Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_034992740.1 DL88_RS04925 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000745425.1:WP_034992740.1
Length = 1107
Score = 1269 bits (3285), Expect = 0.0
Identities = 669/1095 (61%), Positives = 813/1095 (74%), Gaps = 43/1095 (3%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDI +I+I+GAGPI+IGQACEFDYSG QACKALR+EGYR++LVNSNPATIMTDP+M
Sbjct: 1 MPKRTDIGTIMIIGAGPIIIGQACEFDYSGTQACKALRQEGYRIVLVNSNPATIMTDPDM 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDA-----VLPTMGGQTALNCALELERQGVLEEFGVTM 115
AD TY+EPI EVV KII KER A +LPTMGGQTALNCAL L++ GVL+++ V M
Sbjct: 61 ADRTYVEPITPEVVAKIIAKERHAAPGGFALLPTMGGQTALNCALSLKKMGVLDDYDVEM 120
Query: 116 IGATADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMG 175
IGATA+AIDKAEDR F AM KIGL T RS T+ +AL + D+G P IIRPSFTMG
Sbjct: 121 IGATAEAIDKAEDRELFREAMTKIGLSTPRSHQIKTLNQALDILDDIGLPAIIRPSFTMG 180
Query: 176 GSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIE 235
G+GGGIAYN+ E+ +I RG+D SPT E+L++ES++GWKEYEMEVVRD+NDNCIIVCSIE
Sbjct: 181 GTGGGIAYNKAEYIDIIERGIDASPTNEVLVEESVLGWKEYEMEVVRDRNDNCIIVCSIE 240
Query: 236 NFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRL 295
N D MG+HTGDSITVAPA TLTDKEYQ+MR+AS+AVLREIGVETGGSNVQFAVNP++GR+
Sbjct: 241 NIDPMGVHTGDSITVAPALTLTDKEYQVMRDASLAVLREIGVETGGSNVQFAVNPQDGRM 300
Query: 296 IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYV 355
IVIEMNPRVSRSSALASKATGFPIAKVAA+LAVGYTLDE+ NDITGG TPASFEPSIDYV
Sbjct: 301 IVIEMNPRVSRSSALASKATGFPIAKVAARLAVGYTLDEIANDITGGATPASFEPSIDYV 360
Query: 356 VTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSL 415
VTKIPRF FEKF GA D LTT MKSVGE MAIGRT ESLQKALR L+ G TG D ++++
Sbjct: 361 VTKIPRFAFEKFPGAEDTLTTAMKSVGETMAIGRTFAESLQKALRSLDTGLTGLD-EIAI 419
Query: 416 DD---PEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRL 472
D + + +R L DR+ +A A R G+S++ + +IDRWFL QI ++ L
Sbjct: 420 DGLGLGDDMNALRGALGRPTPDRLLKVAQAMREGMSIEEIHEACSIDRWFLDQIAGILDL 479
Query: 473 EEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTC 532
E KV G+ +A LR+LK GF+DARLA L G E+ LR + + PVYKR+DTC
Sbjct: 480 EAKVRAFGLP-QDAANLRRLKAAGFSDARLATLTGTGPREVAALRAELGVEPVYKRIDTC 538
Query: 533 AAEFATDTAYMYSTYEEE------CEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHAS 586
AAEFA+ TAY+YSTY CEA PS +R+K+++LGGGPNRIGQGIEFDYCC A
Sbjct: 539 AAEFASPTAYLYSTYAPPFAGPPVCEARPS-NRDKVVILGGGPNRIGQGIEFDYCCCQAC 597
Query: 587 LALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKP----KGVIVQY 642
AL + G ETIM+NCNPETVSTDYDTSDRLYFEP+T+EDVL I+ E+ KGVIVQ+
Sbjct: 598 FALHDAGLETIMINCNPETVSTDYDTSDRLYFEPLTIEDVLSILAKEQQAGTLKGVIVQF 657
Query: 643 GGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAV 702
GGQTPLKLA ALE AGVP++GTS D+ID AEDR+RF+ +E++ LKQP N ++E +
Sbjct: 658 GGQTPLKLAHALERAGVPILGTSVDSIDLAEDRDRFKRLLEKIGLKQPMNGIAFSVEQSR 717
Query: 703 EKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAV-------------------- 742
A ++G PLVVRPSYVLGGRAM I+ D A Y +
Sbjct: 718 LVAADLGLPLVVRPSYVLGGRAMAIIRDNAAFDDYLLGTLPGLVSSEIKSRYPNDKTGQI 777
Query: 743 -SVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTL 801
+V P+L D +L DAVEVDVDA+CDG+ V I GIMEHIE+AG+HSGDSACSLP +L
Sbjct: 778 NTVLGKNPLLFDRYLSDAVEVDVDALCDGKEVFICGIMEHIEEAGIHSGDSACSLPPRSL 837
Query: 802 SQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPL 861
E + Q +KLA LQV G MNVQ+A+K++E+Y++EVNPRAARTVPFV+K GVPL
Sbjct: 838 GPEKIAALEDQTRKLALALQVGGFMNVQYALKDDEIYVLEVNPRAARTVPFVAKVIGVPL 897
Query: 862 AKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVG 921
AK+AAR+M G+ LA+ + + + + VKE V PF +FPGVD +LGPEMRSTGEVMG+
Sbjct: 898 AKIAARLMTGERLADFKLESKKL-RHVGVKEAVFPFARFPGVDTVLGPEMRSTGEVMGID 956
Query: 922 RTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVL 981
+FA AFAK+QLG + + G +SVR+ DK R V+ L+ GF++ AT GTA L
Sbjct: 957 YSFAIAFAKSQLGGGTKVPTKGTVFVSVRDEDKHRAVETIRLLVTLGFKICATGGTARFL 1016
Query: 982 GEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYD 1041
GI + +NKV EGRPH+ D IKNG ++NTT G +A+ DSR +RR+AL +KV Y
Sbjct: 1017 EAEGIPAQRLNKVSEGRPHVVDAIKNGLIQLVLNTTEGAQALADSRSLRRAALLHKVPYY 1076
Query: 1042 TTLNGGFATAMALNA 1056
TTL G A A + A
Sbjct: 1077 TTLAGAIAAAQGIRA 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: 3165
Number of extensions: 162
Number of successful extensions: 19
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_034992740.1 DL88_RS04925 (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.26347.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 1442.1 0.0 0 1441.3 0.0 1.3 1 lcl|NCBI__GCF_000745425.1:WP_034992740.1 DL88_RS04925 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745425.1:WP_034992740.1 DL88_RS04925 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1441.3 0.0 0 0 1 1049 [. 2 1086 .. 2 1089 .. 0.96
Alignments for each domain:
== domain 1 score: 1441.3 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+di ++++iG+Gpi+igqA+EFDYsG+qa+kal++eg+++vLvnsn+At+mtd+++ad++Y+eP
lcl|NCBI__GCF_000745425.1:WP_034992740.1 2 PKRTDIGTIMIIGAGPIIIGQACEFDYSGTQACKALRQEGYRIVLVNSNPATIMTDPDMADRTYVEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpD.....ailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRe 129
+t+e+v+kii kEr a+l+t+GGqtaLn+a++l+++GvL+ y+v+++G++ eai+kaedRe
lcl|NCBI__GCF_000745425.1:WP_034992740.1 69 ITPEVVAKIIAKERHAapggfALLPTMGGQTALNCALSLKKMGVLDDYDVEMIGATAEAIDKAEDRE 135
**************763334469******************************************** PP
TIGR01369 130 kFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalk 196
+F+ea+++i++++++s+ +++ ++al++ ++ig+P i+R++ft+gGtG+gia+n++e ++e++++
lcl|NCBI__GCF_000745425.1:WP_034992740.1 136 LFREAMTKIGLSTPRSHQIKTLNQALDILDDIGLPAIIRPSFTMGGTGGGIAYNKAEYIDIIERGID 202
******************************************************************* PP
TIGR01369 197 aspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqll 263
asp+++vlve+s+ gwkE+E+EvvRD++dnciivc+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq +
lcl|NCBI__GCF_000745425.1:WP_034992740.1 203 ASPTNEVLVEESVLGWKEYEMEVVRDRNDNCIIVCSIENIDPMGVHTGDSITVAPALTLTDKEYQVM 269
******************************************************************* PP
TIGR01369 264 Rdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGys 329
Rdasl+++re+gve++ +nvqfa++P++ r++viE+npRvsRssALAskAtG+PiAkvaa+lavGy+
lcl|NCBI__GCF_000745425.1:WP_034992740.1 270 RDASLAVLREIGVETGgSNVQFAVNPQDGRMIVIEMNPRVSRSSALASKATGFPIAKVAARLAVGYT 336
**************988************************************************** PP
TIGR01369 330 Ldelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqka 395
Lde+ nd+t+ t+AsfEPs+DYvv+kiPr++++kf +++++l+t mksvGE maigrtf e+lqka
lcl|NCBI__GCF_000745425.1:WP_034992740.1 337 LDEIANDITGgATPASFEPSIDYVVTKIPRFAFEKFPGAEDTLTTAMKSVGETMAIGRTFAESLQKA 403
*********878******************************************************* PP
TIGR01369 396 lrsleekllglklkek...ea.esdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffl 458
lrsl+++l+gl++ + ++l+ al +p+++Rl+ +a+a+r+g+s+ee++e++ idr+fl
lcl|NCBI__GCF_000745425.1:WP_034992740.1 404 LRSLDTGLTGLDEIAIdglGLgDDMNALRGALGRPTPDRLLKVAQAMREGMSIEEIHEACSIDRWFL 470
**********66543311133144556778999********************************** PP
TIGR01369 459 eklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvD 525
++++ +++le +++ l ++ +l+++k+ Gfsd+++a+l+++ +ev +lr elg+ pv+kr+D
lcl|NCBI__GCF_000745425.1:WP_034992740.1 471 DQIAGILDLEAKVRAFGLP-QDAANLRRLKAAGFSDARLATLTGTGPREVAALRAELGVEPVYKRID 536
**************88887.7999******************************************* PP
TIGR01369 526 tvaaEfeaktpYlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalrea 587
t+aaEf + t+YlYsty+ +++ ++++kv++lG+Gp+Rigqg+EFDyc+ +a+ al++a
lcl|NCBI__GCF_000745425.1:WP_034992740.1 537 TCAAEFASPTAYLYSTYAPPfagppVCEARPSNRDKVVILGGGPNRIGQGIEFDYCCCQACFALHDA 603
*****************998666665677777788******************************** PP
TIGR01369 588 gyktilinynPEtvstDydiadrLyFeeltvedvldiiekek....vegvivqlgGqtalnlakele 650
g +ti+in+nPEtvstDyd++drLyFe+lt+edvl+i+ ke+ +gvivq+gGqt+l+la++le
lcl|NCBI__GCF_000745425.1:WP_034992740.1 604 GLETIMINCNPETVSTDYDTSDRLYFEPLTIEDVLSILAKEQqagtLKGVIVQFGGQTPLKLAHALE 670
****************************************983333478****************** PP
TIGR01369 651 eagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgG 717
+agv+ilGts++sid aEdR++F++ll+++g+kqp + +a sve+ + +a+++g+P++vRpsyvlgG
lcl|NCBI__GCF_000745425.1:WP_034992740.1 671 RAGVPILGTSVDSIDLAEDRDRFKRLLEKIGLKQPMNGIAFSVEQSRLVAADLGLPLVVRPSYVLGG 737
******************************************************************* PP
TIGR01369 718 rameiveneeeleryle.....................eavevskekPvlidkyledavEvdvDava 763
ram+i+++++ + +yl ++++v ++P+l d+yl+davEvdvDa++
lcl|NCBI__GCF_000745425.1:WP_034992740.1 738 RAMAIIRDNAAFDDYLLgtlpglvsseiksrypndktgQINTVLGKNPLLFDRYLSDAVEVDVDALC 804
************999977788888888888888887777778889********************** PP
TIGR01369 764 dgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkde 830
dg+ev+i+gi+eHiEeaG+HsGDs+++lpp++l e +++++++k+a +l+v G +n+q+++kd+
lcl|NCBI__GCF_000745425.1:WP_034992740.1 805 DGKEVFICGIMEHIEEAGIHSGDSACSLPPRSLGPEKIAALEDQTRKLALALQVGGFMNVQYALKDD 871
******************************************************************* PP
TIGR01369 831 evyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfskl 897
e+yv+Evn+Ra+RtvPfv+k++gvpl+k+a+++++g++l++ + ++kk ++v+vk+avf+f+++
lcl|NCBI__GCF_000745425.1:WP_034992740.1 872 EIYVLEVNPRAARTVPFVAKVIGVPLAKIAARLMTGERLADFKL---ESKKLRHVGVKEAVFPFARF 935
*****************************************876...99999*************** PP
TIGR01369 898 agvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaek 964
gvd vlgpem+stGEvmgi+++++ a++k++l ++k+++kg+v++sv+d+dk++++e+++ l+++
lcl|NCBI__GCF_000745425.1:WP_034992740.1 936 PGVDTVLGPEMRSTGEVMGIDYSFAIAFAKSQLGGGTKVPTKGTVFVSVRDEDKHRAVETIRLLVTL 1002
******************************************************************* PP
TIGR01369 965 glkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirrea 1031
g+k++at gta++le +gi a+ ++kvse ++++++++k++ i+lv+n+t+ +++a ++ ++rr+a
lcl|NCBI__GCF_000745425.1:WP_034992740.1 1003 GFKICATGGTARFLEAEGIPAQRLNKVSEGRPHVVDAIKNGLIQLVLNTTE-GAQALADSRSLRRAA 1068
************************************************997.88899999******* PP
TIGR01369 1032 veykvplvteletaeall 1049
+ +kvp+ t+l++a a++
lcl|NCBI__GCF_000745425.1:WP_034992740.1 1069 LLHKVPYYTTLAGAIAAA 1086
**********99887765 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: 00:00:00.15
# Mc/sec: 7.32
//
[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