Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate HSERO_RS06925 HSERO_RS06925 carbamoyl phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>FitnessBrowser__HerbieS:HSERO_RS06925
Length = 1077
Score = 1440 bits (3727), Expect = 0.0
Identities = 742/1084 (68%), Positives = 865/1084 (79%), Gaps = 20/1084 (1%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDIKSILI+GAGPI+IGQACEFDYSGAQACKALREEG++VILVNSNPATIMTDPEM
Sbjct: 1 MPKRTDIKSILIIGAGPIIIGQACEFDYSGAQACKALREEGFKVILVNSNPATIMTDPEM 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADATYIEPI W+ V +II KE+PDA+LPTMGGQTALNCAL+L R GVLE++ V +IGAT
Sbjct: 61 ADATYIEPITWQAVERIIAKEKPDAILPTMGGQTALNCALDLHRHGVLEKYKVELIGATP 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
+AIDKAEDR +F AM KIGL +ARSG++HTMEE+ AV +GFP IIRPSFTMGG+GGG
Sbjct: 121 EAIDKAEDRSKFKEAMTKIGLGSARSGVSHTMEESWAVQKTIGFPVIIRPSFTMGGTGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYN EEFE IC RGL+ SPT ELLI+ESLIGWKEYEMEVVRDK DNCIIVCSIEN D M
Sbjct: 181 IAYNAEEFETICKRGLEASPTSELLIEESLIGWKEYEMEVVRDKADNCIIVCSIENLDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPAQTLTDKEYQIMRNAS+AVLREIGV+TGGSNVQF+VNP +GR+IVIEM
Sbjct: 241 GVHTGDSITVAPAQTLTDKEYQIMRNASLAVLREIGVDTGGSNVQFSVNPADGRMIVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAK+AAKLAVG+TLDEL N+ITGG TPASFEPSIDYVVTKIP
Sbjct: 301 NPRVSRSSALASKATGFPIAKIAAKLAVGFTLDELRNEITGGATPASFEPSIDYVVTKIP 360
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
RF FEKF A+ LTTQMKSVGEVMAIGRT QES QKALRGLEVG G + K + D E
Sbjct: 361 RFTFEKFPQADKHLTTQMKSVGEVMAIGRTFQESFQKALRGLEVGVDGMNEKTT--DREL 418
Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLE---EKVA 477
I +EL + G DRIWY+ DAF G S++ V LT+ID WFL QI+E+V +E EK
Sbjct: 419 ---IEKELGEPGPDRIWYVGDAFAQGFSLEEVHGLTHIDPWFLSQIKEIVDIELWLEK-- 473
Query: 478 EVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFA 537
+V + L+ L QLK+KGF+D RLAKL + +R+ R + + PV+KRVDTCA EF+
Sbjct: 474 DVALESLDKATLFQLKQKGFSDRRLAKLLKTTDTAVREQRKKLGVRPVFKRVDTCAGEFS 533
Query: 538 TDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETI 597
TDTAYMYSTY+EECE+NP TD++KIMVLGGGPNRIGQGIEFDYCCVHA+LA+R+DGYETI
Sbjct: 534 TDTAYMYSTYDEECESNP-TDKKKIMVLGGGPNRIGQGIEFDYCCVHAALAMRDDGYETI 592
Query: 598 MVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAA 657
MVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIV EKP GVIVQYGGQTPLKLA LEA
Sbjct: 593 MVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVDKEKPVGVIVQYGGQTPLKLALDLEAN 652
Query: 658 GVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPS 717
GVP++GTSPD ID AEDRERFQ ++ L L+QP N T A++ A+EIGYPLVVRPS
Sbjct: 653 GVPIVGTSPDMIDAAEDRERFQKLLQDLGLRQPPNRTARTEADALQLAQEIGYPLVVRPS 712
Query: 718 YVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGG 777
YVLGGRAMEIV+++ DL RY + AV VS+D+PVLLD FL+DA+EVDVD + DGE IGG
Sbjct: 713 YVLGGRAMEIVHEQRDLERYMREAVKVSHDSPVLLDRFLNDAIEVDVDCLSDGERTFIGG 772
Query: 778 IMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNE- 836
+MEHIEQAGVHSGDSACSLP Y+LS++ + +++Q +A L V GLMNVQFA++ +E
Sbjct: 773 VMEHIEQAGVHSGDSACSLPPYSLSKDTIEELKRQTALMAKGLNVVGLMNVQFAIQQSEV 832
Query: 837 -------VYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYS 889
V+++EVNPRA+RTVPFVSKATG+ LAK+AAR M G+SL QG+ EV+PPYYS
Sbjct: 833 DGKTVDTVFVLEVNPRASRTVPFVSKATGLQLAKIAARCMVGQSLDSQGIKNEVVPPYYS 892
Query: 890 VKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSV 949
VKE V PF KFPGVD +LGPEM+STGEVMGVG+TF EAF K+Q+G+ + K G+ LSV
Sbjct: 893 VKEAVFPFVKFPGVDTILGPEMKSTGEVMGVGKTFGEAFVKSQMGAGVKLPKSGKVFLSV 952
Query: 950 REGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGE 1009
+ DK R V +A L+ GF + AT GTA + AGI VNKV EGRPHI D +KN E
Sbjct: 953 KNSDKPRAVQVARDLVALGFSIVATKGTAAAISAAGIPVATVNKVVEGRPHIVDMVKNNE 1012
Query: 1010 YTYIINTTSGRR-AIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEM 1068
++NT +R AI DS IR SAL +V TT+ G A + + V +Q +
Sbjct: 1013 IALVVNTVEEKRNAIADSGAIRTSALAARVTTFTTIAGAEAAVEGMRHLESLDVYDLQGL 1072
Query: 1069 HAQI 1072
H I
Sbjct: 1073 HKAI 1076
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: 3125
Number of extensions: 119
Number of successful extensions: 16
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: 1077
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1032
Effective search space: 1060896
Effective search space used: 1060896
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 HSERO_RS06925 HSERO_RS06925 (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.10422.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 1553.4 0.0 0 1553.2 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS06925 HSERO_RS06925 carbamoyl phosphat
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS06925 HSERO_RS06925 carbamoyl phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1553.2 0.0 0 0 1 1050 [. 2 1056 .. 2 1058 .. 0.98
Alignments for each domain:
== domain 1 score: 1553.2 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYie 66
pkr+dik++l+iG+Gpi+igqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+e+ad++Yie
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 2 PKRTDIKSILIIGAGPIIIGQACEFDYSGAQACKALREEGFKVILVNSNPATIMTDPEMADATYIE 67
689*************************************************************** PP
TIGR01369 67 PltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFk 132
P+t++ave+ii kE+pDail+t+GGqtaLn+a++l+++GvLeky v+l+G++ eai+kaedR kFk
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 68 PITWQAVERIIAKEKPDAILPTMGGQTALNCALDLHRHGVLEKYKVELIGATPEAIDKAEDRSKFK 133
****************************************************************** PP
TIGR01369 133 ealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkas 198
ea+++i++ a+s + +++ee+ +++++ig+Pvi+R++ft+gGtG+gia+n+ee++++++++l+as
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 134 EAMTKIGLGSARSGVSHTMEESWAVQKTIGFPVIIRPSFTMGGTGGGIAYNAEEFETICKRGLEAS 199
****************************************************************** PP
TIGR01369 199 pikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllR 264
p++++l+e+sl gwkE+E+EvvRD++dnciivc+iEnlDp+GvHtGdsi+vaP+qtLtdkeyq++R
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 200 PTSELLIEESLIGWKEYEMEVVRDKADNCIIVCSIENLDPMGVHTGDSITVAPAQTLTDKEYQIMR 265
****************************************************************** PP
TIGR01369 265 daslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGys 329
+asl+++re+gv+++ +nvqf+++P + r++viE+npRvsRssALAskAtG+PiAk+aaklavG++
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 266 NASLAVLREIGVDTGgSNVQFSVNPADGRMIVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGFT 331
************9988************************************************** PP
TIGR01369 330 Ldelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqk 394
Ldel+n++t+ t+AsfEPs+DYvv+kiPr+ ++kf ++d++l+tqmksvGEvmaigrtf+e++qk
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 332 LDELRNEITGgATPASFEPSIDYVVTKIPRFTFEKFPQADKHLTTQMKSVGEVMAIGRTFQESFQK 397
*********878****************************************************** PP
TIGR01369 395 alrsleekllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrfflek 460
alr le ++ g+++k ++++e +e++l +p ++R++++ +a+ +g+s+eev+ lt+id +fl++
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 398 ALRGLEVGVDGMNEK---TTDRELIEKELGEPGPDRIWYVGDAFAQGFSLEEVHGLTHIDPWFLSQ 460
*******99998876...777888899*************************************** PP
TIGR01369 461 lkklvelekeleee.klkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvD 525
+k++v++e le+ +l+ l+k +l ++k++Gfsd+++akl+k+++++vr+ rk+lg+ pv+krvD
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 461 IKEIVDIELWLEKDvALESLDKATLFQLKQKGFSDRRLAKLLKTTDTAVREQRKKLGVRPVFKRVD 526
***********9876899************************************************ PP
TIGR01369 526 tvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagykt 591
t+a+Ef+++t+Y+Ysty ee +++ t+kkk++vlG+Gp+Rigqg+EFDyc+vha+la+r+ gy+t
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 527 TCAGEFSTDTAYMYSTYDEE-CESNPTDKKKIMVLGGGPNRIGQGIEFDYCCVHAALAMRDDGYET 591
********************.566667777************************************ PP
TIGR01369 592 ilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkil 657
i++n+nPEtvstDyd++drLyFe++t+edvl+i++kek+ gvivq+gGqt+l+la +le++gv+i+
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 592 IMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVDKEKPVGVIVQYGGQTPLKLALDLEANGVPIV 657
****************************************************************** PP
TIGR01369 658 GtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiv 723
Gts++ id aEdRe+F+kll++lg+ qp +++a++ +a ++a+eigyP++vRpsyvlgGrameiv
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 658 GTSPDMIDAAEDRERFQKLLQDLGLRQPPNRTARTEADALQLAQEIGYPLVVRPSYVLGGRAMEIV 723
****************************************************************** PP
TIGR01369 724 eneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstl 789
+++ +lery++eav+vs+++Pvl+d++l+da+EvdvD ++dge+ +i g++eHiE+aGvHsGDs++
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 724 HEQRDLERYMREAVKVSHDSPVLLDRFLNDAIEVDVDCLSDGERTFIGGVMEHIEQAGVHSGDSAC 789
****************************************************************** PP
TIGR01369 790 vlppqklseevkkkikeivkkiakelkvkGllniqfvvkde........evyviEvnvRasRtvPf 847
+lpp +ls+++ +++k++++ +ak l+v+Gl+n+qf++++ +v v+Evn+RasRtvPf
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 790 SLPPYSLSKDTIEELKRQTALMAKGLNVVGLMNVQFAIQQSevdgktvdTVFVLEVNPRASRTVPF 855
*************************************987512222222578************** PP
TIGR01369 848 vskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGE 913
vska+g++l+k+a+++++g++l + +g+k+e + +++vk+avf+f k+ gvd +lgpemkstGE
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 856 VSKATGLQLAKIAARCMVGQSLDS--QGIKNEVVPPYYSVKEAVFPFVKFPGVDTILGPEMKSTGE 919
***********************9..789************************************* PP
TIGR01369 914 vmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvle 979
vmg+g+++ ea++k+++ ++ k++k g+v+lsvk++dk +++++a+ l+++g++++at+gta++++
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 920 VMGVGKTFGEAFVKSQMGAGVKLPKSGKVFLSVKNSDKPRAVQVARDLVALGFSIVATKGTAAAIS 985
****************************************************************** PP
TIGR01369 980 eagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteleta 1045
agi + +v+kv e +++i++++k++ei lv+n+ ++k++a ++ ir +a+ +v+++t++++a
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 986 AAGIPVATVNKVVEGRPHIVDMVKNNEIALVVNTVEEKRNAIADSGAIRTSALAARVTTFTTIAGA 1051
****************************************************************** PP
TIGR01369 1046 ealle 1050
ea++e
lcl|FitnessBrowser__HerbieS:HSERO_RS06925 1052 EAAVE 1056
99886 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1077 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.10
# Mc/sec: 10.79
//
[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