Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_020565795.1 A3OW_RS0122885 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000372865.1:WP_020565795.1
Length = 1075
Score = 1522 bits (3940), Expect = 0.0
Identities = 760/1072 (70%), Positives = 898/1072 (83%), Gaps = 1/1072 (0%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDIKSIL+LGAGPIVIGQACEFDYSG QACKALREEG+RV+LVNSNPATIMTDP+M
Sbjct: 1 MPKRTDIKSILLLGAGPIVIGQACEFDYSGTQACKALREEGFRVVLVNSNPATIMTDPDM 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADA YIEPI W+ V KIIEKERPDA+LPTMGGQTALNCAL L+ GVLE++GV MIGAT
Sbjct: 61 ADAVYIEPIDWQTVEKIIEKERPDAILPTMGGQTALNCALALDANGVLEKYGVEMIGATK 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
+AI+KAEDR F+ AM++IG E ARS AH++EEALA +VG+P IIRPSFTMGGSGGG
Sbjct: 121 EAINKAEDRELFNQAMRRIGFEVARSKTAHSIEEALAAQEEVGYPTIIRPSFTMGGSGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYNREEF EIC RGLDLSPT ELLI+ES++GWKE+EMEVVRD DNCIIVCSIENFD M
Sbjct: 181 IAYNREEFIEICERGLDLSPTNELLIEESVLGWKEFEMEVVRDSKDNCIIVCSIENFDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPAQTLTDKEYQI+RN ++AVLREIGV+TGGSNVQ A+NPK+GRLIVIEM
Sbjct: 241 GVHTGDSITVAPAQTLTDKEYQILRNVAVAVLREIGVDTGGSNVQVAINPKDGRLIVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL N+ITGG TPASFEP+IDYVVTK+P
Sbjct: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELQNEITGGATPASFEPTIDYVVTKVP 360
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
RF FEKF A+DRLTTQMKSVGEVMAIGRT QESLQKALRGLE+G +G D + +++ +A
Sbjct: 361 RFTFEKFPQADDRLTTQMKSVGEVMAIGRTFQESLQKALRGLEIGISGLDEVIDMEEVDA 420
Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
K++REL+ G DR+ Y+ADAFR+G+S++ V ID WFL QIE+L+ E+ +A
Sbjct: 421 HEKMQRELRHPGPDRLRYVADAFRSGMSLEEVHEACKIDPWFLAQIEDLIVSEKSLATKT 480
Query: 481 ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
+ L L +LKRKGF+D RLAKL G E+E+R +R ++ + PVYKR+D+CAAEF++DT
Sbjct: 481 LATLKEGELYRLKRKGFSDQRLAKLLGTTESEVRNVRHRHGIRPVYKRIDSCAAEFSSDT 540
Query: 541 AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
AY+YSTYEEECEA S DREKI++LGGGPNRIGQGIEFDYCCVHA+LALREDGYETIM+N
Sbjct: 541 AYLYSTYEEECEARVS-DREKIIILGGGPNRIGQGIEFDYCCVHAALALREDGYETIMIN 599
Query: 601 CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
CNPETVSTD+DTSDRLYFE +TLEDVLEIV IEKPKGVIVQYGGQTPLKLARALEAAGVP
Sbjct: 600 CNPETVSTDFDTSDRLYFESLTLEDVLEIVHIEKPKGVIVQYGGQTPLKLARALEAAGVP 659
Query: 661 VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
+IGTSPD+ID AEDRERFQ +ERL LKQP NAT ++E A+ AKE+GYPLVVRPSYVL
Sbjct: 660 IIGTSPDSIDLAEDRERFQKLLERLDLKQPPNATARSVEQALTAAKELGYPLVVRPSYVL 719
Query: 721 GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
GGRAMEIV++E L+RY + AV+VSND+PVLLD FLDDAVE+DVDAI DGE VLIGG+ME
Sbjct: 720 GGRAMEIVFNEEGLQRYMKEAVTVSNDSPVLLDRFLDDAVEMDVDAIYDGERVLIGGLME 779
Query: 781 HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
HIEQAGVHSGDSACSLP Y L +IQD +R+QV+ LA L V+GLMN QFA++ ++Y++
Sbjct: 780 HIEQAGVHSGDSACSLPPYELPLKIQDRLREQVKALAEALGVQGLMNTQFAIQGEDIYVL 839
Query: 841 EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
EVNPRA+RT PFVSKATG PLAK+AAR M GK+LA+QG+T+E IP YYSVKE V PF KF
Sbjct: 840 EVNPRASRTAPFVSKATGYPLAKIAARCMVGKTLAQQGMTEERIPGYYSVKEAVFPFVKF 899
Query: 901 PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
PGVDPLLGPEM+STGEVMGVG+TF EAFAK+Q + + G+ L+S+R+ DK + D+
Sbjct: 900 PGVDPLLGPEMKSTGEVMGVGKTFGEAFAKSQRAAGVKLNHSGKVLISIRDADKVKAPDI 959
Query: 961 AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
A L+ + +E+ AT GTA L EAGI +V KV++GRP+ D IKNG+ +INTT G+
Sbjct: 960 ARMLVDKKYEIVATPGTARFLQEAGIPCEVVYKVNQGRPNTVDMIKNGQIQLVINTTEGK 1019
Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQI 1072
+AI DS +RR ALQ++V Y TT+ G A AL +V+ +Q++H +
Sbjct: 1020 KAIADSFTMRREALQHRVTYYTTMAGAKAACYALGELEAREVVCLQDLHKSL 1071
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: 3165
Number of extensions: 130
Number of successful extensions: 12
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 WP_020565795.1 A3OW_RS0122885 (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.16638.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 1581.9 0.0 0 1581.8 0.0 1.0 1 lcl|NCBI__GCF_000372865.1:WP_020565795.1 A3OW_RS0122885 carbamoyl-phospha
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000372865.1:WP_020565795.1 A3OW_RS0122885 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1581.8 0.0 0 0 1 1051 [. 2 1052 .. 2 1053 .. 0.99
Alignments for each domain:
== domain 1 score: 1581.8 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+dik++l++G+GpivigqA+EFDYsG+qa+kal+eeg++vvLvnsn+At+mtd+++ad+vYieP
lcl|NCBI__GCF_000372865.1:WP_020565795.1 2 PKRTDIKSILLLGAGPIVIGQACEFDYSGTQACKALREEGFRVVLVNSNPATIMTDPDMADAVYIEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
+++++vekiiekErpDail+t+GGqtaLn+a+ l+ +GvLekygv+++G++ eai+kaedRe+F++a
lcl|NCBI__GCF_000372865.1:WP_020565795.1 69 IDWQTVEKIIEKERPDAILPTMGGQTALNCALALDANGVLEKYGVEMIGATKEAINKAEDRELFNQA 135
******************************************************************* PP
TIGR01369 135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201
++ i+ eva+s++++s+eeal+a+ee+gyP i+R++ft+gG+G+gia+n+ee+ e++e++l++sp++
lcl|NCBI__GCF_000372865.1:WP_020565795.1 136 MRRIGFEVARSKTAHSIEEALAAQEEVGYPTIIRPSFTMGGSGGGIAYNREEFIEICERGLDLSPTN 202
******************************************************************* PP
TIGR01369 202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268
++l+e+s+ gwkE+E+EvvRDskdnciivc+iEn+Dp+GvHtGdsi+vaP+qtLtdkeyq+lR++++
lcl|NCBI__GCF_000372865.1:WP_020565795.1 203 ELLIEESVLGWKEFEMEVVRDSKDNCIIVCSIENFDPMGVHTGDSITVAPAQTLTDKEYQILRNVAV 269
******************************************************************* PP
TIGR01369 269 kiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelk 334
+++re+gv+++ +nvq a++P++ r++viE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldel+
lcl|NCBI__GCF_000372865.1:WP_020565795.1 270 AVLREIGVDTGgSNVQVAINPKDGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELQ 336
********9988******************************************************* PP
TIGR01369 335 ndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsle 400
n++t+ t+AsfEP++DYvv+k+Pr+ ++kf ++d++l+tqmksvGEvmaigrtf+e+lqkalr le
lcl|NCBI__GCF_000372865.1:WP_020565795.1 337 NEITGgATPASFEPTIDYVVTKVPRFTFEKFPQADDRLTTQMKSVGEVMAIGRTFQESLQKALRGLE 403
****878************************************************************ PP
TIGR01369 401 ekllglk..lkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklv 465
++++gl+ ++ +e+ ++e+++++l++p ++Rl ++a+a+r+g+s+eev+e++kid +fl ++++l+
lcl|NCBI__GCF_000372865.1:WP_020565795.1 404 IGISGLDevIDMEEVDAHEKMQRELRHPGPDRLRYVADAFRSGMSLEEVHEACKIDPWFLAQIEDLI 470
*****65115566778889999********************************************* PP
TIGR01369 466 elekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfe 532
ek+l++++l lk+ +l ++k++Gfsd+++akl++++e+evr++r++ gi pv+kr+D +aaEf+
lcl|NCBI__GCF_000372865.1:WP_020565795.1 471 VSEKSLATKTLATLKEGELYRLKRKGFSDQRLAKLLGTTESEVRNVRHRHGIRPVYKRIDSCAAEFS 537
******************************************************************* PP
TIGR01369 533 aktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPE 599
++t+YlYstyeee +++v++++k+++lG+Gp+Rigqg+EFDyc+vha+lalre gy+ti+in+nPE
lcl|NCBI__GCF_000372865.1:WP_020565795.1 538 SDTAYLYSTYEEE-CEARVSDREKIIILGGGPNRIGQGIEFDYCCVHAALALREDGYETIMINCNPE 603
*************.788899999******************************************** PP
TIGR01369 600 tvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidr 666
tvstD+d++drLyFe+lt+edvl+i++ ek++gvivq+gGqt+l+la++le+agv+i+Gts++sid
lcl|NCBI__GCF_000372865.1:WP_020565795.1 604 TVSTDFDTSDRLYFESLTLEDVLEIVHIEKPKGVIVQYGGQTPLKLARALEAAGVPIIGTSPDSIDL 670
******************************************************************* PP
TIGR01369 667 aEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryl 733
aEdRe+F+kll++l++kqp +++a+sve+a ++ake+gyP++vRpsyvlgGrameiv nee l+ry+
lcl|NCBI__GCF_000372865.1:WP_020565795.1 671 AEDRERFQKLLERLDLKQPPNATARSVEQALTAAKELGYPLVVRPSYVLGGRAMEIVFNEEGLQRYM 737
******************************************************************* PP
TIGR01369 734 eeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseev 800
+eav+vs+++Pvl+d++l+davE+dvDa+ dge+vli g++eHiE+aGvHsGDs+++lpp +l ++
lcl|NCBI__GCF_000372865.1:WP_020565795.1 738 KEAVTVSNDSPVLLDRFLDDAVEMDVDAIYDGERVLIGGLMEHIEQAGVHSGDSACSLPPYELPLKI 804
******************************************************************* PP
TIGR01369 801 kkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgk 867
+++++e+vk++a++l v+Gl+n qf++++e++yv+Evn+RasRt Pfvska+g pl+k+a+++++gk
lcl|NCBI__GCF_000372865.1:WP_020565795.1 805 QDRLREQVKALAEALGVQGLMNTQFAIQGEDIYVLEVNPRASRTAPFVSKATGYPLAKIAARCMVGK 871
******************************************************************* PP
TIGR01369 868 kleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaska 934
+l++ +g+++e + +++vk+avf+f k+ gvd++lgpemkstGEvmg+g+++ ea++k+++a++
lcl|NCBI__GCF_000372865.1:WP_020565795.1 872 TLAQ--QGMTEERIPGYYSVKEAVFPFVKFPGVDPLLGPEMKSTGEVMGVGKTFGEAFAKSQRAAGV 936
***9..77899******************************************************** PP
TIGR01369 935 kikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaekilel 1001
k+++ g+vl+s++d+dk ++ ++a++l++k ++++at gta++l+eagi +evv+kv++ +++++++
lcl|NCBI__GCF_000372865.1:WP_020565795.1 937 KLNHSGKVLISIRDADKVKAPDIARMLVDKKYEIVATPGTARFLQEAGIPCEVVYKVNQGRPNTVDM 1003
******************************************************************* PP
TIGR01369 1002 lkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
+k+++i+lvin+t+ +kka +++++rrea++++v++ t++++a+a++ a
lcl|NCBI__GCF_000372865.1:WP_020565795.1 1004 IKNGQIQLVINTTE-GKKAIADSFTMRREALQHRVTYYTTMAGAKAACYA 1052
***********997.78889999*********************998876 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: 9.58
//
[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