Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_011373096.1 SUDEN_RS07665 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000012965.1:WP_011373096.1
Length = 1085
Score = 1159 bits (2999), Expect = 0.0
Identities = 609/1078 (56%), Positives = 773/1078 (71%), Gaps = 34/1078 (3%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDI +IL++G+GPI+IGQACEFDYSG QA K L+E GYRV+L+NSNPATIMTDPE
Sbjct: 1 MPKRTDIHTILLIGSGPIIIGQACEFDYSGTQAVKTLKELGYRVVLINSNPATIMTDPEF 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
AD TYIEPI +++ KII+ E+ DAVLPTMGGQTALN A + ++G+LE GV +GA+
Sbjct: 61 ADRTYIEPIREDIIAKIIKDEKVDAVLPTMGGQTALNVATSMYKKGMLE--GVEFLGASP 118
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
+AI K EDR F+ AM KIG++ +S A+++EEAL VA ++GFP I R SFT+ G G G
Sbjct: 119 EAIHKGEDRSAFNKAMIKIGMDLPKSRNAYSVEEALEVALEIGFPVISRASFTLAGGGSG 178
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
+AYN EEF+ + G+ SP E+ I ES++GWKEYEMEV+RDK DNCIIVCSIENFD M
Sbjct: 179 VAYNMEEFKILAQEGISASPVSEIEIMESMLGWKEYEMEVIRDKADNCIIVCSIENFDPM 238
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPA TLTDKEYQ MR+AS +LREIGV+TGGSNVQF+++PK GR+IVIEM
Sbjct: 239 GVHTGDSITVAPALTLTDKEYQRMRDASFDILREIGVDTGGSNVQFSIDPKTGRMIVIEM 298
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATG+PIAKVA LAVG+TLDE+ NDITG TPASFEP IDYVVTKIP
Sbjct: 299 NPRVSRSSALASKATGYPIAKVATLLAVGFTLDEITNDITG--TPASFEPVIDYVVTKIP 356
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
RF FEKF A L+T MKSVGEVMAIGRT +ES+QKAL LE G GFDP + D
Sbjct: 357 RFTFEKFPEAQSTLSTSMKSVGEVMAIGRTFKESIQKALCSLETGLCGFDP-IDAD---- 411
Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
I+ E++ ADRI Y+A+ FR G+S++ +F+ NID WFL QIEE++++E + +
Sbjct: 412 FDFIKHEIRRPNADRILYVAEGFRRGMSIEEMFDTCNIDPWFLYQIEEMIKVESIIDKKI 471
Query: 481 ITGLNADFLRQLKRKGFADARLAKLAG------VREAEIRKLRDQYDLHPVYKRVDTCAA 534
++ + F+R +K GF+D R+A+L + E ++ K + ++ Y VDTCAA
Sbjct: 472 LS--DETFMRSVKVDGFSDKRIAQLISQKSETKITEDDVYKAKKTLGVNLEYNEVDTCAA 529
Query: 535 EFATDTAYMYSTYEEECEANPS---TDREKIMVLGGGPNRIGQGIEFDYCCVHASLALRE 591
EF T Y+YST N ++ +K+++LGGGPNRIGQGIEFDYCCVHA+ AL+E
Sbjct: 530 EFEALTPYLYSTTNITKLPNVKNRVSEAKKVLILGGGPNRIGQGIEFDYCCVHAAFALKE 589
Query: 592 DGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLA 651
G ETIM NCNPETVSTDYDTSD LYFEP+ E V E++ EKP GVIV +GGQTPLKLA
Sbjct: 590 MGIETIMYNCNPETVSTDYDTSDVLYFEPIDFEHVREVIENEKPDGVIVHFGGQTPLKLA 649
Query: 652 RALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYP 711
AL G + GT ID AEDRE+F + V LKQPAN + A + A +G+P
Sbjct: 650 NALTKIGANIAGTPSHVIDLAEDREQFSNFVNSHGLKQPANGLARTKDEAHDIALRLGFP 709
Query: 712 LVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGE 771
++VRPSYVLGGR M IVY + +LR+Y AV VSNDAPVL+D FLD A+E+DVDAICDG
Sbjct: 710 VLVRPSYVLGGRGMRIVYSQEELRQYMDLAVLVSNDAPVLVDKFLDQAIELDVDAICDGV 769
Query: 772 MVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFA 831
V IG +M+HIE+AG+HSGDSACSLP +LS+E+ D + Q + +A L VRGLMNVQ+A
Sbjct: 770 DVYIGSVMQHIEEAGIHSGDSACSLPPVSLSKELIDQVEAQTKTIALGLGVRGLMNVQYA 829
Query: 832 VKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSL--------------AEQ 877
+ +E+YLIEVNPRA+RTVPFVSKATG+PLAKVA RVM G++L E
Sbjct: 830 IYQDEIYLIEVNPRASRTVPFVSKATGMPLAKVATRVMVGETLKNALNYYDKYNIVMEEN 889
Query: 878 GVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNS 937
G+ K + + SVKE V PF+K G D +LGPEM+STGEVMG+ F +FAKAQ+ + +
Sbjct: 890 GLLKPRLKGHISVKEAVFPFHKLYGADLVLGPEMKSTGEVMGISSNFGISFAKAQIAAGN 949
Query: 938 TMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEG 997
+ G LS + DK+ ++A+ L + GF+L AT GT + EAGI +V K+ EG
Sbjct: 950 RIVTEGTCFLSFVDTDKKYASEIASALHRHGFKLLATKGTQASIEEAGIPCEVVLKISEG 1009
Query: 998 RPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALN 1055
RP+I+D +KN INT+ + +D+ VIR+ L+ + Y TTL+ A +AL+
Sbjct: 1010 RPNIEDSMKNDAIDMAINTSDNNTSKKDAIVIRQEVLKRNIPYFTTLSAARALILALD 1067
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: 2895
Number of extensions: 126
Number of successful extensions: 18
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: 1085
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1039
Effective search space: 1067053
Effective search space used: 1067053
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 WP_011373096.1 SUDEN_RS07665 (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.17996.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 1452.0 2.1 0 1451.8 2.1 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011373096.1 SUDEN_RS07665 carbamoyl-phosphat
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012965.1:WP_011373096.1 SUDEN_RS07665 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1451.8 2.1 0 0 1 1051 [. 2 1065 .. 2 1066 .. 0.97
Alignments for each domain:
== domain 1 score: 1451.8 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+di+++l+iGsGpi+igqA+EFDYsG+qa+k+lke g++vvL+nsn+At+mtd+e+ad++YieP
lcl|NCBI__GCF_000012965.1:WP_011373096.1 2 PKRTDIHTILLIGSGPIIIGQACEFDYSGTQAVKTLKELGYRVVLINSNPATIMTDPEFADRTYIEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
+ + +++kii+ E++Da+l+t+GGqtaLn+a ++ +kG+Le v+ lG++ eai+k+edR +F++a
lcl|NCBI__GCF_000012965.1:WP_011373096.1 69 IREDIIAKIIKDEKVDAVLPTMGGQTALNVATSMYKKGMLEG--VEFLGASPEAIHKGEDRSAFNKA 133
****************************************96..*********************** PP
TIGR01369 135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201
+ +i+++++ks+ + sveeale+a eig+Pvi Ra+ftl+G Gsg+a+n+ee+k l++++++asp++
lcl|NCBI__GCF_000012965.1:WP_011373096.1 134 MIKIGMDLPKSRNAYSVEEALEVALEIGFPVISRASFTLAGGGSGVAYNMEEFKILAQEGISASPVS 200
******************************************************************* PP
TIGR01369 202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268
++ + +s+ gwkE+E+Ev+RD++dnciivc+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++Rdas+
lcl|NCBI__GCF_000012965.1:WP_011373096.1 201 EIEIMESMLGWKEYEMEVIRDKADNCIIVCSIENFDPMGVHTGDSITVAPALTLTDKEYQRMRDASF 267
******************************************************************* PP
TIGR01369 269 kiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelk 334
i+re+gv+++ +nvqf++dP++ r++viE+npRvsRssALAskAtGyPiAkva+ lavG++Lde++
lcl|NCBI__GCF_000012965.1:WP_011373096.1 268 DILREIGVDTGgSNVQFSIDPKTGRMIVIEMNPRVSRSSALASKATGYPIAKVATLLAVGFTLDEIT 334
********9988******************************************************* PP
TIGR01369 335 ndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrslee 401
nd+t+ t+AsfEP +DYvv+kiPr+ ++kf +++++l+t+mksvGEvmaigrtf+e++qkal+sle+
lcl|NCBI__GCF_000012965.1:WP_011373096.1 335 NDITG-TPASFEPVIDYVVTKIPRFTFEKFPEAQSTLSTSMKSVGEVMAIGRTFKESIQKALCSLET 400
****9.99*********************************************************** PP
TIGR01369 402 kllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvele 468
+l g++ + + +++++++pn++R++++ae +rrg+s+ee++++++id +fl+++++++++e
lcl|NCBI__GCF_000012965.1:WP_011373096.1 401 GLCGFDPI---DADFDFIKHEIRRPNADRILYVAEGFRRGMSIEEMFDTCNIDPWFLYQIEEMIKVE 464
****9986...4455556789********************************************** PP
TIGR01369 469 keleeeklkelkkellkkakklGfsdeqiaklvkvseae......vrklrkelgivpvvkrvDtvaa 529
+ ++++ l+ ++ ++++k Gfsd++ia+l+++++++ v k++k+lg+ +++vDt+aa
lcl|NCBI__GCF_000012965.1:WP_011373096.1 465 SIIDKKILS--DETFMRSVKVDGFSDKRIAQLISQKSETkiteddVYKAKKTLGVNLEYNEVDTCAA 529
***977776..8899*****************9955444455555********************** PP
TIGR01369 530 EfeaktpYlYstyeee...kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktil 593
Efea tpYlYst + + + +++v+e kkvl+lG+Gp+Rigqg+EFDyc+vha+ al+e+g++ti+
lcl|NCBI__GCF_000012965.1:WP_011373096.1 530 EFEALTPYLYSTTNITklpNVKNRVSEAKKVLILGGGPNRIGQGIEFDYCCVHAAFALKEMGIETIM 596
************99884433456677889************************************** PP
TIGR01369 594 inynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGts 660
n+nPEtvstDyd++d LyFe++ +e+v ++ie+ek++gviv++gGqt+l+la++l++ g++i Gt
lcl|NCBI__GCF_000012965.1:WP_011373096.1 597 YNCNPETVSTDYDTSDVLYFEPIDFEHVREVIENEKPDGVIVHFGGQTPLKLANALTKIGANIAGTP 663
******************************************************************* PP
TIGR01369 661 aesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameivenee 727
++id aEdRe+Fs+++++ g+kqp++ a++++ea++ia ++g+PvlvRpsyvlgGr+m+iv+++e
lcl|NCBI__GCF_000012965.1:WP_011373096.1 664 SHVIDLAEDREQFSNFVNSHGLKQPANGLARTKDEAHDIALRLGFPVLVRPSYVLGGRGMRIVYSQE 730
******************************************************************* PP
TIGR01369 728 eleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppq 794
el++y++ av vs+++Pvl+dk+l++a+E+dvDa++dg +v+i ++++HiEeaG+HsGDs+++lpp
lcl|NCBI__GCF_000012965.1:WP_011373096.1 731 ELRQYMDLAVLVSNDAPVLVDKFLDQAIELDVDAICDGVDVYIGSVMQHIEEAGIHSGDSACSLPPV 797
******************************************************************* PP
TIGR01369 795 klseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklav 861
+ls+e+ +++++++k+ia l v+Gl+n+q+++ ++e+y+iEvn+RasRtvPfvska+g+pl+k+a+
lcl|NCBI__GCF_000012965.1:WP_011373096.1 798 SLSKELIDQVEAQTKTIALGLGVRGLMNVQYAIYQDEIYLIEVNPRASRTVPFVSKATGMPLAKVAT 864
******************************************************************* PP
TIGR01369 862 kvllgkkleele............kgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmg 916
+v++g++l+++ +g+ k + +++vk+avf+f+kl+g+d+vlgpemkstGEvmg
lcl|NCBI__GCF_000012965.1:WP_011373096.1 865 RVMVGETLKNALnyydkynivmeeNGLLKPRLKGHISVKEAVFPFHKLYGADLVLGPEMKSTGEVMG 931
**********88999***999999899999999********************************** PP
TIGR01369 917 igrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagi 983
i++++ +++ka++a++++i ++g+++ls d+dk+++ e+a+ l+++g+k++at+gt++ +eeagi
lcl|NCBI__GCF_000012965.1:WP_011373096.1 932 ISSNFGISFAKAQIAAGNRIVTEGTCFLSFVDTDKKYASEIASALHRHGFKLLATKGTQASIEEAGI 998
******************************************************************* PP
TIGR01369 984 kaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaealle 1050
+evvlk+se +++i + +k++ i+++in+++ ++++++++ +ir+e++++++p++t+l++a+al+
lcl|NCBI__GCF_000012965.1:WP_011373096.1 999 PCEVVLKISEGRPNIEDSMKNDAIDMAINTSD-NNTSKKDAIVIRQEVLKRNIPYFTTLSAARALIL 1064
*****************************998.55688899*********************99887 PP
TIGR01369 1051 a 1051
a
lcl|NCBI__GCF_000012965.1:WP_011373096.1 1065 A 1065
6 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1085 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 0.04s 00:00:00.13 Elapsed: 00:00:00.13
# Mc/sec: 8.74
//
[ok]
This GapMind analysis is from Apr 10 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