Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_074200862.1 BUQ81_RS02830 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_900141795.1:WP_074200862.1 Length = 381 Score = 546 bits (1407), Expect = e-160 Identities = 272/372 (73%), Positives = 305/372 (81%), Gaps = 2/372 (0%) Query: 4 SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63 +A+L LEDGT F G++IGA G VGEVVFNTSMTGYQEILTDPSY RQIVTLTYPHIGNV Sbjct: 6 TAILALEDGTVFWGQSIGAEGETVGEVVFNTSMTGYQEILTDPSYFRQIVTLTYPHIGNV 65 Query: 64 GTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLR 123 G N DEES ++ AQGLVIRDLP + SNFR DL SYL++ N+VAIADIDTRKLTR+LR Sbjct: 66 GVNHEDEESPRIMAQGLVIRDLPPLHSNFRAQSDLQSYLRQQNVVAIADIDTRKLTRILR 125 Query: 124 EKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPE 183 EKGAQNG I AGDN D A+ +A+AF GL GMDLA+EVTT E Y WT+G+W L G Sbjct: 126 EKGAQNGVIQAGDNLDPDGAIAQAKAFAGLKGMDLAQEVTTPETYVWTEGTWRLGEG--H 183 Query: 184 AKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPG 243 + E +HVVAYDFG KRNILRML DRGC+LT+VPA+T AEDVL MNPDGIFLSNGPG Sbjct: 184 VDRSAEAKYHVVAYDFGVKRNILRMLADRGCKLTVVPAKTPAEDVLAMNPDGIFLSNGPG 243 Query: 244 DPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKN 303 DP PCDYAI AIQ L+TDIPVFGICLGHQLLALA+GA+TVKMKFGHHG NHPV+D++ Sbjct: 244 DPEPCDYAIEAIQTILKTDIPVFGICLGHQLLALAAGARTVKMKFGHHGANHPVQDLDSG 303 Query: 304 VVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDA 363 V IT+QNHGFAVDEA+LP N+ VTHKSLFDG+LQGI D+ AFSFQGHPEASPGPHD Sbjct: 304 RVYITSQNHGFAVDEASLPDNVDVTHKSLFDGSLQGIRLKDRAAFSFQGHPEASPGPHDV 363 Query: 364 APLFDHFIELIE 375 A LFD FI IE Sbjct: 364 AYLFDQFIADIE 375 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: 500 Number of extensions: 17 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: 381 Length adjustment: 30 Effective length of query: 352 Effective length of database: 351 Effective search space: 123552 Effective search space used: 123552 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 WP_074200862.1 BUQ81_RS02830 (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.1464.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-155 501.0 0.0 1e-154 500.8 0.0 1.0 1 lcl|NCBI__GCF_900141795.1:WP_074200862.1 BUQ81_RS02830 carbamoyl-phosphat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900141795.1:WP_074200862.1 BUQ81_RS02830 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 500.8 0.0 1e-154 1e-154 1 360 [. 7 375 .. 7 376 .. 0.96 Alignments for each domain: == domain 1 score: 500.8 bits; conditional E-value: 1e-154 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a+l+ledGtvf g+s+gae+e+vGevvFnTsmtGYqEiltDpsY +qiv+ltyp+ign+gvn+ed+es lcl|NCBI__GCF_900141795.1:WP_074200862.1 7 AILALEDGTVFWGQSIGAEGETVGEVVFNTSMTGYQEILTDPSYFRQIVTLTYPHIGNVGVNHEDEESP 75 689****************************************************************** PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse.kee 137 +i ++glv+++l sn+ra+++L+++l+++++vai+++DTR+l++ lRekg++++vi++ ++ + lcl|NCBI__GCF_900141795.1:WP_074200862.1 76 RIMAQGLVIRDLPPLHSNFRAQSDLQSYLRQQNVVAIADIDTRKLTRILREKGAQNGVIQAGDNLdPDG 144 ***********************************************************9987543788 PP TIGR01368 138 lvekakespkvkevnlvkevstkeayeleq........k.akkegkklrvvvidlGvKenilreLvkrg 197 ++++ak+ + +k+++l++ev+t e+y +++ + ++ + k++vv++d+GvK+nilr+L++rg lcl|NCBI__GCF_900141795.1:WP_074200862.1 145 AIAQAKAFAGLKGMDLAQEVTTPETYVWTEgtwrlgegHvDRSAEAKYHVVAYDFGVKRNILRMLADRG 213 9999*************************9877766552566667779********************* PP TIGR01368 198 vevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgak 266 +++tvvpa+t+ae++ ++npdgi+lsnGPGdP+ +++aie ++++l+++iP+fGIclGhqllala+ga+ lcl|NCBI__GCF_900141795.1:WP_074200862.1 214 CKLTVVPAKTPAEDVLAMNPDGIFLSNGPGDPEPCDYAIEAIQTILKTDIPVFGICLGHQLLALAAGAR 282 ********************************************************************* PP TIGR01368 267 tyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsv 335 t+k+kfGh+GaNhpv+dl++grv+itsqNHg+avde+sl+ ++++vth++l+Dg+++g++ k+ ++fs lcl|NCBI__GCF_900141795.1:WP_074200862.1 283 TVKMKFGHHGANHPVQDLDSGRVYITSQNHGFAVDEASLP-DNVDVTHKSLFDGSLQGIRLKDRAAFSF 350 **************************************87.66************************** PP TIGR01368 336 QyHPeaspGphdteylFdefvelik 360 Q HPeaspGphd +ylFd+f+ i+ lcl|NCBI__GCF_900141795.1:WP_074200862.1 351 QGHPEASPGPHDVAYLFDQFIADIE 375 *********************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (381 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.65 // [ok]
This GapMind analysis is from Apr 10 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