Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_026606814.1 METAC_RS0109340 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000427445.1:WP_026606814.1
Length = 1107
Score = 1268 bits (3280), Expect = 0.0
Identities = 669/1096 (61%), Positives = 810/1096 (73%), Gaps = 45/1096 (4%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDI++ILI+GAGPI+IGQACEFDYSG QACKALR EGYR++LVNSNPATIMTDP+M
Sbjct: 1 MPKRTDIETILIIGAGPIIIGQACEFDYSGTQACKALRAEGYRIVLVNSNPATIMTDPDM 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPD-----AVLPTMGGQTALNCALELERQGVLEEFGVTM 115
AD TY+EPI E+V KII KER A+LPTMGGQTALNCAL L+R GVLE+F V +
Sbjct: 61 ADRTYVEPITSEIVAKIIAKERYARPGGFALLPTMGGQTALNCALSLKRMGVLEKFDVEL 120
Query: 116 IGATADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMG 175
IGA+A+AIDKAEDR F AM +IGL T RS T+ +AL+ D+G P IIRPSFTMG
Sbjct: 121 IGASAEAIDKAEDRELFREAMTRIGLSTPRSQQIKTLSQALSALEDIGLPAIIRPSFTMG 180
Query: 176 GSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIE 235
G+GGGIAYN+ EF +I RG+D SPT E+L++ES++GWKE+EMEVVRDK DNCIIVCSIE
Sbjct: 181 GTGGGIAYNKAEFIDIIERGIDASPTSEVLVEESVLGWKEFEMEVVRDKADNCIIVCSIE 240
Query: 236 NFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRL 295
N D MG+HTGDSITVAPA TLTDKEYQIMR+AS+AVLREIGVETGGSNVQFAVNP +GR+
Sbjct: 241 NIDPMGVHTGDSITVAPALTLTDKEYQIMRDASLAVLREIGVETGGSNVQFAVNPADGRM 300
Query: 296 IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYV 355
IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDE+ NDITGG TPASFEP+IDYV
Sbjct: 301 IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEIANDITGGATPASFEPTIDYV 360
Query: 356 VTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFD----P 411
VTKIPRF FEKF GA+ LTT MKSVGE MAIGRT ESLQKALR L+ G G D
Sbjct: 361 VTKIPRFAFEKFPGADQILTTAMKSVGETMAIGRTFAESLQKALRSLDTGLDGLDEVEIE 420
Query: 412 KVSLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVR 471
+ L D + + +R L DR+ IA A R G++ + + ++D WF+ ++ E++
Sbjct: 421 GLGLGDDKNV--LRAALGRPTPDRLLVIAQALRHGMTPEEIHEACSVDPWFIARLREILD 478
Query: 472 LEEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDT 531
LE KV G+ + D LR LK GF+DARLA LA V+ +++ LR + +HP +KR+DT
Sbjct: 479 LEGKVRAHGLPN-DPDNLRMLKAAGFSDARLASLAHVKRSDVAALRKRQGVHPAFKRIDT 537
Query: 532 CAAEFATDTAYMYSTY------EEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHA 585
CAAEFA+ TAYMYSTY E CEA PS REKI++LGGGPNRIGQGIEFDYCC HA
Sbjct: 538 CAAEFASPTAYMYSTYAPPFGEEPSCEARPSA-REKIVILGGGPNRIGQGIEFDYCCCHA 596
Query: 586 SLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIE----KPKGVIVQ 641
S ALRE G+ETIMVNCNPETVSTDYDTSDRLYFEP+T EDVLEI+ +E + KG IVQ
Sbjct: 597 SFALREAGFETIMVNCNPETVSTDYDTSDRLYFEPLTTEDVLEILAVENAAGRLKGAIVQ 656
Query: 642 YGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMA 701
+GGQTPLKLA ALE AG+P++GTS D+ID AEDR+RF+ ++R+ LKQP N ++E +
Sbjct: 657 FGGQTPLKLAHALERAGIPILGTSVDSIDLAEDRDRFKRLLDRIGLKQPLNGIAYSVEQS 716
Query: 702 VEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYF----------QTAVSVSNDA--- 748
A E+G PLVVRPSYVLGGRAM I+ D A Y + ND
Sbjct: 717 RIVAGELGLPLVVRPSYVLGGRAMAIIRDAAAFDDYLLGTLPGLVPSEVKARYPNDKTGQ 776
Query: 749 --------PVLLDHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYT 800
P+L D +L DAVE+DVDA+CDG V I GIMEHIE+AG+HSGDSACSLP +
Sbjct: 777 INTVLGKNPLLFDRYLTDAVEIDVDALCDGADVFICGIMEHIEEAGIHSGDSACSLPPRS 836
Query: 801 LSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVP 860
LS E + +Q ++LA L V GLMNVQ+A+K+ E+Y++EVNPRAARTVPFV+K G P
Sbjct: 837 LSPEKIAALERQTRELALALGVGGLMNVQYALKDGEIYVLEVNPRAARTVPFVAKVIGAP 896
Query: 861 LAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGV 920
+AK+AAR+MAG+ L + +T + VKE V PF +FPGVD +LGPEMRSTGEVMG+
Sbjct: 897 IAKIAARIMAGEKLRDFSLT-PASGDHVGVKESVFPFARFPGVDTVLGPEMRSTGEVMGL 955
Query: 921 GRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIV 980
R+FA AFAK+QLG + + G +SVR+ DK R+++ L GF + AT GT+
Sbjct: 956 DRSFAVAFAKSQLGGGTKVPTKGAVFVSVRDADKPRMLETVKLLAGLGFMIRATGGTSRY 1015
Query: 981 LGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHY 1040
L G+ + +NKV EGRPH+ D IKNG ++NTT G +A+ DSR +RR+AL +KV Y
Sbjct: 1016 LESEGVPAQRINKVSEGRPHVVDAIKNGGIQLVLNTTEGAQALADSRSLRRAALLHKVPY 1075
Query: 1041 DTTLNGGFATAMALNA 1056
TTL G A + A
Sbjct: 1076 YTTLAGAIAACEGIKA 1091
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: 3166
Number of extensions: 143
Number of successful extensions: 20
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: 1107
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1061
Effective search space: 1089647
Effective search space used: 1089647
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_026606814.1 METAC_RS0109340 (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.3150.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 1428.3 0.0 0 1427.5 0.0 1.3 1 lcl|NCBI__GCF_000427445.1:WP_026606814.1 METAC_RS0109340 carbamoyl-phosph
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000427445.1:WP_026606814.1 METAC_RS0109340 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1427.5 0.0 0 0 1 1050 [. 2 1087 .. 2 1089 .. 0.96
Alignments for each domain:
== domain 1 score: 1427.5 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+di+++l+iG+Gpi+igqA+EFDYsG+qa+kal+ eg+++vLvnsn+At+mtd+++ad++Y+eP
lcl|NCBI__GCF_000427445.1:WP_026606814.1 2 PKRTDIETILIIGAGPIIIGQACEFDYSGTQACKALRAEGYRIVLVNSNPATIMTDPDMADRTYVEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpD.....ailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRe 129
+t e+v+kii kEr a+l+t+GGqtaLn+a++l+++GvLek++v+l+G++ eai+kaedRe
lcl|NCBI__GCF_000427445.1:WP_026606814.1 69 ITSEIVAKIIAKERYArpggfALLPTMGGQTALNCALSLKRMGVLEKFDVELIGASAEAIDKAEDRE 135
*************8543334579******************************************** PP
TIGR01369 130 kFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalk 196
+F+ea++ i++++++s+ +++ ++al+a e+ig+P i+R++ft+gGtG+gia+n++e+ ++e++++
lcl|NCBI__GCF_000427445.1:WP_026606814.1 136 LFREAMTRIGLSTPRSQQIKTLSQALSALEDIGLPAIIRPSFTMGGTGGGIAYNKAEFIDIIERGID 202
******************************************************************* PP
TIGR01369 197 aspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqll 263
asp+++vlve+s+ gwkE+E+EvvRD++dnciivc+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++
lcl|NCBI__GCF_000427445.1:WP_026606814.1 203 ASPTSEVLVEESVLGWKEFEMEVVRDKADNCIIVCSIENIDPMGVHTGDSITVAPALTLTDKEYQIM 269
******************************************************************* PP
TIGR01369 264 Rdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGys 329
Rdasl+++re+gve++ +nvqfa++P + r++viE+npRvsRssALAskAtG+PiAkvaaklavGy+
lcl|NCBI__GCF_000427445.1:WP_026606814.1 270 RDASLAVLREIGVETGgSNVQFAVNPADGRMIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYT 336
**************988************************************************** PP
TIGR01369 330 Ldelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqka 395
Lde+ nd+t+ t+AsfEP++DYvv+kiPr++++kf ++d+ l+t mksvGE maigrtf e+lqka
lcl|NCBI__GCF_000427445.1:WP_026606814.1 337 LDEIANDITGgATPASFEPTIDYVVTKIPRFAFEKFPGADQILTTAMKSVGETMAIGRTFAESLQKA 403
*********878******************************************************* PP
TIGR01369 396 lrsleekllglklkeke...ae.sdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffl 458
lrsl+++l gl++ e e +++ l+ al +p+++Rl++ia+alr+g++ ee++e++ +d +f+
lcl|NCBI__GCF_000427445.1:WP_026606814.1 404 LRSLDTGLDGLDEVEIEglgLGdDKNVLRAALGRPTPDRLLVIAQALRHGMTPEEIHEACSVDPWFI 470
*********966554431114414455677899********************************** PP
TIGR01369 459 eklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvD 525
+l+++++le +++ + l + ++l+ +k+ Gfsd+++a+l++v++++v +lrk++g++p++kr+D
lcl|NCBI__GCF_000427445.1:WP_026606814.1 471 ARLREILDLEGKVRAHGLP-NDPDNLRMLKAAGFSDARLASLAHVKRSDVAALRKRQGVHPAFKRID 536
*************988777.899******************************************** PP
TIGR01369 526 tvaaEfeaktpYlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalrea 587
t+aaEf + t+Y+Ysty+ + +++ + ++k+++lG+Gp+Rigqg+EFDyc+ ha+ alrea
lcl|NCBI__GCF_000427445.1:WP_026606814.1 537 TCAAEFASPTAYMYSTYAPPfgeepSCEARPSAREKIVILGGGPNRIGQGIEFDYCCCHASFALREA 603
*****************876333333455556679******************************** PP
TIGR01369 588 gyktilinynPEtvstDydiadrLyFeeltvedvldiiekekv....egvivqlgGqtalnlakele 650
g++ti++n+nPEtvstDyd++drLyFe+lt+edvl+i+ e+ +g ivq+gGqt+l+la++le
lcl|NCBI__GCF_000427445.1:WP_026606814.1 604 GFETIMVNCNPETVSTDYDTSDRLYFEPLTTEDVLEILAVENAagrlKGAIVQFGGQTPLKLAHALE 670
***************************************99752222789***************** PP
TIGR01369 651 eagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgG 717
+ag++ilGts++sid aEdR++F++lld++g+kqp + +a sve+ + +a e+g+P++vRpsyvlgG
lcl|NCBI__GCF_000427445.1:WP_026606814.1 671 RAGIPILGTSVDSIDLAEDRDRFKRLLDRIGLKQPLNGIAYSVEQSRIVAGELGLPLVVRPSYVLGG 737
******************************************************************* PP
TIGR01369 718 rameiveneeeleryle.....................eavevskekPvlidkyledavEvdvDava 763
ram+i+++ + + +yl ++++v ++P+l d+yl+davE+dvDa++
lcl|NCBI__GCF_000427445.1:WP_026606814.1 738 RAMAIIRDAAAFDDYLLgtlpglvpsevkarypndktgQINTVLGKNPLLFDRYLTDAVEIDVDALC 804
*************99977788888888888888887777778889********************** PP
TIGR01369 764 dgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkde 830
dg +v+i+gi+eHiEeaG+HsGDs+++lpp++ls e +++++++++a +l v Gl+n+q+++kd+
lcl|NCBI__GCF_000427445.1:WP_026606814.1 805 DGADVFICGIMEHIEEAGIHSGDSACSLPPRSLSPEKIAALERQTRELALALGVGGLMNVQYALKDG 871
******************************************************************* PP
TIGR01369 831 evyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfskl 897
e+yv+Evn+Ra+RtvPfv+k++g p++k+a+++++g+kl++ + + ++ ++v+vk++vf+f+++
lcl|NCBI__GCF_000427445.1:WP_026606814.1 872 EIYVLEVNPRAARTVPFVAKVIGAPIAKIAARIMAGEKLRDFSL---TPASGDHVGVKESVFPFARF 935
*****************************************776...788889************** PP
TIGR01369 898 agvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaek 964
gvd vlgpem+stGEvmg++r+++ a++k++l ++k+++kg v++sv+d+dk ++le++k la +
lcl|NCBI__GCF_000427445.1:WP_026606814.1 936 PGVDTVLGPEMRSTGEVMGLDRSFAVAFAKSQLGGGTKVPTKGAVFVSVRDADKPRMLETVKLLAGL 1002
******************************************************************* PP
TIGR01369 965 glkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirrea 1031
g+ + at gt+++le +g+ a+ ++kvse ++++++++k++ i+lv+n+t+ +++a ++ ++rr+a
lcl|NCBI__GCF_000427445.1:WP_026606814.1 1003 GFMIRATGGTSRYLESEGVPAQRINKVSEGRPHVVDAIKNGGIQLVLNTTE-GAQALADSRSLRRAA 1068
************************************************997.88899999******* PP
TIGR01369 1032 veykvplvteletaealle 1050
+ +kvp+ t+l++a a++e
lcl|NCBI__GCF_000427445.1:WP_026606814.1 1069 LLHKVPYYTTLAGAIAACE 1087
**********999887765 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1107 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: 0.18u 0.02s 00:00:00.20 Elapsed: 00:00:00.20
# Mc/sec: 5.73
//
[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