Align Ornithine carbamoyltransferase subunit F; OTCase-2; EC 2.1.3.3 (characterized)
to candidate BWI76_RS03010 BWI76_RS03010 ornithine carbamoyltransferase
Query= SwissProt::P06960 (334 letters) >FitnessBrowser__Koxy:BWI76_RS03010 Length = 334 Score = 608 bits (1569), Expect = e-179 Identities = 299/334 (89%), Positives = 317/334 (94%) Query: 1 MSDLYKKHFLKLLDFTPAQFTSLLTLAAQLKADKKNGKEVQKLTGKNIALIFEKDSTRTR 60 MS Y+KHFLKLLDFTPA+ T+LL LAA+LKADKKN E+Q LTGKNIALIFEKDSTRTR Sbjct: 1 MSAFYQKHFLKLLDFTPAEITALLELAARLKADKKNNIEIQHLTGKNIALIFEKDSTRTR 60 Query: 61 CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQY 120 CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLA+Y Sbjct: 61 CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAEY 120 Query: 121 AGVPVWNGLTNEFHPTQLLADLMTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALT 180 AGVPVWNGLTNEFHPTQLLADL+TMQEHLPGKAFN+MTLVYAGDARNNMGNSMLEAAALT Sbjct: 121 AGVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNQMTLVYAGDARNNMGNSMLEAAALT 180 Query: 181 GLDLRLLAPKACWPEESLVAECSALAEKHGGKITLTEDVAAGVKGADFIYTDVWVSMGEA 240 GLDLRL+AP ACWPEE LV +C ALA+K+GG ITLTED+AAGVKGADFIYTDVWVSMGEA Sbjct: 181 GLDLRLVAPTACWPEEKLVEQCRALAQKNGGNITLTEDIAAGVKGADFIYTDVWVSMGEA 240 Query: 241 KEKWAERIALLRGYQVNAQMMALTDNPNVKFLHCLPAFHDDQTTLGKQMAKEFDLHGGME 300 KEKWAERIALLR YQVN++MMALT NP VKFLHCLPAFHDDQTTLGKQMA E+ LHGGME Sbjct: 241 KEKWAERIALLRAYQVNSEMMALTGNPQVKFLHCLPAFHDDQTTLGKQMAAEYGLHGGME 300 Query: 301 VTDEVFESAASIVFDQAENRMHTIKAVMMATLGE 334 VTDEVFESAASIVFDQAENRMHTIKAVM+ATLG+ Sbjct: 301 VTDEVFESAASIVFDQAENRMHTIKAVMVATLGK 334 Lambda K H 0.318 0.132 0.385 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: 486 Number of extensions: 12 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: 334 Length of database: 334 Length adjustment: 28 Effective length of query: 306 Effective length of database: 306 Effective search space: 93636 Effective search space used: 93636 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate BWI76_RS03010 BWI76_RS03010 (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.1116.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-140 451.4 0.0 8e-140 451.2 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS03010 BWI76_RS03010 ornithine carbamoy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS03010 BWI76_RS03010 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.2 0.0 8e-140 8e-140 1 303 [. 7 332 .. 7 333 .. 0.99 Alignments for each domain: == domain 1 score: 451.2 bits; conditional E-value: 8e-140 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlyl 71 +h+l+lld++++e++ llela++lk++kk++ e ++l+gk++aliFek+stRtR+sfevaa+++Ga+v+yl lcl|FitnessBrowser__Koxy:BWI76_RS03010 7 KHFLKLLDFTPAEITALLELAARLKADKKNNIEIQHLTGKNIALIFEKDSTRTRCSFEVAAFDQGARVTYL 77 79********************************************************************* PP TIGR00658 72 nkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikek 142 +++ +q+g+kesikDtarvl+r++d+i++R++ +e ve+la+ya+vPv+ngLt+++hP+q+laDllt++e+ lcl|FitnessBrowser__Koxy:BWI76_RS03010 78 GPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAEYAGVPVWNGLTNEFHPTQLLADLLTMQEH 148 *********************************************************************** PP TIGR00658 143 lg..klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedp 210 l ++++++lvy GDa nn++ns+l aaa++Gld+++++P +++pe+++v++++++a++ngg+++lted+ lcl|FitnessBrowser__Koxy:BWI76_RS03010 149 LPgkAFNQMTLVYAGDArNNMGNSMLEAAALTGLDLRLVAPTACWPEEKLVEQCRALAQKNGGNITLTEDI 219 *8889****************************************************************** PP TIGR00658 211 kkavkdadviytDvwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr........... 268 + +vk+ad+iytDvwvsmGe +ek++er++ll+ yqvn+e+++l+ +p+vkflhCLPa++ lcl|FitnessBrowser__Koxy:BWI76_RS03010 220 AAGVKGADFIYTDVWVSMGEaKEKWAERIALLRAYQVNSEMMALTgNPQVKFLHCLPAFHddqttlgkqma 290 ********************9999*********************************************** PP TIGR00658 269 .......GeevtdevlegeasivfdeaenRlhaqkavlkall 303 G+evtdev+e++asivfd+aenR+h++kav++a+l lcl|FitnessBrowser__Koxy:BWI76_RS03010 291 aeyglhgGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATL 332 ***************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (334 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.76 // [ok]
This GapMind analysis is from Apr 09 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