Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_106710507.1 CU102_RS07170 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_003010955.1:WP_106710507.1 Length = 407 Score = 353 bits (905), Expect = e-102 Identities = 190/382 (49%), Positives = 246/382 (64%), Gaps = 14/382 (3%) Query: 4 SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63 +A+LVL DGT G+ +GATG EV FNT++TGY+EILTDPSY+ QIVT T+PHIGNV Sbjct: 17 TAVLVLADGTVIEGKGLGATGICEAEVCFNTALTGYEEILTDPSYAGQIVTFTFPHIGNV 76 Query: 64 GTNDADEE----SSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLT 119 GTN D E +++ A G + + S++R E L +LK ++A+A DTR LT Sbjct: 77 GTNKEDIEDLTPANRAGAVGAIFKADITAPSSYRAAEHLDHWLKARGVIALAGADTRALT 136 Query: 120 RLLREKGAQNGCIIAGDNPDAALALE----KARAFPGLNGMDLAKEVTTAEAYSWTQGSW 175 L+REKG N +IA D PD + +A A+ GL +DLAK+VT+ ++ WT+ W Sbjct: 137 VLIREKGMPNA-VIAHD-PDGKFDIPALKARAAAWHGLLDLDLAKDVTSGQSSVWTEKPW 194 Query: 176 TLTGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDG 235 G + + + FHVVA D+G KRNILR++ G ++TI+PA +A DVL PDG Sbjct: 195 VWNEGFDD---QSDPEFHVVAIDYGIKRNILRLIAGLGAKVTILPASATAADVLAYKPDG 251 Query: 236 IFLSNGPGDPAPCD-YAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGN 294 IFLSNGPGDPA YA+ AI++ ++TDIPVFGICLGHQ+LALA G T KM GHHG N Sbjct: 252 IFLSNGPGDPAATGKYAVPAIKELIKTDIPVFGICLGHQMLALALGGDTKKMHQGHHGAN 311 Query: 295 HPVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHP 354 HPV+D V I + NHGFAVD + P + TH SLFDG+ G+ +P FS Q HP Sbjct: 312 HPVRDDTTGKVEIVSMNHGFAVDAGSFPDGVEETHVSLFDGSNCGLRVVGRPVFSVQHHP 371 Query: 355 EASPGPHDAAPLFDHFIELIEQ 376 EASPGP D+ LF F LI + Sbjct: 372 EASPGPQDSHYLFRRFFNLIRE 393 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: 479 Number of extensions: 21 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: 407 Length adjustment: 31 Effective length of query: 351 Effective length of database: 376 Effective search space: 131976 Effective search space used: 131976 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_106710507.1 CU102_RS07170 (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.3348140.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-124 400.1 0.0 4.8e-124 399.9 0.0 1.0 1 NCBI__GCF_003010955.1:WP_106710507.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106710507.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.9 0.0 4.8e-124 4.8e-124 1 360 [. 18 392 .. 18 393 .. 0.93 Alignments for each domain: == domain 1 score: 399.9 bits; conditional E-value: 4.8e-124 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneeda....esk 69 a+lvl+dGtv+egk++ga++ + +ev+FnT++tGY+EiltDpsY+gqiv++t p+ign+g+n+ed+ ++ NCBI__GCF_003010955.1:WP_106710507.1 18 AVLVLADGTVIEGKGLGATGICEAEVCFNTALTGYEEILTDPSYAGQIVTFTFPHIGNVGTNKEDIedltPAN 90 689***************************************************************3333367 PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...keelv 139 + + g + k +++s+yra e L+++lk +g++a++g DTRal+ +Rekg +avi+++ l+ NCBI__GCF_003010955.1:WP_106710507.1 91 RAGAVGAIFKADITAPSSYRAAEHLDHWLKARGVIALAGADTRALTVLIREKGMPNAVIAHDPDGkfdIPALK 163 88999*******************************************************9986544355677 PP TIGR01368 140 ekakespkvkevnlvkevstkeayeleqk........akkegkklrvvvidlGvKenilreLvkrgvevtvvp 204 ++a++ + + +++l+k+v+ + + +++k +++ + +vv+id+G+K+nilr ++ g++vt++p NCBI__GCF_003010955.1:WP_106710507.1 164 ARAAAWHGLLDLDLAKDVTSGQSSVWTEKpwvwnegfDDQSDPEFHVVAIDYGIKRNILRLIAGLGAKVTILP 236 77778888999*************999955556667677788889**************************** PP TIGR01368 205 adtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrG 276 a+++a+++ +++pdgi+lsnGPGdPaa ++a+ +k+l++++iP+fGIclGhq+lalalg++t k++ Gh+G NCBI__GCF_003010955.1:WP_106710507.1 237 ASATAADVLAYKPDGIFLSNGPGDPAATgKYAVPAIKELIKTDIPVFGICLGHQMLALALGGDTKKMHQGHHG 309 *************************776377899*************************************** PP TIGR01368 277 aNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdte 349 aNhpv+d +tg+vei s NHg+avd s + + +e thv+l+Dg++ gl+ pvfsvQ+HPeaspGp+d++ NCBI__GCF_003010955.1:WP_106710507.1 310 ANHPVRDDTTGKVEIVSMNHGFAVDAGSFP-DGVEETHVSLFDGSNCGLRVVGRPVFSVQHHPEASPGPQDSH 381 ****************************77.55**************************************** PP TIGR01368 350 ylFdefvelik 360 ylF++f++li+ NCBI__GCF_003010955.1:WP_106710507.1 382 YLFRRFFNLIR 392 ********997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (407 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 28.30 // [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