Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate N515DRAFT_2713 N515DRAFT_2713 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>FitnessBrowser__Dyella79:N515DRAFT_2713
Length = 1075
Score = 1474 bits (3815), Expect = 0.0
Identities = 743/1075 (69%), Positives = 879/1075 (81%), Gaps = 3/1075 (0%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDIKS+LI+GAGPIVIGQACEFDYSGAQACKAL+EEGYRVILVNSNPATIMTDPE
Sbjct: 1 MPKRTDIKSVLIIGAGPIVIGQACEFDYSGAQACKALKEEGYRVILVNSNPATIMTDPET 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADA YIEPI+W+ V +II KERPDAVLPTMGGQT LNCAL+L GVLE++GV +IGA+
Sbjct: 61 ADAVYIEPINWQTVERIIAKERPDAVLPTMGGQTGLNCALDLADNGVLEKYGVELIGASR 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
+AI AEDR F +AMK IGLE ++ +A T E+AL + VGFP IIRPSFT+GGSGGG
Sbjct: 121 EAIRMAEDRELFRIAMKDIGLECPKAEVAKTFEQALEIQTKVGFPTIIRPSFTLGGSGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYN+EEFEEI RGLDLSP E+L++ES++GWKE+EMEVVRDK DNCIIVCSIEN D M
Sbjct: 181 IAYNKEEFEEIAKRGLDLSPVHEILVEESVLGWKEFEMEVVRDKADNCIIVCSIENLDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPAQTLTDKEYQ +R+AS+AVLR+IGV+TGGSNVQF +N ++GR++VIEM
Sbjct: 241 GVHTGDSITVAPAQTLTDKEYQRLRDASIAVLRKIGVDTGGSNVQFGINAEDGRVVVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAK+AAKLAVGYTLDEL NDITGG TPASFEP+IDYVVTKIP
Sbjct: 301 NPRVSRSSALASKATGFPIAKIAAKLAVGYTLDELKNDITGGLTPASFEPTIDYVVTKIP 360
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPK-VSLDDPE 419
RF FEKF A+ RLTTQMKSVGEVMA+GRT ESLQKALRGLE+G TG +P V E
Sbjct: 361 RFAFEKFPSADARLTTQMKSVGEVMAMGRTFHESLQKALRGLEIGKTGLNPTGVDFSTDE 420
Query: 420 ALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEV 479
L ++REL++ DR++++ DAFRAGLS++ V+ L+ +D WFL E++V E +V
Sbjct: 421 GLAALKRELREPRPDRVFHLGDAFRAGLSLEEVYGLSRVDPWFLAAFEDIVLTENEVQAQ 480
Query: 480 GITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATD 539
GI+ L+A +R+LKR GF+DAR+A+L EA +R LR + PVYKRVD+CAAEFAT
Sbjct: 481 GISALDALRMRELKRMGFSDARIAELTDTDEAAVRHLRRTLGVRPVYKRVDSCAAEFATT 540
Query: 540 TAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMV 599
TAYMYSTYEEECEANP T+R+KIMVLGGGPNRIGQGIEFDYCCVHA+LALREDG+ETIMV
Sbjct: 541 TAYMYSTYEEECEANP-TNRDKIMVLGGGPNRIGQGIEFDYCCVHAALALREDGFETIMV 599
Query: 600 NCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGV 659
NCNPETVSTDYDTSDRLYFEP+TLEDVLEIV +EKPKGVIVQYGGQTPLKLARALEAAG
Sbjct: 600 NCNPETVSTDYDTSDRLYFEPLTLEDVLEIVDLEKPKGVIVQYGGQTPLKLARALEAAGA 659
Query: 660 PVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYV 719
PVIGTSPD+ID AEDRERFQ +E++ LKQP N T + A+ A+EIGYPLVVRPSYV
Sbjct: 660 PVIGTSPDSIDLAEDRERFQQMIEKIGLKQPPNRTARNADEALALAREIGYPLVVRPSYV 719
Query: 720 LGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGE-MVLIGGI 778
LGGRAMEIVY +ADL RY + AV VSND+PVLLD FLD AVEVDVD I D E VL+GGI
Sbjct: 720 LGGRAMEIVYGDADLSRYIREAVQVSNDSPVLLDRFLDHAVEVDVDIIADAEGNVLVGGI 779
Query: 779 MEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVY 838
MEHIE+AGVHSGDS+CSLP Y+LS+++QD +R+QV +A EL+V GLMN QFA++ + V+
Sbjct: 780 MEHIEEAGVHSGDSSCSLPPYSLSKDVQDELRRQVALMAKELKVIGLMNTQFAIQGDTVF 839
Query: 839 LIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFN 898
++EVNPRA+RTVPFVSKATGVPLAK+AAR MAG++L Q T+EVIP YYSVKE + PF
Sbjct: 840 ILEVNPRASRTVPFVSKATGVPLAKIAARAMAGRTLIAQNATREVIPSYYSVKEAIFPFL 899
Query: 899 KFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVV 958
KF VDP+LGPEMRSTGEVMGVGR+F AFA+ + G+ +SVR+ DK+R++
Sbjct: 900 KFQNVDPILGPEMRSTGEVMGVGRSFGAAFARGHDAAGIKTPPKGKVFVSVRDADKDRLL 959
Query: 959 DLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTS 1018
+A + +GF L AT GTA L G+ +NKV EGRPHI D IKNGE YI+NTT
Sbjct: 960 PVAKDAVSRGFSLVATEGTAAYLAGHGVACERINKVAEGRPHIVDLIKNGEIVYIVNTTE 1019
Query: 1019 GRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
G++AI DS IRR ALQ++V Y TT+ G A +L+ +V S+QE+H ++K
Sbjct: 1020 GKQAIADSFSIRREALQHRVTYSTTVAGARALVHSLDYHGAGEVHSLQELHKELK 1074
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: 3128
Number of extensions: 128
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: 1073
Length of database: 1075
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1030
Effective search space: 1058840
Effective search space used: 1058840
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 N515DRAFT_2713 N515DRAFT_2713 (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.9893.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 1538.0 0.0 0 1537.8 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 N515DRAFT_2713 carbamoyl-phospha
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 N515DRAFT_2713 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1537.8 0.0 0 0 1 1051 [. 2 1054 .. 2 1055 .. 0.98
Alignments for each domain:
== domain 1 score: 1537.8 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvY 64
pkr+dik+vl+iG+GpivigqA+EFDYsG+qa+kalkeeg++v+Lvnsn+At+mtd+e ad+vY
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 2 PKRTDIKSVLIIGAGPIVIGQACEFDYSGAQACKALKEEGYRVILVNSNPATIMTDPETADAVY 65
689************************************************************* PP
TIGR01369 65 iePltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedR 128
ieP+++++ve+ii kErpDa+l+t+GGqt+Ln+a++l ++GvLekygv+l+G++ eai+ aedR
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 66 IEPINWQTVERIIAKERPDAVLPTMGGQTGLNCALDLADNGVLEKYGVELIGASREAIRMAEDR 129
**************************************************************** PP
TIGR01369 129 ekFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelve 192
e+F+ a+k+i++e +k+e++++ e+ale+++++g+P i+R++ftlgG+G+gia+n+ee++e+++
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 130 ELFRIAMKDIGLECPKAEVAKTFEQALEIQTKVGFPTIIRPSFTLGGSGGGIAYNKEEFEEIAK 193
**************************************************************** PP
TIGR01369 193 kalkaspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLt 256
++l++sp++++lve+s+ gwkE+E+EvvRD++dnciivc+iEnlDp+GvHtGdsi+vaP+qtLt
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 194 RGLDLSPVHEILVEESVLGWKEFEMEVVRDKADNCIIVCSIENLDPMGVHTGDSITVAPAQTLT 257
**************************************************************** PP
TIGR01369 257 dkeyqllRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAk 319
dkeyq+lRdas++++r++gv+++ +nvqf+++ e+ r+vviE+npRvsRssALAskAtG+PiAk
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 258 DKEYQRLRDASIAVLRKIGVDTGgSNVQFGINAEDGRVVVIEMNPRVSRSSALASKATGFPIAK 321
********************9988**************************************** PP
TIGR01369 320 vaaklavGysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvm 382
+aaklavGy+Ldelknd+t+ t+AsfEP++DYvv+kiPr++++kf ++d +l+tqmksvGEvm
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 322 IAAKLAVGYTLDELKNDITGgLTPASFEPTIDYVVTKIPRFAFEKFPSADARLTTQMKSVGEVM 385
*******************867****************************************** PP
TIGR01369 383 aigrtfeealqkalrsleekllglklkekeaesde...eleealkkpndrRlfaiaealrrgvs 443
a+grtf+e+lqkalr le++ +gl+ + +de +l+++l++p ++R+f + +a+r+g+s
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 386 AMGRTFHESLQKALRGLEIGKTGLNPTGVDFSTDEglaALKRELREPRPDRVFHLGDAFRAGLS 449
***********************8877665555442227899********************** PP
TIGR01369 444 veevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseae 507
+eevy l+++d +fl ++++v +e+e++ + ++ l++ ++++k++Gfsd++ia+l++++ea+
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 450 LEEVYGLSRVDPWFLAAFEDIVLTENEVQAQGISALDALRMRELKRMGFSDARIAELTDTDEAA 513
**************************************************************** PP
TIGR01369 508 vrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgv 571
vr+lr++lg+ pv+krvD +aaEf ++t+Y+Ystyeee++ ++++++ k++vlG+Gp+Rigqg+
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 514 VRHLRRTLGVRPVYKRVDSCAAEFATTTAYMYSTYEEECEANPTNRD-KIMVLGGGPNRIGQGI 576
**************************************766666555.**************** PP
TIGR01369 572 EFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegviv 635
EFDyc+vha+lalre g++ti++n+nPEtvstDyd++drLyFe+lt+edvl+i++ ek++gviv
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 577 EFDYCCVHAALALREDGFETIMVNCNPETVSTDYDTSDRLYFEPLTLEDVLEIVDLEKPKGVIV 640
**************************************************************** PP
TIGR01369 636 qlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakei 699
q+gGqt+l+la++le+ag++++Gts++sid aEdRe+F+++++++g+kqp +++a++ +ea +
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 641 QYGGQTPLKLARALEAAGAPVIGTSPDSIDLAEDRERFQQMIEKIGLKQPPNRTARNADEALAL 704
**************************************************************** PP
TIGR01369 700 akeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDava 763
a+eigyP++vRpsyvlgGrameiv+ +++l+ry++eav+vs+++Pvl+d++l++avEvdvD++a
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 705 AREIGYPLVVRPSYVLGGRAMEIVYGDADLSRYIREAVQVSNDSPVLLDRFLDHAVEVDVDIIA 768
**************************************************************** PP
TIGR01369 764 dge.evliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfv 826
d e +vl+ gi+eHiEeaGvHsGDs ++lpp +ls++v+++++++v+ +akelkv Gl+n qf+
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 769 DAEgNVLVGGIMEHIEEAGVHSGDSSCSLPPYSLSKDVQDELRRQVALMAKELKVIGLMNTQFA 832
96439*********************************************************** PP
TIGR01369 827 vkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaa 890
+++++v ++Evn+RasRtvPfvska+gvpl+k+a+++++g++l ++ +++e +++++vk+a
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 833 IQGDTVFILEVNPRASRTVPFVSKATGVPLAKIAARAMAGRTLIAQN--ATREVIPSYYSVKEA 894
*******************************************9955..589999********* PP
TIGR01369 891 vfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeel 954
f+f k+++vd++lgpem+stGEvmg+gr++ a+++ a++ k++ kg+v++sv+d+dk++l
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 895 IFPFLKFQNVDPILGPEMRSTGEVMGVGRSFGAAFARGHDAAGIKTPPKGKVFVSVRDADKDRL 958
**************************************************************** PP
TIGR01369 955 lelakklaekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkk 1018
l++ak +++g++++ategta++l+ +g+ +e ++kv e +++i++l+k++ei +++n+t+ +k
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 959 LPVAKDAVSRGFSLVATEGTAAYLAGHGVACERINKVAEGRPHIVDLIKNGEIVYIVNTTE-GK 1021
**********************************************************997.78 PP
TIGR01369 1019 kaaekgykirreaveykvplvteletaeallea 1051
+a ++++irrea++++v++ t++++a+al+++
lcl|FitnessBrowser__Dyella79:N515DRAFT_2713 1022 QAIADSFSIRREALQHRVTYSTTVAGARALVHS 1054
899999********************9998875 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: 0.09u 0.03s 00:00:00.12 Elapsed: 00:00:00.11
# Mc/sec: 9.99
//
[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