Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate 7023737 Shewana3_0967 carbamoyl phosphate synthase small subunit (RefSeq)
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__ANA3:7023737 Length = 386 Score = 605 bits (1560), Expect = e-178 Identities = 295/382 (77%), Positives = 331/382 (86%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 + KSALLVLEDGT F G AIGA G +VGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI Sbjct: 5 LTKSALLVLEDGTVFTGTAIGADGLSVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 64 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GN GTN+ D ES+ VHA GL+IRDLPL+AS+FRN + LS YLK +N+V IADIDTRKLTR Sbjct: 65 GNTGTNNEDVESNGVHACGLIIRDLPLVASSFRNQQTLSDYLKANNVVGIADIDTRKLTR 124 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LREKGAQ GCI+AG + D A AL A+AFPGL GMDLAKEVTT +AY W +GSW L GG Sbjct: 125 ILREKGAQAGCIMAGADLDEAKALAAAKAFPGLKGMDLAKEVTTDKAYPWRKGSWRLVGG 184 Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240 LPE + L + VVAYD+G K+NILRMLVDRGC +T+VPA+TSA DVL MNPDG+FLSN Sbjct: 185 LPEDTPAEALKYKVVAYDYGVKQNILRMLVDRGCDVTVVPAKTSAADVLAMNPDGVFLSN 244 Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300 GPGDP PCDYAI AIQ+ L+TD P+FGICLGHQLLALASGAKT+KMKFGHHG NHPV ++ Sbjct: 245 GPGDPEPCDYAIEAIQQILKTDTPIFGICLGHQLLALASGAKTLKMKFGHHGANHPVSNI 304 Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360 EK VMIT+QNHGFA DEATLPAN++VTHKSLFDG+LQGIH TDKPAFSFQGHPEASPGP Sbjct: 305 EKGNVMITSQNHGFAADEATLPANIKVTHKSLFDGSLQGIHLTDKPAFSFQGHPEASPGP 364 Query: 361 HDAAPLFDHFIELIEQYRKTAK 382 +DAAPLFDHFIELIEQYR+ AK Sbjct: 365 NDAAPLFDHFIELIEQYRQNAK 386 Lambda K H 0.318 0.135 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: 551 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: 382 Length of database: 386 Length adjustment: 30 Effective length of query: 352 Effective length of database: 356 Effective search space: 125312 Effective search space used: 125312 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: 50 (23.9 bits)
Align candidate 7023737 Shewana3_0967 (carbamoyl phosphate synthase small subunit (RefSeq))
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))
# 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/TIGR01368.hmm # target sequence database: /tmp/gapView.28663.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01368 [M=361] Accession: TIGR01368 Description: CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-152 491.6 0.0 7.1e-152 491.5 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7023737 Shewana3_0967 carbamoyl phosphat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023737 Shewana3_0967 carbamoyl phosphate synthase small subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 491.5 0.0 7.1e-152 7.1e-152 1 360 [. 9 379 .. 9 380 .. 0.96 Alignments for each domain: == domain 1 score: 491.5 bits; conditional E-value: 7.1e-152 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglv 77 a lvledGtvf+g+++ga++ vGevvFnTsmtGYqEiltDpsY++qiv+ltyp+ign+g+n+ed+es+ +++ gl+ lcl|FitnessBrowser__ANA3:7023737 9 ALLVLEDGTVFTGTAIGADGLSVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNTGTNNEDVESNGVHACGLI 85 579************************************************************************** PP TIGR01368 78 vkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistek.sekeelvekakespkvkevnl 153 +++l +s++r++++L+++lk +++v+i+++DTR+l++ lRekg+++++i++ + ++ ++ ++ak+ p +k+++l lcl|FitnessBrowser__ANA3:7023737 86 IRDLPLVASSFRNQQTLSDYLKANNVVGIADIDTRKLTRILREKGAQAGCIMAGAdLDEAKALAAAKAFPGLKGMDL 162 ***************************************************987615677888999*********** PP TIGR01368 154 vkevstkeayeleq...........kakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdg 219 +kev+t++ay +++ ++ +e k++vv++d+GvK+nilr+Lv+rg++vtvvpa+tsa+++ ++npdg lcl|FitnessBrowser__ANA3:7023737 163 AKEVTTDKAYPWRKgswrlvgglpeDTPAEALKYKVVAYDYGVKQNILRMLVDRGCDVTVVPAKTSAADVLAMNPDG 239 *************9877776665533556666699****************************************** PP TIGR01368 220 illsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNH 296 ++lsnGPGdP+ +++aie ++++l++++PifGIclGhqllala+gakt+k+kfGh+GaNhpv ++++g+v+itsqNH lcl|FitnessBrowser__ANA3:7023737 240 VFLSNGPGDPEPCDYAIEAIQQILKTDTPIFGICLGHQLLALASGAKTLKMKFGHHGANHPVSNIEKGNVMITSQNH 316 ***************************************************************************** PP TIGR01368 297 gyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 g+a de++l+++ ++vth++l+Dg+++g++ +++p+fs Q HPeaspGp+d++ lFd+f+eli+ lcl|FitnessBrowser__ANA3:7023737 317 GFAADEATLPAN-IKVTHKSLFDGSLQGIHLTDKPAFSFQGHPEASPGPNDAAPLFDHFIELIE 379 ********8866.************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (386 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.52 // [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