Alignments for a candidate for arcB in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Pseudomonas fluorescens GW456-L13

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate PfGW456L13_1873 Ornithine carbamoyltransferase (EC 2.1.3.3)

Query= SwissProt::P08308
         (336 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1873
          Length = 336

 Score =  617 bits (1591), Expect = 0.0
 Identities = 300/336 (89%), Positives = 320/336 (95%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           MAFN+HNRNLLSL HH+ RELRYLLDLSRDLKRAKYTGTEQQHLK  NIALIFEKTSTRT
Sbjct: 1   MAFNIHNRNLLSLEHHTPRELRYLLDLSRDLKRAKYTGTEQQHLKGNNIALIFEKTSTRT 60

Query: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120
           RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK
Sbjct: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120

Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180
           FAGVPVFNGLTDEYHPTQM+ADVLTMREH+DKP+H+ISYAYLGDARNNMGNSLLLIGAKL
Sbjct: 121 FAGVPVFNGLTDEYHPTQMIADVLTMREHADKPIHEISYAYLGDARNNMGNSLLLIGAKL 180

Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240
           GMDVRI APKALWP D+ VA+CK++ EESGA++TLTEDPK AVKGVDF+HTDVWVSMGEP
Sbjct: 181 GMDVRICAPKALWPADDLVARCKQYGEESGARITLTEDPKAAVKGVDFIHTDVWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
           VEAW ERI++LLPYQVN E+MKATGNPR KFMHCLPAFHN +TKVGKQIAEQYP L+NGI
Sbjct: 241 VEAWAERIQQLLPYQVNAELMKATGNPRTKFMHCLPAFHNCDTKVGKQIAEQYPYLSNGI 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: 481
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 PfGW456L13_1873 (Ornithine carbamoyltransferase (EC 2.1.3.3))
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.carbon/TIGR00658.hmm
# target sequence database:        /tmp/gapView.18370.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   4.6e-137  442.2   0.0   5.2e-137  442.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1873  Ornithine carbamoyltransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1873  Ornithine carbamoyltransferase (EC 2.1.3.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.0   0.0  5.2e-137  5.2e-137       1     303 [.       8     333 ..       8     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 442.0 bits;  conditional E-value: 5.2e-137
                                               TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRv 55 
                                                             r+llsl +++++el++ll+l+++lk++k++g+e+++lkg+++aliFek+stRtR+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1873   8 RNLLSLEHHTPRELRYLLDLSRDLKRAKYTGTEQQHLKGNNIALIFEKTSTRTRC 62 
                                                             78***************************************************** PP

                                               TIGR00658  56 sfevaayelGaqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedvee 110
                                                             +fevaay++Ga+v+y++++++q+g+kes+kDtarvl+r++dai +R++k+e+vee
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1873  63 AFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEE 117
                                                             ******************************************************* PP

                                               TIGR00658 111 lakyasvPvingLtdlehPcqilaDlltikeklg.klkevklvyvGDa.nnvans 163
                                                             lak+a+vPv+ngLtd+ hP+q++aD+lt++e+ +  ++e++++y+GDa nn++ns
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1873 118 LAKFAGVPVFNGLTDEYHPTQMIADVLTMREHADkPIHEISYAYLGDArNNMGNS 172
                                                             **********************************99******************* PP

                                               TIGR00658 164 lllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdad 218
                                                             lll++aklG+dv++++P++l+p  ++v ++k+  +e+g++++ltedpk avk++d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1873 173 LLLIGAKLGMDVRICAPKALWPADDLVARCKQYGEESGARITLTEDPKAAVKGVD 227
                                                             ******************************************************* PP

                                               TIGR00658 219 viytDvwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr... 268
                                                             +i+tDvwvsmGe  e+++er+++l pyqvn el++ + +p +kf+hCLPa++   
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1873 228 FIHTDVWVSMGEpVEAWAERIQQLLPYQVNAELMKATgNPRTKFMHCLPAFHncd 282
                                                             ************9999*************************************** PP

                                               TIGR00658 269 ................GeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                                                             G evtd+v+e++a i f++aenR+h++ka+l+ +l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1873 283 tkvgkqiaeqypylsnGIEVTDDVFESPACIAFEQAENRMHTIKAILVSTL 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.65
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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, or view the source code.

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 catabolism of small carbon sources