Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate Pf1N1B4_1172 Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)
Query= BRENDA::P00968
(1073 letters)
>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172
Length = 1073
Score = 1601 bits (4146), Expect = 0.0
Identities = 808/1073 (75%), Positives = 916/1073 (85%), Gaps = 1/1073 (0%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDP M
Sbjct: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPAM 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADATYIEPI W+ V KIIEKERPDA+LPTMGGQTALNCAL+LER+GVLE+FGV MIGA A
Sbjct: 61 ADATYIEPIKWQTVAKIIEKERPDALLPTMGGQTALNCALDLEREGVLEKFGVEMIGANA 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
D IDKAEDR RFD AMK IGL+ RSGIAH+MEEA AV +GFPCIIRPSFTMGG+GGG
Sbjct: 121 DTIDKAEDRSRFDKAMKSIGLDCPRSGIAHSMEEANAVLERLGFPCIIRPSFTMGGTGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDK DNCIIVCSIENFD M
Sbjct: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKKDNCIIVCSIENFDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPAQTLTDKEYQI+RNAS+AVLREIGVETGGSNVQF + P GR++VIEM
Sbjct: 241 GVHTGDSITVAPAQTLTDKEYQILRNASLAVLREIGVETGGSNVQFGICPNTGRMVVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL NDITGG+TPASFEPSIDYVVTK+P
Sbjct: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELSNDITGGKTPASFEPSIDYVVTKLP 360
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
RF FEKF A+ RLTTQMKSVGEVMAIGRT QESLQKALRGLEVG G D K+ L +PE+
Sbjct: 361 RFAFEKFPKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDEKLDLSNPES 420
Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
++ ++REL GA+RIWY+ADAFRAGLSV+ +F + ID WFLVQIE+L++ EEKV +G
Sbjct: 421 MSILKRELTVPGAERIWYVADAFRAGLSVEDIFGMNMIDPWFLVQIEDLIKEEEKVKTLG 480
Query: 481 ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
+ ++ D + +LKRKGF+D RLAKL GV E +R+ R + ++ PVYKRVDTCAAEFATDT
Sbjct: 481 LASIDHDVMFRLKRKGFSDMRLAKLLGVTEKALRRHRHKLEIFPVYKRVDTCAAEFATDT 540
Query: 541 AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
AY+YSTYEEECEA PS R+KIM+LGGGPNRIGQGIEFDYCCVHA+LALREDGYETIMVN
Sbjct: 541 AYLYSTYEEECEAAPS-GRDKIMILGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVN 599
Query: 601 CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
CNPETVSTDYDTSDRLYFEPVTLEDVLEIVR+EKPKGVIVQYGGQTPLKLARALE AGVP
Sbjct: 600 CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRVEKPKGVIVQYGGQTPLKLARALEEAGVP 659
Query: 661 VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
+IGTSPDAIDRAEDRERFQ VERL L+QP NATV + + A+ A +IGYPLVVRPSYVL
Sbjct: 660 IIGTSPDAIDRAEDRERFQQMVERLNLRQPPNATVRSEDEAIRAAAKIGYPLVVRPSYVL 719
Query: 721 GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
GGRAMEIVY+E +L+RY + AV VSND+PVLLDHFL+ A+E+DVDA+CDG V+IG IM+
Sbjct: 720 GGRAMEIVYEEEELKRYLRDAVKVSNDSPVLLDHFLNCAIEMDVDAVCDGTDVVIGAIMQ 779
Query: 781 HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
HIEQAGVHSGDSACSLP Y+L IQD MR+QV+K+A EL V GLMNVQ A++ ++Y+I
Sbjct: 780 HIEQAGVHSGDSACSLPPYSLPAHIQDEMREQVKKMALELGVVGLMNVQLALQGEDIYVI 839
Query: 841 EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
EVNPRA+RTVPFVSK GV LA +AARVMAGK+L E G TKE+IP +YSVKE V PF KF
Sbjct: 840 EVNPRASRTVPFVSKCIGVSLAMIAARVMAGKTLKEIGFTKEIIPNFYSVKEAVFPFAKF 899
Query: 901 PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
PGVDP+LGPEM+STGEVMGVG TF EAFAKAQ+G++ + G A +SVR+ DK V +
Sbjct: 900 PGVDPILGPEMKSTGEVMGVGDTFGEAFAKAQMGASEVLPTGGTAFISVRDDDKPLVAGV 959
Query: 961 AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
A L+ GFE+ AT GTA ++ AG+ R VNKV EGRPH+ D IKN E T IINTT GR
Sbjct: 960 ARDLINLGFEVVATAGTAKLIEAAGLKVRRVNKVTEGRPHVVDMIKNDEVTLIINTTEGR 1019
Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
++I DS IRR+ALQ+K++ TT+ G A AL + V +Q++HA +K
Sbjct: 1020 QSIADSYSIRRNALQHKIYCTTTIAAGEAICEALKFGPEKTVRRLQDLHAGLK 1072
Lambda K H
0.318 0.135 0.383
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: 3216
Number of extensions: 137
Number of successful extensions: 12
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: 1073
Length of database: 1073
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1028
Effective search space: 1056784
Effective search space used: 1056784
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: 58 (26.9 bits)
Align candidate Pf1N1B4_1172 (Carbamoyl-phosphate synthase large chain (EC 6.3.5.5))
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.20574.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 1574.9 0.0 0 1574.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 Carbamoyl-phosphate synthase lar
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1574.7 0.0 0 0 1 1052 [] 2 1053 .. 2 1053 .. 0.98
Alignments for each domain:
== domain 1 score: 1574.7 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladk 62
pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+++ad+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPAMADA 63
689*********************************************************** PP
TIGR01369 63 vYiePltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikk 124
+YieP+++++v+kiiekErpDa+l+t+GGqtaLn+a++le++GvLek+gv+++G++ ++i+k
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 64 TYIEPIKWQTVAKIIEKERPDALLPTMGGQTALNCALDLEREGVLEKFGVEMIGANADTIDK 125
************************************************************** PP
TIGR01369 125 aedRekFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneee 186
aedR +F++a+k i+++ ++s i++s+eea ++ e++g+P+i+R++ft+gGtG+gia+n+ee
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 126 AEDRSRFDKAMKSIGLDCPRSGIAHSMEEANAVLERLGFPCIIRPSFTMGGTGGGIAYNREE 187
************************************************************** PP
TIGR01369 187 lkelvekalkaspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsiv 248
++e+++++l++sp+k++l+++sl gwkE+E+EvvRD+kdnciivc+iEn+Dp+GvHtGdsi+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 188 FEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKKDNCIIVCSIENFDPMGVHTGDSIT 249
************************************************************** PP
TIGR01369 249 vaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALA 309
vaP+qtLtdkeyq+lR+asl+++re+gve++ +nvqf++ P++ r+vviE+npRvsRssALA
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 250 VAPAQTLTDKEYQILRNASLAVLREIGVETGgSNVQFGICPNTGRMVVIEMNPRVSRSSALA 311
*****************************988****************************** PP
TIGR01369 310 skAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrk 370
skAtG+PiAkvaaklavGy+Ldel+nd+t+ +t+AsfEPs+DYvv+k+Pr++++kf k+d +
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 312 SKATGFPIAKVAAKLAVGYTLDELSNDITGgKTPASFEPSIDYVVTKLPRFAFEKFPKADAR 373
*****************************879****************************** PP
TIGR01369 371 lgtqmksvGEvmaigrtfeealqkalrsleekllglklkeke..aesdeeleealkkpndrR 430
l+tqmksvGEvmaigrtf+e+lqkalr le ++ gl++k + es + l+++l+ p ++R
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 374 LTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDEKLDLsnPESMSILKRELTVPGAER 435
***********************************887755400455667899********* PP
TIGR01369 431 lfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGf 492
++++a+a+r+g+sve+++ + id +fl ++++l++ e+++++ l ++++++ ++k++Gf
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 436 IWYVADAFRAGLSVEDIFGMNMIDPWFLVQIEDLIKEEEKVKTLGLASIDHDVMFRLKRKGF 497
************************************************************** PP
TIGR01369 493 sdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtek 554
sd ++akl++v+e+++r+ r++l+i pv+krvDt+aaEf ++t+YlYstyeee++ +++ ++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 498 SDMRLAKLLGVTEKALRRHRHKLEIFPVYKRVDTCAAEFATDTAYLYSTYEEECEAAPSGRD 559
*****************************************************766666665 PP
TIGR01369 555 kkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeel 616
k+++lG+Gp+Rigqg+EFDyc+vha+lalre gy+ti++n+nPEtvstDyd++drLyFe++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 560 -KIMILGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVNCNPETVSTDYDTSDRLYFEPV 620
.************************************************************* PP
TIGR01369 617 tvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklld 678
t+edvl+i++ ek++gvivq+gGqt+l+la++leeagv+i+Gts+++idraEdRe+F+++++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 621 TLEDVLEIVRVEKPKGVIVQYGGQTPLKLARALEEAGVPIIGTSPDAIDRAEDRERFQQMVE 682
************************************************************** PP
TIGR01369 679 elgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevs 740
+l++ qp +++++s +ea ++a++igyP++vRpsyvlgGrameiv++eeel+ryl++av+vs
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 683 RLNLRQPPNATVRSEDEAIRAAAKIGYPLVVRPSYVLGGRAMEIVYEEEELKRYLRDAVKVS 744
************************************************************** PP
TIGR01369 741 kekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkk 802
+++Pvl+d++l+ a+E+dvDav+dg++v+i +i++HiE+aGvHsGDs+++lpp +l +++++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 745 NDSPVLLDHFLNCAIEMDVDAVCDGTDVVIGAIMQHIEQAGVHSGDSACSLPPYSLPAHIQD 806
************************************************************** PP
TIGR01369 803 kikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvl 864
+++e+vkk+a el v+Gl+n+q+++++e++yviEvn+RasRtvPfvsk +gv+l+ +a++v+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 807 EMREQVKKMALELGVVGLMNVQLALQGEDIYVIEVNPRASRTVPFVSKCIGVSLAMIAARVM 868
************************************************************** PP
TIGR01369 865 lgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeall 926
+gk+l+e g +ke +++++vk+avf+f+k+ gvd++lgpemkstGEvmg+g+++ ea++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 869 AGKTLKE--IGFTKEIIPNFYSVKEAVFPFAKFPGVDPILGPEMKSTGEVMGVGDTFGEAFA 928
*******..6789************************************************* PP
TIGR01369 927 kallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevv 988
ka++ +++++++ g++++sv+d dk + +a+ l ++g++v+at+gtak +e ag k++ v
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 929 KAQMGASEVLPTGGTAFISVRDDDKPLVAGVARDLINLGFEVVATAGTAKLIEAAGLKVRRV 990
************************************************************** PP
TIGR01369 989 lkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaealle 1050
+kv+e ++++++++k++e++l+in+t+ ++++ ++y+irr+a+++k+ + t++++ ea++e
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 991 NKVTEGRPHVVDMIKNDEVTLIINTTE-GRQSIADSYSIRRNALQHKIYCTTTIAAGEAICE 1051
************************997.77788899***********************999 PP
TIGR01369 1051 al 1052
al
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1172 1052 AL 1053
86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1073 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: 0.10u 0.04s 00:00:00.14 Elapsed: 00:00:00.12
# Mc/sec: 8.77
//
[ok]
This GapMind analysis is from Apr 09 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