Alignments for a candidate for argI in Methyloferula stellata AR4T

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Methyloferula stellata AR4T

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_040580602.1 A3OQ_RS0105025 ornithine carbamoyltransferase

Query= BRENDA::Q98BB6
         (303 letters)



>NCBI__GCF_000385335.1:WP_040580602.1
          Length = 312

 Score =  406 bits (1043), Expect = e-118
 Identities = 202/308 (65%), Positives = 239/308 (77%), Gaps = 10/308 (3%)

Query: 2   SVRHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERT------RPLEGKVLAMIFDKPSTR 55
           + RHF DLS +   DLR +LD A    AR+KAG R       RPL GK+LAMIFDKPSTR
Sbjct: 6   TARHFLDLSEIPAPDLRHILDAA----ARIKAGRRKGQIAAERPLAGKMLAMIFDKPSTR 61

Query: 56  TRVSFDVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELT 115
           TRVSFDVGMR+LGGETIMLTG EMQLGR ETIADTA+VLSR+VDA++IR  SH  + EL 
Sbjct: 62  TRVSFDVGMRELGGETIMLTGQEMQLGRGETIADTARVLSRFVDAVVIRILSHTDMQELA 121

Query: 116 ENATVPVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFR 175
           ++A++PVINGLT  THPCQ+MAD++TFEEHRGP+ G+T+AWTGD NNVL S + A+ RF 
Sbjct: 122 DHASIPVINGLTKKTHPCQVMADVLTFEEHRGPIKGRTVAWTGDANNVLASWVHAAQRFD 181

Query: 176 FNLNVAVPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARG 235
           F +NVA P       + ++W+K    +L+ TR P EAV +AD V++DCWVSMG E     
Sbjct: 182 FEINVATPAELAMPAELVEWAKRSKTRLNVTRDPFEAVRRADAVISDCWVSMGDEDETFR 241

Query: 236 HNVFSPYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKA 295
           HN+ +PYQVNAKLMA A  DA+FMHCLPAHRGEEVTDEVIDGP SVVFDEAENRLHAQK 
Sbjct: 242 HNLLAPYQVNAKLMAAAAKDAIFMHCLPAHRGEEVTDEVIDGPQSVVFDEAENRLHAQKG 301

Query: 296 VLAWCLGA 303
           +LAWCLGA
Sbjct: 302 ILAWCLGA 309


Lambda     K      H
   0.320    0.133    0.400 

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: 386
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: 303
Length of database: 312
Length adjustment: 27
Effective length of query: 276
Effective length of database: 285
Effective search space:    78660
Effective search space used:    78660
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_040580602.1 A3OQ_RS0105025 (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.32676.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-115  371.7   0.0   1.5e-115  371.6   0.0    1.0  1  lcl|NCBI__GCF_000385335.1:WP_040580602.1  A3OQ_RS0105025 ornithine carbamo


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000385335.1:WP_040580602.1  A3OQ_RS0105025 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.6   0.0  1.5e-115  1.5e-115       1     303 [.       8     307 ..       8     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 371.6 bits;  conditional E-value: 1.5e-115
                                 TIGR00658   1 rhllslldlseeelkellelakklkkekkkgke..ekklkgktlaliFekrstRtRvsfevaayelGaq 67 
                                               rh+l+l ++   +l+++l+ a+++k+ ++kg+   e+ l gk la+iF+k+stRtRvsf+v++ elG++
  lcl|NCBI__GCF_000385335.1:WP_040580602.1   8 RHFLDLSEIPAPDLRHILDAAARIKAGRRKGQIaaERPLAGKMLAMIFDKPSTRTRVSFDVGMRELGGE 76 
                                               8****************************997555899******************************* PP

                                 TIGR00658  68 vlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDl 136
                                               +++l  +e+qlgr+e+i+Dtarvlsr+vda+v+R  +h+d++ela++as+PvingLt ++hPcq++aD+
  lcl|NCBI__GCF_000385335.1:WP_040580602.1  77 TIMLTGQEMQLGRGETIADTARVLSRFVDAVVIRILSHTDMQELADHASIPVINGLTKKTHPCQVMADV 145
                                               ********************************************************************* PP

                                 TIGR00658 137 ltikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkle 205
                                               lt +e+ g +k+ ++++ GDannv  s + aa  + ++++vatP +l + ae+v++ak    ++ ++l+
  lcl|NCBI__GCF_000385335.1:WP_040580602.1 146 LTFEEHRGPIKGRTVAWTGDANNVLASWVHAAQRFDFEINVATPAELAMPAELVEWAK----RSKTRLN 210
                                               ********************************************************95....5889*** PP

                                 TIGR00658 206 ltedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtd 274
                                               +t+dp +av+ ad +  D wvsmG+e+++  r +ll pyqvn +l++ a ++++f+hCLPa+rGeevtd
  lcl|NCBI__GCF_000385335.1:WP_040580602.1 211 VTRDPFEAVRRADAVISDCWVSMGDEDET-FRHNLLAPYQVNAKLMAAAAKDAIFMHCLPAHRGEEVTD 278
                                               *************************9987.899************************************ PP

                                 TIGR00658 275 evlegeasivfdeaenRlhaqkavlkall 303
                                               ev++g++s+vfdeaenRlhaqk++l+++l
  lcl|NCBI__GCF_000385335.1:WP_040580602.1 279 EVIDGPQSVVFDEAENRLHAQKGILAWCL 307
                                               *************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (312 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: 9.84
//
[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