Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_011736386.1 PPRO_RS12485 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_000015045.1:WP_011736386.1 Length = 373 Score = 367 bits (941), Expect = e-106 Identities = 196/374 (52%), Positives = 244/374 (65%), Gaps = 3/374 (0%) Query: 5 ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64 ALL L DG F G++ GA G A GEVVFNT+MTGYQE+LTDPSY Q+VT+TY IGN G Sbjct: 3 ALLALADGRIFEGKSFGAGGEARGEVVFNTAMTGYQEVLTDPSYKGQMVTMTYTQIGNTG 62 Query: 65 TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124 N D ES + G ++R+ SN+R L SYLK + ++ I IDTR LTR LR+ Sbjct: 63 INAEDIESRGLFLSGFIVREYQECYSNWRACMSLDSYLKENGVIGIQGIDTRALTRHLRD 122 Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184 KGAQNG II+ + D + KARA P + G+DLA V+ + Y WT+G W L G P+ Sbjct: 123 KGAQNG-IISTIDLDRESLVAKARAIPSMAGLDLATGVSCDKPYHWTEGLWDLKDGYPQV 181 Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244 L + VVAYDFG K NILR LVD GC +T+VPA AE+ L MNPDG+FLSNGPGD Sbjct: 182 DPV-TLKYKVVAYDFGIKYNILRCLVDAGCDVTVVPASFPAEEALAMNPDGVFLSNGPGD 240 Query: 245 PAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNV 304 P P I+K + P+FGICLGHQLL LA G KT+K+ FG+HG N PV D+ Sbjct: 241 PEPLVAVQEEIRKMIGRK-PIFGICLGHQLLGLALGGKTMKLPFGNHGSNLPVMDMATRK 299 Query: 305 VMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDAA 364 V IT+QNHGFAVD +L + H++L D T++GI P FS Q HPEASPGPHD+ Sbjct: 300 VEITSQNHGFAVDLDSLGDAACLGHENLNDQTVEGISHCTLPIFSVQHHPEASPGPHDSH 359 Query: 365 PLFDHFIELIEQYR 378 LF F+E++E+ R Sbjct: 360 YLFGRFVEMMERNR 373 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: 433 Number of extensions: 12 Number of successful extensions: 4 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: 373 Length adjustment: 30 Effective length of query: 352 Effective length of database: 343 Effective search space: 120736 Effective search space used: 120736 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_011736386.1 PPRO_RS12485 (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.3173.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-151 489.9 0.0 2.4e-151 489.7 0.0 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011736386.1 PPRO_RS12485 carbamoyl-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011736386.1 PPRO_RS12485 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 489.7 0.0 2.4e-151 2.4e-151 1 360 [. 3 370 .. 3 371 .. 0.97 Alignments for each domain: == domain 1 score: 489.7 bits; conditional E-value: 2.4e-151 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a l+l+dG++fegksfga +e+ GevvFnT+mtGYqE+ltDpsYkgq+v++ty++ign+g+n+ed+es+ lcl|NCBI__GCF_000015045.1:WP_011736386.1 3 ALLALADGRIFEGKSFGAGGEARGEVVFNTAMTGYQEVLTDPSYKGQMVTMTYTQIGNTGINAEDIESR 71 579****************************************************************** PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138 ++g++v+e+++ +sn+ra sL+++lke+g+++i+g+DTRal+++lR+kg+++++ist + ++e+l lcl|NCBI__GCF_000015045.1:WP_011736386.1 72 GLFLSGFIVREYQECYSNWRACMSLDSYLKENGVIGIQGIDTRALTRHLRDKGAQNGIISTIDLDRESL 140 ********************************************************************* PP TIGR01368 139 vekakespkvkevnlvkevstkeayeleq..........kakkegkklrvvvidlGvKenilreLvkrg 197 v+ka++ p++++++l++ vs++++y++++ + + k++vv++d+G+K nilr+Lv+ g lcl|NCBI__GCF_000015045.1:WP_011736386.1 141 VAKARAIPSMAGLDLATGVSCDKPYHWTEglwdlkdgypQVDPVTLKYKVVAYDFGIKYNILRCLVDAG 209 ****************************988877655543555666699******************** PP TIGR01368 198 vevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgak 266 ++vtvvpa+++aee ++npdg++lsnGPGdP+ + ++ e+++k+++ ++PifGIclGhqll+lalg+k lcl|NCBI__GCF_000015045.1:WP_011736386.1 210 CDVTVVPASFPAEEALAMNPDGVFLSNGPGDPEPLVAVQEEIRKMIG-RKPIFGICLGHQLLGLALGGK 277 ***********************************************.********************* PP TIGR01368 267 tyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsv 335 t+kl fG++G+N pv+d++t +veitsqNHg+avd +sl +++ h nlnD+tveg++h +lp+fsv lcl|NCBI__GCF_000015045.1:WP_011736386.1 278 TMKLPFGNHGSNLPVMDMATRKVEITSQNHGFAVDLDSLG-DAACLGHENLNDQTVEGISHCTLPIFSV 345 **************************************66.66999*********************** PP TIGR01368 336 QyHPeaspGphdteylFdefvelik 360 Q+HPeaspGphd++ylF +fve+++ lcl|NCBI__GCF_000015045.1:WP_011736386.1 346 QHHPEASPGPHDSHYLFGRFVEMME 370 **********************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (373 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.20 // [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