Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate PfGW456L13_5100 Carbamoyl-phosphate synthase small chain (EC 6.3.5.5)
Query= SwissProt::P0A6F1 (382 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5100 Length = 378 Score = 543 bits (1398), Expect = e-159 Identities = 265/371 (71%), Positives = 302/371 (81%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 + K A+L L DG+ F G AIGA G VGEVVFNT+MTGYQEILTDPSY++QIVTLTYPHI Sbjct: 1 LTKPAILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHI 60 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GN GT D ES++V + GLVIRDLPL+ASN+RNT LS YLK +N+VAIA IDTR+LTR Sbjct: 61 GNTGTTPEDAESNRVWSAGLVIRDLPLVASNWRNTMSLSDYLKANNVVAIAGIDTRRLTR 120 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LREKGAQNGCI+AGDN A A+ A+ FPGL GMDLAK V+T E+Y W W L Sbjct: 121 ILREKGAQNGCIMAGDNISEAAAIAAAQGFPGLKGMDLAKVVSTKESYEWRSTVWDLKTD 180 Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240 + ELP+HVVAYD+G K NILRMLV+RGCR+T+VPAQT A DVL + PDG+FLSN Sbjct: 181 SHATIEASELPYHVVAYDYGVKVNILRMLVERGCRVTVVPAQTPAADVLALKPDGVFLSN 240 Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300 GPGDP PCDYAI AI+ LET+IPVFGICLGHQLLALASGAKT+KM GHHG NHPV+D+ Sbjct: 241 GPGDPEPCDYAIQAIKDVLETEIPVFGICLGHQLLALASGAKTLKMGHGHHGANHPVQDL 300 Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360 + VVMIT+QNHGFAVDEATLPAN+R HKSLFDGTLQGI RTDK AFSFQGHPEASPGP Sbjct: 301 DSGVVMITSQNHGFAVDEATLPANVRAIHKSLFDGTLQGIERTDKSAFSFQGHPEASPGP 360 Query: 361 HDAAPLFDHFI 371 +D APLFD FI Sbjct: 361 NDVAPLFDRFI 371 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: 510 Number of extensions: 8 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: 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 PfGW456L13_5100 (Carbamoyl-phosphate synthase small chain (EC 6.3.5.5))
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.9206.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-147 476.8 0.0 2.4e-147 476.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5100 Carbamoyl-phosphate synthase sma Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5100 Carbamoyl-phosphate synthase small chain (EC 6.3.5.5) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 476.6 0.0 2.4e-147 2.4e-147 1 360 [. 5 375 .. 5 376 .. 0.95 Alignments for each domain: == domain 1 score: 476.6 bits; conditional E-value: 2.4e-147 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltypl 55 a+l+l+dG++f+g+++ga++++vGevvFnT+mtGYqEiltDpsY++qiv+ltyp+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5100 5 AILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPH 59 689**************************************************** PP TIGR01368 56 ignygvneedaeskkikvkglvvkelskevsnyrakesLeeflkeegivaiegvD 110 ign+g+++edaes++++ +glv+++l +sn+r++ sL+++lk +++vai+g+D lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5100 60 IGNTGTTPEDAESNRVWSAGLVIRDLPLVASNWRNTMSLSDYLKANNVVAIAGID 114 ******************************************************* PP TIGR01368 111 TRalvkklRekgsmkavistekse.keelvekakespkvkevnlvkevstkeaye 164 TR l++ lRekg+++++i++ ++ + ++++a+ p +k+++l+k vstke ye lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5100 115 TRRLTRILREKGAQNGCIMAGDNIsEAAAIAAAQGFPGLKGMDLAKVVSTKESYE 169 ******************998765266677888999******************* PP TIGR01368 165 leq.........k..akkegkklrvvvidlGvKenilreLvkrgvevtvvpadts 208 +++ + +++++ ++vv++d+GvK nilr+Lv+rg++vtvvpa+t+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5100 170 WRStvwdlktdsHatIEASELPYHVVAYDYGVKVNILRMLVERGCRVTVVPAQTP 224 **977777655414345555559******************************** PP TIGR01368 209 aeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalal 263 a+++ +l+pdg++lsnGPGdP+ +++ai+ +k +le++iP+fGIclGhqllala+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5100 225 AADVLALKPDGVFLSNGPGDPEPCDYAIQAIKDVLETEIPVFGICLGHQLLALAS 279 ******************************************************* PP TIGR01368 264 gaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnln 318 gakt+k+ Gh+GaNhpv+dl++g v+itsqNHg+avde++l+++ +++ h++l+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5100 280 GAKTLKMGHGHHGANHPVQDLDSGVVMITSQNHGFAVDEATLPAN-VRAIHKSLF 333 *****************************************8866.********* PP TIGR01368 319 DgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 Dgt++g+e++++ +fs Q HPeaspGp+d + lFd+f+++++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5100 334 DGTLQGIERTDKSAFSFQGHPEASPGPNDVAPLFDRFITEMA 375 **************************************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: 10.27 // [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