Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate 200321 SO1141 carbamoyl-phosphate synthase, small subunit (NCBI ptt file)
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__MR1:200321 Length = 386 Score = 597 bits (1540), Expect = e-175 Identities = 291/382 (76%), Positives = 328/382 (85%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 + KSALLVLEDGT F G AIGA G +VGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI Sbjct: 5 LTKSALLVLEDGTVFTGTAIGADGLSVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 64 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GN GTN+ D ES+ VHA GL+IRDLPLIAS+FRN ++LS YLK +N+V IADIDTRKLTR Sbjct: 65 GNTGTNNEDVESNGVHACGLIIRDLPLIASSFRNQQNLSDYLKANNVVGIADIDTRKLTR 124 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LREKGAQ GCI+AG + D AL A+AFPGL GMDLAKEVTT +AY W +GSW L GG Sbjct: 125 ILREKGAQAGCIMAGADLDEVKALAAAKAFPGLKGMDLAKEVTTDKAYPWRKGSWRLVGG 184 Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240 LP + L + VVAYD+G K+NILRMLVDRGC +T+VPA+T A +VL MNPDG+FLSN Sbjct: 185 LPADTPAEALKYKVVAYDYGVKQNILRMLVDRGCDVTVVPAKTPASEVLAMNPDGVFLSN 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 +DAAPLFDHFIELIE YR+ AK Sbjct: 365 NDAAPLFDHFIELIEHYRQNAK 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: 554 Number of extensions: 13 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 200321 SO1141 (carbamoyl-phosphate synthase, small subunit (NCBI ptt file))
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.1108.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-151 489.8 0.0 2.6e-151 489.6 0.0 1.0 1 lcl|FitnessBrowser__MR1:200321 SO1141 carbamoyl-phosphate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200321 SO1141 carbamoyl-phosphate synthase, small subunit (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 489.6 0.0 2.6e-151 2.6e-151 1 360 [. 9 379 .. 9 380 .. 0.96 Alignments for each domain: == domain 1 score: 489.6 bits; conditional E-value: 2.6e-151 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkglvvk 79 a lvledGtvf+g+++ga++ vGevvFnTsmtGYqEiltDpsY++qiv+ltyp+ign+g+n+ed+es+ +++ gl+++ lcl|FitnessBrowser__MR1:200321 9 ALLVLEDGTVFTGTAIGADGLSVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNTGTNNEDVESNGVHACGLIIR 87 579**************************************************************************** PP TIGR01368 80 elskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteks.ekeelvekakespkvkevnlvkev 157 +l +s++r++++L+++lk +++v+i+++DTR+l++ lRekg+++++i++ + ++ ++ ++ak+ p +k+++l+kev lcl|FitnessBrowser__MR1:200321 88 DLPLIASSFRNQQNLSDYLKANNVVGIADIDTRKLTRILREKGAQAGCIMAGADlDEVKALAAAKAFPGLKGMDLAKEV 166 *************************************************9876515667888999************** PP TIGR01368 158 stkeayeleq...........kakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgillsnG 225 +t++ay +++ ++ +e k++vv++d+GvK+nilr+Lv+rg++vtvvpa+t+a+e+ ++npdg++lsnG lcl|FitnessBrowser__MR1:200321 167 TTDKAYPWRKgswrlvgglpaDTPAEALKYKVVAYDYGVKQNILRMLVDRGCDVTVVPAKTPASEVLAMNPDGVFLSNG 245 *********9877766655533566666799************************************************ PP TIGR01368 226 PGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdees 304 PGdP+ +++aie ++++l++++PifGIclGhqllala+gakt+k+kfGh+GaNhpv ++++g+v+itsqNHg+a de++ lcl|FitnessBrowser__MR1:200321 246 PGDPEPCDYAIEAIQQILKTDTPIFGICLGHQLLALASGAKTLKMKFGHHGANHPVSNIEKGNVMITSQNHGFAADEAT 324 ******************************************************************************* PP TIGR01368 305 lkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 l+++ ++vth++l+Dg+++g++ +++p+fs Q HPeaspGp+d++ lFd+f+eli+ lcl|FitnessBrowser__MR1:200321 325 LPAN-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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.33 // [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