Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_012755913.1 RLEG_RS00945 ornithine carbamoyltransferase
Query= BRENDA::Q98BB6 (303 letters) >NCBI__GCF_000023185.1:WP_012755913.1 Length = 304 Score = 464 bits (1193), Expect = e-135 Identities = 222/303 (73%), Positives = 255/303 (84%) Query: 1 MSVRHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERTRPLEGKVLAMIFDKPSTRTRVSF 60 MS +HF DLS V+ DLR +++DA+ RK KAG+ +PL GK+LAMIF+KPSTRTRVSF Sbjct: 1 MSPKHFLDLSAVTSADLRTIMNDALARKQAFKAGQGDKPLAGKMLAMIFEKPSTRTRVSF 60 Query: 61 DVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENATV 120 DVGMRQLGGET+ L+GTEMQLGR+ETI DTAKVLSRYVDAIMIRTT H RL+EL ++ATV Sbjct: 61 DVGMRQLGGETLFLSGTEMQLGRAETIGDTAKVLSRYVDAIMIRTTEHSRLVELAQHATV 120 Query: 121 PVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLNV 180 PVIN LTDDTHPCQ+MADIMTFEEHRGP+ GKTIAWTGDGNNVLHSL+E +ARF + +N+ Sbjct: 121 PVINALTDDTHPCQIMADIMTFEEHRGPIKGKTIAWTGDGNNVLHSLVEGAARFGYRMNM 180 Query: 181 AVPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGHNVFS 240 AVP GSEP +++W++ G ++ + AV DCVVTD WVSM QEHRARGHNVF Sbjct: 181 AVPLGSEPKDHYLNWARNEGAEIMLCHDADRAVAGVDCVVTDTWVSMNQEHRARGHNVFQ 240 Query: 241 PYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVLAWC 300 PYQVNA LMA A DALFMHCLPAHRGEEVTDEVIDGP SVVFDEAENRLHAQK++LAWC Sbjct: 241 PYQVNAALMAKAGNDALFMHCLPAHRGEEVTDEVIDGPQSVVFDEAENRLHAQKSILAWC 300 Query: 301 LGA 303 LGA Sbjct: 301 LGA 303 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: 394 Number of extensions: 15 Number of successful extensions: 1 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: 304 Length adjustment: 27 Effective length of query: 276 Effective length of database: 277 Effective search space: 76452 Effective search space used: 76452 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_012755913.1 RLEG_RS00945 (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.15900.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-118 380.0 0.0 4.5e-118 379.8 0.0 1.0 1 lcl|NCBI__GCF_000023185.1:WP_012755913.1 RLEG_RS00945 ornithine carbamoyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023185.1:WP_012755913.1 RLEG_RS00945 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.8 0.0 4.5e-118 4.5e-118 1 303 [. 4 301 .. 4 302 .. 0.98 Alignments for each domain: == domain 1 score: 379.8 bits; conditional E-value: 4.5e-118 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 +h+l+l +++++l+++++ a k++ k+g+ +k l gk la+iFek+stRtRvsf+v++ +lG+++l lcl|NCBI__GCF_000023185.1:WP_012755913.1 4 KHFLDLSAVTSADLRTIMNDALARKQAFKAGQGDKPLAGKMLAMIFEKPSTRTRVSFDVGMRQLGGETL 72 79******************************************************************* PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 +l+ e+qlgr e+i Dta+vlsryvdai++R+++h+ + ela++a+vPvin+Ltd +hPcqi+aD++t lcl|NCBI__GCF_000023185.1:WP_012755913.1 73 FLSGTEMQLGRAETIGDTAKVLSRYVDAIMIRTTEHSRLVELAQHATVPVINALTDDTHPCQIMADIMT 141 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 +e+ g +k+ ++++ GD+nnv +sl+ +aa +G +++a P g ep+ +++++a+ ++g+++ l lcl|NCBI__GCF_000023185.1:WP_012755913.1 142 FEEHRGPIKGKTIAWTGDGNNVLHSLVEGAARFGYRMNMAVPLGSEPKDHYLNWAR----NEGAEIMLC 206 *****************************************************995....59******* PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 +d ++av+++d ++tD+wvsm +e+++ ++++pyqvn l++ a +++ f+hCLPa+rGeevtdev lcl|NCBI__GCF_000023185.1:WP_012755913.1 207 HDADRAVAGVDCVVTDTWVSMNQEHRA-RGHNVFQPYQVNAALMAKAGNDALFMHCLPAHRGEEVTDEV 274 **********************99887.5679************************************* PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 ++g++s+vfdeaenRlhaqk++l+++l lcl|NCBI__GCF_000023185.1:WP_012755913.1 275 IDGPQSVVFDEAENRLHAQKSILAWCL 301 ***********************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (304 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.90 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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