Alignments for a candidate for arcB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Burkholderia phytofirmans PsJN

Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate BPHYT_RS15915 BPHYT_RS15915 ornithine carbamoyltransferase

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



>FitnessBrowser__BFirm:BPHYT_RS15915
          Length = 309

 Score =  453 bits (1166), Expect = e-132
 Identities = 213/303 (70%), Positives = 259/303 (85%), Gaps = 1/303 (0%)

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

Query: 63  GMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVPV 122
           G+ Q+GG A++++TRD+QLGRGEP+EDAAQV+SRM D+IMIRT+GQ+I++RF+++SRVPV
Sbjct: 66  GIFQLGGHAVFMSTRDTQLGRGEPIEDAAQVISRMVDIIMIRTFGQDILQRFSENSRVPV 125

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

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

Query: 242 VDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVHG 301
           VD   MARA  DALFMHCLPAHRGEEV+AEVIDGPQSVVW+EAENRLHVQKAL+EYL+ G
Sbjct: 246 VDADMMARANPDALFMHCLPAHRGEEVSAEVIDGPQSVVWDEAENRLHVQKALMEYLLLG 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: 375
Number of extensions: 11
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 BPHYT_RS15915 BPHYT_RS15915 (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.20160.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.3e-111  357.8   0.0   2.8e-111  357.5   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS15915  BPHYT_RS15915 ornithine carbamoy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS15915  BPHYT_RS15915 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.5   0.0  2.8e-111  2.8e-111       1     303 [.       7     303 ..       7     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 357.5 bits;  conditional E-value: 2.8e-111
                                TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvly 70 
                                              rh+l+++d+s e+ +++le+a+ lk++ k+ ++ + l+ +tla+iFek+stRtR+sfe+++++lG+++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS15915   7 RHYLQFKDFSLEDYEYVLERARILKRKFKNYETYHPLHDRTLAMIFEKNSTRTRLSFEAGIFQLGGHAVF 76 
                                              89*****************************9************************************** PP

                                TIGR00658  71 lnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltik 140
                                              +++ ++qlgr+e+i+D a+v+sr+vd+i++R++ +++++ +++++ vPvingLt++ hPcq+laD++t  
  lcl|FitnessBrowser__BFirm:BPHYT_RS15915  77 MSTRDTQLGRGEPIEDAAQVISRMVDIIMIRTFGQDILQRFSENSRVPVINGLTNEYHPCQVLADIFTYF 146
                                              ********************************************************************** PP

                                TIGR00658 141 eklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedp 210
                                              e+ g + + ++++vGDann+  + + aa  lG++++++tP+g++ + ++v       +e+    e  +dp
  lcl|FitnessBrowser__BFirm:BPHYT_RS15915 147 EHRGPIRDKTVAWVGDANNMLYTWIEAAQILGFKLRLSTPPGYKLDRAMVA------AESAPFYEEFDDP 210
                                              ********************************************9988764......45666778899** PP

                                TIGR00658 211 kkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlege 280
                                              ++a ++ad++ tDvw+smG e+++e+r k++ ++ v+ ++++ a+p++ f+hCLPa+rGeev+ ev++g+
  lcl|FitnessBrowser__BFirm:BPHYT_RS15915 211 NEACTGADLVTTDVWTSMGFEAENEARKKAFADWCVDADMMARANPDALFMHCLPAHRGEEVSAEVIDGP 280
                                              ********************************************************************** PP

                                TIGR00658 281 asivfdeaenRlhaqkavlkall 303
                                              +s+v+deaenRlh+qka++++ll
  lcl|FitnessBrowser__BFirm:BPHYT_RS15915 281 QSVVWDEAENRLHVQKALMEYLL 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: 00:00:00.00
# Mc/sec: 11.49
//
[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
the source code
instructions for running GapMind on your computer

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