Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate PP_4724 PP_4724 Carbamoyl-phosphate synthase small chain
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__Putida:PP_4724 Length = 378 Score = 539 bits (1389), Expect = e-158 Identities = 264/378 (69%), Positives = 301/378 (79%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 M K A+L L DG+ F G AIGA G VGEVVFNT+MTGYQEILTDPSY++QIVTLTYPHI Sbjct: 1 MTKPAILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHI 60 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GN GT D ESS+V + GLVIRDLPL+ASN+RNT+ L YLK +N+VAIA IDTR+LTR Sbjct: 61 GNTGTTPEDAESSRVWSAGLVIRDLPLLASNWRNTQSLPEYLKANNVVAIAGIDTRRLTR 120 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LREKGAQNGCI+AGDN A+ AR FPGL GMDLAK V+T E Y W W L Sbjct: 121 ILREKGAQNGCILAGDNISEEAAIAAARGFPGLKGMDLAKVVSTKERYEWRSSVWELKTD 180 Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240 +LP+HVVA+D+G K NILRMLV RGCR+T+VPAQT A +VL +NPDG+FLSN Sbjct: 181 SHPTIDAADLPYHVVAFDYGVKLNILRMLVARGCRVTVVPAQTPASEVLALNPDGVFLSN 240 Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300 GPGDP PCDYAI AI++ LET+IPVFGICLGHQLLALASGAKTVKM GHHG NHPV+D+ Sbjct: 241 GPGDPEPCDYAIQAIKEILETEIPVFGICLGHQLLALASGAKTVKMGHGHHGANHPVQDL 300 Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360 + VVMIT+QNHGFAVDEATLP N+R HKSLFDGTLQGI RTDK AFSFQGHPEASPGP Sbjct: 301 DTGVVMITSQNHGFAVDEATLPGNVRAIHKSLFDGTLQGIERTDKSAFSFQGHPEASPGP 360 Query: 361 HDAAPLFDHFIELIEQYR 378 D APLFD F + + + R Sbjct: 361 TDVAPLFDRFTDAMAKRR 378 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: 514 Number of extensions: 10 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: 378 Length adjustment: 30 Effective length of query: 352 Effective length of database: 348 Effective search space: 122496 Effective search space used: 122496 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 PP_4724 PP_4724 (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.32029.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-147 474.7 0.0 9.8e-147 474.5 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_4724 PP_4724 Carbamoyl-phosphate synt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4724 PP_4724 Carbamoyl-phosphate synthase small chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 474.5 0.0 9.8e-147 9.8e-147 1 360 [. 5 375 .. 5 376 .. 0.95 Alignments for each domain: == domain 1 score: 474.5 bits; conditional E-value: 9.8e-147 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvkg 75 a+l+l+dG++f+g+++ga++++vGevvFnT+mtGYqEiltDpsY++qiv+ltyp+ign+g+++edaes++++ +g lcl|FitnessBrowser__Putida:PP_4724 5 AILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHIGNTGTTPEDAESSRVWSAG 79 689************************************************************************ PP TIGR01368 76 lvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.keelvekakespkvk 149 lv+++l +sn+r+++sL e+lk +++vai+g+DTR l++ lRekg+++++i + ++ +e ++++a+ p +k lcl|FitnessBrowser__Putida:PP_4724 80 LVIRDLPLLASNWRNTQSLPEYLKANNVVAIAGIDTRRLTRILREKGAQNGCILAGDNIsEEAAIAAARGFPGLK 154 ****************************************************998775427778889999***** PP TIGR01368 150 evnlvkevstkeayeleq.......k....akkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeik 213 +++l+k vstke+ye+++ + + + + ++vv++d+GvK nilr+Lv+rg++vtvvpa+t+a+e+ lcl|FitnessBrowser__Putida:PP_4724 155 GMDLAKVVSTKERYEWRSsvwelktDshptIDAADLPYHVVAFDYGVKLNILRMLVARGCRVTVVPAQTPASEVL 229 *****************977766551555455566669************************************* PP TIGR01368 214 klnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgr 288 +lnpdg++lsnGPGdP+ +++ai+ +k++le++iP+fGIclGhqllala+gakt+k+ Gh+GaNhpv+dl+tg lcl|FitnessBrowser__Putida:PP_4724 230 ALNPDGVFLSNGPGDPEPCDYAIQAIKEILETEIPVFGICLGHQLLALASGAKTVKMGHGHHGANHPVQDLDTGV 304 *************************************************************************** PP TIGR01368 289 veitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 v+itsqNHg+avde++l+ +++++ h++l+Dgt++g+e++++ +fs Q HPeaspGp+d + lFd+f+++++ lcl|FitnessBrowser__Putida:PP_4724 305 VMITSQNHGFAVDEATLP-GNVRAIHKSLFDGTLQGIERTDKSAFSFQGHPEASPGPTDVAPLFDRFTDAMA 375 ***************977.66***********************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (378 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: 12.16 // [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