Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_057509125.1 ABB28_RS13565 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_001431535.1:WP_057509125.1
Length = 1080
Score = 1475 bits (3818), Expect = 0.0
Identities = 756/1079 (70%), Positives = 883/1079 (81%), Gaps = 8/1079 (0%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
M KRTD+K+ILI+GAGPIVIGQACEFDYSGAQACKALR+EGYRV+LVNSNPATIMTDPEM
Sbjct: 1 MAKRTDLKTILIIGAGPIVIGQACEFDYSGAQACKALRDEGYRVVLVNSNPATIMTDPEM 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADA YIEPI+W+ V KII KE+PDA+LPTMGGQTALNCAL+L GVLE++ V +IGA
Sbjct: 61 ADAVYIEPINWQTVEKIIAKEKPDALLPTMGGQTALNCALDLADNGVLEKYNVELIGAKR 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
+AI AEDR F VAM +IGLE + +AHT+EEAL + VG+P IIRPSFT+GGSGGG
Sbjct: 121 EAIRMAEDRELFRVAMGEIGLECPSAAVAHTLEEALDIQTRVGYPTIIRPSFTLGGSGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYNREE +I RGL+LSPT E+L++ES++GWKE+EMEVVRD DNCIIVCSIEN D M
Sbjct: 181 IAYNREELIDIVTRGLELSPTTEVLVEESVLGWKEFEMEVVRDTADNCIIVCSIENLDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPAQTLTDKEYQ +R+AS+AVLR+IGV+TGGSNVQF +NP GR++VIEM
Sbjct: 241 GVHTGDSITVAPAQTLTDKEYQRLRDASIAVLRKIGVDTGGSNVQFGINPHTGRVVVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL N+ITGG TPASFEPSIDYVVTKIP
Sbjct: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELKNEITGGLTPASFEPSIDYVVTKIP 360
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDP-KVSLDDPE 419
RF FEKF A+ RLTTQMKSVGEVMA+GRT QES+QKALRGLE G GFDP ++ L + +
Sbjct: 361 RFAFEKFPAADARLTTQMKSVGEVMAMGRTFQESMQKALRGLETGKVGFDPTELDLGNED 420
Query: 420 ALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEV 479
+ +RRELK G +R++Y+AD FRAG+SV+ + L+ ID WFL QIEE++ E +VA
Sbjct: 421 DMQTLRRELKAPGPERLFYVADGFRAGMSVEEIHALSFIDPWFLDQIEEIITAEGEVAAG 480
Query: 480 GITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATD 539
GI L+A LR+LKR GF+DARLA+L G EA +R LR + + PVYKRVD+CA EFAT
Sbjct: 481 GIDSLDAARLRKLKRAGFSDARLAQLTGTNEAAVRALRRAHKVRPVYKRVDSCAGEFATG 540
Query: 540 TAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMV 599
TAY+YSTYE+ECEA PS +R+KIM+LGGGPNRIGQGIEFDYCCVHA+LALREDGYETIMV
Sbjct: 541 TAYLYSTYEDECEAAPS-NRDKIMILGGGPNRIGQGIEFDYCCVHAALALREDGYETIMV 599
Query: 600 NCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGV 659
NCNPETVSTDYDTSDRLYFEP+TLEDVLEIV +E+PKGVIVQYGGQTPLKLARALEA GV
Sbjct: 600 NCNPETVSTDYDTSDRLYFEPLTLEDVLEIVELEQPKGVIVQYGGQTPLKLARALEANGV 659
Query: 660 PVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYV 719
PVIGTSPD+ID AEDRERFQ V+ L LKQP N + A+ A+EIGYPLVVRPSYV
Sbjct: 660 PVIGTSPDSIDLAEDRERFQQLVDNLGLKQPPNRIARNDQEALLLAREIGYPLVVRPSYV 719
Query: 720 LGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGE-MVLIGGI 778
LGGRAMEIVY E+DL RY + AV VSND+PVLLD FLD+AVEVDVD I D + VLIGG+
Sbjct: 720 LGGRAMEIVYGESDLARYVRDAVKVSNDSPVLLDRFLDNAVEVDVDIIADSQGNVLIGGV 779
Query: 779 MEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNE-- 836
MEHIE+AGVHSGDS+CSLP Y+LS E Q +R+QV +LA L V GLMN QFA++ E
Sbjct: 780 MEHIEEAGVHSGDSSCSLPPYSLSAETQAELRRQVVELAKALNVVGLMNTQFAIQAGENG 839
Query: 837 ---VYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEV 893
VYL+EVNPRA+RTVPFVSKATG+PLAK+AAR MAGK+LAEQG TKE++P YYSVKE
Sbjct: 840 EDIVYLLEVNPRASRTVPFVSKATGMPLAKIAARCMAGKTLAEQGATKEIVPDYYSVKEA 899
Query: 894 VLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGD 953
+ PF KF GVDP+LGPEMRSTGEVMGVGR+F+ AFA+AQ G+A +SVR+ D
Sbjct: 900 IFPFAKFQGVDPILGPEMRSTGEVMGVGRSFSAAFARAQEAGGIKAPPVGKAFVSVRDPD 959
Query: 954 KERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYI 1013
K+RV+ +A LL +G+ L AT GTA L + G+ +VNKV EGRPHI DRIKNGE YI
Sbjct: 960 KQRVLPVAEALLAKGYSLVATRGTAAWLQQHGMECEIVNKVVEGRPHIVDRIKNGEIVYI 1019
Query: 1014 INTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQI 1072
+NTT GR AI DS IRR ALQ++V Y TT+ G A +L T V S+QE+H ++
Sbjct: 1020 VNTTEGRAAINDSFSIRREALQHRVTYSTTIAGAKALVHSLEFRGTGPVWSLQELHKEL 1078
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: 3123
Number of extensions: 120
Number of successful extensions: 14
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: 1080
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1034
Effective search space: 1061918
Effective search space used: 1061918
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_057509125.1 ABB28_RS13565 (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.32175.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 1544.0 0.0 0 1543.8 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509125.1 ABB28_RS13565 carbamoyl-phosphat
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509125.1 ABB28_RS13565 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1543.8 0.0 0 0 2 1051 .. 3 1059 .. 2 1060 .. 0.97
Alignments for each domain:
== domain 1 score: 1543.8 bits; conditional E-value: 0
TIGR01369 2 kredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePl 68
kr+d+k++l+iG+GpivigqA+EFDYsG+qa+kal++eg++vvLvnsn+At+mtd+e+ad+vYieP+
lcl|NCBI__GCF_001431535.1:WP_057509125.1 3 KRTDLKTILIIGAGPIVIGQACEFDYSGAQACKALRDEGYRVVLVNSNPATIMTDPEMADAVYIEPI 69
799**************************************************************** PP
TIGR01369 69 tveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkeal 135
++++vekii kE+pDa+l+t+GGqtaLn+a++l ++GvLeky+v+l+G+k eai+ aedRe+F+ a+
lcl|NCBI__GCF_001431535.1:WP_057509125.1 70 NWQTVEKIIAKEKPDALLPTMGGQTALNCALDLADNGVLEKYNVELIGAKREAIRMAEDRELFRVAM 136
******************************************************************* PP
TIGR01369 136 keineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikq 202
ei++e ++++++++ eeal++++++gyP i+R++ftlgG+G+gia+n+eel +v ++l++sp+++
lcl|NCBI__GCF_001431535.1:WP_057509125.1 137 GEIGLECPSAAVAHTLEEALDIQTRVGYPTIIRPSFTLGGSGGGIAYNREELIDIVTRGLELSPTTE 203
******************************************************************* PP
TIGR01369 203 vlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslk 269
vlve+s+ gwkE+E+EvvRD++dnciivc+iEnlDp+GvHtGdsi+vaP+qtLtdkeyq+lRdas++
lcl|NCBI__GCF_001431535.1:WP_057509125.1 204 VLVEESVLGWKEFEMEVVRDTADNCIIVCSIENLDPMGVHTGDSITVAPAQTLTDKEYQRLRDASIA 270
******************************************************************* PP
TIGR01369 270 iirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkn 335
++r++gv+++ +nvqf+++P++ r+vviE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldelkn
lcl|NCBI__GCF_001431535.1:WP_057509125.1 271 VLRKIGVDTGgSNVQFGINPHTGRVVVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELKN 337
*******9988******************************************************** PP
TIGR01369 336 dvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrslee 401
++t+ t+AsfEPs+DYvv+kiPr++++kf +d +l+tqmksvGEvma+grtf+e++qkalr le+
lcl|NCBI__GCF_001431535.1:WP_057509125.1 338 EITGgLTPASFEPSIDYVVTKIPRFAFEKFPAADARLTTQMKSVGEVMAMGRTFQESMQKALRGLET 404
***867************************************************************* PP
TIGR01369 402 kllglklkeke...aesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklv 465
+ +g++ +e + + ++l+++lk p ++Rlf++a+ +r+g+svee++ l+ id +fl+++++++
lcl|NCBI__GCF_001431535.1:WP_057509125.1 405 GKVGFDPTELDlgnEDDMQTLRRELKAPGPERLFYVADGFRAGMSVEEIHALSFIDPWFLDQIEEII 471
****88776551113445567899******************************************* PP
TIGR01369 466 elekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfe 532
++e e++ ++ l++ l+k+k+ Gfsd+++a+l++++ea+vr+lr++ ++ pv+krvD +a+Ef
lcl|NCBI__GCF_001431535.1:WP_057509125.1 472 TAEGEVAAGGIDSLDAARLRKLKRAGFSDARLAQLTGTNEAAVRALRRAHKVRPVYKRVDSCAGEFA 538
******************************************************************* PP
TIGR01369 533 aktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPE 599
+ t+YlYstye+e++ ++++++ k+++lG+Gp+Rigqg+EFDyc+vha+lalre gy+ti++n+nPE
lcl|NCBI__GCF_001431535.1:WP_057509125.1 539 TGTAYLYSTYEDECEAAPSNRD-KIMILGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVNCNPE 604
*************766666655.******************************************** PP
TIGR01369 600 tvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidr 666
tvstDyd++drLyFe+lt+edvl+i+e e+++gvivq+gGqt+l+la++le++gv+++Gts++sid
lcl|NCBI__GCF_001431535.1:WP_057509125.1 605 TVSTDYDTSDRLYFEPLTLEDVLEIVELEQPKGVIVQYGGQTPLKLARALEANGVPVIGTSPDSIDL 671
******************************************************************* PP
TIGR01369 667 aEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryl 733
aEdRe+F++l+d+lg+kqp +++a++ +ea +a+eigyP++vRpsyvlgGrameiv+ e +l+ry+
lcl|NCBI__GCF_001431535.1:WP_057509125.1 672 AEDRERFQQLVDNLGLKQPPNRIARNDQEALLLAREIGYPLVVRPSYVLGGRAMEIVYGESDLARYV 738
******************************************************************* PP
TIGR01369 734 eeavevskekPvlidkyledavEvdvDavad.geevliagileHiEeaGvHsGDstlvlppqklsee 799
++av+vs+++Pvl+d++l++avEvdvD++ad +++vli g++eHiEeaGvHsGDs ++lpp +ls+e
lcl|NCBI__GCF_001431535.1:WP_057509125.1 739 RDAVKVSNDSPVLLDRFLDNAVEVDVDIIADsQGNVLIGGVMEHIEEAGVHSGDSSCSLPPYSLSAE 805
******************************93469******************************** PP
TIGR01369 800 vkkkikeivkkiakelkvkGllniqfvvkdee.....vyviEvnvRasRtvPfvskalgvplvklav 861
++ +++++v ++ak+l+v+Gl+n qf+++ +e vy++Evn+RasRtvPfvska+g+pl+k+a+
lcl|NCBI__GCF_001431535.1:WP_057509125.1 806 TQAELRRQVVELAKALNVVGLMNTQFAIQAGEngediVYLLEVNPRASRTVPFVSKATGMPLAKIAA 872
***************************98743344459***************************** PP
TIGR01369 862 kvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallka 928
++++gk+l+e +g++ke +++++vk+a f+f+k++gvd++lgpem+stGEvmg+gr+++ a+++a
lcl|NCBI__GCF_001431535.1:WP_057509125.1 873 RCMAGKTLAE--QGATKEIVPDYYSVKEAIFPFAKFQGVDPILGPEMRSTGEVMGVGRSFSAAFARA 937
**********..7789*************************************************** PP
TIGR01369 929 llaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseea 995
+ a + k + g++++sv+d dk+++l++a+ l +kg++++at+gta+ l+++g+++e v+kv e +
lcl|NCBI__GCF_001431535.1:WP_057509125.1 938 QEAGGIKAPPVGKAFVSVRDPDKQRVLPVAEALLAKGYSLVATRGTAAWLQQHGMECEIVNKVVEGR 1004
******************************************************************* PP
TIGR01369 996 ekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
++i++ +k++ei +++n+t+ +++a +++++irrea++++v++ t++++a+al+++
lcl|NCBI__GCF_001431535.1:WP_057509125.1 1005 PHIVDRIKNGEIVYIVNTTE-GRAAINDSFSIRREALQHRVTYSTTIAGAKALVHS 1059
*****************997.77799999*********************999875 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1080 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.12
# Mc/sec: 9.39
//
[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