Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_036259910.1 DL86_RS06900 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000746085.1:WP_036259910.1
Length = 1107
Score = 1275 bits (3300), Expect = 0.0
Identities = 671/1095 (61%), Positives = 813/1095 (74%), Gaps = 43/1095 (3%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDI +ILI+GAGPI+IGQACEFDYSG QACKALR+EGYR++LVNSNPATIMTDP+M
Sbjct: 1 MPKRTDIGTILIIGAGPIIIGQACEFDYSGTQACKALRQEGYRIVLVNSNPATIMTDPDM 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPD-----AVLPTMGGQTALNCALELERQGVLEEFGVTM 115
AD TY+EPI E+V KII KER A+LPTMGGQTALNCAL L++ GVL+ F V M
Sbjct: 61 ADRTYVEPITPEIVAKIIAKERYASPGGFALLPTMGGQTALNCALSLKKMGVLDTFDVEM 120
Query: 116 IGATADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMG 175
IGA+ADAID AEDR RF AM +IGL T RS T+ +ALA+ D+G P IIRPSFTMG
Sbjct: 121 IGASADAIDMAEDRERFREAMTRIGLSTPRSRQIKTLSQALAILDDIGLPAIIRPSFTMG 180
Query: 176 GSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIE 235
G+GGGIAYN+ EF +I RG+D SPT E+L++ES++GWKEYEMEVVRDK DNCII+CSIE
Sbjct: 181 GTGGGIAYNKAEFIDIIERGIDASPTSEVLVEESVLGWKEYEMEVVRDKADNCIIICSIE 240
Query: 236 NFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRL 295
N D MG+HTGDSITVAPA TLTDKEYQIMR+AS+AVLREIGVETGGSNVQFAVNP++GR+
Sbjct: 241 NIDPMGVHTGDSITVAPALTLTDKEYQIMRDASLAVLREIGVETGGSNVQFAVNPEDGRM 300
Query: 296 IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYV 355
IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDE+ NDITGG TPASFEP+IDYV
Sbjct: 301 IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEIANDITGGATPASFEPTIDYV 360
Query: 356 VTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSL 415
VTKIPRF FEKF GA + LTT MKSVGE MAIG T ESLQKALR L+ G G D ++ +
Sbjct: 361 VTKIPRFAFEKFPGAENTLTTAMKSVGETMAIGLTFAESLQKALRSLDTGLDGLD-EIEI 419
Query: 416 DD---PEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRL 472
D + + +R L DR+ +A A R G++ D + IDRWF+ +++E++ L
Sbjct: 420 DGLGLGDDMNVLRAALGCPTPDRLLVVAQALRRGMTPDEIHEACRIDRWFIERLQEILDL 479
Query: 473 EEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTC 532
E KV G+ G +A LR LK GF+DARLA LA A++ LR + +HPVYKR+DTC
Sbjct: 480 EAKVRAHGLPG-DAANLRLLKAAGFSDARLASLAHAPRADVSALRKRLGVHPVYKRIDTC 538
Query: 533 AAEFATDTAYMYSTY------EEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHAS 586
AAEFA+ TAYMYSTY CEA PS+ REKI++LGGGPNRIGQGIEFDYCC HA
Sbjct: 539 AAEFASPTAYMYSTYAPPFAGAPACEARPSS-REKIVILGGGPNRIGQGIEFDYCCCHAC 597
Query: 587 LALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIE----KPKGVIVQY 642
ALRE GYETIM+NCNPETVSTDYDTSDRLYFEP+T EDVLEI+ E + KG IVQ+
Sbjct: 598 FALREVGYETIMINCNPETVSTDYDTSDRLYFEPLTDEDVLEILAKESEAGRLKGAIVQF 657
Query: 643 GGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAV 702
GGQTPLKLA ALE AG+P++GTS D ID AEDR+RF+ ++++ LKQP N ++E +
Sbjct: 658 GGQTPLKLAHALEKAGIPILGTSVDCIDLAEDRDRFKRLLDKIGLKQPMNGIAYSVEQSR 717
Query: 703 EKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYF----------QTAVSVSNDA---- 748
A E+G PLVVRPSYVLGGRAM I++D A Y + ND
Sbjct: 718 IVAAELGLPLVVRPSYVLGGRAMAIIHDTATFDDYLLGTLPGLVPSEVKARYPNDKTGQI 777
Query: 749 -------PVLLDHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTL 801
P+L D +L DAVE+DVDA+CDG+ I GIMEHIE+AG+HSGDSACSLP +L
Sbjct: 778 NTVLGKNPLLFDRYLSDAVEIDVDALCDGKDAFICGIMEHIEEAGIHSGDSACSLPPRSL 837
Query: 802 SQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPL 861
S E + Q ++LA L V GLMNVQ+A+K+ E+Y++EVNPRAARTVPFV+K G P+
Sbjct: 838 SPEKIAELESQTRELALALSVGGLMNVQYALKDGEIYVLEVNPRAARTVPFVAKVIGAPI 897
Query: 862 AKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVG 921
AK+AAR+MAG+SL+ G++ + + VKE V PF +FPGVD +LGPEMRSTGEVMG+
Sbjct: 898 AKIAARIMAGESLSSFGLSSTPL-DHVGVKESVFPFARFPGVDTVLGPEMRSTGEVMGLD 956
Query: 922 RTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVL 981
R+FA AFAK+QLG + + G +SVR+ DK RV++ L GF++ AT GT L
Sbjct: 957 RSFAIAFAKSQLGGGTKVPTTGAVFVSVRDADKPRVLETVQLLAGLGFKIYATGGTLRFL 1016
Query: 982 GEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYD 1041
G+ + +NKV EGRPH+ D IKNG ++NTT G +A+ DSR +RR+AL +KV Y
Sbjct: 1017 ESKGVQAQRINKVSEGRPHVVDAIKNGGIQLVLNTTEGAQALADSRSLRRAALLHKVPYY 1076
Query: 1042 TTLNGGFATAMALNA 1056
TTL G A + + A
Sbjct: 1077 TTLAGAIAASEGIKA 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: 3150
Number of extensions: 151
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_036259910.1 DL86_RS06900 (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.32232.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 1423.5 0.0 0 1422.7 0.0 1.3 1 lcl|NCBI__GCF_000746085.1:WP_036259910.1 DL86_RS06900 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000746085.1:WP_036259910.1 DL86_RS06900 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1422.7 0.0 0 0 1 1048 [. 2 1085 .. 2 1089 .. 0.96
Alignments for each domain:
== domain 1 score: 1422.7 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_000746085.1:WP_036259910.1 2 PKRTDIGTILIIGAGPIIIGQACEFDYSGTQACKALRQEGYRIVLVNSNPATIMTDPDMADRTYVEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpD.....ailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRe 129
+t+e+v+kii kEr a+l+t+GGqtaLn+a++l+++GvL+ ++v+++G++ +ai+ aedRe
lcl|NCBI__GCF_000746085.1:WP_036259910.1 69 ITPEIVAKIIAKERYAspggfALLPTMGGQTALNCALSLKKMGVLDTFDVEMIGASADAIDMAEDRE 135
**************754444479******************************************** PP
TIGR01369 130 kFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalk 196
+F+ea++ i++++++s+ +++ ++al++ ++ig+P i+R++ft+gGtG+gia+n++e+ ++e++++
lcl|NCBI__GCF_000746085.1:WP_036259910.1 136 RFREAMTRIGLSTPRSRQIKTLSQALAILDDIGLPAIIRPSFTMGGTGGGIAYNKAEFIDIIERGID 202
******************************************************************* PP
TIGR01369 197 aspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqll 263
asp+++vlve+s+ gwkE+E+EvvRD++dncii+c+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++
lcl|NCBI__GCF_000746085.1:WP_036259910.1 203 ASPTSEVLVEESVLGWKEYEMEVVRDKADNCIIICSIENIDPMGVHTGDSITVAPALTLTDKEYQIM 269
******************************************************************* PP
TIGR01369 264 Rdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGys 329
Rdasl+++re+gve++ +nvqfa++Pe+ r++viE+npRvsRssALAskAtG+PiAkvaaklavGy+
lcl|NCBI__GCF_000746085.1:WP_036259910.1 270 RDASLAVLREIGVETGgSNVQFAVNPEDGRMIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYT 336
**************988************************************************** PP
TIGR01369 330 Ldelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqka 395
Lde+ nd+t+ t+AsfEP++DYvv+kiPr++++kf +++++l+t mksvGE maig tf e+lqka
lcl|NCBI__GCF_000746085.1:WP_036259910.1 337 LDEIANDITGgATPASFEPTIDYVVTKIPRFAFEKFPGAENTLTTAMKSVGETMAIGLTFAESLQKA 403
*********878******************************************************* PP
TIGR01369 396 lrsleekllg...lklkekeaesdee.leealkkpndrRlfaiaealrrgvsveevyeltkidrffl 458
lrsl+++l g ++++ +d++ l+ al p+++Rl+++a+alrrg++ +e++e+++idr+f+
lcl|NCBI__GCF_000746085.1:WP_036259910.1 404 LRSLDTGLDGldeIEIDGLGLGDDMNvLRAALGCPTPDRLLVVAQALRRGMTPDEIHEACRIDRWFI 470
*********9433334444445555415678999********************************* PP
TIGR01369 459 eklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvD 525
e+l+++++le +++ + l ++ +l+ +k+ Gfsd+++a+l++ +a+v +lrk+lg++pv+kr+D
lcl|NCBI__GCF_000746085.1:WP_036259910.1 471 ERLQEILDLEAKVRAHGLP-GDAANLRLLKAAGFSDARLASLAHAPRADVSALRKRLGVHPVYKRID 536
*************988777.8999******************************************* PP
TIGR01369 526 tvaaEfeaktpYlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalrea 587
t+aaEf + t+Y+Ysty+ +++ ++++k+++lG+Gp+Rigqg+EFDyc+ ha+ alre
lcl|NCBI__GCF_000746085.1:WP_036259910.1 537 TCAAEFASPTAYMYSTYAPPfagapACEARPSSREKIVILGGGPNRIGQGIEFDYCCCHACFALREV 603
*****************987555555566777778******************************** PP
TIGR01369 588 gyktilinynPEtvstDydiadrLyFeeltvedvldiieke....kvegvivqlgGqtalnlakele 650
gy+ti+in+nPEtvstDyd++drLyFe+lt edvl+i+ ke + +g ivq+gGqt+l+la++le
lcl|NCBI__GCF_000746085.1:WP_036259910.1 604 GYETIMINCNPETVSTDYDTSDRLYFEPLTDEDVLEILAKEseagRLKGAIVQFGGQTPLKLAHALE 670
**************************************99844445789****************** PP
TIGR01369 651 eagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgG 717
+ag++ilGts++ id aEdR++F++lld++g+kqp + +a sve+ + +a+e+g+P++vRpsyvlgG
lcl|NCBI__GCF_000746085.1:WP_036259910.1 671 KAGIPILGTSVDCIDLAEDRDRFKRLLDKIGLKQPMNGIAYSVEQSRIVAAELGLPLVVRPSYVLGG 737
******************************************************************* PP
TIGR01369 718 rameiveneeeleryle.....................eavevskekPvlidkyledavEvdvDava 763
ram+i+++++++ +yl ++++v ++P+l d+yl+davE+dvDa++
lcl|NCBI__GCF_000746085.1:WP_036259910.1 738 RAMAIIHDTATFDDYLLgtlpglvpsevkarypndktgQINTVLGKNPLLFDRYLSDAVEIDVDALC 804
**************9977788888888888888887777778889********************** PP
TIGR01369 764 dgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkde 830
dg++ +i+gi+eHiEeaG+HsGDs+++lpp++ls e +++++++++a +l+v Gl+n+q+++kd+
lcl|NCBI__GCF_000746085.1:WP_036259910.1 805 DGKDAFICGIMEHIEEAGIHSGDSACSLPPRSLSPEKIAELESQTRELALALSVGGLMNVQYALKDG 871
******************************************************************* PP
TIGR01369 831 evyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfskl 897
e+yv+Evn+Ra+RtvPfv+k++g p++k+a+++++g++l++ + +++ ++v+vk++vf+f+++
lcl|NCBI__GCF_000746085.1:WP_036259910.1 872 EIYVLEVNPRAARTVPFVAKVIGAPIAKIAARIMAGESLSSFGL---SSTPLDHVGVKESVFPFARF 935
*****************************************886...78889*************** PP
TIGR01369 898 agvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaek 964
gvd vlgpem+stGEvmg++r+++ a++k++l ++k+++ g v++sv+d+dk ++le+++ la +
lcl|NCBI__GCF_000746085.1:WP_036259910.1 936 PGVDTVLGPEMRSTGEVMGLDRSFAIAFAKSQLGGGTKVPTTGAVFVSVRDADKPRVLETVQLLAGL 1002
******************************************************************* PP
TIGR01369 965 glkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirrea 1031
g+k+yat gt ++le +g++a+ ++kvse ++++++++k++ i+lv+n+t+ +++a ++ ++rr+a
lcl|NCBI__GCF_000746085.1:WP_036259910.1 1003 GFKIYATGGTLRFLESKGVQAQRINKVSEGRPHVVDAIKNGGIQLVLNTTE-GAQALADSRSLRRAA 1068
************************************************997.88899999******* PP
TIGR01369 1032 veykvplvteletaeal 1048
+ +kvp+ t+l++a a+
lcl|NCBI__GCF_000746085.1:WP_036259910.1 1069 LLHKVPYYTTLAGAIAA 1085
*********99987665 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: 0.14u 0.02s 00:00:00.16 Elapsed: 00:00:00.16
# Mc/sec: 7.22
//
[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