Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_010530473.1 ON01_RS07815 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit
Query= SwissProt::P25993 (364 letters) >NCBI__GCF_000224785.1:WP_010530473.1 Length = 364 Score = 451 bits (1159), Expect = e-131 Identities = 216/358 (60%), Positives = 275/358 (76%), Gaps = 3/358 (0%) Query: 2 KRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGNY 61 +R+L+LE+ +F GE FG+ GEVVFNTGMTGYQE+++DPSYCGQ+V +TYPLIGNY Sbjct: 3 ERQLILEDSTIFTGEGFGADISATGEVVFNTGMTGYQEVITDPSYCGQMVVMTYPLIGNY 62 Query: 62 GINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMIR 121 GINRDDFE++TPF+ GLI+KE E PSN+RS TL +YLK IPG+ G+DTRKLT++IR Sbjct: 63 GINRDDFETVTPFIHGLIVKEFSEFPSNFRSDETLHDYLKANGIPGISGLDTRKLTKIIR 122 Query: 122 TAGALKGTFASSDEDIEAVLKRLNETELPRNQVSQVSAKTAYPSPGRGKRIVLVDFGMKH 181 G +K A + E +++ L +QV+Q S Y PGRGKRIVLVDFGMKH Sbjct: 123 KHGTMKAIMADAGMPAEELIESLKGLPDQTDQVNQTSTIKPYVVPGRGKRIVLVDFGMKH 182 Query: 182 GILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGDPKDVPEAIEMIKGVLGKVP 241 ILREL KR C V VVPYN +A ++L+LKPDGIML+NGPGDPK+VPE+IEM++ VLGK+P Sbjct: 183 SILRELTKRDCHVTVVPYNYSAGDILRLKPDGIMLTNGPGDPKNVPESIEMVQTVLGKIP 242 Query: 242 LFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKVALTSQNHGYTVS--SISKT 299 LFGICLGHQLFALACGA+T+KM FGHRG N PVK+ K +TSQNH Y V+ S+ T Sbjct: 243 LFGICLGHQLFALACGADTKKMAFGHRGVNQPVKDTEKNKTFMTSQNHSYAVTHDSLIGT 302 Query: 300 ELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHLFDRFIEMI-ETTEKE 356 +L++ ++ND+++EG++H T PAF+VQYHPE+SPGPED LFD F++MI E +KE Sbjct: 303 DLDLIQFSLNDNSVEGIRHLTYPAFSVQYHPESSPGPEDTPQLFDEFLQMISEFRQKE 360 Lambda K H 0.317 0.136 0.397 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: 441 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: 364 Length of database: 364 Length adjustment: 29 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_010530473.1 ON01_RS07815 (glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit)
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.3341405.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-145 469.4 0.0 4.1e-145 469.2 0.0 1.0 1 NCBI__GCF_000224785.1:WP_010530473.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010530473.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 469.2 0.0 4.1e-145 4.1e-145 2 360 .. 5 354 .. 4 355 .. 0.98 Alignments for each domain: == domain 1 score: 469.2 bits; conditional E-value: 4.1e-145 TIGR01368 2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvk 74 +l+led t+f+g++fga+ +++GevvFnT+mtGYqE++tDpsY gq+vv+typlignyg+n++d+e ++ ++ NCBI__GCF_000224785.1:WP_010530473.1 5 QLILEDSTIFTGEGFGADISATGEVVFNTGMTGYQEVITDPSYCGQMVVMTYPLIGNYGINRDDFETVTPFIH 77 699********************************************************************** PP TIGR01368 75 glvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespk 147 gl+vke+s+ +sn+r+ e+L+++lk +gi++i g+DTR+l+k +R++g+mka+++++ + +eel+e++k p+ NCBI__GCF_000224785.1:WP_010530473.1 78 GLIVKEFSEFPSNFRSDETLHDYLKANGIPGISGLDTRKLTKIIRKHGTMKAIMADAGMPAEELIESLKGLPD 150 *******************************************************************999999 PP TIGR01368 148 vkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgi 220 + + v++ st ++y + +gk r+v++d+G+K++ilreL+kr+++vtvvp+++sa +i +l+pdgi NCBI__GCF_000224785.1:WP_010530473.1 151 QT--DQVNQTSTIKPYVVPG----RGK--RIVLVDFGMKHSILRELTKRDCHVTVVPYNYSAGDILRLKPDGI 215 97..99**********9994....344..6******************************************* PP TIGR01368 221 llsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveits 293 +l+nGPGdP++v e ie+v+++l+ kiP+fGIclGhql+ala ga+t k+ fGhrG N+pvkd+++++ ++ts NCBI__GCF_000224785.1:WP_010530473.1 216 MLTNGPGDPKNVPESIEMVQTVLG-KIPLFGICLGHQLFALACGADTKKMAFGHRGVNQPVKDTEKNKTFMTS 287 ************************.************************************************ PP TIGR01368 294 qNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 qNH+yav ++sl ++l+ + +lnD++veg++h ++p+fsvQyHPe+spGp+dt +lFdef+++i+ NCBI__GCF_000224785.1:WP_010530473.1 288 QNHSYAVTHDSLIGTDLDLIQFSLNDNSVEGIRHLTYPAFSVQYHPESSPGPEDTPQLFDEFLQMIS 354 ****************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (364 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 14.41 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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