GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Paraburkholderia bryophila 376MFSha3.1

Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate H281DRAFT_04119 H281DRAFT_04119 ornithine carbamoyltransferase

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



>FitnessBrowser__Burk376:H281DRAFT_04119
          Length = 309

 Score =  456 bits (1174), Expect = e-133
 Identities = 215/303 (70%), Positives = 260/303 (85%), Gaps = 1/303 (0%)

Query: 3   IKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFEA 62
           I+HYLQF DF+LD+YEYV+ER+R++KRKFKNYE +H L DRTL M+FEKNSTRTRLSFEA
Sbjct: 6   IRHYLQFKDFSLDDYEYVLERARILKRKFKNYETYHPLHDRTLAMIFEKNSTRTRLSFEA 65

Query: 63  GMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVPV 122
           G+ Q+GG A++++TRD+QLGRGEP+EDAAQV+SRM D+IMIRT+GQ+II+RFA++SRVPV
Sbjct: 66  GIFQLGGHAVFMSTRDTQLGRGEPIEDAAQVISRMVDIIMIRTFGQDIIQRFAENSRVPV 125

Query: 123 INGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNVST 182
           INGLTNE HPCQVLAD+FTY EH G I+GK VAWVGDANNMLY+W++AA++ GF + +ST
Sbjct: 126 INGLTNEYHPCQVLADIFTYFEHRGPIRGKTVAWVGDANNMLYTWIEAAQILGFKLRLST 185

Query: 183 PKGYDIDPAQVSPGNKN-YTFFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGWI 241
           P GY +D A V+  +   +  F DP +AC  ADLVTTDVWTSMGFEAEN AR KAF  W 
Sbjct: 186 PPGYKLDRALVAAESAPFFQEFDDPNEACAGADLVTTDVWTSMGFEAENEARKKAFADWC 245

Query: 242 VDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVHG 301
           VD   M+RA  DALFMHCLPAHRGEEV+AEVIDGPQSVVW+EAENRLHVQKAL+EYL+ G
Sbjct: 246 VDAEMMSRANADALFMHCLPAHRGEEVSAEVIDGPQSVVWDEAENRLHVQKALMEYLLLG 305

Query: 302 RFD 304
           + +
Sbjct: 306 KLN 308


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: 377
Number of extensions: 14
Number of successful extensions: 2
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: 309
Length adjustment: 27
Effective length of query: 277
Effective length of database: 282
Effective search space:    78114
Effective search space used:    78114
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 H281DRAFT_04119 H281DRAFT_04119 (ornithine carbamoyltransferase)
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.23565.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.8e-112  359.7   0.0   6.8e-112  359.5   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04119  H281DRAFT_04119 ornithine carbam


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04119  H281DRAFT_04119 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.5   0.0  6.8e-112  6.8e-112       1     303 [.       7     303 ..       7     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 359.5 bits;  conditional E-value: 6.8e-112
                                    TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGa 66 
                                                  rh+l+++d+s ++ +++le+a+ lk++ k+ ++ + l+ +tla+iFek+stRtR+sfe+++++lG+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04119   7 RHYLQFKDFSLDDYEYVLERARILKRKFKNYETYHPLHDRTLAMIFEKNSTRTRLSFEAGIFQLGG 72 
                                                  89*****************************9********************************** PP

                                    TIGR00658  67 qvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqi 132
                                                  +++++++ ++qlgr+e+i+D a+v+sr+vd+i++R++ +++++ +a+++ vPvingLt++ hPcq+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04119  73 HAVFMSTRDTQLGRGEPIEDAAQVISRMVDIIMIRTFGQDIIQRFAENSRVPVINGLTNEYHPCQV 138
                                                  ****************************************************************** PP

                                    TIGR00658 133 laDlltikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiak 198
                                                  laD++t  e+ g + + ++++vGDann+  + + aa  lG++++++tP+g++ + ++v      a+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04119 139 LADIFTYFEHRGPIRGKTVAWVGDANNMLYTWIEAAQILGFKLRLSTPPGYKLDRALV------AA 198
                                                  *****************************************************99987......45 PP

                                    TIGR00658 199 enggkleltedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCL 264
                                                  e+   ++  +dp++a ++ad++ tDvw+smG e+++e+r k++ ++ v+ e+++ a+ ++ f+hCL
  lcl|FitnessBrowser__Burk376:H281DRAFT_04119 199 ESAPFFQEFDDPNEACAGADLVTTDVWTSMGFEAENEARKKAFADWCVDAEMMSRANADALFMHCL 264
                                                  677889999********************************************************* PP

                                    TIGR00658 265 PavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                                  Pa+rGeev+ ev++g++s+v+deaenRlh+qka++++ll
  lcl|FitnessBrowser__Burk376:H281DRAFT_04119 265 PAHRGEEVSAEVIDGPQSVVWDEAENRLHVQKALMEYLL 303
                                                  ***********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (309 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: 00:00:00.01
# Mc/sec: 7.76
//
[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