Alignments for a candidate for argI in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Clostridium acetobutylicum ATCC 824

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate NP_346957.1 CA_C0316 ornithine carbomoyltransferase

Query= metacyc::ORNCARBAMTRANSFERST-MONOMER
         (332 letters)



>NCBI__GCF_000008765.1:NP_346957.1
          Length = 333

 Score =  409 bits (1050), Expect = e-119
 Identities = 197/330 (59%), Positives = 259/330 (78%), Gaps = 2/330 (0%)

Query: 5   LKGRSFLTLKHFTPEEINYLLDLSADLKAKKRAGIKGNLLEGKNVVLLFEKTSTRTRCAF 64
           LK R+FL+L  FTP++INY+LDL+  LK  KR G++   L+ KN+ L+FEK STRTRC+F
Sbjct: 4   LKNRNFLSLMDFTPQDINYMLDLAKKLKEDKRNGLEEQYLKKKNIALIFEKDSTRTRCSF 63

Query: 65  EVGVLDEGGHVTFLGSGDSQMGKKESIEDTAKVLGRFYDGIEFRGFKQETVEILAANAGV 124
           EV   D+G H  ++GS  SQ+ KKESI+DTA+VLGR +D IE+RG+ QE VEILA ++ V
Sbjct: 64  EVAAHDQGAHAVYIGSTGSQISKKESIKDTARVLGRMFDAIEYRGYGQEVVEILAEHSNV 123

Query: 125 PVWNGLTDLYHPTQILADFLTIKEHVAKPLNKVKFVYAGDARNNMGNSLMIGAAKMGMEF 184
           PVWNGLTD  HPTQ++A+F+T+KE   KPLN++KFVY GDARNN+ N+LMIGAAKMGM+F
Sbjct: 124 PVWNGLTDEEHPTQVIANFMTLKEKFNKPLNEIKFVYCGDARNNVSNALMIGAAKMGMDF 183

Query: 185 WGLAPKELWPSEELVAEMKEVAKETGASINFSENVDD-VKNADVIYTDVWVSMGEE-AMF 242
              APK L+PS ELV +  ++A+ TG  I  S+ VD+ V  ADV+YTDVWVSMGE+  ++
Sbjct: 184 RIAAPKSLFPSSELVKKCMDIAELTGGKITLSDEVDEAVFGADVLYTDVWVSMGEDREVW 243

Query: 243 EERIKQLKPYQVNMDMIKKTENPDVLFLHCLPAFHDLNTTVGKDIYEKFGLESMEVTDEV 302
           +ER+K LKPYQ+NM+MI KT+NP+V F+HCLPAFHD +T   K+IY++F     EVTDEV
Sbjct: 244 KERLKMLKPYQINMEMISKTKNPNVKFMHCLPAFHDFSTDAAKEIYDEFNEIPFEVTDEV 303

Query: 303 FRSRHSKVFDEAENRMHTIKAVMVATIGNL 332
           F S +S  FDEAENR+H+IKA+MVAT+G++
Sbjct: 304 FESDYSLAFDEAENRLHSIKAIMVATLGDI 333


Lambda     K      H
   0.317    0.135    0.389 

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: 357
Number of extensions: 8
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: 332
Length of database: 333
Length adjustment: 28
Effective length of query: 304
Effective length of database: 305
Effective search space:    92720
Effective search space used:    92720
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate NP_346957.1 CA_C0316 (ornithine carbomoyltransferase)
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.7031.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
     2e-132  426.9   0.2   2.3e-132  426.8   0.2    1.0  1  lcl|NCBI__GCF_000008765.1:NP_346957.1  CA_C0316 ornithine carbomoyltran


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_346957.1  CA_C0316 ornithine carbomoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.8   0.2  2.3e-132  2.3e-132       1     303 [.       7     330 ..       7     331 .. 0.99

  Alignments for each domain:
  == domain 1  score: 426.8 bits;  conditional E-value: 2.3e-132
                              TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlyln 72 
                                            r++lsl+d+++++++++l+lakklk++k++g ee++lk+k++aliFek+stRtR+sfevaa ++Ga+++y++
  lcl|NCBI__GCF_000008765.1:NP_346957.1   7 RNFLSLMDFTPQDINYMLDLAKKLKEDKRNGLEEQYLKKKNIALIFEKDSTRTRCSFEVAAHDQGAHAVYIG 78 
                                            789********************************************************************* PP

                              TIGR00658  73 keelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg 144
                                            +  +q+++kesikDtarvl+r++dai +R+y +e ve la++++vPv+ngLtd+ehP+q++a+++t+kek++
  lcl|NCBI__GCF_000008765.1:NP_346957.1  79 STGSQISKKESIKDTARVLGRMFDAIEYRGYGQEVVEILAEHSNVPVWNGLTDEEHPTQVIANFMTLKEKFN 150
                                            ************************************************************************ PP

                              TIGR00658 145 .klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkav 214
                                              l+e+k+vy GDa nnv n l+++aak+G+d+++a+P+ l p++e+vkk+ +ia+ +ggk++l +++++av
  lcl|NCBI__GCF_000008765.1:NP_346957.1 151 kPLNEIKFVYCGDArNNVSNALMIGAAKMGMDFRIAAPKSLFPSSELVKKCMDIAELTGGKITLSDEVDEAV 222
                                            99********************************************************************** PP

                              TIGR00658 215 kdadviytDvwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr................ 268
                                             +adv+ytDvwvsmGe  e ++erlk+lkpyq+n+e+++ + +p+vkf+hCLPa++                
  lcl|NCBI__GCF_000008765.1:NP_346957.1 223 FGADVLYTDVWVSMGEdREVWKERLKMLKPYQINMEMISKTkNPNVKFMHCLPAFHdfstdaakeiydefne 294
                                            ****************66789*******************999***************************** PP

                              TIGR00658 269 .GeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                               evtdev+e++ s+ fdeaenRlh++ka+++a+l
  lcl|NCBI__GCF_000008765.1:NP_346957.1 295 iPFEVTDEVFESDYSLAFDEAENRLHSIKAIMVATL 330
                                            99*******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (333 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: 7.79
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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:

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
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