Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_092483171.1 BM299_RS08950 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit
Query= SwissProt::P25993 (364 letters) >NCBI__GCF_900115975.1:WP_092483171.1 Length = 359 Score = 402 bits (1033), Expect = e-117 Identities = 186/354 (52%), Positives = 259/354 (73%), Gaps = 4/354 (1%) Query: 1 MKRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGN 60 MK L LE+G +F G +FG+ GEVVFNTGMTGYQEIL+DPSYCGQIV +TYPLIGN Sbjct: 1 MKAVLALEDGTLFTGRSFGATGEQWGEVVFNTGMTGYQEILTDPSYCGQIVVMTYPLIGN 60 Query: 61 YGINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMI 120 YGINR+DFE+ FV+G ++++ C+ PSNWR+ Y + +YL + IPG+ G+DTR LTR + Sbjct: 61 YGINREDFEAEKSFVRGFVVRQACDHPSNWRAGYRISDYLAREGIPGISGVDTRALTRHL 120 Query: 121 RTAGALKGTFASSDEDIEAVLKRLNETELPRNQ--VSQVSAKTAYPSPGRGKRIVLVDFG 178 R+ G ++G A+ + D + ++++ + Q V++V+ Y G G R+VL+D G Sbjct: 121 RSYGTMRGVIAAGEVDTDELVEKARTSPHLSGQQLVAEVAVTEPYTIEGSGPRVVLIDLG 180 Query: 179 MKHGILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGDPKDVPEAIEMIKGVLG 238 K I+R L R C VIVVP T E++ L PDG++LSNGPGDP DVP +E + ++G Sbjct: 181 AKQNIVRRLLDRGCTVIVVPPASTPEQIGALAPDGVLLSNGPGDPVDVPGTVETTRALVG 240 Query: 239 KVPLFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKVALTSQNHGYTV--SSI 296 + PLFGICLGHQ+ +LA GA T KMKFGHRG+NHPVK+L +G+V +TSQNHG+ V S+ Sbjct: 241 RYPLFGICLGHQVLSLALGAKTYKMKFGHRGANHPVKDLHSGRVYITSQNHGFAVDAGSL 300 Query: 297 SKTELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHLFDRFIEMI 350 + ++ V+HI +ND+T+EG++HK LP F VQYHPEASPGP D++++FD+F++M+ Sbjct: 301 AGLDVAVSHINLNDNTVEGIRHKQLPLFAVQYHPEASPGPHDSDYIFDQFMDMM 354 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: 397 Number of extensions: 12 Number of successful extensions: 3 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: 359 Length adjustment: 29 Effective length of query: 335 Effective length of database: 330 Effective search space: 110550 Effective search space used: 110550 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_092483171.1 BM299_RS08950 (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.4025882.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-159 514.6 0.0 7.5e-159 514.4 0.0 1.0 1 NCBI__GCF_900115975.1:WP_092483171.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900115975.1:WP_092483171.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 514.4 0.0 7.5e-159 7.5e-159 1 360 [. 3 355 .. 3 356 .. 0.99 Alignments for each domain: == domain 1 score: 514.4 bits; conditional E-value: 7.5e-159 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikv 73 a+l+ledGt f+g+sfga++e+ GevvFnT+mtGYqEiltDpsY gqivv+typlignyg+n+ed+e++k v NCBI__GCF_900115975.1:WP_092483171.1 3 AVLALEDGTLFTGRSFGATGEQWGEVVFNTGMTGYQEILTDPSYCGQIVVMTYPLIGNYGINREDFEAEKSFV 75 689********************************************************************** PP TIGR01368 74 kglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakesp 146 +g+vv+++++++sn+ra ++++l++egi++i gvDTRal+++lR+ g+m++vi++ +++++elveka++sp NCBI__GCF_900115975.1:WP_092483171.1 76 RGFVVRQACDHPSNWRAGYRISDYLAREGIPGISGVDTRALTRHLRSYGTMRGVIAAGEVDTDELVEKARTSP 148 ************************************************************************* PP TIGR01368 147 kvkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdg 219 ++++++lv+ev+++e+y++e +g rvv+idlG K+ni+r+L++rg++v+vvp ++ e+i +l pdg NCBI__GCF_900115975.1:WP_092483171.1 149 HLSGQQLVAEVAVTEPYTIEG----SGP--RVVLIDLGAKQNIVRRLLDRGCTVIVVPPASTPEQIGALAPDG 215 *****************9994....455..5****************************************** PP TIGR01368 220 illsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveit 292 +llsnGPGdP +v ++et+++l++ ++P+fGIclGhq+l+lalgaktyk+kfGhrGaNhpvkdl++grv+it NCBI__GCF_900115975.1:WP_092483171.1 216 VLLSNGPGDPVDVPGTVETTRALVG-RYPLFGICLGHQVLSLALGAKTYKMKFGHRGANHPVKDLHSGRVYIT 287 *************************.*********************************************** PP TIGR01368 293 sqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360 sqNHg+avd sl ++ v h nlnD+tveg++hk+lp+f+vQyHPeaspGphd++y+Fd+f+++++ NCBI__GCF_900115975.1:WP_092483171.1 288 SQNHGFAVDAGSLAGLDVAVSHINLNDNTVEGIRHKQLPLFAVQYHPEASPGPHDSDYIFDQFMDMMR 355 *****************************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (359 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: 28.31 // [ok]
This GapMind analysis is from Jul 25 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