIGQWAAVIGGSLGGMQALQWTITYPDRVRHCLAIASAPKLSA 188

Query: 184 QQIAFNEVGRIAIVSDPNWNSGNYYGEKE-PTHGLALARMIGHITYLSDDSMHQKFGRRL 242
           Q IAFNEV R AI++DP ++ G++      P  GL LARM+GHITYLSDDSM +KFGR L
Sbjct: 189 QNIAFNEVARQAILTDPEFHGGSFQEHGVIPKRGLMLARMVGHITYLSDDSMGEKFGRGL 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
             N  AKF V+SFT+DW + P + RE+V AL A   DV Y EI++  GHD+FL+   +  
Sbjct: 308 FANATAKFCVMSFTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFLIPIPRYL 367

Query: 360 YVLNNFLS 367
               N+++
Sbjct: 368 QAFGNYMN 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: 500
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 AO356_13410 AO356_13410 (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.4772.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   5.4e-142  458.9   0.0   6.2e-142  458.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410  AO356_13410 homoserine O-acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410  AO356_13410 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.8   0.0  6.2e-142  6.2e-142       3     345 ..      22     369 ..      20     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 458.8 bits;  conditional E-value: 6.2e-142
                                       TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellG 63 
                                                     e+l l +G  l+ +++ y+tyGtlna  +Navl+cHal+g++h+ag+++ +d+  GWWd+ +G
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410  22 EPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGYHSIDDRkpGWWDSCIG 84 
                                                     789*******************************************998777678******** PP

                                       TIGR01392  64 pgraldtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgv 126
                                                     pg+++dts++fvv+lN+lG+c+GstgP+s+np+tgkp+ga+fP++t++D+v+ q++l+d+Lg+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410  85 PGKPIDTSKFFVVSLNNLGGCNGSTGPSSLNPDTGKPFGADFPVLTVEDWVHSQARLADRLGI 147
                                                     *************************************************************** PP

                                       TIGR01392 127 eklaavvGgSlGGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndG 189
                                                      ++aav+GgSlGGmqal+w+++yp+rv++++++a+++++saq+iafnev+rqail+Dpe+++G
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 148 GQWAAVIGGSLGGMQALQWTITYPDRVRHCLAIASAPKLSAQNIAFNEVARQAILTDPEFHGG 210
                                                     *************************************************************** PP

                                       TIGR01392 190 eyaeee.qPekGLalARmlalltYrseesleerfgreakseeslassleeefsvesylryqgk 251
                                                     +++e++  P++GL lARm++++tY+s++s+ e+fgr  kse+     ++ ef+vesylryqg+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 211 SFQEHGvIPKRGLMLARMVGHITYLSDDSMGEKFGRGLKSEKLNYDFHSVEFQVESYLRYQGE 273
                                                     ******9********************************9977777779************** PP

                                       TIGR01392 252 kfverFdAnsYllltkaldthdlargrrdslkealkkikapvlvvgiesDllftleeqeelak 314
                                                     +f  rFdAn+Yll+tkald++d a++ +d+l++++++++a+++v+++++D++f++++++el++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 274 EFSGRFDANTYLLMTKALDYFDPAANFDDNLAKTFANATAKFCVMSFTTDWRFSPARSRELVD 336
                                                     *************************************************************** PP

                                       TIGR01392 315 alkaakle..yaeieseeGHDaFllekekveel 345
                                                     al aa+++  y ei+ ++GHDaFl+   ++ ++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 337 ALMAARKDvcYLEIDAPQGHDAFLIPIPRYLQA 369
                                                     ****999999**************988776665 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: 12.65
//
[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