Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate GFF3136 HP15_3078 carbamoyl-phosphate synthase small chain
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__Marino:GFF3136 Length = 376 Score = 536 bits (1381), Expect = e-157 Identities = 261/375 (69%), Positives = 304/375 (81%), Gaps = 3/375 (0%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 M A+L L DG+ F+G AIGA G GEVVFNT+MTGYQEILTDPSYSRQIVTLTYPHI Sbjct: 1 MSTPAILALADGSLFYGTAIGADGETSGEVVFNTAMTGYQEILTDPSYSRQIVTLTYPHI 60 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GN G N+ D ES ++ A GL+IRDLPL+AS++R+ L YL+ +NIV IADIDTR+LTR Sbjct: 61 GNTGVNEEDVESDRIQAAGLIIRDLPLLASSWRSKGTLDDYLRSNNIVGIADIDTRRLTR 120 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LR+KG+QNG I+AG+N A ALE A+AFPGL GMDLAKEVT+ + +SW + WTL G Sbjct: 121 ILRDKGSQNGAIVAGENATAERALELAKAFPGLKGMDLAKEVTSDKTWSWKETEWTLEEG 180 Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240 E +E F VVA+D+G K NILRML RGC +T+VPAQT A +VL MNPDG+FLSN Sbjct: 181 YGE---REESRFKVVAWDYGVKLNILRMLASRGCDITVVPAQTPASEVLAMNPDGVFLSN 237 Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300 GPGDP PCDYAITAI++ LET+IPVFGICLGHQLLALASGAKT+KM GHHG NHPV+++ Sbjct: 238 GPGDPEPCDYAITAIKEVLETEIPVFGICLGHQLLALASGAKTMKMGHGHHGANHPVQEI 297 Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360 VMIT+QNHGFAVDEATLPAN+ THKSLFDGTLQGI RTDKPA+SFQGHPEASPGP Sbjct: 298 ATGTVMITSQNHGFAVDEATLPANVEATHKSLFDGTLQGIRRTDKPAYSFQGHPEASPGP 357 Query: 361 HDAAPLFDHFIELIE 375 HD APLFD FI L+E Sbjct: 358 HDVAPLFDEFIRLME 372 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: 519 Number of extensions: 9 Number of successful extensions: 2 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: 376 Length adjustment: 30 Effective length of query: 352 Effective length of database: 346 Effective search space: 121792 Effective search space used: 121792 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 GFF3136 HP15_3078 (carbamoyl-phosphate synthase small chain)
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.19547.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-149 483.9 0.0 1.6e-149 483.7 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF3136 HP15_3078 carbamoyl-phosphate sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3136 HP15_3078 carbamoyl-phosphate synthase small chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 483.7 0.0 1.6e-149 1.6e-149 1 360 [. 5 372 .. 5 373 .. 0.96 Alignments for each domain: == domain 1 score: 483.7 bits; conditional E-value: 1.6e-149 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkg 75 a+l+l+dG+ f g+++ga++e+ GevvFnT+mtGYqEiltDpsY++qiv+ltyp+ign+gvneed+es++i+++g lcl|FitnessBrowser__Marino:GFF3136 5 AILALADGSLFYGTAIGADGETSGEVVFNTAMTGYQEILTDPSYSRQIVTLTYPHIGNTGVNEEDVESDRIQAAG 79 689************************************************************************ PP TIGR01368 76 lvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.keelvekakespkvk 149 l++++l +s++r+k +L+++l++++iv+i+++DTR l++ lR+kgs++++i++ +++ +e++ e ak+ p +k lcl|FitnessBrowser__Marino:GFF3136 80 LIIRDLPLLASSWRSKGTLDDYLRSNNIVGIADIDTRRLTRILRDKGSQNGAIVAGENAtAERALELAKAFPGLK 154 ***************************************************99987765378889999******* PP TIGR01368 150 evnlvkevstkeayeleq.....k...akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikkln 216 +++l+kev+ +++ ++++ + ++e+++ +vv+ d+GvK nilr+L++rg+++tvvpa+t+a+e+ ++n lcl|FitnessBrowser__Marino:GFF3136 155 GMDLAKEVTSDKTWSWKEtewtlEegyGEREESRFKVVAWDYGVKLNILRMLASRGCDITVVPAQTPASEVLAMN 229 *****************966655156667888889**************************************** PP TIGR01368 217 pdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrvei 291 pdg++lsnGPGdP+ +++ai+ +k++le++iP+fGIclGhqllala+gakt+k+ Gh+GaNhpv++++tg+v+i lcl|FitnessBrowser__Marino:GFF3136 230 PDGVFLSNGPGDPEPCDYAITAIKEVLETEIPVFGICLGHQLLALASGAKTMKMGHGHHGANHPVQEIATGTVMI 304 *************************************************************************** PP TIGR01368 292 tsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 tsqNHg+avde++l+++ +e+th++l+Dgt++g++++++p++s Q HPeaspGphd + lFdef++l++ lcl|FitnessBrowser__Marino:GFF3136 305 TSQNHGFAVDEATLPAN-VEATHKSLFDGTLQGIRRTDKPAYSFQGHPEASPGPHDVAPLFDEFIRLME 372 *************8866.************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (376 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: 7.63 // [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