Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_006748500.1 THITH_RS12630 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_000227685.2:WP_006748500.1 Length = 377 Score = 523 bits (1346), Expect = e-153 Identities = 253/378 (66%), Positives = 295/378 (78%), Gaps = 2/378 (0%) Query: 1 MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60 M A+LVLEDGT FHG+++GA G VGEVVFNTSMTGYQEILTDPSY+RQIVTLTYPHI Sbjct: 1 MSAPAVLVLEDGTVFHGQSVGAAGETVGEVVFNTSMTGYQEILTDPSYARQIVTLTYPHI 60 Query: 61 GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120 GNVGT D+ES++VHA GL++RD+P + SN+R+ E L +L RH +VAIA IDTR+LTR Sbjct: 61 GNVGTTPEDDESAKVHAAGLIVRDVPPLVSNWRSRESLPDFLMRHGVVAIAGIDTRRLTR 120 Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180 +LREKGAQN C+ G+ D ALE+ARAFPG+ GMDLA+EV+TA Y W G W L G Sbjct: 121 ILREKGAQNACLQGGE-VDTGRALEQARAFPGIKGMDLAREVSTANRYEWLDGPWRLDGP 179 Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240 P+ D+ FHVVAYDFG K NILRMLV RGCR+T+VPA+T A+D L + PDGIFLSN Sbjct: 180 APQLPP-DQAEFHVVAYDFGIKHNILRMLVGRGCRVTVVPAETPADDALALEPDGIFLSN 238 Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300 GPGDP PCDYAI I++F PVFGICLGHQLL LASGA TVKMKFGHHG NHP++D+ Sbjct: 239 GPGDPEPCDYAIATIRRFCAEKRPVFGICLGHQLLGLASGASTVKMKFGHHGANHPIQDL 298 Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360 VMI++QNHGFAVDEA LP L TH+SLFDG+LQGI R+D PAF FQGHPEASPGP Sbjct: 299 RSGRVMISSQNHGFAVDEANLPETLVATHRSLFDGSLQGIARSDCPAFGFQGHPEASPGP 358 Query: 361 HDAAPLFDHFIELIEQYR 378 HD AP FD FI + R Sbjct: 359 HDVAPGFDEFIAAMRTAR 376 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: 520 Number of extensions: 17 Number of successful extensions: 3 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: 377 Length adjustment: 30 Effective length of query: 352 Effective length of database: 347 Effective search space: 122144 Effective search space used: 122144 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_006748500.1 THITH_RS12630 (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.5627.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-148 478.5 0.0 6.8e-148 478.4 0.0 1.0 1 lcl|NCBI__GCF_000227685.2:WP_006748500.1 THITH_RS12630 carbamoyl-phosphat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000227685.2:WP_006748500.1 THITH_RS12630 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 478.4 0.0 6.8e-148 6.8e-148 1 360 [. 5 373 .. 5 374 .. 0.97 Alignments for each domain: == domain 1 score: 478.4 bits; conditional E-value: 6.8e-148 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a+lvledGtvf+g+s+ga +e+vGevvFnTsmtGYqEiltDpsY++qiv+ltyp+ign+g+++ed es lcl|NCBI__GCF_000227685.2:WP_006748500.1 5 AVLVLEDGTVFHGQSVGAAGETVGEVVFNTSMTGYQEILTDPSYARQIVTLTYPHIGNVGTTPEDDESA 73 689****************************************************************** PP TIGR01368 70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138 k++++gl+v+++ vsn+r++esL +fl ++g+vai+g+DTR l++ lRekg+++a+++ ++++ ++ lcl|NCBI__GCF_000227685.2:WP_006748500.1 74 KVHAAGLIVRDVPPLVSNWRSRESLPDFLMRHGVVAIAGIDTRRLTRILREKGAQNACLQGGEVDTGRA 142 ********************************************************************* PP TIGR01368 139 vekakespkvkevnlvkevstkeayeleq..........kakkegkklrvvvidlGvKenilreLvkrg 197 e+a++ p +k+++l++evst+++ye+ + + ++ + +vv++d+G+K+nilr+Lv rg lcl|NCBI__GCF_000227685.2:WP_006748500.1 143 LEQARAFPGIKGMDLAREVSTANRYEWLDgpwrldgpapQLPPDQAEFHVVAYDFGIKHNILRMLVGRG 211 ****************************988877666543455555699******************** PP TIGR01368 198 vevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgak 266 ++vtvvpa+t+a++ +l+pdgi+lsnGPGdP+ +++ai+t+++++ +k P+fGIclGhqll+la+ga+ lcl|NCBI__GCF_000227685.2:WP_006748500.1 212 CRVTVVPAETPADDALALEPDGIFLSNGPGDPEPCDYAIATIRRFCAEKRPVFGICLGHQLLGLASGAS 280 ********************************************************************* PP TIGR01368 267 tyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsv 335 t+k+kfGh+GaNhp++dl++grv+i+sqNHg+avde+ l+e +l +th++l+Dg+++g+++++ p+f lcl|NCBI__GCF_000227685.2:WP_006748500.1 281 TVKMKFGHHGANHPIQDLRSGRVMISSQNHGFAVDEANLPE-TLVATHRSLFDGSLQGIARSDCPAFGF 348 **************************************885.5************************** PP TIGR01368 336 QyHPeaspGphdteylFdefvelik 360 Q HPeaspGphd + Fdef+ +++ lcl|NCBI__GCF_000227685.2:WP_006748500.1 349 QGHPEASPGPHDVAPGFDEFIAAMR 373 *********************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (377 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: 7.23 // [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