Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate Ac3H11_436 Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)
Query= BRENDA::P00968
(1073 letters)
>FitnessBrowser__acidovorax_3H11:Ac3H11_436
Length = 1081
Score = 1467 bits (3798), Expect = 0.0
Identities = 759/1085 (69%), Positives = 873/1085 (80%), Gaps = 19/1085 (1%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTD+KSILI+GAGPI+IGQACEFDYSG QACKALREEGY+VIL+NSNPATIMTDP
Sbjct: 1 MPKRTDLKSILIIGAGPIIIGQACEFDYSGVQACKALREEGYKVILINSNPATIMTDPAT 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
AD TYIEPI W+ V KII KERPDA+LPTMGGQTALNCAL+L R GVL+++ V +IGAT
Sbjct: 61 ADVTYIEPITWQTVEKIIAKERPDAILPTMGGQTALNCALDLWRNGVLDKYKVELIGATP 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
+AIDKAEDR +F AM KIGL +ARSGIAH+M+EA AV VGFP +IRPSFT+GG+GGG
Sbjct: 121 EAIDKAEDRLKFKDAMTKIGLGSARSGIAHSMDEAWAVQKSVGFPTVIRPSFTLGGTGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYN EEFE IC RGL+ SPT ELLI+ESL+GWKEYEMEVVRDK DNCII+CSIEN D M
Sbjct: 181 IAYNPEEFETICKRGLEASPTNELLIEESLLGWKEYEMEVVRDKADNCIIICSIENLDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPAQTLTDKEYQIMRNAS+AVLREIGV+TGGSNVQF+VNPK+GR+IVIEM
Sbjct: 241 GVHTGDSITVAPAQTLTDKEYQIMRNASLAVLREIGVDTGGSNVQFSVNPKDGRMIVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL N+ITGG TPASFEPSIDYVVTKIP
Sbjct: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELRNEITGGATPASFEPSIDYVVTKIP 360
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
RF FEKF A+ RLTTQMKSVGEVMA+GRT QES QKALRGLEVG G + K D E
Sbjct: 361 RFAFEKFPTADSRLTTQMKSVGEVMAMGRTFQESFQKALRGLEVGVDGMNEKT--QDREV 418
Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKV---- 476
L K EL + G +RIWY+ DAF GLSVD V++LT ID+WFLVQIEE+V++E ++
Sbjct: 419 LEK---ELGEPGPERIWYVGDAFAMGLSVDEVYDLTKIDKWFLVQIEEIVKIELELDQLA 475
Query: 477 ---AEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCA 533
E + L+AD LR LK+KGF+D RLAKL E +R+ R ++ PVYKRVDTCA
Sbjct: 476 ADKGEGALAALDADTLRTLKKKGFSDRRLAKLLKTTEKSVREARRALNVRPVYKRVDTCA 535
Query: 534 AEFATDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDG 593
AEFAT+TAYMYSTYEEECEA P TD++KIMVLGGGPNRIGQGIEFDYCCVHA+LA+REDG
Sbjct: 536 AEFATNTAYMYSTYEEECEAEP-TDKKKIMVLGGGPNRIGQGIEFDYCCVHAALAMREDG 594
Query: 594 YETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARA 653
YETIMVNCNPETVSTDYDTSDRLYFEP+TLEDVLEIV EKP GVIVQYGGQTPLKLA
Sbjct: 595 YETIMVNCNPETVSTDYDTSDRLYFEPLTLEDVLEIVDKEKPHGVIVQYGGQTPLKLALG 654
Query: 654 LEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLV 713
LEA GVP+IGTSPD ID AEDRERFQ + L L+QP NAT A+EKA +GYPLV
Sbjct: 655 LEAEGVPIIGTSPDMIDAAEDRERFQKLLGDLGLRQPPNATARTEAEALEKAATLGYPLV 714
Query: 714 VRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGE-M 772
VRPSYVLGGRAMEIV+++ DL RY + AV VSND+PVLLD FL+DA+E DVD + D E
Sbjct: 715 VRPSYVLGGRAMEIVHEQRDLERYMREAVKVSNDSPVLLDRFLNDAIECDVDCLRDPEGK 774
Query: 773 VLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAV 832
IGG+MEHIEQAGVHSGDSACSLP Y L Q D +++Q +A L V GLMNVQFA+
Sbjct: 775 TFIGGVMEHIEQAGVHSGDSACSLPPYYLKQATVDELKRQSAAMAEGLNVVGLMNVQFAI 834
Query: 833 K----NNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYY 888
+ + +Y++EVNPRA+RTVPFVSKATG+ LAKVAAR MAG++LA QG+TKEV PPY+
Sbjct: 835 QEVDGKDVIYVLEVNPRASRTVPFVSKATGIQLAKVAARCMAGQTLASQGITKEVTPPYF 894
Query: 889 SVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLS 948
SVKE V PF KFPGVD +LGPEM+STGEVMGVG+TF EAF K+QLG+ + + G+ L+
Sbjct: 895 SVKEAVFPFVKFPGVDTILGPEMKSTGEVMGVGKTFGEAFVKSQLGAGTKLPTSGKVFLT 954
Query: 949 VREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNG 1008
V+ DK R VD+A +L+ GF+L AT GTA + +AG+ +VNKV EGRPHI D IKN
Sbjct: 955 VKNNDKPRAVDIARQLVALGFDLVATKGTAAAIADAGVPVVVVNKVTEGRPHIVDMIKNN 1014
Query: 1009 EYTYIINTTSGRR-AIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQE 1067
E +INT RR AI DSR IR S+L +V TT+ G A + V SVQE
Sbjct: 1015 EIVMVINTVEERRNAIADSRAIRTSSLLARVTTFTTIFGAEAAVEGMKYLDKLDVYSVQE 1074
Query: 1068 MHAQI 1072
+HAQ+
Sbjct: 1075 LHAQL 1079
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: 3125
Number of extensions: 132
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: 1073
Length of database: 1081
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1035
Effective search space: 1062945
Effective search space used: 1062945
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 Ac3H11_436 (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.26181.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 1538.2 0.0 0 1538.1 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 Carbamoyl-phosphate synthase lar
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 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 ! 1538.1 0.0 0 0 1 1050 [. 2 1059 .. 2 1061 .. 0.98
Alignments for each domain:
== domain 1 score: 1538.1 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeelad 61
pkr+d+k++l+iG+Gpi+igqA+EFDYsG qa+kal+eeg++v+L+nsn+At+mtd++ ad
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 2 PKRTDLKSILIIGAGPIIIGQACEFDYSGVQACKALREEGYKVILINSNPATIMTDPATAD 62
689********************************************************** PP
TIGR01369 62 kvYiePltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveai 122
+YieP+t+++vekii kErpDail+t+GGqtaLn+a++l ++GvL+ky v+l+G++ eai
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 63 VTYIEPITWQTVEKIIAKERPDAILPTMGGQTALNCALDLWRNGVLDKYKVELIGATPEAI 123
************************************************************* PP
TIGR01369 123 kkaedRekFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaen 183
+kaedR kFk+a+++i++ a+s i++s++ea ++++++g+P ++R++ftlgGtG+gia+n
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 124 DKAEDRLKFKDAMTKIGLGSARSGIAHSMDEAWAVQKSVGFPTVIRPSFTLGGTGGGIAYN 184
************************************************************* PP
TIGR01369 184 eeelkelvekalkaspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtG 244
ee++++++++l+asp++++l+e+sl gwkE+E+EvvRD++dncii+c+iEnlDp+GvHtG
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 185 PEEFETICKRGLEASPTNELLIEESLLGWKEYEMEVVRDKADNCIIICSIENLDPMGVHTG 245
************************************************************* PP
TIGR01369 245 dsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsR 304
dsi+vaP+qtLtdkeyq++R+asl+++re+gv+++ +nvqf+++P++ r++viE+npRvsR
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 246 DSITVAPAQTLTDKEYQIMRNASLAVLREIGVDTGgSNVQFSVNPKDGRMIVIEMNPRVSR 306
********************************9988************************* PP
TIGR01369 305 ssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkf 364
ssALAskAtG+PiAkvaaklavGy+Ldel+n++t+ t+AsfEPs+DYvv+kiPr++++kf
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 307 SSALASKATGFPIAKVAAKLAVGYTLDELRNEITGgATPASFEPSIDYVVTKIPRFAFEKF 367
**********************************878************************ PP
TIGR01369 365 ekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkekeaesdeeleealkk 425
++d++l+tqmksvGEvma+grtf+e++qkalr le ++ g+++k ++++e le++l +
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 368 PTADSRLTTQMKSVGEVMAMGRTFQESFQKALRGLEVGVDGMNEK---TQDREVLEKELGE 425
*************************************99998886...667777889**** PP
TIGR01369 426 pndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklk.......el 479
p ++R++++ +a+ g+sv+evy+ltkid++fl +++++v++e el++ +++ l
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 426 PGPERIWYVGDAFAMGLSVDEVYDLTKIDKWFLVQIEEIVKIELELDQLAADkgegalaAL 486
*********************************************9987433333444489 PP
TIGR01369 480 kkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYs 540
++++l+++kk+Gfsd+++akl+k++e++vr++r++l++ pv+krvDt+aaEf ++t+Y+Ys
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 487 DADTLRTLKKKGFSDRRLAKLLKTTEKSVREARRALNVRPVYKRVDTCAAEFATNTAYMYS 547
************************************************************* PP
TIGR01369 541 tyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtv 601
tyeee ++e t+kkk++vlG+Gp+Rigqg+EFDyc+vha+la+re gy+ti++n+nPEtv
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 548 TYEEE-CEAEPTDKKKIMVLGGGPNRIGQGIEFDYCCVHAALAMREDGYETIMVNCNPETV 607
*****.677888888********************************************** PP
TIGR01369 602 stDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsae 662
stDyd++drLyFe+lt+edvl+i++kek++gvivq+gGqt+l+la le++gv+i+Gts++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 608 STDYDTSDRLYFEPLTLEDVLEIVDKEKPHGVIVQYGGQTPLKLALGLEAEGVPIIGTSPD 668
************************************************************* PP
TIGR01369 663 sidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiv 723
id aEdRe+F+kll +lg+ qp +++a++ ea e+a+++gyP++vRpsyvlgGrameiv
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 669 MIDAAEDRERFQKLLGDLGLRQPPNATARTEAEALEKAATLGYPLVVRPSYVLGGRAMEIV 729
************************************************************* PP
TIGR01369 724 eneeeleryleeavevskekPvlidkyledavEvdvDavad.geevliagileHiEeaGvH 783
+++ +lery++eav+vs+++Pvl+d++l+da+E+dvD + d +++ +i g++eHiE+aGvH
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 730 HEQRDLERYMREAVKVSNDSPVLLDRFLNDAIECDVDCLRDpEGKTFIGGVMEHIEQAGVH 790
***************************************99456999************** PP
TIGR01369 784 sGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkd....eevyviEvnvR 840
sGDs+++lpp l++ +++++k++++++a+ l+v+Gl+n+qf++++ + +yv+Evn+R
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 791 SGDSACSLPPYYLKQATVDELKRQSAAMAEGLNVVGLMNVQFAIQEvdgkDVIYVLEVNPR 851
*******************************************9875544669******** PP
TIGR01369 841 asRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvd 901
asRtvPfvska+g++l+k+a+++++g++l++ +g++ke ++ +++vk+avf+f k+ gvd
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 852 ASRTVPFVSKATGIQLAKVAARCMAGQTLAS--QGITKEVTPPYFSVKEAVFPFVKFPGVD 910
******************************9..789************************* PP
TIGR01369 902 vvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakkla 962
+lgpemkstGEvmg+g+++ ea++k++l +++k+++ g+v+l+vk++dk +++++a++l+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 911 TILGPEMKSTGEVMGVGKTFGEAFVKSQLGAGTKLPTSGKVFLTVKNNDKPRAVDIARQLV 971
************************************************************* PP
TIGR01369 963 ekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaek 1023
++g+ ++at+gta+++++ag+ + vv+kv+e +++i++++k++ei +vin+ +++++a +
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 972 ALGFDLVATKGTAAAIADAGVPVVVVNKVTEGRPHIVDMIKNNEIVMVINTVEERRNAIAD 1032
************************************************************* PP
TIGR01369 1024 gykirreaveykvplvteletaealle 1050
+ ir +++ +v+++t++ +aea++e
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_436 1033 SRAIRTSSLLARVTTFTTIFGAEAAVE 1059
******************999998876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1081 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.08
# Mc/sec: 12.72
//
[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