Alignments for a candidate for metX in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Caulobacter crescentus NA1000

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate CCNA_00559 CCNA_00559 homoserine O-acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>FitnessBrowser__Caulo:CCNA_00559
          Length = 382

 Score =  775 bits (2000), Expect = 0.0
 Identities = 382/382 (100%), Positives = 382/382 (100%)

Query: 1   MAALDPITPAGGGTWRFPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTG 60
           MAALDPITPAGGGTWRFPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTG
Sbjct: 1   MAALDPITPAGGGTWRFPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTG 60

Query: 61  DQHVASPHPTTGKPGWWQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTY 120
           DQHVASPHPTTGKPGWWQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTY
Sbjct: 61  DQHVASPHPTTGKPGWWQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTY 120

Query: 121 GLSFPVITIADMVRAQAMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLAS 180
           GLSFPVITIADMVRAQAMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLAS
Sbjct: 121 GLSFPVITIADMVRAQAMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLAS 180

Query: 181 ASRHSAQNIAFHEVGRQAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQR 240
           ASRHSAQNIAFHEVGRQAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQR
Sbjct: 181 ASRHSAQNIAFHEVGRQAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQR 240

Query: 241 KFGRELQRDGLSWGFDADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGV 300
           KFGRELQRDGLSWGFDADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGV
Sbjct: 241 KFGRELQRDGLSWGFDADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGV 300

Query: 301 LAKAFTRARNVRFCVLSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLD 360
           LAKAFTRARNVRFCVLSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLD
Sbjct: 301 LAKAFTRARNVRFCVLSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLD 360

Query: 361 EPVMDAALEGFLASAERDRGLV 382
           EPVMDAALEGFLASAERDRGLV
Sbjct: 361 EPVMDAALEGFLASAERDRGLV 382


Lambda     K      H
   0.321    0.135    0.417 

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: 701
Number of extensions: 20
Number of successful extensions: 1
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate CCNA_00559 CCNA_00559 (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.2947918.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-147  477.1   0.0   1.9e-147  476.9   0.0    1.0  1  FitnessBrowser__Caulo:CCNA_00559  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_00559  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  476.9   0.0  1.9e-147  1.9e-147       2     350 ..      20     372 ..      19     373 .. 0.97

  Alignments for each domain:
  == domain 1  score: 476.9 bits;  conditional E-value: 1.9e-147
                         TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldtsryfvvc 77 
                                       +e+l l+sG+v++ +e+ay+tyG+lna+++Navl+cHaltg++hva+ + ++ k GWW++l+Gpg++ld++r+f++c
  FitnessBrowser__Caulo:CCNA_00559  20 NEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKpGWWQRLVGPGKPLDPARHFIIC 96 
                                       5799******************************************999877667********************** PP

                         TIGR01392  78 lNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewalsypervk 154
                                       +Nv+G+c GstgP+sinp+tgk+yg +fP++ti D+v+aq++l+ +Lgve+l+avvGgS+GGmq+ +wa++yper+ 
  FitnessBrowser__Caulo:CCNA_00559  97 SNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQAMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMF 173
                                       ***************************************************************************** PP

                         TIGR01392 155 kivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesleerfgreaksee 230
                                       ++vvla++ r+saq+iaf+ev rqai++Dp++++G yae++ +PekGLa+ARm a++tY+se +l+++fgre +++ 
  FitnessBrowser__Caulo:CCNA_00559 174 SAVVLASASRHSAQNIAFHEVGRQAIMADPDWRGGAYAEHGvRPEKGLAVARMAAHITYLSEPALQRKFGRELQRD- 249
                                       ************************************************************************9998. PP

                         TIGR01392 231 slassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkik.apvlvvgiesDllftl 306
                                        l+  ++++f+vesylr+qg++fv+rFdAnsYl++t+a+d++d+a+ + + l++a+++++ ++++v++++sD+l+++
  FitnessBrowser__Caulo:CCNA_00559 250 GLSWGFDADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARnVRFCVLSFSSDWLYPT 326
                                       778889**************************************************9886278************** PP

                         TIGR01392 307 eeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350
                                       +e+++l++al+aa+++  +aeies++GHDaFll++  ++++++ fl
  FitnessBrowser__Caulo:CCNA_00559 327 AENRHLVRALTAAGARaaFAEIESDKGHDAFLLDEPVMDAALEGFL 372
                                       ************999999*********************9999887 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 21.21
//
[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