Aligments for a candidate for argI in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Aligments for a candidate for argI in Cupriavidus basilensis 4G11

Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate RR42_RS17175 RR42_RS17175 ornithine carbamoyltransferase

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



>FitnessBrowser__Cup4G11:RR42_RS17175
          Length = 307

 Score =  457 bits (1177), Expect = e-133
 Identities = 222/303 (73%), Positives = 253/303 (83%), Gaps = 1/303 (0%)

Query: 2   AIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFE 61
           +IKHYLQFSD T DEYEY+++R+R++K KFKNYE  H L DRTL M+FEKNSTRTRLSFE
Sbjct: 5   SIKHYLQFSDLTPDEYEYLLDRARILKTKFKNYETWHPLHDRTLSMIFEKNSTRTRLSFE 64

Query: 62  AGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVP 121
           AG+HQ+GG A++LNTRDSQLGRGEP+EDAAQV+SRM D+IMIRT+GQEIIERFA HSRVP
Sbjct: 65  AGIHQLGGHAVFLNTRDSQLGRGEPIEDAAQVISRMVDIIMIRTFGQEIIERFAAHSRVP 124

Query: 122 VINGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNVS 181
           VINGLTNE HPCQVLADVFTYIE  GSI+GK VAW+GDANNM Y+W+QAAE  GF  + S
Sbjct: 125 VINGLTNEYHPCQVLADVFTYIEQRGSIRGKTVAWIGDANNMAYTWIQAAERLGFTFHFS 184

Query: 182 TPKGYDIDPAQVSPGNKNYT-FFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGW 240
            P GY +DPA V     +    F DP  ACQ ADLVTTDVWTSMG+EAEN+AR +AF  W
Sbjct: 185 APPGYQLDPAMVPATAAHLVKVFDDPLTACQGADLVTTDVWTSMGYEAENDARKRAFQNW 244

Query: 241 IVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVH 300
           +V  A M RA  DALFMHCLPAHRGEEV A VIDGP+SVVWEEAENRLHVQKAL+EYL+ 
Sbjct: 245 MVTTAMMDRAGDDALFMHCLPAHRGEEVEAAVIDGPKSVVWEEAENRLHVQKALMEYLLC 304

Query: 301 GRF 303
           GR+
Sbjct: 305 GRY 307


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: 383
Number of extensions: 10
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 RR42_RS17175 RR42_RS17175 (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.aa/TIGR00658.hmm
# target sequence database:        /tmp/gapView.13407.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-110  354.0   0.0   3.8e-110  353.8   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS17175  RR42_RS17175 ornithine carbamoyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS17175  RR42_RS17175 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.8   0.0  3.8e-110  3.8e-110       1     303 [.       7     303 ..       7     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 353.8 bits;  conditional E-value: 3.8e-110
                                 TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 
                                               +h+l++ dl+++e ++ll++a+ lk++ k+ ++ + l+ +tl++iFek+stRtR+sfe+++ +lG++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS17175   7 KHYLQFSDLTPDEYEYLLDRARILKTKFKNYETWHPLHDRTLSMIFEKNSTRTRLSFEAGIHQLGGHAV 75 
                                               799***************************9999*********************************** PP

                                 TIGR00658  70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138
                                               +ln+ ++qlgr+e+i+D a+v+sr+vd+i++R++ +e++e +a ++ vPvingLt++ hPcq+laD++t
  lcl|FitnessBrowser__Cup4G11:RR42_RS17175  76 FLNTRDSQLGRGEPIEDAAQVISRMVDIIMIRTFGQEIIERFAAHSRVPVINGLTNEYHPCQVLADVFT 144
                                               ********************************************************************* PP

                                 TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207
                                                +e+ g++ + +++++GDann+a + + aa  lG++++ ++P+g++ ++++v  +          +++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS17175 145 YIEQRGSIRGKTVAWIGDANNMAYTWIQAAERLGFTFHFSAPPGYQLDPAMVPATA------AHLVKVF 207
                                               **************************************************998763......35799** PP

                                 TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276
                                               +dp  a ++ad++ tDvw+smG e+++++r ++++++ v++ +++ a +++ f+hCLPa+rGeev   v
  lcl|FitnessBrowser__Cup4G11:RR42_RS17175 208 DDPLTACQGADLVTTDVWTSMGYEAENDARKRAFQNWMVTTAMMDRAGDDALFMHCLPAHRGEEVEAAV 276
                                               ********************************************************************* PP

                                 TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303
                                               ++g++s+v++eaenRlh+qka++++ll
  lcl|FitnessBrowser__Cup4G11:RR42_RS17175 277 IDGPKSVVWEEAENRLHVQKALMEYLL 303
                                               ***********************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.67
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis