Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_013076160.1 BTUS_RS11060 ornithine carbamoyltransferase
Query= BRENDA::O93656 (317 letters) >NCBI__GCF_000092905.1:WP_013076160.1 Length = 318 Score = 363 bits (933), Expect = e-105 Identities = 185/310 (59%), Positives = 225/310 (72%) Query: 3 VSLKGRDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRV 62 + L+GRD L L D+T +E+ +L A +LK QK G+ + L GKTL MIF+K STRTRV Sbjct: 6 IDLRGRDFLDLADFTSDELRGLLRLAAVLKEKQKAGERVQPLAGKTLGMIFEKSSTRTRV 65 Query: 63 SFEVAMAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYA 122 SFEV M LGGHAL+L + D QL RGE I DTARVLSRYVD IM R + H+ V +LA+YA Sbjct: 66 SFEVGMVQLGGHALFLASHDTQLGRGEPIPDTARVLSRYVDGIMIRTFSHESVRELAEYA 125 Query: 123 SVPVINGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGDGNNVAHSLMIAGTKLGADV 182 +VPVINGL+D HPCQ LAD MTI E K ++GV V YVGDGNN+A+S ++ G ++ Sbjct: 126 TVPVINGLTDLHHPCQVLADAMTILEHKSRLEGVTVAYVGDGNNMANSWLVGAPLFGMNL 185 Query: 183 VVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEAE 242 VATP+GYE D V A++ AA +G L+HDP +AV ADVIYTDVWASMGQEAE E Sbjct: 186 RVATPQGYECDPGVAARAQELAARAGTEMSLVHDPREAVAGADVIYTDVWASMGQEAERE 245 Query: 243 ERRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDEAENRLHAQ 302 ER + F F+V LV A PDY+FMHCLPAHRGEEV DVID P+SV++DEAENRLHAQ Sbjct: 246 ERLRAFAGFEVTPALVARAAPDYLFMHCLPAHRGEEVAPDVIDGPHSVIFDEAENRLHAQ 305 Query: 303 KAVLALLLGG 312 KA+L + G Sbjct: 306 KAILVATMAG 315 Lambda K H 0.319 0.134 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: 287 Number of extensions: 8 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: 317 Length of database: 318 Length adjustment: 27 Effective length of query: 290 Effective length of database: 291 Effective search space: 84390 Effective search space used: 84390 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_013076160.1 BTUS_RS11060 (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.24377.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-136 440.8 0.0 1.4e-136 440.6 0.0 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013076160.1 BTUS_RS11060 ornithine carbamoyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013076160.1 BTUS_RS11060 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 440.6 0.0 1.4e-136 1.4e-136 1 303 [. 11 313 .. 11 314 .. 0.99 Alignments for each domain: == domain 1 score: 440.6 bits; conditional E-value: 1.4e-136 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 r++l+l+d++++el+ ll la+ lk+++k+g++ + l gktl++iFek+stRtRvsfev++++lG+++l lcl|NCBI__GCF_000092905.1:WP_013076160.1 11 RDFLDLADFTSDELRGLLRLAAVLKEKQKAGERVQPLAGKTLGMIFEKSSTRTRVSFEVGMVQLGGHAL 79 79******************************************************************* PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 +l ++++qlgr+e+i Dtarvlsryvd+i++R+++he v+ela+ya+vPvingLtdl hPcq+laD +t lcl|NCBI__GCF_000092905.1:WP_013076160.1 80 FLASHDTQLGRGEPIPDTARVLSRYVDGIMIRTFSHESVRELAEYATVPVINGLTDLHHPCQVLADAMT 148 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 i e++ +l++v+++yvGD+nn+ans l++a ++G++++vatP+g+e ++ + +a+++a++ g++++l+ lcl|NCBI__GCF_000092905.1:WP_013076160.1 149 ILEHKSRLEGVTVAYVGDGNNMANSWLVGAPLFGMNLRVATPQGYECDPGVAARAQELAARAGTEMSLV 217 ********************************************************************* PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 +dp +av++adviytDvw+smG+e+++eerl+++ ++ v+ l++ a p++ f+hCLPa+rGeev+ +v lcl|NCBI__GCF_000092905.1:WP_013076160.1 218 HDPREAVAGADVIYTDVWASMGQEAEREERLRAFAGFEVTPALVARAAPDYLFMHCLPAHRGEEVAPDV 286 ********************************************************************* PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 ++g++s++fdeaenRlhaqka+l+a++ lcl|NCBI__GCF_000092905.1:WP_013076160.1 287 IDGPHSVIFDEAENRLHAQKAILVATM 313 ***********************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (318 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: 7.36 // [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