Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_011938757.1 GURA_RS09445 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000016745.1:WP_011938757.1
Length = 1082
Score = 1360 bits (3520), Expect = 0.0
Identities = 685/1087 (63%), Positives = 849/1087 (78%), Gaps = 19/1087 (1%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDIK ILI+GAGPIVIGQACEFDYSG QACKAL+EEG++V+L+NSNPATIMTDP+
Sbjct: 1 MPKRTDIKKILIIGAGPIVIGQACEFDYSGTQACKALKEEGFQVVLLNSNPATIMTDPDF 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
AD TYIEP+ E++ IIEKERPDAVLPT+GGQTALN A+ + GVLE++GV +IGA
Sbjct: 61 ADRTYIEPVTPEILAMIIEKERPDAVLPTLGGQTALNTAVAVAESGVLEKYGVELIGAKL 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
AI AEDR F AM++I L RSG+AH EA+ + ++GFP IIRPSFT+GG+GGG
Sbjct: 121 PAIKMAEDRTLFKEAMQRINLTVPRSGLAHNHAEAMEIIKEIGFPAIIRPSFTLGGTGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYN EE+E++ G++ SPT E+LI+ES+IGWKEYE+EV+RD DN +I+CSIENFD M
Sbjct: 181 IAYNMEEYEKMSVAGIEASPTSEILIEESVIGWKEYELEVMRDTADNVVIICSIENFDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPAQTLTDKEYQI+R+AS+ ++REIGV+TGGSN+QF +NP++GRL+VIEM
Sbjct: 241 GVHTGDSITVAPAQTLTDKEYQILRDASLKIIREIGVDTGGSNIQFGINPRDGRLVVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAK+AAKLAVGYTLDE+ NDIT TPA FEP+IDYVVTK+P
Sbjct: 301 NPRVSRSSALASKATGFPIAKIAAKLAVGYTLDEITNDITR-ETPACFEPTIDYVVTKVP 359
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
RF FEKF A+ LTTQMKSVGEVMAIGRT +ESLQKA+R LE+G++GF+ + L D +A
Sbjct: 360 RFTFEKFPAADATLTTQMKSVGEVMAIGRTFKESLQKAIRSLEIGSSGFESR--LFDSKA 417
Query: 421 LTK----------IRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELV 470
T+ + +L+ +R+WY+ DAFR+G++V+ +F +T D WFL I++++
Sbjct: 418 ETRRALTGKEQQLLMEKLRTPNWERLWYLGDAFRSGMTVEEIFAVTAFDPWFLHNIKQII 477
Query: 471 RLEEKVAEVGITGLNADFL----RQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVY 526
E+++ +V + D L R+ K+ GF+D L L G E E+R+LR + PV+
Sbjct: 478 DKEDELKQVNVEEEANDNLKEVIREAKQYGFSDKHLGNLWGKTEDEVRQLRLSLGIKPVF 537
Query: 527 KRVDTCAAEFATDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHAS 586
KRVDTCAAEF T Y+YSTYEEECEA P TDR+KIM+LGGGPNRIGQGIEFDYCCVH
Sbjct: 538 KRVDTCAAEFVAYTPYLYSTYEEECEAEP-TDRKKIMILGGGPNRIGQGIEFDYCCVHGV 596
Query: 587 LALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQT 646
AL EDGYETIMVNCNPETVSTDYDTSDRLYFEP+T EDVL IV +EKP+GVIVQ+GGQT
Sbjct: 597 FALAEDGYETIMVNCNPETVSTDYDTSDRLYFEPLTYEDVLNIVELEKPEGVIVQFGGQT 656
Query: 647 PLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAK 706
PLKLA +LE AGVP+IGTSPDAIDRAEDRERFQ + +L L+QP N T + E A + A
Sbjct: 657 PLKLAVSLEKAGVPIIGTSPDAIDRAEDRERFQEMLHKLGLRQPENGTARSFEEAEKVAD 716
Query: 707 EIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDA 766
IGYP+VVRPSYVLGGRAMEIVYD +LRRY TAV S + P+L+D FLD+A+E+DVDA
Sbjct: 717 RIGYPVVVRPSYVLGGRAMEIVYDVDNLRRYMHTAVQASPEHPILIDKFLDEAIEIDVDA 776
Query: 767 ICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLM 826
+CDG +IGGIMEHIE+AG+HSGDSACSLP Y++S+EI D +R+Q + +A EL VRGLM
Sbjct: 777 LCDGTEAVIGGIMEHIEEAGIHSGDSACSLPPYSISREIADEIRRQTKMMALELNVRGLM 836
Query: 827 NVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPP 886
NVQ+A+K++ +Y++EVNPRA+RT PFVSKATG PLAK+AAR+M+GK+L E G+T+E+ P
Sbjct: 837 NVQYAIKDDVIYILEVNPRASRTAPFVSKATGRPLAKLAARIMSGKTLRELGITEEIEPT 896
Query: 887 YYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRAL 946
+ SVKE V PF KFPGVD +LGPEM+STGEVMG+ FA+AFAKAQLG+ + G+
Sbjct: 897 HISVKEAVFPFVKFPGVDTILGPEMKSTGEVMGIDDNFAKAFAKAQLGAGVKLPTSGKVF 956
Query: 947 LSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIK 1006
+SVR+ DK+ +V A KL GFEL AT GTA L E GI +VNKV EGRPHI D IK
Sbjct: 957 ISVRDADKKHIVSAAKKLYDNGFELVATRGTAAYLQEKGIPVLVVNKVLEGRPHIVDSIK 1016
Query: 1007 NGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQ 1066
N E +INTT G +A+ DS IRR+AL + Y TT +G A + A E+ +SV+
Sbjct: 1017 NNEICMVINTTQGAQAVADSFSIRRNALVSNIAYYTTASGARAVVDGIIAMRQEE-LSVK 1075
Query: 1067 EMHAQIK 1073
+ +K
Sbjct: 1076 PIQDYLK 1082
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: 3097
Number of extensions: 126
Number of successful extensions: 15
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 WP_011938757.1 GURA_RS09445 (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.1178203.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 1573.4 0.1 0 1573.2 0.1 1.0 1 NCBI__GCF_000016745.1:WP_011938757.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016745.1:WP_011938757.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1573.2 0.1 0 0 1 1049 [. 2 1061 .. 2 1064 .. 0.97
Alignments for each domain:
== domain 1 score: 1573.2 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71
pkr+dikk+l+iG+GpivigqA+EFDYsG+qa+kalkeeg++vvL+nsn+At+mtd+++ad++YieP+t+e
NCBI__GCF_000016745.1:WP_011938757.1 2 PKRTDIKKILIIGAGPIVIGQACEFDYSGTQACKALKEEGFQVVLLNSNPATIMTDPDFADRTYIEPVTPE 72
689******************************************************************** PP
TIGR01369 72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142
+++ iiekErpDa+l+tlGGqtaLn av + e+GvLekygv+l+G+k+ aik aedR +Fkea++ in+ v
NCBI__GCF_000016745.1:WP_011938757.1 73 ILAMIIEKERPDAVLPTLGGQTALNTAVAVAESGVLEKYGVELIGAKLPAIKMAEDRTLFKEAMQRINLTV 143
*********************************************************************** PP
TIGR01369 143 akseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwk 213
++s +++ +ea+e+++eig+P i+R++ftlgGtG+gia+n+ee +++ +++asp++++l+e+s+ gwk
NCBI__GCF_000016745.1:WP_011938757.1 144 PRSGLAHNHAEAMEIIKEIGFPAIIRPSFTLGGTGGGIAYNMEEYEKMSVAGIEASPTSEILIEESVIGWK 214
*********************************************************************** PP
TIGR01369 214 EiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvq 283
E+E+Ev+RD++dn++i+c+iEn+Dp+GvHtGdsi+vaP+qtLtdkeyq+lRdaslkiire+gv+++ +n+q
NCBI__GCF_000016745.1:WP_011938757.1 215 EYELEVMRDTADNVVIICSIENFDPMGVHTGDSITVAPAQTLTDKEYQILRDASLKIIREIGVDTGgSNIQ 285
***************************************************************9988**** PP
TIGR01369 284 faldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvv 354
f+++P++ r+vviE+npRvsRssALAskAtG+PiAk+aaklavGy+Lde++nd+t+et+A+fEP++DYvv+
NCBI__GCF_000016745.1:WP_011938757.1 286 FGINPRDGRLVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYTLDEITNDITRETPACFEPTIDYVVT 356
*********************************************************************** PP
TIGR01369 355 kiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklk..........ekeaes 415
k+Pr+ ++kf +d +l+tqmksvGEvmaigrtf+e+lqka+rsle++ +g++++ + ++
NCBI__GCF_000016745.1:WP_011938757.1 357 KVPRFTFEKFPAADATLTTQMKSVGEVMAIGRTFKESLQKAIRSLEIGSSGFESRlfdskaetrrALTGKE 427
**************************************************965541111111100123345 PP
TIGR01369 416 deeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklk....elkke 482
++ l+e+l++pn +Rl+++ +a+r+g++vee++ +t +d +fl+++k++++ e el++++++ + ke
NCBI__GCF_000016745.1:WP_011938757.1 428 QQLLMEKLRTPNWERLWYLGDAFRSGMTVEEIFAVTAFDPWFLHNIKQIIDKEDELKQVNVEeeanDNLKE 498
667899***************************************************99665222255567 PP
TIGR01369 483 llkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevte 553
++++ak++Gfsd+++++l++++e+evr+lr +lgi pv+krvDt+aaEf a tpYlYstyeee ++e t+
NCBI__GCF_000016745.1:WP_011938757.1 499 VIREAKQYGFSDKHLGNLWGKTEDEVRQLRLSLGIKPVFKRVDTCAAEFVAYTPYLYSTYEEE-CEAEPTD 568
77899**********************************************************.6778888 PP
TIGR01369 554 kkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldi 624
+kk+++lG+Gp+Rigqg+EFDyc+vh+v al e gy+ti++n+nPEtvstDyd++drLyFe+lt+edvl+i
NCBI__GCF_000016745.1:WP_011938757.1 569 RKKIMILGGGPNRIGQGIEFDYCCVHGVFALAEDGYETIMVNCNPETVSTDYDTSDRLYFEPLTYEDVLNI 639
88********************************************************************* PP
TIGR01369 625 iekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsvee 695
+e ek+egvivq+gGqt+l+la +le+agv+i+Gts+++idraEdRe+F+++l++lg+ qp++ +a+s ee
NCBI__GCF_000016745.1:WP_011938757.1 640 VELEKPEGVIVQFGGQTPLKLAVSLEKAGVPIIGTSPDAIDRAEDRERFQEMLHKLGLRQPENGTARSFEE 710
*********************************************************************** PP
TIGR01369 696 akeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadge 766
a+++a++igyPv+vRpsyvlgGrameiv++ ++l+ry+++av++s+e+P+lidk+l++a+E+dvDa++dg+
NCBI__GCF_000016745.1:WP_011938757.1 711 AEKVADRIGYPVVVRPSYVLGGRAMEIVYDVDNLRRYMHTAVQASPEHPILIDKFLDEAIEIDVDALCDGT 781
*********************************************************************** PP
TIGR01369 767 evliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEv 837
e +i gi+eHiEeaG+HsGDs+++lpp ++s+e+ ++i++++k +a el+v+Gl+n+q+++kd+ +y++Ev
NCBI__GCF_000016745.1:WP_011938757.1 782 EAVIGGIMEHIEEAGIHSGDSACSLPPYSISREIADEIRRQTKMMALELNVRGLMNVQYAIKDDVIYILEV 852
*********************************************************************** PP
TIGR01369 838 nvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpem 908
n+RasRt Pfvska+g pl+kla++++ gk+l+e g+++e ++++++vk+avf+f k+ gvd +lgpem
NCBI__GCF_000016745.1:WP_011938757.1 853 NPRASRTAPFVSKATGRPLAKLAARIMSGKTLRE--LGITEEIEPTHISVKEAVFPFVKFPGVDTILGPEM 921
**********************************..6689******************************* PP
TIGR01369 909 kstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvle 979
kstGEvmgi++++++a++ka+l ++ k+++ g+v++sv+d+dk++++++akkl ++g++++at+gta++l+
NCBI__GCF_000016745.1:WP_011938757.1 922 KSTGEVMGIDDNFAKAFAKAQLGAGVKLPTSGKVFISVRDADKKHIVSAAKKLYDNGFELVATRGTAAYLQ 992
*********************************************************************** PP
TIGR01369 980 eagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeall 1049
e+gi + vv+kv e +++i++ +k++ei +vin+t+ +++a+ ++++irr+a+ ++++ t++++a+a++
NCBI__GCF_000016745.1:WP_011938757.1 993 EKGIPVLVVNKVLEGRPHIVDSIKNNEICMVINTTQ-GAQAVADSFSIRRNALVSNIAYYTTASGARAVV 1061
*********************************987.88899999*******************999987 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: 0.02u 0.03s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 21.47
//
[ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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