GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI in Rhodomicrobium vannielii ATCC 17100

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_245257982.1 RVAN_RS11965 ornithine carbamoyltransferase

Query= BRENDA::Q98BB6
         (303 letters)



>NCBI__GCF_000166055.1:WP_245257982.1
          Length = 312

 Score =  358 bits (919), Expect = e-104
 Identities = 179/300 (59%), Positives = 220/300 (73%), Gaps = 3/300 (1%)

Query: 4   RHFTDLSTVSEGDLRFMLDDAVVRKARLK---AGERTRPLEGKVLAMIFDKPSTRTRVSF 60
           RHF D+       LR +LD+A   K  +K   A +  +  EGKVLAM+F+K STRTRVSF
Sbjct: 9   RHFLDIDDYDFDTLRLILDNARALKKLIKTSPASDWPKVAEGKVLAMLFEKSSTRTRVSF 68

Query: 61  DVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENATV 120
           DV MRQLGGETI+L   +MQLGR ETIADTA+VLSRYVDAIM+R TSH+ L+EL E++ V
Sbjct: 69  DVAMRQLGGETIVLNRNDMQLGRGETIADTARVLSRYVDAIMMRCTSHEALIELAEHSAV 128

Query: 121 PVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLNV 180
           PVINGL+D +HPCQ++ADIMT EEH+G VA   +AW GD NNV  S + A+ RF F + +
Sbjct: 129 PVINGLSDRSHPCQILADIMTLEEHKGDVAPLKVAWIGDFNNVTASWVHAAVRFGFAMTL 188

Query: 181 AVPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGHNVFS 240
           A P+  +P +  +DW+   GG++     P  AV  ADCVVTD WVSMGQE+ A    + +
Sbjct: 189 ATPKLLQPPRSFLDWANDEGGRITVVEDPAVAVAGADCVVTDVWVSMGQENVAERETLLA 248

Query: 241 PYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVLAWC 300
           PYQVNA LM  A  +A+FMHCLPAHRG EVTD+VIDGP SVVFDEAENRLHAQ+A+LAWC
Sbjct: 249 PYQVNAALMEKADKNAIFMHCLPAHRGREVTDDVIDGPQSVVFDEAENRLHAQRAILAWC 308


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: 336
Number of extensions: 13
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_245257982.1 RVAN_RS11965 (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.1179627.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-120  388.0   0.0   1.6e-120  387.8   0.0    1.0  1  NCBI__GCF_000166055.1:WP_245257982.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166055.1:WP_245257982.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.8   0.0  1.6e-120  1.6e-120       1     303 [.       9     309 ..       9     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: 387.8 bits;  conditional E-value: 1.6e-120
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgke...ekklkgktlaliFekrstRtRvsfevaayelGaqvly 70 
                                           rh+l++ d++ + l+ +l+ a+ lkk  k++      k  +gk la++Fek+stRtRvsf+va+ +lG+++++
  NCBI__GCF_000166055.1:WP_245257982.1   9 RHFLDIDDYDFDTLRLILDNARALKKLIKTSPAsdwPKVAEGKVLAMLFEKSSTRTRVSFDVAMRQLGGETIV 81 
                                           8************************9877755444468899******************************** PP

                             TIGR00658  71 lnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikekl 143
                                           ln++++qlgr+e+i+Dtarvlsryvdai++R ++he + ela++++vPvingL+d +hPcqilaD++t++e++
  NCBI__GCF_000166055.1:WP_245257982.1  82 LNRNDMQLGRGETIADTARVLSRYVDAIMMRCTSHEALIELAEHSAVPVINGLSDRSHPCQILADIMTLEEHK 154
                                           ************************************************************************* PP

                             TIGR00658 144 gklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkd 216
                                           g++  +k++++GD nnv+ s + aa+ +G+ +++atP+ l+p  + +++a    +++gg+++++edp+ av++
  NCBI__GCF_000166055.1:WP_245257982.1 155 GDVAPLKVAWIGDFNNVTASWVHAAVRFGFAMTLATPKLLQPPRSFLDWA----NDEGGRITVVEDPAVAVAG 223
                                           ************************************************99....669**************** PP

                             TIGR00658 217 adviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeae 289
                                           ad ++tDvwvsmG+e+ + er  ll pyqvn  l+e a+++++f+hCLPa+rG+evtd+v++g++s+vfdeae
  NCBI__GCF_000166055.1:WP_245257982.1 224 ADCVVTDVWVSMGQENVA-ERETLLAPYQVNAALMEKADKNAIFMHCLPAHRGREVTDDVIDGPQSVVFDEAE 295
                                           **************9987.899*************************************************** PP

                             TIGR00658 290 nRlhaqkavlkall 303
                                           nRlhaq+a+l++++
  NCBI__GCF_000166055.1:WP_245257982.1 296 NRLHAQRAILAWCF 309
                                           **********9876 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: 17.79
//
[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