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.
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:
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