Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_018124349.1 B149_RS0106375 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_000375485.1:WP_018124349.1 Length = 374 Score = 337 bits (864), Expect = 3e-97 Identities = 181/378 (47%), Positives = 236/378 (62%), Gaps = 6/378 (1%) Query: 5 ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64 A+L LEDGT FHG + G GEV+FNT MTGYQEILTDPSY+ Q+V +TYP IGN G Sbjct: 3 AILALEDGTIFHGTSFTGEGETGGEVIFNTGMTGYQEILTDPSYNGQLVCMTYPLIGNYG 62 Query: 65 TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124 ND D ES V A GL++++ SN+R T+ L YL+ + + I DIDTR LTR LR Sbjct: 63 VNDVDVESLSVKAAGLIVKECCKTPSNWRATKSLPDYLRENGVTGIEDIDTRALTRHLRL 122 Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184 GA G I D + A+ +A+ P + G++LA V++ ++W G + +A Sbjct: 123 NGAMRGYITTEDISEEE-AVRRAQGQPDMEGLNLADGVSSDRPFAWVDGRPRFFESIDQA 181 Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244 + + P + YDFG K NILR+L D+G L +VP+ A +V + PD IFLSNGPGD Sbjct: 182 EWQGNGP-RLAVYDFGIKFNILRLLADQGFDLLVVPSSARAAEVRNLKPDAIFLSNGPGD 240 Query: 245 PAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNV 304 PA + A+ A + E D PV GICLGHQ+L LA GAK+ K+KFGHHG NHPV D+ Sbjct: 241 PAAVENAVEAARDLTE-DHPVAGICLGHQILGLAMGAKSYKLKFGHHGCNHPVMDLTTRK 299 Query: 305 VMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDAA 364 + I++QNHGF VD A L L THK+L D TL+G +KP + Q HPEA+PGPHD+ Sbjct: 300 IEISSQNHGFCVDIAGLDF-LEPTHKNLNDDTLEGFAHKEKPILAIQYHPEAAPGPHDSR 358 Query: 365 PLFDHFIELIEQYRKTAK 382 F F EL+ + KT K Sbjct: 359 YFFSRFRELVRE--KTGK 374 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: 428 Number of extensions: 15 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: 374 Length adjustment: 30 Effective length of query: 352 Effective length of database: 344 Effective search space: 121088 Effective search space used: 121088 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_018124349.1 B149_RS0106375 (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.16265.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-149 483.2 0.0 2.7e-149 483.0 0.0 1.0 1 lcl|NCBI__GCF_000375485.1:WP_018124349.1 B149_RS0106375 carbamoyl-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000375485.1:WP_018124349.1 B149_RS0106375 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 483.0 0.0 2.7e-149 2.7e-149 1 360 [. 3 369 .. 3 370 .. 0.97 Alignments for each domain: == domain 1 score: 483.0 bits; conditional E-value: 2.7e-149 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a+l+ledGt+f+g+sf e+e+ Gev+FnT+mtGYqEiltDpsY+gq+v +typlignygvn+ d+es lcl|NCBI__GCF_000375485.1:WP_018124349.1 3 AILALEDGTIFHGTSFTGEGETGGEVIFNTGMTGYQEILTDPSYNGQLVCMTYPLIGNYGVNDVDVESL 71 689****************************************************************** PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138 ++k++gl+vke++k++sn+ra++sL ++l+e+g+ +ie++DTRal+++lR +g+m+++i+te++++ee+ lcl|NCBI__GCF_000375485.1:WP_018124349.1 72 SVKAAGLIVKECCKTPSNWRATKSLPDYLRENGVTGIEDIDTRALTRHLRLNGAMRGYITTEDISEEEA 140 ********************************************************************* PP TIGR01368 139 vekakespkvkevnlvkevstkeayeleq..........kakkegkklrvvvidlGvKenilreLvkrg 197 v++a+ +p+++++nl++ vs +++ ++ + +a+ +g+ r++v+d+G+K nilr L+++g lcl|NCBI__GCF_000375485.1:WP_018124349.1 141 VRRAQGQPDMEGLNLADGVSSDRPFAWVDgrprffesidQAEWQGNGPRLAVYDFGIKFNILRLLADQG 209 ****************************988887776654777777789******************** PP TIGR01368 198 vevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgak 266 +++ vvp +++a+e+ +l+pd+i+lsnGPGdPaave+a+e + l+e + P+ GIclGhq+l+la+gak lcl|NCBI__GCF_000375485.1:WP_018124349.1 210 FDLLVVPSSARAAEVRNLKPDAIFLSNGPGDPAAVENAVEAARDLTE-DHPVAGICLGHQILGLAMGAK 277 ***********************************************.********************* PP TIGR01368 267 tyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsv 335 yklkfGh+G Nhpv+dl+t ++ei+sqNHg+ vd + l+ le+th+nlnD+t+eg +hke+p++++ lcl|NCBI__GCF_000375485.1:WP_018124349.1 278 SYKLKFGHHGCNHPVMDLTTRKIEISSQNHGFCVDIAGLD--FLEPTHKNLNDDTLEGFAHKEKPILAI 344 ************************************9966..68************************* PP TIGR01368 336 QyHPeaspGphdteylFdefvelik 360 QyHPea+pGphd++y+F++f el++ lcl|NCBI__GCF_000375485.1:WP_018124349.1 345 QYHPEAAPGPHDSRYFFSRFRELVR 369 ********************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (374 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: 11.39 // [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