Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate PfGW456L13_5099 Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)
Query= BRENDA::P00968
(1073 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099
Length = 1073
Score = 1602 bits (4148), Expect = 0.0
Identities = 807/1073 (75%), Positives = 918/1073 (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 DTIDKAEDRSRFDKAMKSIGLACPRSGIAHSMEEANAVLEKLGFPCIIRPSFTMGGTGGG 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 KV L +PE+
Sbjct: 361 RFAFEKFSKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDEKVDLANPES 420
Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
++ ++REL GA+RIWY+ADA RAG+SV+ +F +T ID WFLVQ+E+L++ EEKV +G
Sbjct: 421 MSVLKRELTVPGAERIWYVADAMRAGMSVEDIFGMTMIDPWFLVQMEDLIKDEEKVKTLG 480
Query: 481 ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
+T ++ D + +LKRKGF+D RLAKL GV E +R R + ++ PVYKRVDTCAAEFATDT
Sbjct: 481 LTSIDRDLMFRLKRKGFSDMRLAKLLGVTEKSLRAHRHKLEIFPVYKRVDTCAAEFATDT 540
Query: 541 AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
AY+YSTYEEECEA PS R+KIM+LGGGPNRIGQGIEFDYCCVHA+LALR+DGYETIMVN
Sbjct: 541 AYLYSTYEEECEAAPS-GRDKIMILGGGPNRIGQGIEFDYCCVHAALALRDDGYETIMVN 599
Query: 601 CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
CNPETVSTDYDTSDRLYFEPVTLEDVLEIVR+EKPKGVIVQYGGQTPLKLARALEAAGVP
Sbjct: 600 CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRVEKPKGVIVQYGGQTPLKLARALEAAGVP 659
Query: 661 VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
+IGTSPDAIDRAEDRERFQ V+RL L+QP NATV + + A+ A +IGYPLVVRPSYVL
Sbjct: 660 IIGTSPDAIDRAEDRERFQQMVQRLNLRQPPNATVRSEDEAIRAAAKIGYPLVVRPSYVL 719
Query: 721 GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
GGRAMEIVY+E +L+RY + AV VSND+PVLLDHFL+ A+E+DVDA+CDG+ V+IG IM+
Sbjct: 720 GGRAMEIVYEEEELKRYLREAVQVSNDSPVLLDHFLNCAIEMDVDAVCDGKDVVIGAIMQ 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 EVNPRASRTVPFVSKCIGVSLAMIAARVMAGKTLKELGFTKEIIPNFYSVKEAVFPFAKF 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: 3179
Number of extensions: 139
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 PfGW456L13_5099 (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.18565.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 1577.0 0.0 0 1576.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 Carbamoyl-phosphate synthase lar
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 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 ! 1576.9 0.0 0 0 1 1052 [] 2 1053 .. 2 1053 .. 0.98
Alignments for each domain:
== domain 1 score: 1576.9 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtv 53
pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 2 PKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATI 54
689************************************************** PP
TIGR01369 54 mtdeeladkvYiePltveavekiiekErpDailltlGGqtaLnlaveleekGv 106
mtd+++ad++YieP+++++v+kiiekErpDa+l+t+GGqtaLn+a++le++Gv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 55 MTDPAMADATYIEPIKWQTVAKIIEKERPDALLPTMGGQTALNCALDLEREGV 107
***************************************************** PP
TIGR01369 107 LekygvkllGtkveaikkaedRekFkealkeineevakseivesveealeaae 159
Lek+gv+++G++ ++i+kaedR +F++a+k i++ ++s i++s+eea ++ e
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 108 LEKFGVEMIGANADTIDKAEDRSRFDKAMKSIGLACPRSGIAHSMEEANAVLE 160
***************************************************** PP
TIGR01369 160 eigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagw 212
++g+P+i+R++ft+gGtG+gia+n+ee++e+++++l++sp+k++l+++sl gw
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 161 KLGFPCIIRPSFTMGGTGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGW 213
***************************************************** PP
TIGR01369 213 kEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRd 265
kE+E+EvvRD+kdnciivc+iEn+Dp+GvHtGdsi+vaP+qtLtdkeyq+lR+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 214 KEYEMEVVRDKKDNCIIVCSIENFDPMGVHTGDSITVAPAQTLTDKEYQILRN 266
***************************************************** PP
TIGR01369 266 aslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPi 317
asl+++re+gve++ +nvqf++ P++ r+vviE+npRvsRssALAskAtG+Pi
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 267 ASLAVLREIGVETGgSNVQFGICPNTGRMVVIEMNPRVSRSSALASKATGFPI 319
************988************************************** PP
TIGR01369 318 AkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdr 369
AkvaaklavGy+Ldel+nd+t+ +t+AsfEPs+DYvv+k+Pr++++kf+k+d
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 320 AKVAAKLAVGYTLDELSNDITGgKTPASFEPSIDYVVTKLPRFAFEKFSKADA 372
*********************879***************************** PP
TIGR01369 370 klgtqmksvGEvmaigrtfeealqkalrsleekllglklkekea..esdeele 420
+l+tqmksvGEvmaigrtf+e+lqkalr le ++ gl++k + a es + l+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 373 RLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDEKVDLAnpESMSVLK 425
************************************88776554115566789 PP
TIGR01369 421 ealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekelee 473
++l+ p ++R++++a+a+r+g+sve+++ +t id +fl ++++l++ e+++++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 426 RELTVPGAERIWYVADAMRAGMSVEDIFGMTMIDPWFLVQMEDLIKDEEKVKT 478
9**************************************************** PP
TIGR01369 474 eklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDt 526
l+ ++++l+ ++k++Gfsd ++akl++v+e+++r+ r++l+i pv+krvDt
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 479 LGLTSIDRDLMFRLKRKGFSDMRLAKLLGVTEKSLRAHRHKLEIFPVYKRVDT 531
***************************************************** PP
TIGR01369 527 vaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavh 579
+aaEf ++t+YlYstyeee++ +++ ++ k+++lG+Gp+Rigqg+EFDyc+vh
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 532 CAAEFATDTAYLYSTYEEECEAAPSGRD-KIMILGGGPNRIGQGIEFDYCCVH 583
*******************766666665.************************ PP
TIGR01369 580 avlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekveg 632
a+lalr+ gy+ti++n+nPEtvstDyd++drLyFe++t+edvl+i++ ek++g
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 584 AALALRDDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRVEKPKG 636
***************************************************** PP
TIGR01369 633 vivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqp 685
vivq+gGqt+l+la++le+agv+i+Gts+++idraEdRe+F++++++l++ qp
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 637 VIVQYGGQTPLKLARALEAAGVPIIGTSPDAIDRAEDRERFQQMVQRLNLRQP 689
***************************************************** PP
TIGR01369 686 kgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeave 738
+++++s +ea ++a++igyP++vRpsyvlgGrameiv++eeel+ryl+eav+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 690 PNATVRSEDEAIRAAAKIGYPLVVRPSYVLGGRAMEIVYEEEELKRYLREAVQ 742
***************************************************** PP
TIGR01369 739 vskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvl 791
vs+++Pvl+d++l+ a+E+dvDav+dg++v+i +i++HiE+aGvHsGDs+++l
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 743 VSNDSPVLLDHFLNCAIEMDVDAVCDGKDVVIGAIMQHIEQAGVHSGDSACSL 795
***************************************************** PP
TIGR01369 792 ppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRt 844
pp +l ++++++++e+vkk+a el v+Gl+n+q+++++e++yviEvn+RasRt
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 796 PPYSLPAHIQDEMREQVKKMALELGVVGLMNVQLALQGEDIYVIEVNPRASRT 848
***************************************************** PP
TIGR01369 845 vPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfskl 897
vPfvsk +gv+l+ +a++v++gk+l+e g +ke +++++vk+avf+f+k+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 849 VPFVSKCIGVSLAMIAARVMAGKTLKE--LGFTKEIIPNFYSVKEAVFPFAKF 899
***************************..5679******************** PP
TIGR01369 898 agvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkd 950
gvd++lgpemkstGEvmg+g+++ ea++ka++ +++++++ g++++sv+d d
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 900 PGVDPILGPEMKSTGEVMGVGDTFGEAFAKAQMGASEVLPTGGTAFISVRDDD 952
***************************************************** PP
TIGR01369 951 keellelakklaekglkvyategtakvleeagikaevvlkvseeaekilellk 1003
k + +a+ l ++g++v+at+gtak +e ag k++ v+kv+e ++++++++k
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 953 KPLVAGVARDLINLGFEVVATAGTAKLIEAAGLKVRRVNKVTEGRPHVVDMIK 1005
***************************************************** PP
TIGR01369 1004 eeeielvinltskkkkaaekgykirreaveykvplvteletaealleal 1052
++e++l+in+t+ ++++ ++y+irr+a+++k+ + t++++ ea++eal
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5099 1006 NDEVTLIINTTE-GRQSIADSYSIRRNALQHKIYCTTTIAAGEAICEAL 1053
*********997.77788899***********************99986 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: 0.09u 0.03s 00:00:00.12 Elapsed: 00:00:00.12
# Mc/sec: 9.24
//
[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