GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Acidovorax sp. GW101-3H11

Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate Ac3H11_1333 Ornithine carbamoyltransferase (EC 2.1.3.3)

Query= reanno::HerbieS:HSERO_RS07185
         (304 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1333
          Length = 328

 Score =  418 bits (1074), Expect = e-121
 Identities = 201/314 (64%), Positives = 247/314 (78%), Gaps = 14/314 (4%)

Query: 3   IKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFEA 62
           +KHYLQF+D   DEY Y+ ER+ +IK+KFK Y+ HH L DRTL M+FEK STRTR+SFEA
Sbjct: 13  LKHYLQFTDLNADEYAYLFERAALIKKKFKAYDKHHPLVDRTLAMIFEKASTRTRVSFEA 72

Query: 63  GMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVPV 122
           GM+Q+GG+ ++L T DSQLGR EP+ED+A+V+SRM D++MIRTY Q  IERFA +SRVPV
Sbjct: 73  GMYQLGGSVVHLTTGDSQLGRAEPIEDSAKVISRMTDLVMIRTYEQAKIERFAANSRVPV 132

Query: 123 INGLTNEQHPCQVLADVFTYIEHHG----------SIQGKIVAWVGDANNMLYSWLQAAE 172
           INGLTNE HPCQ+LAD+FT+IEH G           ++GK VAWVGD NNM  +W+QAA 
Sbjct: 133 INGLTNEYHPCQILADIFTFIEHRGPKDGTGNLTDCLKGKTVAWVGDGNNMANTWVQAAS 192

Query: 173 VFGFHVNVSTPKGYDIDPAQVSPGN----KNYTFFADPADACQDADLVTTDVWTSMGFEA 228
           + GF V+VSTP+GY+ID    +  +     +Y FF++P +AC+ ADLVTTDVWTSMG+EA
Sbjct: 193 LLGFKVHVSTPRGYEIDEKLAAGAHGISADSYQFFSNPMEACRGADLVTTDVWTSMGYEA 252

Query: 229 ENNARLKAFDGWIVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRL 288
           EN AR KAF  W VD   MA A+ DALFMHCLPAHRGEEV A+VIDGPQSVVW+EAENR+
Sbjct: 253 ENEARKKAFADWCVDTEMMAAAQPDALFMHCLPAHRGEEVEADVIDGPQSVVWDEAENRM 312

Query: 289 HVQKALLEYLVHGR 302
           HVQKAL+EYL+ GR
Sbjct: 313 HVQKALMEYLLLGR 326


Lambda     K      H
   0.321    0.135    0.409 

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: 374
Number of extensions: 14
Number of successful extensions: 3
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: 304
Length of database: 328
Length adjustment: 27
Effective length of query: 277
Effective length of database: 301
Effective search space:    83377
Effective search space used:    83377
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: 48 (23.1 bits)

Align candidate Ac3H11_1333 (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.23168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   7.2e-113  362.7   0.0   8.4e-113  362.5   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333  Ornithine carbamoyltransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333  Ornithine carbamoyltransferase (EC 2.1.3.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.5   0.0  8.4e-113  8.4e-113       1     303 [.      14     323 ..      14     324 .. 0.97

  Alignments for each domain:
  == domain 1  score: 362.5 bits;  conditional E-value: 8.4e-113
                                        TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaay 62 
                                                      +h+l+++dl+ +e  +l e+a+ +kk+ k+  +++ l  +tla+iFek+stRtRvsfe+++y
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333  14 KHYLQFTDLNADEYAYLFERAALIKKKFKAYDKHHPLVDRTLAMIFEKASTRTRVSFEAGMY 75 
                                                      799*********************************************************** PP

                                        TIGR00658  63 elGaqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLt 124
                                                      +lG+ v++l + ++qlgr e+i+D a+v+sr+ d +++R+y++ ++e +a ++ vPvingLt
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333  76 QLGGSVVHLTTGDSQLGRAEPIEDSAKVISRMTDLVMIRTYEQAKIERFAANSRVPVINGLT 137
                                                      ************************************************************** PP

                                        TIGR00658 125 dlehPcqilaDlltikeklgklkev..........klvyvGDannvanslllaaaklGldvv 176
                                                      ++ hPcqilaD++t +e+ g  ++           ++++vGD+nn+an+ + aa +lG++v+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 138 NEYHPCQILADIFTFIEHRGPKDGTgnltdclkgkTVAWVGDGNNMANTWVQAASLLGFKVH 199
                                                      ******************99777767778889998*************************** PP

                                        TIGR00658 177 vatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGeeekkeerl 238
                                                      v+tP+g+e ++++   a+ i+++   + ++ ++p +a ++ad++ tDvw+smG e+++e+r 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 200 VSTPRGYEIDEKLAAGAHGISAD---SYQFFSNPMEACRGADLVTTDVWTSMGYEAENEARK 258
                                                      *****************998765...6899******************************** PP

                                        TIGR00658 239 kllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlk 300
                                                      k++ ++ v++e+++ a+p++ f+hCLPa+rGeev  +v++g++s+v+deaenR+h+qka+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 259 KAFADWCVDTEMMAAAQPDALFMHCLPAHRGEEVEADVIDGPQSVVWDEAENRMHVQKALME 320
                                                      *************************************************************9 PP

                                        TIGR00658 301 all 303
                                                      +ll
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 321 YLL 323
                                                      987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (328 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: 10.52
//
[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:

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