Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_012172547.1 AZC_RS20655 ornithine carbamoyltransferase
Query= BRENDA::Q98BB6 (303 letters) >NCBI__GCF_000010525.1:WP_012172547.1 Length = 309 Score = 402 bits (1032), Expect = e-117 Identities = 197/299 (65%), Positives = 235/299 (78%) Query: 3 VRHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERTRPLEGKVLAMIFDKPSTRTRVSFDV 62 VRHF DL+ + DLR +L+ + KA+ KAG +PL GK LAM+FDKPSTRTRVSFD+ Sbjct: 6 VRHFLDLTDLEAVDLRGVLELSKQLKAKRKAGTEEKPLAGKSLAMVFDKPSTRTRVSFDL 65 Query: 63 GMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENATVPV 122 MRQLGGETIMLTG EMQLGR E+IADTA+VLSR+VDAIMIR SH+ LLEL + ATVPV Sbjct: 66 AMRQLGGETIMLTGAEMQLGRGESIADTARVLSRFVDAIMIRILSHEDLLELAKFATVPV 125 Query: 123 INGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLNVAV 182 INGLT +HPCQ+MAD++TFEEH+G + G+++AWTGD NNVL S + A+A+F F +NVA Sbjct: 126 INGLTRVSHPCQVMADVLTFEEHKGSIEGRSVAWTGDANNVLASWVHAAAQFDFTINVAT 185 Query: 183 PEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGHNVFSPY 242 P+ P Q ++ K K+ F R PEEAV+ DCV+TD WVSMG + R HN+ PY Sbjct: 186 PKELSPRQALKEFVKRTQAKVRFMRDPEEAVEGVDCVITDTWVSMGDKEAERRHNLLKPY 245 Query: 243 QVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVLAWCL 301 QVNAKLMA A PDA+FMHCLPAHRGEEVTDEV+DGP SVVFDEAENRLHAQK +LAWCL Sbjct: 246 QVNAKLMARAAPDAIFMHCLPAHRGEEVTDEVMDGPQSVVFDEAENRLHAQKGILAWCL 304 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: 370 Number of extensions: 11 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: 309 Length adjustment: 27 Effective length of query: 276 Effective length of database: 282 Effective search space: 77832 Effective search space used: 77832 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_012172547.1 AZC_RS20655 (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.9892.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-122 395.0 0.0 1.2e-122 394.8 0.0 1.0 1 lcl|NCBI__GCF_000010525.1:WP_012172547.1 AZC_RS20655 ornithine carbamoylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_012172547.1 AZC_RS20655 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 394.8 0.0 1.2e-122 1.2e-122 1 303 [. 7 304 .. 7 305 .. 0.98 Alignments for each domain: == domain 1 score: 394.8 bits; conditional E-value: 1.2e-122 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 rh+l+l+dl+ +l+ +lel+k+lk+++k+g+eek l gk+la++F+k+stRtRvsf+ a+ +lG++++ lcl|NCBI__GCF_000010525.1:WP_012172547.1 7 RHFLDLTDLEAVDLRGVLELSKQLKAKRKAGTEEKPLAGKSLAMVFDKPSTRTRVSFDLAMRQLGGETI 75 8******************************************************************** PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 +l e+qlgr+esi+Dtarvlsr+vdai++R +hed+ elak+a+vPvingLt +hPcq++aD+lt lcl|NCBI__GCF_000010525.1:WP_012172547.1 76 MLTGAEMQLGRGESIADTARVLSRFVDAIMIRILSHEDLLELAKFATVPVINGLTRVSHPCQVMADVLT 144 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 +e++g++++ ++++ GDannv s + aaa++ ++++vatP++l+p++++ k+++k++ +k++++ lcl|NCBI__GCF_000010525.1:WP_012172547.1 145 FEEHKGSIEGRSVAWTGDANNVLASWVHAAAQFDFTINVATPKELSPRQAL----KEFVKRTQAKVRFM 209 ***********************************************9876....678999******** PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 +dp++av+++d + tD+wvsmG++e+ e r +llkpyqvn +l++ a p+++f+hCLPa+rGeevtdev lcl|NCBI__GCF_000010525.1:WP_012172547.1 210 RDPEEAVEGVDCVITDTWVSMGDKEA-ERRHNLLKPYQVNAKLMARAAPDAIFMHCLPAHRGEEVTDEV 277 **********************9765.5899************************************** PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 ++g++s+vfdeaenRlhaqk++l+++l lcl|NCBI__GCF_000010525.1:WP_012172547.1 278 MDGPQSVVFDEAENRLHAQKGILAWCL 304 ***********************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (309 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: 7.96 // [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