Align Carbamoyl-phosphate synthase pyrimidine-specific large chain; Carbamoyl-phosphate synthetase ammonia chain; EC 6.3.5.5 (characterized)
to candidate WP_013430297.1 CALKRO_RS06735 carbamoyl-phosphate synthase large subunit
Query= SwissProt::P25994 (1071 letters) >NCBI__GCF_000166775.1:WP_013430297.1 Length = 1075 Score = 1249 bits (3233), Expect = 0.0 Identities = 624/1053 (59%), Positives = 811/1053 (77%), Gaps = 5/1053 (0%) Query: 1 MPKRVDINKILVIGSGPIIIGQAAEFDYAGTQACLALKEEGYEVILVNSNPATIMTDTEM 60 MP R DI K+LVIGSGPIIIGQAAEFDY+G+QAC ALKEEG EVIL+NSNPATIMTD M Sbjct: 1 MPLRKDIKKVLVIGSGPIIIGQAAEFDYSGSQACKALKEEGIEVILINSNPATIMTDKTM 60 Query: 61 ADRVYIEPLTPEFLTRIIRKERPDAILPTLGGQTGLNLAVELSERGVLAECGVEVLGTKL 120 AD +YIEP+T E + +II+KER DAILPTLGGQTGLN AVEL + G+L + V+V+GT + Sbjct: 61 ADSIYIEPITCEIIEKIIQKERVDAILPTLGGQTGLNTAVELYKSGILDKYNVKVIGTNI 120 Query: 121 SAIQQAEDRDLFRTLMNELNEPVPESEIIHSLEEAEKFVSQIGFPVIVRPAYTLGGTGGG 180 AI+ AEDR LF+ LM ++ EPV SE+++ +E+ F +IGFPVI+RPAYTLGGTGGG Sbjct: 121 EAIEFAEDRQLFKQLMIKIGEPVVPSEVVNCVEDGLAFAKKIGFPVIIRPAYTLGGTGGG 180 Query: 181 ICSNETELKEIVENGLKLSPVHQCLLEKSIAGYKEIEYEVMRDSQDHAIVVCNMENIDPV 240 I +NE E EI GL SPVHQ L+EKSI G+KEIEYEVMRDS I VCNMENIDPV Sbjct: 181 IANNEEEFVEIARRGLSYSPVHQILVEKSIKGWKEIEYEVMRDSNGCLITVCNMENIDPV 240 Query: 241 GIHTGDSIVVAPSQTLSDREYQLLRNVSLKLIRALGIEGGCNVQLALDPDSFQYYIIEVN 300 GIHTGDSIV+APSQTLSD+EYQ+LR+ +LK+I AL IEGGCNVQ AL+PDSF+Y +IEVN Sbjct: 241 GIHTGDSIVIAPSQTLSDKEYQMLRSSALKIIDALKIEGGCNVQFALNPDSFEYAVIEVN 300 Query: 301 PRVSRSSALASKATGYPIAKLAAKIAVGLSLDEMMNPVTGKTYAAFEPALDYVVSKIPRW 360 PRVSRSSALASKATGYPIA++AAKIA+G +LDE+ N +T TYA+FEPALDYVV KIPRW Sbjct: 301 PRVSRSSALASKATGYPIARIAAKIALGYTLDEIENAITKMTYASFEPALDYVVLKIPRW 360 Query: 361 PFDKFESANRKLGTQMKATGEVMAIGRTLEESLLKAVRSLEADVYHLELKDAADISDELL 420 PFDKF ANRKLGTQMKATGEVMAIGRT EESLLK +RSL+ + +L+L + + +E L Sbjct: 361 PFDKFTYANRKLGTQMKATGEVMAIGRTFEESLLKGIRSLDIGLDYLDLPELKSLDNESL 420 Query: 421 EKRIKKAGDERLFYLAEAYRRGYTVEDLHEFSAIDVFFLHKLFGIVQFEKELKANAGDTD 480 + I +A D R+F LAEA RR Y VE L+ S +D FFLHK+ I++ E+ ++ ++ Sbjct: 421 SQLIIEADDRRIFALAEAIRRRYEVEYLYRISKVDRFFLHKIKNIIEMEERIRKEDLNSS 480 Query: 481 VLRRAKELGFSDQYISREWKMKESELYSLRKQAGIAPVFKMVDTCAAEFESETPYFYSTY 540 +L AK++GFSD+ I+ ++ E+++ SLRK I PV+KMVDTCAAEFE++TPY+YSTY Sbjct: 481 ILLEAKKMGFSDKTIASLKEISENDVRSLRKSLNITPVYKMVDTCAAEFEAKTPYYYSTY 540 Query: 541 EEENESVVTD----KKSVMVLGSGPIRIGQGVEFDYATVHSVWAIKQAGYEAIIVNNNPE 596 E EN+ V+ ++ ++VLGSGPIRIGQG+EFDY +VHSV+A+ + G +++I+NNNPE Sbjct: 541 ERENDVAVSQTSYTQRKIVVLGSGPIRIGQGIEFDYTSVHSVYALSKLGIKSVIINNNPE 600 Query: 597 TVSTDFSISDKLYFEPLTIEDVMHIIDLEQPMGVVVQFGGQTAINLADELSARGVKILGT 656 TVSTDF SD L+FEPLT EDV+++I+ + GV+VQFGGQTAI L+ +L+ G+KI GT Sbjct: 601 TVSTDFDTSDMLFFEPLTKEDVLNVIETVKAEGVIVQFGGQTAIKLSQQLAKEGIKIFGT 660 Query: 657 SLEDLDRAEDRDKFEQALGELGVPQPLGKTATSVNQAVSIASDIGYPVLVRPSYVLGGRA 716 S E +D AEDR++F++ L +L + +P G T ++ +A+ IA+ +GYPVLVRPSYVLGG+ Sbjct: 661 SAEGIDIAEDRERFDKILNKLNIKRPPGYTCYTLQEALRIANSLGYPVLVRPSYVLGGQG 720 Query: 717 MEIVYHEEELLHYMKNAVKINPQHPVLIDRYLTGKEIEVDAVSDGETVVIPGIMEHIERA 776 M+I + +++++ + A +N HP+LID+Y+ GKEIEVDA+SDGE ++IPGIMEHIERA Sbjct: 721 MKIAFDDDDIVEMLSYAKNLN-NHPILIDKYIVGKEIEVDAISDGEDILIPGIMEHIERA 779 Query: 777 GVHSGDSIAVYPPQSLTEDIKKKIEQYTIALAKGLNIVGLLNIQFVLSQGEVYVLEVNPR 836 G+HSGDSI++YP +++++ I++KI +YT+ +A+ L GL+N+QF++ E+YV+EVNPR Sbjct: 780 GIHSGDSISLYPARNISKYIEEKIVEYTLKIARELECKGLMNVQFIVQNEELYVIEVNPR 839 Query: 837 SSRTVPFLSKITGIPMANLATKIILGQKLAAFGYTEGLQPEQQGVFVKAPVFSFAKLRRV 896 SRTVPFLSK+TG+PM LAT + LG KL T GL P++ K PVFSF KL V Sbjct: 840 GSRTVPFLSKVTGVPMVELATMVSLGYKLKDLVNTVGLLPKKDFYAFKVPVFSFEKLPDV 899 Query: 897 DITLGPEMKSTGEVMGKDSTLEKALYKALIASGIQIPNYGSVLLTVADKDKEEGLAIAKR 956 +++LGPEMKSTGEVMG ALYK L+ASG ++P G VL TVAD DK E + IA++ Sbjct: 900 EVSLGPEMKSTGEVMGISKDYYVALYKGLVASGTKLPLEGGVLFTVADPDKNEIIPIAEK 959 Query: 957 FHAIGYNILATEGTAGYLKEASIPAKVVGKIGQDGPNLLDVIRNGEAQFVINTLTKGKQP 1016 F +G+ I AT TA +L + A V K+ + PN++D+IR GE VINT TKG+QP Sbjct: 960 FEKLGFKIYATSKTAKHLNFYQVAANYVKKVSEGSPNIIDLIRKGEINIVINTPTKGRQP 1019 Query: 1017 ARDGFRIRRESVENGVACLTSLDTAEAILRVLE 1049 RDGF IRR +VEN V TS+DTA+A++ ++E Sbjct: 1020 QRDGFLIRRFAVENKVPIFTSVDTAKAVVEIIE 1052 Lambda K H 0.316 0.135 0.377 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: 2961 Number of extensions: 123 Number of successful extensions: 13 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: 1071 Length of database: 1075 Length adjustment: 45 Effective length of query: 1026 Effective length of database: 1030 Effective search space: 1056780 Effective search space used: 1056780 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 (21.6 bits) S2: 58 (26.9 bits)
Align candidate WP_013430297.1 CALKRO_RS06735 (carbamoyl-phosphate synthase large subunit)
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large 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/TIGR01369.hmm # target sequence database: /tmp/gapView.815045.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01369 [M=1052] Accession: TIGR01369 Description: CPSaseII_lrg: carbamoyl-phosphate synthase, large 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1556.3 7.3 0 1556.1 7.3 1.0 1 NCBI__GCF_000166775.1:WP_013430297.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430297.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1556.1 7.3 0 0 2 1051 .. 3 1050 .. 2 1051 .. 0.99 Alignments for each domain: == domain 1 score: 1556.1 bits; conditional E-value: 0 TIGR01369 2 kredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltvea 72 r+dikkvlviGsGpi+igqAaEFDYsGsqa+kalkeegiev+L+nsn+At+mtd+++ad++YieP+t e+ NCBI__GCF_000166775.1:WP_013430297.1 3 LRKDIKKVLVIGSGPIIIGQAAEFDYSGSQACKALKEEGIEVILINSNPATIMTDKTMADSIYIEPITCEI 73 689******************************************************************** PP TIGR01369 73 vekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineeva 143 +ekii+kEr+Dail+tlGGqt+Ln avel ++G+L+ky+vk++Gt++eai+ aedR++Fk+++ +i+e+v NCBI__GCF_000166775.1:WP_013430297.1 74 IEKIIQKERVDAILPTLGGQTGLNTAVELYKSGILDKYNVKVIGTNIEAIEFAEDRQLFKQLMIKIGEPVV 144 *********************************************************************** PP TIGR01369 144 kseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkE 214 se+v+ ve+ l++a++ig+Pvi+R+a+tlgGtG+gia+neee+ e+++++l+ sp++q+lveks++gwkE NCBI__GCF_000166775.1:WP_013430297.1 145 PSEVVNCVEDGLAFAKKIGFPVIIRPAYTLGGTGGGIANNEEEFVEIARRGLSYSPVHQILVEKSIKGWKE 215 *********************************************************************** PP TIGR01369 215 iEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvegecnvqfa 285 iEyEv+RDs++ i+vcn+En+Dp+G+HtGdsiv+aPsqtL+dkeyq+lR+++lkii +l++eg+cnvqfa NCBI__GCF_000166775.1:WP_013430297.1 216 IEYEVMRDSNGCLITVCNMENIDPVGIHTGDSIVIAPSQTLSDKEYQMLRSSALKIIDALKIEGGCNVQFA 286 *********************************************************************** PP TIGR01369 286 ldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvki 356 l+P+s +y viEvnpRvsRssALAskAtGyPiA++aak+a+Gy+Lde++n +tk t+AsfEP+lDYvv ki NCBI__GCF_000166775.1:WP_013430297.1 287 LNPDSFEYAVIEVNPRVSRSSALASKATGYPIARIAAKIALGYTLDEIENAITKMTYASFEPALDYVVLKI 357 *********************************************************************** PP TIGR01369 357 PrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkekeaesdeeleealkkpn 427 Prw++dkf+ ++rklgtqmk++GEvmaigrtfee+l+k++rsl+++l l+l+e + ++e+l + + +++ NCBI__GCF_000166775.1:WP_013430297.1 358 PRWPFDKFTYANRKLGTQMKATGEVMAIGRTFEESLLKGIRSLDIGLDYLDLPELKSLDNESLSQLIIEAD 428 *********************************************************************** PP TIGR01369 428 drRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqia 498 drR+fa+aea+rr ++ve +y+++k+drffl+k+k+++e+e++++ +++l++ l +akk+Gfsd++ia NCBI__GCF_000166775.1:WP_013430297.1 429 DRRIFALAEAIRRRYEVEYLYRISKVDRFFLHKIKNIIEMEERIR---KEDLNSSILLEAKKMGFSDKTIA 496 ********************************************7...67788****************** PP TIGR01369 499 klvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtek....kkvlvlGsGpi 565 +l + se++vr+lrk+l+i+pv+k+vDt+aaEfeaktpY+Ystye+e +dv+v+++ +k++vlGsGpi NCBI__GCF_000166775.1:WP_013430297.1 497 SLKEISENDVRSLRKSLNITPVYKMVDTCAAEFEAKTPYYYSTYERE-NDVAVSQTsytqRKIVVLGSGPI 566 ***********************************************.8877766545568********** PP TIGR01369 566 RigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivq 636 Rigqg+EFDy++vh+v al++ g+k+++in+nPEtvstD+d++d L+Fe+lt edvl++ie+ k egvivq NCBI__GCF_000166775.1:WP_013430297.1 567 RIGQGIEFDYTSVHSVYALSKLGIKSVIINNNPETVSTDFDTSDMLFFEPLTKEDVLNVIETVKAEGVIVQ 637 *********************************************************************** PP TIGR01369 637 lgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPv 707 +gGqta++l+++l+++g+ki+Gtsae id+aEdRe+F+k+l++l+ik+p g + +++ea +ia+++gyPv NCBI__GCF_000166775.1:WP_013430297.1 638 FGGQTAIKLSQQLAKEGIKIFGTSAEGIDIAEDRERFDKILNKLNIKRPPGYTCYTLQEALRIANSLGYPV 708 *********************************************************************** PP TIGR01369 708 lvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiE 778 lvRpsyvlgG++m+i+ +++++ ++l+ a +++ ++P+lidky+ ++E++vDa++dge++li+gi+eHiE NCBI__GCF_000166775.1:WP_013430297.1 709 LVRPSYVLGGQGMKIAFDDDDIVEMLSYAKNLN-NHPILIDKYIV-GKEIEVDAISDGEDILIPGIMEHIE 777 ***************************998776.9**********.************************* PP TIGR01369 779 eaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvs 849 +aG+HsGDs+ ++p++++s+ +++ki e++ kia+el+ kGl+n+qf+v++ee+yviEvn+R sRtvPf+s NCBI__GCF_000166775.1:WP_013430297.1 778 RAGIHSGDSISLYPARNISKYIEEKIVEYTLKIARELECKGLMNVQFIVQNEELYVIEVNPRGSRTVPFLS 848 *********************************************************************** PP TIGR01369 850 kalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrd 920 k++gvp+v+la+ v lg kl++l ++v +k++++a k++vfsf+kl +v+v lgpemkstGEvmgi++d NCBI__GCF_000166775.1:WP_013430297.1 849 KVTGVPMVELATMVSLGYKLKDLVNTVGLLPKKDFYAFKVPVFSFEKLPDVEVSLGPEMKSTGEVMGISKD 919 *********************************************************************** PP TIGR01369 921 leeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkv 991 + al+k l+as++k++ +g vl +v+d dk+e+ ++a+k++++g+k+yat++tak l+ ++ a+ v+kv NCBI__GCF_000166775.1:WP_013430297.1 920 YYVALYKGLVASGTKLPLEGGVLFTVADPDKNEIIPIAEKFEKLGFKIYATSKTAKHLNFYQVAANYVKKV 990 *********************************************************************** PP TIGR01369 992 seeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051 se +++i++l++++ei++vin+++k+++ +++g+ irr ave+kvp++t+++ta+a++e+ NCBI__GCF_000166775.1:WP_013430297.1 991 SEGSPNIIDLIRKGEINIVINTPTKGRQPQRDGFLIRRFAVENKVPIFTSVDTAKAVVEI 1050 ********************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1052 nodes) Target sequences: 1 (1075 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 0.02s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 32.12 // [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