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

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.16018.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: 11.93
//
[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