Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_012590640.1 MSIL_RS08265 carbamoyl-phosphate synthase small subunit
Query= SwissProt::P0A6F1 (382 letters) >NCBI__GCF_000021745.1:WP_012590640.1 Length = 398 Score = 368 bits (945), Expect = e-106 Identities = 193/382 (50%), Positives = 244/382 (63%), Gaps = 14/382 (3%) Query: 4 SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63 +ALLVL +G G +GATG AVGEV FNT+MTGYQEILTDPSY+ QIVT T+PHIGNV Sbjct: 19 TALLVLANGLVLEGVGLGATGEAVGEVCFNTAMTGYQEILTDPSYAGQIVTFTFPHIGNV 78 Query: 64 GTNDADEESSQVHA----QGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLT 119 G ND D E+S A +G ++ SN+R+T +LK I+ + +DTR LT Sbjct: 79 GANDEDIETSNPAAAAGVRGAIVHAPITGPSNYRSTRHFDGWLKSRGIIGLCGVDTRALT 138 Query: 120 RLLREKGAQNGCIIAGDNPDAALALEK----ARAFPGLNGMDLAKEVTTAEAYSWTQGSW 175 L+R+ G N I +PD LE A +PGL GMDL V + + Y W+Q W Sbjct: 139 ALIRDSGMPNAVI--AHSPDGEFDLEHLKRLAAQWPGLEGMDLVPSVASTQRYEWSQTPW 196 Query: 176 TLTGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDG 235 T G A+ F VVA D+G K ILR+L D GC +T+ P+ +A ++L + PDG Sbjct: 197 TQANGYGSAEGGK---FKVVAIDYGVKSTILRLLTDAGCDVTVAPSTATAAEILALKPDG 253 Query: 236 IFLSNGPGDPAPCD-YAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGN 294 IFLSNGPGDPA YA+ I+ L+ IP FGICLGHQ+LALA G +TVKM+ GHHG N Sbjct: 254 IFLSNGPGDPAETGKYAVPVIKALLDEKIPTFGICLGHQMLALALGGRTVKMRQGHHGAN 313 Query: 295 HPVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHP 354 HPV+D V I + NHGFAVD +LP N R TH+SLFDG+ G+ TD+PAFS Q HP Sbjct: 314 HPVQDFTTGKVEIVSMNHGFAVDPLSLPENARETHRSLFDGSNCGLELTDRPAFSVQHHP 373 Query: 355 EASPGPHDAAPLFDHFIELIEQ 376 EASPGP D+ LF F +++E+ Sbjct: 374 EASPGPRDSHYLFRRFAQMMEK 395 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: 454 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: 398 Length adjustment: 30 Effective length of query: 352 Effective length of database: 368 Effective search space: 129536 Effective search space used: 129536 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_012590640.1 MSIL_RS08265 (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.2250.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-131 422.5 0.0 7.2e-131 422.4 0.0 1.0 1 lcl|NCBI__GCF_000021745.1:WP_012590640.1 MSIL_RS08265 carbamoyl-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021745.1:WP_012590640.1 MSIL_RS08265 carbamoyl-phosphate synthase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.4 0.0 7.2e-131 7.2e-131 1 361 [] 20 395 .. 20 395 .. 0.94 Alignments for each domain: == domain 1 score: 422.4 bits; conditional E-value: 7.2e-131 TIGR01368 1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 a lvl++G v+eg ++ga++e+vGev+FnT+mtGYqEiltDpsY+gqiv++t p+ign+g n+ed+e + lcl|NCBI__GCF_000021745.1:WP_012590640.1 20 ALLVLANGLVLEGVGLGATGEAVGEVCFNTAMTGYQEILTDPSYAGQIVTFTFPHIGNVGANDEDIETS 88 579***************************************************************987 PP TIGR01368 70 ....kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse 134 v+g +v+ + +snyr+++ ++ +lk++gi+++ gvDTRal+ +R++g +avi+++ lcl|NCBI__GCF_000021745.1:WP_012590640.1 89 npaaAAGVRGAIVHAPITGPSNYRSTRHFDGWLKSRGIIGLCGVDTRALTALIRDSGMPNAVIAHSPDG 157 23334568899*****************************************************98765 PP TIGR01368 135 ...keelvekakespkvkevnlvkevstkeayeleq....k....akkegkklrvvvidlGvKenilre 192 e+l++ a++ p +++++lv +v+ +++ye++q + ++eg k +vv+id+GvK++ilr lcl|NCBI__GCF_000021745.1:WP_012590640.1 158 efdLEHLKRLAAQWPGLEGMDLVPSVASTQRYEWSQtpwtQangyGSAEGGKFKVVAIDYGVKSTILRL 226 444677778888999********************976661556667888889**************** PP TIGR01368 193 LvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqlla 260 L++ g++vtv p +++a+ei +l+pdgi+lsnGPGdPa+ ++a+ +k+ll++kiP+fGIclGhq+la lcl|NCBI__GCF_000021745.1:WP_012590640.1 227 LTDAGCDVTVAPSTATAAEILALKPDGIFLSNGPGDPAETgKYAVPVIKALLDEKIPTFGICLGHQMLA 295 *************************************77627789999********************* PP TIGR01368 261 lalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehke 329 lalg++t+k++ Gh+GaNhpv+d++tg+vei s NHg+avd+ sl+e+ ++ th++l+Dg++ gle ++ lcl|NCBI__GCF_000021745.1:WP_012590640.1 296 LALGGRTVKMRQGHHGANHPVQDFTTGKVEIVSMNHGFAVDPLSLPEN-ARETHRSLFDGSNCGLELTD 363 ********************************************8865.99****************** PP TIGR01368 330 lpvfsvQyHPeaspGphdteylFdefvelikk 361 p+fsvQ+HPeaspGp+d++ylF++f ++++k lcl|NCBI__GCF_000021745.1:WP_012590640.1 364 RPAFSVQHHPEASPGPRDSHYLFRRFAQMMEK 395 ****************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (361 nodes) Target sequences: 1 (398 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: 00:00:00.02 # Mc/sec: 6.97 // [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