Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate RR42_RS13510 RR42_RS13510 carbamoyl phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>FitnessBrowser__Cup4G11:RR42_RS13510
Length = 1082
Score = 1449 bits (3750), Expect = 0.0
Identities = 750/1087 (68%), Positives = 867/1087 (79%), Gaps = 21/1087 (1%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDIKSILI+GAGPI+IGQACEFDYSGAQACKALREEG++V+LVNSNPATIMTDP
Sbjct: 1 MPKRTDIKSILIIGAGPIIIGQACEFDYSGAQACKALREEGFKVVLVNSNPATIMTDPNT 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
AD TYIEPI WEVV +II KERPDA+LPTMGGQTALNCAL+L R GVL ++ V +IGA+
Sbjct: 61 ADVTYIEPITWEVVERIIAKERPDAILPTMGGQTALNCALDLHRHGVLAKYNVELIGASP 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADV-------GFPCIIRPSFT 173
+AIDKAEDR++F AM KIGL +A+SGIAH+MEEALAV + G+P +IRPSFT
Sbjct: 121 EAIDKAEDRQKFKEAMTKIGLGSAKSGIAHSMEEALAVQTQIAKETATGGYPIVIRPSFT 180
Query: 174 MGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCS 233
+GGSGGGIAYNREEFEEIC RGLDLSPT+ELLI+ESL+GWKEYEMEVVRDK DNCII+CS
Sbjct: 181 LGGSGGGIAYNREEFEEICKRGLDLSPTRELLIEESLLGWKEYEMEVVRDKKDNCIIICS 240
Query: 234 IENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNG 293
IEN D MGIHTGDSITVAPAQTLTDKEYQI+RNAS+AVLREIGV+TGGSNVQF++NP +G
Sbjct: 241 IENLDPMGIHTGDSITVAPAQTLTDKEYQILRNASLAVLREIGVDTGGSNVQFSINPADG 300
Query: 294 RLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSID 353
R+IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL N+ITGG TPASFEPSID
Sbjct: 301 RMIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELKNEITGGATPASFEPSID 360
Query: 354 YVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKV 413
YVVTK+PRF FEKF A+ LTTQMKSVGEVMA+GRT QES QKALRGLEVG G D K
Sbjct: 361 YVVTKVPRFAFEKFPQADSHLTTQMKSVGEVMAMGRTFQESFQKALRGLEVGVDGLDDKS 420
Query: 414 SLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLE 473
+ D +I E+ +AG DRIWY+ DAFR G+S++ V T ID WFL QIE++V+ E
Sbjct: 421 TDRD-----EIVEEIGEAGPDRIWYVGDAFRIGMSLEEVHAETAIDPWFLAQIEDIVKTE 475
Query: 474 EKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCA 533
V + L+A LR LK+KGF+D RLAKL G A +R R + PVYKRVDTCA
Sbjct: 476 TLVKARKLDSLSAAELRHLKQKGFSDRRLAKLMGAEPAAVRVARHAAGVRPVYKRVDTCA 535
Query: 534 AEFATDTAYMYSTYEE---ECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALR 590
AEFAT+TAYMY TYE ECEA+P+ +R KIMVLGGGPNRIGQGIEFDYCCVHA+LALR
Sbjct: 536 AEFATNTAYMYGTYEAEHGECEADPTANR-KIMVLGGGPNRIGQGIEFDYCCVHAALALR 594
Query: 591 EDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKL 650
EDGYETIMVNCNPETVSTDYDTSDRLYFEP+TLEDVLEIV EKP GVIVQYGGQTPLKL
Sbjct: 595 EDGYETIMVNCNPETVSTDYDTSDRLYFEPLTLEDVLEIVDREKPVGVIVQYGGQTPLKL 654
Query: 651 ARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGY 710
A LEA GVP+IGTSPD ID AEDRERFQ + L L+QP N T A + A+ A EIGY
Sbjct: 655 ALDLEANGVPIIGTSPDMIDAAEDRERFQKLLHELGLRQPPNRTARAEDEALRLATEIGY 714
Query: 711 PLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDG 770
PLVVRPSYVLGGRAMEIV++ DL RY + AV VS+D+PVLLD FL+DA+E DVDA+CDG
Sbjct: 715 PLVVRPSYVLGGRAMEIVHEPRDLERYMREAVKVSHDSPVLLDRFLNDAIECDVDALCDG 774
Query: 771 EMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQF 830
+ V IGG+MEHIEQAGVHSGDSACSLP Y+L+Q D +++Q +A L V GLMNVQF
Sbjct: 775 QRVFIGGVMEHIEQAGVHSGDSACSLPPYSLAQATVDELKRQTAAMAKALNVIGLMNVQF 834
Query: 831 AVK--NNE--VYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPP 886
A++ N E VY++EVNPRA+RTVP+VSKATG+ LAK+AAR MAG++L QGV EV+PP
Sbjct: 835 AIQQVNGEDIVYVLEVNPRASRTVPYVSKATGLSLAKIAARCMAGQTLDSQGVFDEVVPP 894
Query: 887 YYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRAL 946
Y+SVKE V PFNKFPGVDP+LGPEMRSTGEVMGVG+TF EA K+QL + S + + G L
Sbjct: 895 YFSVKEAVFPFNKFPGVDPVLGPEMRSTGEVMGVGKTFGEALFKSQLAAGSRLPEKGTVL 954
Query: 947 LSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIK 1006
L+V++ DK V +A L G+ + AT GTA + AGI R+VNKV +GRPHI D +K
Sbjct: 955 LTVKDSDKPHAVGVARMLHDMGYPIVATRGTASAIEAAGIPVRVVNKVKDGRPHIVDMLK 1014
Query: 1007 NGEYTYIINTT-SGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISV 1065
NGE + T R AI DSR IR SAL +V Y TT+ G A L + +V +
Sbjct: 1015 NGELALVFTTVDETRTAIADSRSIRISALASRVPYYTTIAGARAAVEGLKHMQSLEVYDL 1074
Query: 1066 QEMHAQI 1072
Q +HA +
Sbjct: 1075 QSLHASL 1081
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: 3119
Number of extensions: 137
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: 1082
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1036
Effective search space: 1063972
Effective search space used: 1063972
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 RR42_RS13510 RR42_RS13510 (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.22699.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 1533.3 0.0 0 1533.2 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS13510 RR42_RS13510 carbamoyl phosphate
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS13510 RR42_RS13510 carbamoyl phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1533.2 0.0 0 0 1 1050 [. 2 1061 .. 2 1063 .. 0.98
Alignments for each domain:
== domain 1 score: 1533.2 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+dik++l+iG+Gpi+igqA+EFDYsG+qa+kal+eeg++vvLvnsn+At+mtd++ ad +YieP
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 2 PKRTDIKSILIIGAGPIIIGQACEFDYSGAQACKALREEGFKVVLVNSNPATIMTDPNTADVTYIEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
+t+e+ve+ii kErpDail+t+GGqtaLn+a++l+++GvL+ky+v+l+G++ eai+kaedR+kFkea
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 69 ITWEVVERIIAKERPDAILPTMGGQTALNCALDLHRHGVLAKYNVELIGASPEAIDKAEDRQKFKEA 135
******************************************************************* PP
TIGR01369 135 lkeineevakseivesveealeaaeei.......gyPvivRaaftlgGtGsgiaeneeelkelveka 194
+++i++ aks i++s+eeal+++++i gyP+++R++ftlgG+G+gia+n+ee++e+++++
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 136 MTKIGLGSAKSGIAHSMEEALAVQTQIaketatgGYPIVIRPSFTLGGSGGGIAYNREEFEEICKRG 202
********************999887766666668******************************** PP
TIGR01369 195 lkaspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyq 261
l++sp++++l+e+sl gwkE+E+EvvRD+kdncii+c+iEnlDp+G+HtGdsi+vaP+qtLtdkeyq
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 203 LDLSPTRELLIEESLLGWKEYEMEVVRDKKDNCIIICSIENLDPMGIHTGDSITVAPAQTLTDKEYQ 269
******************************************************************* PP
TIGR01369 262 llRdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavG 327
+lR+asl+++re+gv+++ +nvqf+++P + r++viE+npRvsRssALAskAtG+PiAkvaaklavG
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 270 ILRNASLAVLREIGVDTGgSNVQFSINPADGRMIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVG 336
***************9988************************************************ PP
TIGR01369 328 ysLdelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealq 393
y+Ldelkn++t+ t+AsfEPs+DYvv+k+Pr++++kf ++d++l+tqmksvGEvma+grtf+e++q
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 337 YTLDELKNEITGgATPASFEPSIDYVVTKVPRFAFEKFPQADSHLTTQMKSVGEVMAMGRTFQESFQ 403
***********878***************************************************** PP
TIGR01369 394 kalrsleekllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrfflek 460
kalr le ++ gl+ k ++++e+ e++ ++ ++R++++ +a+r g+s+eev+ t id +fl +
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 404 KALRGLEVGVDGLDDK---STDRDEIVEEIGEAGPDRIWYVGDAFRIGMSLEEVHAETAIDPWFLAQ 467
********99998776...778888999*************************************** PP
TIGR01369 461 lkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtv 527
++++v++e+ ++ kl+ l++ +l+++k++Gfsd+++akl++ + a+vr +r+++g+ pv+krvDt+
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 468 IEDIVKTETLVKARKLDSLSAAELRHLKQKGFSDRRLAKLMGAEPAAVRVARHAAGVRPVYKRVDTC 534
******************************************************************* PP
TIGR01369 528 aaEfeaktpYlYstyeeekddve..vtekkkvlvlGsGpiRigqgvEFDycavhavlalreagykti 592
aaEf ++t+Y+Y tye+e+ + e t ++k++vlG+Gp+Rigqg+EFDyc+vha+lalre gy+ti
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 535 AAEFATNTAYMYGTYEAEHGECEadPTANRKIMVLGGGPNRIGQGIEFDYCCVHAALALREDGYETI 601
*****************9665541156779************************************* PP
TIGR01369 593 linynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGt 659
++n+nPEtvstDyd++drLyFe+lt+edvl+i+++ek+ gvivq+gGqt+l+la +le++gv+i+Gt
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 602 MVNCNPETVSTDYDTSDRLYFEPLTLEDVLEIVDREKPVGVIVQYGGQTPLKLALDLEANGVPIIGT 668
******************************************************************* PP
TIGR01369 660 saesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameivene 726
s++ id aEdRe+F+kll+elg+ qp +++a++ +ea ++a+eigyP++vRpsyvlgGrameiv++
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 669 SPDMIDAAEDRERFQKLLHELGLRQPPNRTARAEDEALRLATEIGYPLVVRPSYVLGGRAMEIVHEP 735
******************************************************************* PP
TIGR01369 727 eeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlpp 793
+lery++eav+vs+++Pvl+d++l+da+E+dvDa++dg++v+i g++eHiE+aGvHsGDs+++lpp
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 736 RDLERYMREAVKVSHDSPVLLDRFLNDAIECDVDALCDGQRVFIGGVMEHIEQAGVHSGDSACSLPP 802
******************************************************************* PP
TIGR01369 794 qklseevkkkikeivkkiakelkvkGllniqfvvkd....eevyviEvnvRasRtvPfvskalgvpl 856
+l + +++++k++++++ak+l+v Gl+n+qf++++ + vyv+Evn+RasRtvP+vska+g++l
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 803 YSLAQATVDELKRQTAAMAKALNVIGLMNVQFAIQQvngeDIVYVLEVNPRASRTVPYVSKATGLSL 869
*********************************9875543569************************ PP
TIGR01369 857 vklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdlee 923
+k+a+++++g++l + +gv e + +++vk+avf+f+k+ gvd+vlgpem+stGEvmg+g+++ e
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 870 AKIAARCMAGQTLDS--QGVFDEVVPPYFSVKEAVFPFNKFPGVDPVLGPEMRSTGEVMGVGKTFGE 934
**************9..889*********************************************** PP
TIGR01369 924 allkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlk 990
al+k++la+++++++kg+vll+vkd+dk +++ +a++l+++g+ ++at+gta+++e agi ++vv+k
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 935 ALFKSQLAAGSRLPEKGTVLLTVKDSDKPHAVGVARMLHDMGYPIVATRGTASAIEAAGIPVRVVNK 1001
******************************************************************* PP
TIGR01369 991 vseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaealle 1050
v++ +++i+++lk++e+ lv+++ +++++a ++ +ir +a+ +vp+ t++++a+a++e
lcl|FitnessBrowser__Cup4G11:RR42_RS13510 1002 VKDGRPHIVDMLKNGELALVFTTVDETRTAIADSRSIRISALASRVPYYTTIAGARAAVE 1061
*****************************************************9999876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1082 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 0.05s 00:00:00.14 Elapsed: 00:00:00.12
# Mc/sec: 8.76
//
[ok]
This GapMind analysis is from Apr 09 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