GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Lentibacillus jeotgali Grbi

Align ArgF (EC 2.1.3.3) (characterized)
to candidate WP_010532213.1 ON01_RS16960 ornithine carbamoyltransferase

Query= metacyc::ARGFBACSU-MONOMER
         (319 letters)



>NCBI__GCF_000224785.1:WP_010532213.1
          Length = 320

 Score =  347 bits (889), Expect = e-100
 Identities = 183/310 (59%), Positives = 220/310 (70%), Gaps = 4/310 (1%)

Query: 5   TQTSLYGKDLLTLKDLSEEDINALLAEAGELKQNKIQPIFH----GKTLAMIFEKSSTRT 60
           T   L G+  L L DL+ +++  LL  AGELKQ     +       KTL M+FEK STRT
Sbjct: 10  TGNELKGRKFLKLTDLNIQELGYLLELAGELKQKHKSGLHEEPLKAKTLGMLFEKPSTRT 69

Query: 61  RVSFEAGMAQLGGSALFLSQKDLQLGRGETVADTAKVLSGYVDAIMIRTFEHEKVEELAK 120
           RVSFE G+ QLGGS +FL+  +LQLGRGE++ADTAKVLSGYVD +MIRTF HE +EE A+
Sbjct: 70  RVSFETGIFQLGGSGIFLNSDNLQLGRGESMADTAKVLSGYVDGMMIRTFSHEVLEEFAQ 129

Query: 121 EADIPVINGLTDKYHPCQALADLLTIKEIKGKLKGVKVAYIGDGNNVAHSLMIGCAKMGC 180
            A +PVINGLTD YHPCQ LADL TI+EIK  L GVK+AYIGDGNN+AHSLMIG A  G 
Sbjct: 130 NATVPVINGLTDMYHPCQVLADLQTIREIKNGLSGVKLAYIGDGNNMAHSLMIGAAMTGM 189

Query: 181 DISIASPKGYEVLDEAAEAAKTYALQSGSSVTLTDDPIEAVKDADVIYSDVFTSMGQEAE 240
           DI+IA+P  Y       + A T A Q+G  V +T DP  A + ADVIY+DV+ SMGQE E
Sbjct: 190 DINIAAPDDYMPNTSIVQEALTIAEQTGGHVEVTSDPQAAAEQADVIYTDVWASMGQEDE 249

Query: 241 EQERLAVFAPYQVNAALVSHAKPDYTFLHCLPAHREEEVTAEIIDGPNSAVFQQAENRLH 300
           +  R   F+ +QVN  L S AK D  F+HCLPAHR EEVTA++IDG  S VFQQAENRLH
Sbjct: 250 QGNRKQAFSDFQVNVRLCSLAKNDAFFMHCLPAHRGEEVTADVIDGKQSVVFQQAENRLH 309

Query: 301 VQKALLKAIL 310
            QKAL+ A++
Sbjct: 310 AQKALMMALM 319


Lambda     K      H
   0.315    0.131    0.361 

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: 292
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: 319
Length of database: 320
Length adjustment: 28
Effective length of query: 291
Effective length of database: 292
Effective search space:    84972
Effective search space used:    84972
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 48 (23.1 bits)

Align candidate WP_010532213.1 ON01_RS16960 (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.1739196.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-136  440.3   0.1   1.9e-136  440.2   0.1    1.0  1  NCBI__GCF_000224785.1:WP_010532213.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010532213.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.2   0.1  1.9e-136  1.9e-136       1     303 [.      17     319 ..      17     320 .] 0.99

  Alignments for each domain:
  == domain 1  score: 440.2 bits;  conditional E-value: 1.9e-136
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 
                                           r++l+l+dl+ +el +llela +lk+++k+g +e+ lk ktl+++Fek+stRtRvsfe+++++lG+  ++ln+
  NCBI__GCF_000224785.1:WP_010532213.1  17 RKFLKLTDLNIQELGYLLELAGELKQKHKSGLHEEPLKAKTLGMLFEKPSTRTRVSFETGIFQLGGSGIFLNS 89 
                                           689********************************************************************** PP

                             TIGR00658  74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146
                                           ++lqlgr+es++Dta+vls yvd++++R+++he +ee+a++a+vPvingLtd+ hPcq+laDl+ti+e ++ l
  NCBI__GCF_000224785.1:WP_010532213.1  90 DNLQLGRGESMADTAKVLSGYVDGMMIRTFSHEVLEEFAQNATVPVINGLTDMYHPCQVLADLQTIREIKNGL 162
                                           ************************************************************************* PP

                             TIGR00658 147 kevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219
                                           ++vkl+y+GD+nn+a+sl+++aa++G+d+++a+P+++ p+++iv++a  ia+++gg++e+t+dp+ a+++adv
  NCBI__GCF_000224785.1:WP_010532213.1 163 SGVKLAYIGDGNNMAHSLMIGAAMTGMDINIAAPDDYMPNTSIVQEALTIAEQTGGHVEVTSDPQAAAEQADV 235
                                           ************************************************************************* PP

                             TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRl 292
                                           iytDvw+smG+e+++ +r +++ ++qvn +l +lak+++ f+hCLPa+rGeevt +v++g++s+vf++aenRl
  NCBI__GCF_000224785.1:WP_010532213.1 236 IYTDVWASMGQEDEQGNRKQAFSDFQVNVRLCSLAKNDAFFMHCLPAHRGEEVTADVIDGKQSVVFQQAENRL 308
                                           ************************************************************************* PP

                             TIGR00658 293 haqkavlkall 303
                                           haqka++ al+
  NCBI__GCF_000224785.1:WP_010532213.1 309 HAQKALMMALM 319
                                           *******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (320 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: 00:00:00.00
# Mc/sec: 14.63
//
[ok]

This GapMind analysis is from Jul 26 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