Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_012172161.1 AZC_RS18745 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_000010525.1:WP_012172161.1 Length = 401 Score = 380 bits (977), Expect = e-110 Identities = 198/387 (51%), Positives = 255/387 (65%), Gaps = 14/387 (3%) Query: 4 SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63 +ALLVL DGT G GA VGEV FNT++TGY+EILTDPSY+ QI+T T+PHIGNV Sbjct: 20 TALLVLADGTVLEGFGFGAATEGVGEVCFNTAITGYEEILTDPSYAGQIITFTFPHIGNV 79 Query: 64 GTNDADEESSQVHA----QGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLT 119 GTN+ D E+ A +G+V+R SN+R T L ++LK +I AI+ IDTR LT Sbjct: 80 GTNEEDIETVSAAAVSGVRGVVVRGSVTDPSNYRATRHLDAWLKARDIPAISGIDTRALT 139 Query: 120 RLLREKGAQNGCIIAGDNPDAALALE----KARAFPGLNGMDLAKEVTTAEAYSWTQGSW 175 L+RE G N + NP +E KA+ +PGL GMDL VT+ + ++W + W Sbjct: 140 ALIREGGMPNA--VLAHNPAGVFDIEALKAKAKEWPGLVGMDLVPGVTSVQRFNWDETEW 197 Query: 176 TLTGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDG 235 GG + +HVVA D+G KRNILR+L GC++T+VPA TSA DVL + PDG Sbjct: 198 QWNGGYGH---QGAPKYHVVAIDYGVKRNILRLLATAGCKVTVVPATTSAADVLALQPDG 254 Query: 236 IFLSNGPGDPAPC-DYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGN 294 +FLSNGPGDPA +YA+ I++ + +IP FGICLGHQ++ LA G +T+KM GHHG N Sbjct: 255 VFLSNGPGDPAATGEYAVPVIRELIAKEIPTFGICLGHQMIGLAVGGRTLKMHQGHHGAN 314 Query: 295 HPVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHP 354 HPVKD+ V IT+ NHGFAVD +LPAN + TH SLFDG+ GI DKP FS Q HP Sbjct: 315 HPVKDLTTGKVEITSMNHGFAVDRDSLPANAQETHVSLFDGSNAGIALADKPVFSVQYHP 374 Query: 355 EASPGPHDAAPLFDHFIELIEQYRKTA 381 EASPGP D+ LF F+EL+ +++ A Sbjct: 375 EASPGPRDSHYLFTRFVELMAKHKTAA 401 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: 498 Number of extensions: 26 Number of successful extensions: 5 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: 401 Length adjustment: 31 Effective length of query: 351 Effective length of database: 370 Effective search space: 129870 Effective search space used: 129870 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_012172161.1 AZC_RS18745 (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.1046.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-137 444.6 0.0 1.4e-137 444.4 0.0 1.0 1 lcl|NCBI__GCF_000010525.1:WP_012172161.1 AZC_RS18745 carbamoyl-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_012172161.1 AZC_RS18745 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 444.4 0.0 1.4e-137 1.4e-137 1 360 [. 21 395 .. 21 396 .. 0.94 Alignments for each domain: == domain 1 score: 444.4 bits; conditional E-value: 1.4e-137 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a lvl+dGtv+eg +fga +e vGev+FnT++tGY+EiltDpsY+gqi+++t p+ign+g+need+e lcl|NCBI__GCF_000010525.1:WP_012172161.1 21 ALLVLADGTVLEGFGFGAATEGVGEVCFNTAITGYEEILTDPSYAGQIITFTFPHIGNVGTNEEDIETV 89 579***************************************************************865 PP TIGR01368 70 ....kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse 134 v+g+vv+ +++snyra++ L+++lk ++i+ai g+DTRal+ +Re g +av++++ lcl|NCBI__GCF_000010525.1:WP_012172161.1 90 saaaVSGVRGVVVRGSVTDPSNYRATRHLDAWLKARDIPAISGIDTRALTALIREGGMPNAVLAHNPAG 158 222244689********************************************************9976 PP TIGR01368 135 ...keelvekakespkvkevnlvkevstkeayeleq...k.....akkegkklrvvvidlGvKenilre 192 e l++kake p + +++lv v+ ++ ++ + + ++ k++vv+id+GvK+nilr lcl|NCBI__GCF_000010525.1:WP_012172161.1 159 vfdIEALKAKAKEWPGLVGMDLVPGVTSVQRFNWDEtewQwnggyGHQGAPKYHVVAIDYGVKRNILRL 227 6668999999************************9966515566445556669**************** PP TIGR01368 193 LvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqlla 260 L++ g++vtvvpa+tsa+++ +l+pdg++lsnGPGdPaa e+a+ +++l+ ++iP+fGIclGhq+++ lcl|NCBI__GCF_000010525.1:WP_012172161.1 228 LATAGCKVTVVPATTSAADVLALQPDGVFLSNGPGDPAATgEYAVPVIRELIAKEIPTFGICLGHQMIG 296 *************************************8763778999********************** PP TIGR01368 261 lalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehke 329 la+g++t+k++ Gh+GaNhpvkdl+tg+veits NHg+avd++sl+++ ++ thv+l+Dg+++g++ + lcl|NCBI__GCF_000010525.1:WP_012172161.1 297 LAVGGRTLKMHQGHHGANHPVKDLTTGKVEITSMNHGFAVDRDSLPAN-AQETHVSLFDGSNAGIALAD 364 ********************************************9866.99****************** PP TIGR01368 330 lpvfsvQyHPeaspGphdteylFdefvelik 360 +pvfsvQyHPeaspGp+d++ylF +fvel++ lcl|NCBI__GCF_000010525.1:WP_012172161.1 365 KPVFSVQYHPEASPGPRDSHYLFTRFVELMA 395 ****************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (401 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.29 // [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