Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate CCNA_02325 CCNA_02325 ornithine carbamoyltransferase
Query= BRENDA::Q98BB6 (303 letters) >FitnessBrowser__Caulo:CCNA_02325 Length = 311 Score = 320 bits (821), Expect = 2e-92 Identities = 170/307 (55%), Positives = 206/307 (67%), Gaps = 9/307 (2%) Query: 4 RHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERTR-----PLEGKVLAMIFDKPSTRTRV 58 RHF DL + LR +LDDA RKA K + + P + +VL+MIF K STRTR Sbjct: 5 RHFIDLWKLDGATLRLLLDDAHARKAARKGWPQGKVDADAPAKDRVLSMIFQKNSTRTRF 64 Query: 59 SFDVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENA 118 SFD MRQLGG I+ T ++MQLGR ETI DTAKVLSR VDA+MIR SH + + + Sbjct: 65 SFDAAMRQLGGSAIISTASDMQLGRGETIEDTAKVLSRMVDAVMIRANSHADVERFAQVS 124 Query: 119 TVPVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNL 178 TVP+INGLTD +HPCQ+MADI+T EEHRGP+AGKTIAW GDGNNV S + A+ F L Sbjct: 125 TVPIINGLTDKSHPCQIMADILTIEEHRGPIAGKTIAWVGDGNNVCSSFIHAAPLLGFEL 184 Query: 179 NVAVPEGSEPAQKHIDWSKAHG--GKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGH 236 +A P A H D ++A G GK+ T P+ AV AD VV D WVSMG Sbjct: 185 KIACP-AVYHADLH-DLARAEGLQGKVSMTTDPKAAVSGADVVVADTWVSMGDTDHDERL 242 Query: 237 NVFSPYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAV 296 PYQV+ +LM A + +F+HCLPAHRGEEVTD V+DGP S+V+DEAENR+HAQK+V Sbjct: 243 AALEPYQVDDRLMDLAAGNGVFLHCLPAHRGEEVTDAVLDGPRSLVWDEAENRIHAQKSV 302 Query: 297 LAWCLGA 303 LAWC GA Sbjct: 303 LAWCFGA 309 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: 335 Number of extensions: 10 Number of successful extensions: 3 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: 311 Length adjustment: 27 Effective length of query: 276 Effective length of database: 284 Effective search space: 78384 Effective search space used: 78384 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 CCNA_02325 CCNA_02325 (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.carbon/TIGR00658.hmm # target sequence database: /tmp/gapView.3491.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-111 358.4 0.0 1.7e-111 358.2 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_02325 CCNA_02325 ornithine carbamoyltr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02325 CCNA_02325 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 358.2 0.0 1.7e-111 1.7e-111 1 303 [. 5 307 .. 5 308 .. 0.94 Alignments for each domain: == domain 1 score: 358.2 bits; conditional E-value: 1.7e-111 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgke.....ekklkgktlaliFekrstRtRvsfevaayelGaqv 68 rh+++l++l+ + l+ ll+ a+ k+++k + ++ k + l++iF+k+stRtR sf++a+ +lG+ + lcl|FitnessBrowser__Caulo:CCNA_02325 5 RHFIDLWKLDGATLRLLLDDAHARKAARKGWPQgkvdaDAPAKDRVLSMIFQKNSTRTRFSFDAAMRQLGGSA 77 8*********************9999887533333455778999***************************** PP TIGR00658 69 lylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltike 141 ++ ++++qlgr+e+i+Dta+vlsr+vda+++R+++h dve +a+ ++vP+ingLtd++hPcqi+aD+lti+e lcl|FitnessBrowser__Caulo:CCNA_02325 78 IISTASDMQLGRGETIEDTAKVLSRMVDAVMIRANSHADVERFAQVSTVPIINGLTDKSHPCQIMADILTIEE 150 ************************************************************************* PP TIGR00658 142 klgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkav 214 + g + + ++++vGD+nnv+ s++ aa +lG+++++a+P ++ + + + +a + gk+++t dpk av lcl|FitnessBrowser__Caulo:CCNA_02325 151 HRGPIAGKTIAWVGDGNNVCSSFIHAAPLLGFELKIACPAVYHADLHDLARA----EGLQGKVSMTTDPKAAV 219 ****************************************998765555554....6788************* PP TIGR00658 215 kdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfde 287 ++adv++ D+wvsmG+ ++ erl++l+pyqv+++l++la + +flhCLPa+rGeevtd vl+g++s+v+de lcl|FitnessBrowser__Caulo:CCNA_02325 220 SGADVVVADTWVSMGDTDHD-ERLAALEPYQVDDRLMDLAAGNGVFLHCLPAHRGEEVTDAVLDGPRSLVWDE 291 ***************98765.9*************************************************** PP TIGR00658 288 aenRlhaqkavlkall 303 aenR+haqk+vl++++ lcl|FitnessBrowser__Caulo:CCNA_02325 292 AENRIHAQKSVLAWCF 307 ************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (311 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: 7.04 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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