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.19084.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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.10
# Mc/sec: 11.18
//
[ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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