GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Pseudomonas putida KT2440

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate PP_1000 PP_1000 ornithine carbamoyltransferase, catabolic

Query= SwissProt::P08308
         (336 letters)



>FitnessBrowser__Putida:PP_1000
          Length = 336

 Score =  634 bits (1634), Expect = 0.0
 Identities = 309/336 (91%), Positives = 325/336 (96%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           MAFN+HNRNLLSL HH+TRELRYLLDLSRDLKRAKYTGTEQQHLK  NIALIFEKTSTRT
Sbjct: 1   MAFNIHNRNLLSLEHHTTRELRYLLDLSRDLKRAKYTGTEQQHLKGNNIALIFEKTSTRT 60

Query: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120
           RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK
Sbjct: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120

Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180
           FAGVPVFNGLTDEYHPTQM+ADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL
Sbjct: 121 FAGVPVFNGLTDEYHPTQMIADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180

Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240
           GMDVRIAAPKALWPHD+ V +CK++AEESGA++TLTEDPK AVKGVDFVHTDVWVSMGEP
Sbjct: 181 GMDVRIAAPKALWPHDDLVERCKQYAEESGARITLTEDPKAAVKGVDFVHTDVWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
           +EAWGERIK+L PYQVN E+MK+TGNPR KFMHCLPAFHNSETKVGKQIAEQYP+LANGI
Sbjct: 241 IEAWGERIKQLKPYQVNAELMKSTGNPRTKFMHCLPAFHNSETKVGKQIAEQYPDLANGI 300

Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLADI 336
           EVT+DVFESP  IAFEQAENRMHTIKAILVSTLAD+
Sbjct: 301 EVTDDVFESPACIAFEQAENRMHTIKAILVSTLADL 336


Lambda     K      H
   0.318    0.133    0.387 

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: 6
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: 336
Length of database: 336
Length adjustment: 28
Effective length of query: 308
Effective length of database: 308
Effective search space:    94864
Effective search space used:    94864
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: 49 (23.5 bits)

Align candidate PP_1000 PP_1000 (ornithine carbamoyltransferase, catabolic)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

# 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/TIGR00658.hmm
# target sequence database:        /tmp/gapView.2473027.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00658  [M=304]
Accession:   TIGR00658
Description: orni_carb_tr: ornithine carbamoyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.8e-138  446.2   0.0   3.2e-138  446.0   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_1000  PP_1000 ornithine carbamoyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1000  PP_1000 ornithine carbamoyltransferase, catabolic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.0   0.0  3.2e-138  3.2e-138       1     303 [.       8     333 ..       8     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 446.0 bits;  conditional E-value: 3.2e-138
                           TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkee 75 
                                         r+llsl +++++el++ll+l+++lk++k++g+e+++lkg+++aliFek+stRtR++fevaay++Ga+v+y+++++
  lcl|FitnessBrowser__Putida:PP_1000   8 RNLLSLEHHTTRELRYLLDLSRDLKRAKYTGTEQQHLKGNNIALIFEKTSTRTRCAFEVAAYDQGANVTYIDPNS 82 
                                         78************************************************************************* PP

                           TIGR00658  76 lqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg.klkev 149
                                         +q+g+kes+kDtarvl+r++dai +R++k+e+veelak+a+vPv+ngLtd+ hP+q++aD+lt++e+ +  l+++
  lcl|FitnessBrowser__Putida:PP_1000  83 SQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAKFAGVPVFNGLTDEYHPTQMIADVLTMREHSDkPLHDI 157
                                         *********************************************************************99**** PP

                           TIGR00658 150 klvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytD 223
                                         +++y+GDa nn++nslll++aklG+dv++a+P++l+p+ ++v+++k+ a+e+g++++ltedpk avk++d+++tD
  lcl|FitnessBrowser__Putida:PP_1000 158 SYAYLGDArNNMGNSLLLIGAKLGMDVRIAAPKALWPHDDLVERCKQYAEESGARITLTEDPKAAVKGVDFVHTD 232
                                         *************************************************************************** PP

                           TIGR00658 224 vwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr...................Geevtdevl 277
                                         vwvsmGe  e++ er+k+lkpyqvn el++ + +p +kf+hCLPa++                   G evtd+v+
  lcl|FitnessBrowser__Putida:PP_1000 233 VWVSMGEpIEAWGERIKQLKPYQVNAELMKSTgNPRTKFMHCLPAFHnsetkvgkqiaeqypdlanGIEVTDDVF 307
                                         *******8899*********************9****************************************** PP

                           TIGR00658 278 egeasivfdeaenRlhaqkavlkall 303
                                         e++a i f++aenR+h++ka+l+ +l
  lcl|FitnessBrowser__Putida:PP_1000 308 ESPACIAFEQAENRMHTIKAILVSTL 333
                                         **********************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (336 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: 26.08
//
[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