GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Thermus aquaticus YT-1

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_053767952.1 BVI061214_RS08055 ornithine carbamoyltransferase

Query= BRENDA::Q5SJ15
         (301 letters)



>NCBI__GCF_001280255.1:WP_053767952.1
          Length = 301

 Score =  532 bits (1370), Expect = e-156
 Identities = 266/301 (88%), Positives = 277/301 (92%)

Query: 1   MGGEALTLPKDLLDFSGYGPKELQALLDLAEQLKRERYRGEDLKGKVLALLFEKPSLRTR 60
           MGGE LTLPKDLLDFSGY  + L+ LLDLAE LKRERYRGEDLKGK LALLFEKPSLRTR
Sbjct: 1   MGGETLTLPKDLLDFSGYTKEALKRLLDLAEALKRERYRGEDLKGKSLALLFEKPSLRTR 60

Query: 61  TTLEVAMVHLGGHAVYLDQKQVGIGEREPVRDVAKNLERFVEGIAARVFRHETVEALARH 120
           TTLEVAMVHLGGHA+YLDQKQVGIGEREPVRD+AKNLERFVEGIAARV+RH TVE LARH
Sbjct: 61  TTLEVAMVHLGGHALYLDQKQVGIGEREPVRDIAKNLERFVEGIAARVYRHRTVEELARH 120

Query: 121 AKVPVVNALSDRAHPLQALADLLTLKEVFGGLAGLEVAWVGDGNNVLNSLLEVAPLAGLK 180
           A++PV+NALSDRAHPLQALADLLTLKE FGGL GLEVAWVGDGNNVL SLLEVAPL GLK
Sbjct: 121 ARIPVINALSDRAHPLQALADLLTLKEAFGGLEGLEVAWVGDGNNVLASLLEVAPLVGLK 180

Query: 181 VRVATPKGYEPDPGLLKRANAFFTHDPKEAALGAHALYTDVWTSMGQEAEREKRLRDFQG 240
           VRVATP+GYEP+  LL RA AF THDPKEA LGAHALYTDVWTSMGQEAEREKRLRDFQG
Sbjct: 181 VRVATPRGYEPEAALLARAGAFLTHDPKEAVLGAHALYTDVWTSMGQEAEREKRLRDFQG 240

Query: 241 FQVNGELLKLLRPEGVFLHCLPAHYGEETTEEAVHGPRSRVFDQAENRLHTAKAVLLTLL 300
           FQ NG LL LL PEG+FLHCLPAHYGEETTEEAV GPRSRVFDQAENRLHTAKAVLLTLL
Sbjct: 241 FQANGPLLDLLHPEGIFLHCLPAHYGEETTEEAVFGPRSRVFDQAENRLHTAKAVLLTLL 300

Query: 301 K 301
           K
Sbjct: 301 K 301


Lambda     K      H
   0.319    0.137    0.396 

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: 444
Number of extensions: 16
Number of successful extensions: 1
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: 301
Length of database: 301
Length adjustment: 27
Effective length of query: 274
Effective length of database: 274
Effective search space:    75076
Effective search space used:    75076
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_053767952.1 BVI061214_RS08055 (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.3411131.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-110  353.0   0.0   7.7e-110  352.8   0.0    1.1  1  NCBI__GCF_001280255.1:WP_053767952.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280255.1:WP_053767952.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.8   0.0  7.7e-110  7.7e-110       1     303 [.      10     300 ..      10     301 .] 0.98

  Alignments for each domain:
  == domain 1  score: 352.8 bits;  conditional E-value: 7.7e-110
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 
                                           ++ll++  +++e lk+ll+la+ lk+e+++    + lkgk+lal+Fek+s RtR ++eva+++lG+++lyl++
  NCBI__GCF_001280255.1:WP_053767952.1  10 KDLLDFSGYTKEALKRLLDLAEALKRERYR---GEDLKGKSLALLFEKPSLRTRTTLEVAMVHLGGHALYLDQ 79 
                                           799**************************9...589************************************* PP

                             TIGR00658  74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146
                                           +++ +g++e+++D a+ l+r+v++i++Rvy+h++veela++a +Pvin+L+d +hP+q+laDllt+ke +g l
  NCBI__GCF_001280255.1:WP_053767952.1  80 KQVGIGEREPVRDIAKNLERFVEGIAARVYRHRTVEELARHARIPVINALSDRAHPLQALADLLTLKEAFGGL 152
                                           ************************************************************************* PP

                             TIGR00658 147 kevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219
                                           +++++++vGD+nnv  sll  a ++Gl+v+vatP+g+epea+++ +a +          lt+dpk+av +a+ 
  NCBI__GCF_001280255.1:WP_053767952.1 153 EGLEVAWVGDGNNVLASLLEVAPLVGLKVRVATPRGYEPEAALLARAGA---------FLTHDPKEAVLGAHA 216
                                           *******************************************999954.........59************* PP

                             TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRl 292
                                           +ytDvw+smG+e+++e+rl+ ++++q n  ll+l +pe +flhCLPa+ Gee+t+e + g++s+vfd+aenRl
  NCBI__GCF_001280255.1:WP_053767952.1 217 LYTDVWTSMGQEAEREKRLRDFQGFQANGPLLDLLHPEGIFLHCLPAHYGEETTEEAVFGPRSRVFDQAENRL 289
                                           ************************************************************************* PP

                             TIGR00658 293 haqkavlkall 303
                                           h++kavl +ll
  NCBI__GCF_001280255.1:WP_053767952.1 290 HTAKAVLLTLL 300
                                           *******9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (301 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: 00:00:00.00
# Mc/sec: 14.82
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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