Align Carbamoyl-phosphate synthase pyrimidine-specific large chain; Carbamoyl-phosphate synthetase ammonia chain; EC 6.3.5.5 (characterized)
to candidate WP_013430148.1 CALKRO_RS05915 carbamoyl-phosphate synthase (glutamine-hydrolyzing) large subunit
Query= SwissProt::P25994 (1071 letters) >NCBI__GCF_000166775.1:WP_013430148.1 Length = 1077 Score = 1221 bits (3158), Expect = 0.0 Identities = 626/1056 (59%), Positives = 791/1056 (74%), Gaps = 13/1056 (1%) Query: 1 MPKRVDINKILVIGSGPIIIGQAAEFDYAGTQACLALKEEGYEVILVNSNPATIMTDTEM 60 MPKR DI K+L+IGSGPI+IGQAAEFDY+GTQAC ALKEEG EV+LVNSNPATIMTDTE+ Sbjct: 1 MPKRKDIKKVLIIGSGPIVIGQAAEFDYSGTQACRALKEEGIEVVLVNSNPATIMTDTEI 60 Query: 61 ADRVYIEPLTPEFLTRIIRKERPDAILPTLGGQTGLNLAVELSERGVLAECGVEVLGTKL 120 ADRVYIEP++ +++ II+KERP +L LGGQT LN+A EL+E G+L + GV +LGT L Sbjct: 61 ADRVYIEPISVDYIEEIIKKERPQGLLAGLGGQTALNMAFELAEAGILEKYGVCLLGTSL 120 Query: 121 SAIQQAEDRDLFRTLMNELNEPVPESEIIHSLEEAEKFVSQIGFPVIVRPAYTLGGTGGG 180 I++AEDR+LF+ M E+ EPVP+S I HS++EA +F ++G+PVIVRPAYTLGGTGGG Sbjct: 121 ETIKKAEDRELFKKTMIEIGEPVPKSIIAHSVQEAIEFAREVGYPVIVRPAYTLGGTGGG 180 Query: 181 ICSNETELKEIVENGLKLSPVHQCLLEKSIAGYKEIEYEVMRDSQDHAIVVCNMENIDPV 240 I NE EL+ I GLKLS +HQ L+E+S+ G+KEIEYEVMRDS D+ I VCNMENIDPV Sbjct: 181 IAYNEEELRYIASKGLKLSLIHQVLIEQSVLGWKEIEYEVMRDSNDNCITVCNMENIDPV 240 Query: 241 GIHTGDSIVVAPSQTLSDREYQLLRNVSLKLIRALGIEGGCNVQLALDPDSFQYYIIEVN 300 GIHTGDSIVVAPSQTLSD+EYQ+LR+ SL +IR+L IEGGCNVQ AL+P++ +Y +IEVN Sbjct: 241 GIHTGDSIVVAPSQTLSDKEYQMLRSASLNIIRSLKIEGGCNVQFALNPNNMEYVVIEVN 300 Query: 301 PRVSRSSALASKATGYPIAKLAAKIAVGLSLDEMMNPVTGKTYAAFEPALDYVVSKIPRW 360 PRVSRSSALASKATGYPIA++AAKIA+GL+LDE++NP+T TYA+FEP++DYVV K+PRW Sbjct: 301 PRVSRSSALASKATGYPIARIAAKIAIGLTLDEIINPITQNTYASFEPSIDYVVVKVPRW 360 Query: 361 PFDKFESANRKLGTQMKATGEVMAIGRTLEESLLKAVRSLEADV-YHLELKDAADISDEL 419 PFDKFE A+R+LGTQMK+TGEVMAIGRT EE+ LKA+ SL+ + Y L LK ++ D+ Sbjct: 361 PFDKFEKADRRLGTQMKSTGEVMAIGRTFEEAFLKAIDSLDVKINYQLGLKKFEEMPDDQ 420 Query: 420 LEKRIKKAGDERLFYLAEAYRRGYTVEDLHEFSAIDVFFLHKLFGIVQFEKELKANAGDT 479 L + IK DER+F + EA R Y + + + S ID FF+ K IV K+LK ++ Sbjct: 421 LLEYIKTPNDERVFAICEALSRNYDCKFISDLSKIDYFFIEKFKNIVDMSKQLKKYDIES 480 Query: 480 ---DVLRRAKELGFSDQYISREWKMKESELYSLRKQAGIAPVFKMVDTCAAEFESETPYF 536 D+L++AK LGF D YI+ K E+ +R++ + P FKMVDTCA EFE++TPYF Sbjct: 481 LPYDLLQKAKRLGFGDSYIANLLKEDVDEVIEIREKCKLKPSFKMVDTCAGEFEAKTPYF 540 Query: 537 YSTYEEENESVVTDKKSVMVLGSGPIRIGQGVEFDYATVHSVWAIKQAGYEAIIVNNNPE 596 YSTYE+E + VV+ K +V+GSGPIRIGQG+EFDY VHS++A+K+ G EAII+NNNPE Sbjct: 541 YSTYEKETDLVVSSKPKAIVIGSGPIRIGQGIEFDYCCVHSIFALKEEGVEAIIINNNPE 600 Query: 597 TVSTDFSISDKLYFEPLTIEDVMHIIDLEQPMGVVVQFGGQTAINLADELSARGVKILGT 656 TVSTDF SDKL+FEPLT E V+ II E+PMGV+VQFGGQTAIN+A L+ GVKILGT Sbjct: 601 TVSTDFDTSDKLFFEPLTKECVLDIIKQEKPMGVIVQFGGQTAINMASYLAKNGVKILGT 660 Query: 657 SLEDLDRAEDRDKFEQALGELGVPQPLGKTATSVNQAVSIASDIGYPVLVRPSYVLGGRA 716 S+E +D AEDRDKF L L +P P G A S+ AV +A IGYPVLVRPSYVLGGRA Sbjct: 661 SMESIDTAEDRDKFLNLLKNLNIPYPPGGAAYSLEDAVKVAQQIGYPVLVRPSYVLGGRA 720 Query: 717 MEIVYHEEELLHYMKNAVKINPQHPVLIDRYLTGKEIEVDAVSDGETVVIPGIMEHIERA 776 MEIVY EEL Y+K A++I+ +HP+LID+Y+ GKE EVD +SDGE V+IPGIMEHIERA Sbjct: 721 MEIVYSREELEKYIKAAIEISIKHPILIDKYILGKEAEVDGISDGEDVLIPGIMEHIERA 780 Query: 777 GVHSGDSIAVYPPQSLTEDIKKKIEQYTIALAKGLNIVGLLNIQFVLSQGE-VYVLEVNP 835 GVHSGDS+AV+PP +L+E +K+KI YTI LA+ L +VGL NIQFV+ + E VYV+EVNP Sbjct: 781 GVHSGDSMAVFPPHTLSEKVKEKIIDYTIKLARALRVVGLFNIQFVIDKDENVYVIEVNP 840 Query: 836 RSSRTVPFLSKITGIPMANLATKIILGQKLAAFGYTEGLQPEQQGVFVKAPVFSFAKLRR 895 R+SRTVP LSK+TGIPM +ATK+ILG+KL GY GL E VKAPVFSF+KL + Sbjct: 841 RASRTVPILSKVTGIPMIKIATKLILGKKLKDLGYQTGLVKEPDFFAVKAPVFSFSKLSK 900 Query: 896 VDITLGPEMKSTGEVMGKDSTLEKALYKALIASGIQIPNYGSVLLTVADKDKEEGLAIAK 955 VD LGPEMKSTGEV+G L+ ALYKA I+S + GS L+ + +K+ I + Sbjct: 901 VDAYLGPEMKSTGEVLGISKNLKVALYKAFISSNHKFMKNGSCLILAPESEKDAIQQIIR 960 Query: 956 RFHAIGYNILATEGTAGYLKEASIPAKVVGKIGQDGPNLLDVIRNGEAQFVINTLTKGKQ 1015 + + + Y + + Y+K ++ D ++ + FVIN +K K Sbjct: 961 KLYEVNYKVFLVDSMKDYIKGLNVEF-------IDKETAQKLLLEDKFSFVINIPSKDKM 1013 Query: 1016 PARDGFRIRRESVENGVACLTSLDTAEAILRVLESM 1051 GF +RR SVE G+ LTS+DTA + VL S+ Sbjct: 1014 -QEFGFVLRRLSVEFGITTLTSIDTALYYVDVLSSL 1048 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: 2980 Number of extensions: 108 Number of successful extensions: 16 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: 1077 Length adjustment: 45 Effective length of query: 1026 Effective length of database: 1032 Effective search space: 1058832 Effective search space used: 1058832 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_013430148.1 CALKRO_RS05915 (carbamoyl-phosphate synthase (glutamine-hydrolyzing) 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.493526.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 1567.2 5.4 0 1567.0 5.4 1.0 1 NCBI__GCF_000166775.1:WP_013430148.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430148.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1567.0 5.4 0 0 1 1050 [. 2 1043 .. 2 1045 .. 0.98 Alignments for each domain: == domain 1 score: 1567.0 bits; conditional E-value: 0 TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71 pkr+dikkvl+iGsGpivigqAaEFDYsG+qa++alkeegievvLvnsn+At+mtd+e+ad+vYieP+ v NCBI__GCF_000166775.1:WP_013430148.1 2 PKRKDIKKVLIIGSGPIVIGQAAEFDYSGTQACRALKEEGIEVVLVNSNPATIMTDTEIADRVYIEPISVD 72 689******************************************************************** PP TIGR01369 72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142 ++e+ii+kErp ++l++lGGqtaLn+a el e+G+Lekygv llGt++e+ikkaedRe+Fk+++ ei+e+v NCBI__GCF_000166775.1:WP_013430148.1 73 YIEEIIKKERPQGLLAGLGGQTALNMAFELAEAGILEKYGVCLLGTSLETIKKAEDRELFKKTMIEIGEPV 143 *********************************************************************** PP TIGR01369 143 akseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwk 213 +ks i++sv+ea+e+a+e+gyPvivR+a+tlgGtG+gia+neeel+ +++k+lk+s i+qvl+e+s+ gwk NCBI__GCF_000166775.1:WP_013430148.1 144 PKSIIAHSVQEAIEFAREVGYPVIVRPAYTLGGTGGGIAYNEEELRYIASKGLKLSLIHQVLIEQSVLGWK 214 *********************************************************************** PP TIGR01369 214 EiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvegecnvqf 284 EiEyEv+RDs+dnci+vcn+En+Dp+G+HtGdsivvaPsqtL+dkeyq+lR+asl+iir+l++eg+cnvqf NCBI__GCF_000166775.1:WP_013430148.1 215 EIEYEVMRDSNDNCITVCNMENIDPVGIHTGDSIVVAPSQTLSDKEYQMLRSASLNIIRSLKIEGGCNVQF 285 *********************************************************************** PP TIGR01369 285 aldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvk 355 al+P++ +yvviEvnpRvsRssALAskAtGyPiA++aak+a+G++Lde+ n++t++t+AsfEPs+DYvvvk NCBI__GCF_000166775.1:WP_013430148.1 286 ALNPNNMEYVVIEVNPRVSRSSALASKATGYPIARIAAKIAIGLTLDEIINPITQNTYASFEPSIDYVVVK 356 *********************************************************************** PP TIGR01369 356 iPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllg.lklkekeaesdeeleealkk 425 +Prw++dkfek+dr+lgtqmks+GEvmaigrtfeea++ka+ sl+ k+ l lk+ e+++d++l e +k+ NCBI__GCF_000166775.1:WP_013430148.1 357 VPRWPFDKFEKADRRLGTQMKSTGEVMAIGRTFEEAFLKAIDSLDVKINYqLGLKKFEEMPDDQLLEYIKT 427 **********************************************98764889999999*********** PP TIGR01369 426 pndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeq 496 pnd+R+fai+eal+r+++ + + +l+kid ff+ek+k++v+++k+l++ ++ l+ +ll+kak+lGf d+ NCBI__GCF_000166775.1:WP_013430148.1 428 PNDERVFAICEALSRNYDCKFISDLSKIDYFFIEKFKNIVDMSKQLKKYDIESLPYDLLQKAKRLGFGDSY 498 *********************************************************************** PP TIGR01369 497 iaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRi 567 ia+l+k + +ev ++r++ ++ p++k+vDt+a+EfeaktpY+Ystye+e +d v++k k +v+GsGpiRi NCBI__GCF_000166775.1:WP_013430148.1 499 IANLLKEDVDEVIEIREKCKLKPSFKMVDTCAGEFEAKTPYFYSTYEKE-TDLVVSSKPKAIVIGSGPIRI 568 *************************************************.999999999************ PP TIGR01369 568 gqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlg 638 gqg+EFDyc+vh++ al+e+g ++i+in+nPEtvstD+d++d+L+Fe+lt e+vldii++ek++gvivq+g NCBI__GCF_000166775.1:WP_013430148.1 569 GQGIEFDYCCVHSIFALKEEGVEAIIINNNPETVSTDFDTSDKLFFEPLTKECVLDIIKQEKPMGVIVQFG 639 *********************************************************************** PP TIGR01369 639 GqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlv 709 Gqta+n+a+ l+++gvkilGts+esid+aEdR+kF +ll++l+i+ p g +a s+e+a+++a++igyPvlv NCBI__GCF_000166775.1:WP_013430148.1 640 GQTAINMASYLAKNGVKILGTSMESIDTAEDRDKFLNLLKNLNIPYPPGGAAYSLEDAVKVAQQIGYPVLV 710 *********************************************************************** PP TIGR01369 710 RpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEea 780 RpsyvlgGrameiv+++eele+y++ a+e+s ++P+lidky+ ++E++vD ++dge+vli+gi+eHiE+a NCBI__GCF_000166775.1:WP_013430148.1 711 RPSYVLGGRAMEIVYSREELEKYIKAAIEISIKHPILIDKYIL-GKEAEVDGISDGEDVLIPGIMEHIERA 780 ******************************************9.*************************** PP TIGR01369 781 GvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkd.eevyviEvnvRasRtvPfvsk 850 GvHsGDs++v+pp++lse+vk+ki +++ k+a++l+v+Gl+niqfv+++ e+vyviEvn+RasRtvP++sk NCBI__GCF_000166775.1:WP_013430148.1 781 GVHSGDSMAVFPPHTLSEKVKEKIIDYTIKLARALRVVGLFNIQFVIDKdENVYVIEVNPRASRTVPILSK 851 **********************************************976599******************* PP TIGR01369 851 algvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdl 921 ++g+p++k+a+k++lgkkl++l++ k+++++avka+vfsfskl++vd +lgpemkstGEv gi+++l NCBI__GCF_000166775.1:WP_013430148.1 852 VTGIPMIKIATKLILGKKLKDLGYQTGLVKEPDFFAVKAPVFSFSKLSKVDAYLGPEMKSTGEVLGISKNL 922 *********************************************************************** PP TIGR01369 922 eeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvs 992 + al+ka+++s++k+ k+gs+l+ +++k++++++++kl e +kv+ + ++++++ ++e + NCBI__GCF_000166775.1:WP_013430148.1 923 KVALYKAFISSNHKFMKNGSCLILAPESEKDAIQQIIRKLYEVNYKVFLVDSMKDYIKG--LNVEFI---- 987 ***************************************************88766543..333333.... PP TIGR01369 993 eeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaealle 1050 ++e++++ll e+++++vin++sk+k ++e g+++rr +ve++++++t+++ta ++ NCBI__GCF_000166775.1:WP_013430148.1 988 -DKETAQKLLLEDKFSFVINIPSKDK-MQEFGFVLRRLSVEFGITTLTSIDTALYYVD 1043 .3456778899***********9655.8999********************9988776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1052 nodes) Target sequences: 1 (1077 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 41.25 // [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