Alignments for a candidate for arcB in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Dechlorosoma suillum PS

Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate Dsui_3249 Dsui_3249 ornithine carbamoyltransferase

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



>FitnessBrowser__PS:Dsui_3249
          Length = 307

 Score =  432 bits (1112), Expect = e-126
 Identities = 208/302 (68%), Positives = 249/302 (82%), Gaps = 1/302 (0%)

Query: 2   AIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFE 61
           +IKH+LQF DFT +E++Y+  R+R IK +FKNY+ +  L DRTLVM+FEK STRTRLSFE
Sbjct: 3   SIKHFLQFKDFTREEFDYLFARTRWIKDQFKNYKQYWPLTDRTLVMIFEKASTRTRLSFE 62

Query: 62  AGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVP 121
           AGM Q+GG+AIYLNTRDSQLGRGEPVEDAAQV+SRM D++MIRT+ QEIIERFA +SRVP
Sbjct: 63  AGMQQLGGSAIYLNTRDSQLGRGEPVEDAAQVISRMSDIVMIRTFEQEIIERFAANSRVP 122

Query: 122 VINGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNVS 181
           VINGLTNE HPCQ++AD+FTYIEH G IQGK VAW+GD+NN+  +WLQAAEV  F+V+VS
Sbjct: 123 VINGLTNEYHPCQIMADIFTYIEHRGPIQGKTVAWIGDSNNVCNTWLQAAEVLDFNVHVS 182

Query: 182 TPKGYDIDPAQVS-PGNKNYTFFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGW 240
           TP GY+++  +    G  N+  F+DP +A + AD+VTTDVWTSMGFEAEN  RLK F  W
Sbjct: 183 TPPGYEVEAERAGLYGTANFEQFSDPMEAAKGADIVTTDVWTSMGFEAENEERLKDFADW 242

Query: 241 IVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVH 300
            VD   M  AK DA+F+HCLPAHRGEEV AEVIDGPQS VW+EAENRLH QKAL+EYL+ 
Sbjct: 243 QVDGDMMRIAKSDAIFLHCLPAHRGEEVTAEVIDGPQSAVWDEAENRLHTQKALMEYLLL 302

Query: 301 GR 302
           GR
Sbjct: 303 GR 304


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: 371
Number of extensions: 15
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: 307
Length adjustment: 27
Effective length of query: 277
Effective length of database: 280
Effective search space:    77560
Effective search space used:    77560
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 Dsui_3249 Dsui_3249 (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.23801.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.6e-114  367.0   0.0   4.3e-114  366.7   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_3249  Dsui_3249 ornithine carbamoyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3249  Dsui_3249 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.7   0.0  4.3e-114  4.3e-114       1     303 [.       5     301 ..       5     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 366.7 bits;  conditional E-value: 4.3e-114
                         TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelq 77 
                                       +h+l+++d+++ee+ +l  +++ +k + k+ k+   l+ +tl +iFek+stRtR+sfe+++ +lG+ ++yln+ ++q
  lcl|FitnessBrowser__PS:Dsui_3249   5 KHFLQFKDFTREEFDYLFARTRWIKDQFKNYKQYWPLTDRTLVMIFEKASTRTRLSFEAGMQQLGGSAIYLNTRDSQ 81 
                                       79*************************************************************************** PP

                         TIGR00658  78 lgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklvyv 154
                                       lgr+e+++D a+v+sr+ d++++R++++e++e +a ++ vPvingLt++ hPcqi+aD++t +e+ g +++ +++++
  lcl|FitnessBrowser__PS:Dsui_3249  82 LGRGEPVEDAAQVISRMSDIVMIRTFEQEIIERFAANSRVPVINGLTNEYHPCQIMADIFTYIEHRGPIQGKTVAWI 158
                                       ***************************************************************************** PP

                         TIGR00658 155 GDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGee 231
                                       GD+nnv+n+ l aa  l ++v+v+tP+g+e eae             +++e  +dp +a+k+ad++ tDvw+smG e
  lcl|FitnessBrowser__PS:Dsui_3249 159 GDSNNVCNTWLQAAEVLDFNVHVSTPPGYEVEAERAGL------YGTANFEQFSDPMEAAKGADIVTTDVWTSMGFE 229
                                       ******************************99864333......34599**************************** PP

                         TIGR00658 232 ekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                       +++eerlk + ++qv+ +++++ak++++flhCLPa+rGeevt ev++g++s v+deaenRlh+qka++++ll
  lcl|FitnessBrowser__PS:Dsui_3249 230 AENEERLKDFADWQVDGDMMRIAKSDAIFLHCLPAHRGEEVTAEVIDGPQSAVWDEAENRLHTQKALMEYLL 301
                                       ********************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (307 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.04
//
[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