Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_072910070.1 BUB13_RS17565 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_900142125.1:WP_072910070.1
Length = 1085
Score = 1325 bits (3429), Expect = 0.0
Identities = 673/1061 (63%), Positives = 821/1061 (77%), Gaps = 19/1061 (1%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDIK ILI+GAGPI+IGQACEFDYSG QACKAL+EEGY V+L+NSNPATIMTDP+
Sbjct: 1 MPKRTDIKKILIIGAGPIIIGQACEFDYSGTQACKALKEEGYEVVLLNSNPATIMTDPDF 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
AD TY+EP++ V+ +IIEKE+PDA+LPT+GGQTALN A+ + G+LE+ GV +IGA
Sbjct: 61 ADRTYVEPVNPVVLSRIIEKEKPDALLPTLGGQTALNTAVAVAEAGILEKHGVELIGARL 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
I KAEDR F AM+KIG+ RSG+AH+ +EA+ V VGFP IIRPSFT+GG+GGG
Sbjct: 121 GPIKKAEDRTLFKQAMEKIGVAVPRSGLAHSYKEAMEVIDHVGFPAIIRPSFTLGGTGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYN EE+E + G++ SPT E+L++ES+IGWKEYE+EV+RD DN +I+CSIENFDAM
Sbjct: 181 IAYNLEEYERMAIAGIEASPTNEVLVEESVIGWKEYELEVMRDMADNVVIICSIENFDAM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPAQTLTDKEYQI+R+AS+ ++REIGV+TGGSN+QF VNPK+GRL+VIEM
Sbjct: 241 GVHTGDSITVAPAQTLTDKEYQILRDASLKIIREIGVDTGGSNIQFGVNPKDGRLVVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAK+AAKL+VGY LDE+ NDIT T ASFEP+IDYVVTK+P
Sbjct: 301 NPRVSRSSALASKATGFPIAKIAAKLSVGYRLDEIPNDITR-ETLASFEPTIDYVVTKVP 359
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKV------- 413
RF FEKF A LTTQMKSVGE M+IGRT +ESLQKALR +E+G+ GF+ ++
Sbjct: 360 RFTFEKFPQAEAHLTTQMKSVGEAMSIGRTFKESLQKALRSMEIGSHGFESRLFEKPGDY 419
Query: 414 --SLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVR 471
+L E L ++R L+ DR+W++ DA RAG S+D ++ LT ID WFL IE+++
Sbjct: 420 RRTLTQGE-LDELRTNLRVPNCDRMWHLGDAIRAGFSIDEIYQLTGIDPWFLRNIEQIIE 478
Query: 472 LE------EKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPV 525
+E +K+ G D LR K+ GF+D RLA L V E ++R+LR +Y++ PV
Sbjct: 479 MESLLVTQKKLMAAGDQQF-VDLLRNAKQYGFSDKRLAFLWEVTEKDVRELRQKYEVRPV 537
Query: 526 YKRVDTCAAEFATDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHA 585
YKRVDTC AEF T Y+YSTYE ECEA P TD+ KIM+LGGGPNRIGQGIEFDYCCVH
Sbjct: 538 YKRVDTCGAEFEAFTPYLYSTYETECEAEP-TDKRKIMILGGGPNRIGQGIEFDYCCVHG 596
Query: 586 SLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQ 645
AL + G+ETIMVNCNPETVSTDYDTSDRLYFEP+TLEDVLEIV EKP+GVIVQYGGQ
Sbjct: 597 VFALTDAGFETIMVNCNPETVSTDYDTSDRLYFEPLTLEDVLEIVATEKPEGVIVQYGGQ 656
Query: 646 TPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKA 705
TPLKLA LE AGVP+IGTSPDAIDRAEDRERFQ + +L LKQP N + + A + A
Sbjct: 657 TPLKLAVELEKAGVPIIGTSPDAIDRAEDRERFQALLHKLNLKQPENGIARSFDEAEKIA 716
Query: 706 KEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVD 765
IGYP+VVRPSYVLGGRAMEIVYD LRRY + AV S + P+L+D FL DA+E+DVD
Sbjct: 717 GRIGYPVVVRPSYVLGGRAMEIVYDIEQLRRYMKFAVQASPEHPILIDKFLQDAIEIDVD 776
Query: 766 AICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGL 825
A+ DG V+IGGIM+HIE+AG+HSGDSAC+LP Y+L EI +R+Q LA EL+V GL
Sbjct: 777 ALADGTEVVIGGIMQHIEEAGIHSGDSACALPPYSLPDEIIAEIRRQTIALALELKVVGL 836
Query: 826 MNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIP 885
MN+QFAVK +YLIEVNPRA+RTVPFVSKATG LA++AA+VMAG+SLAEQGV ++IP
Sbjct: 837 MNIQFAVKGGTIYLIEVNPRASRTVPFVSKATGRQLAQIAAKVMAGQSLAEQGVAGDIIP 896
Query: 886 PYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRA 945
+ SVKE V PF KFPGVD LLGPEM+STGEVMG+ F +AFAKAQLG+ + G+
Sbjct: 897 EHVSVKEAVFPFVKFPGVDTLLGPEMKSTGEVMGIDMDFGKAFAKAQLGAGVKLPTSGKI 956
Query: 946 LLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRI 1005
+SV++ DKE +V+ KL GF++ AT GTA L E G+ VNKV EGRPH D I
Sbjct: 957 FISVKDSDKEHIVEPVLKLANAGFKIMATAGTAKYLNEHGVITEHVNKVKEGRPHCVDAI 1016
Query: 1006 KNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNG 1046
K+ E + NTT G +++ DS IRRSAL ++ Y TT+ G
Sbjct: 1017 KSREICMVFNTTLGAQSVADSFSIRRSALMQEIAYFTTVAG 1057
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: 3131
Number of extensions: 146
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: 1085
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1039
Effective search space: 1067053
Effective search space used: 1067053
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_072910070.1 BUB13_RS17565 (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.2683755.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 1533.7 0.0 0 1533.5 0.0 1.0 1 NCBI__GCF_900142125.1:WP_072910070.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900142125.1:WP_072910070.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1533.5 0.0 0 0 1 1049 [. 2 1062 .. 2 1065 .. 0.97
Alignments for each domain:
== domain 1 score: 1533.5 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71
pkr+dikk+l+iG+Gpi+igqA+EFDYsG+qa+kalkeeg+evvL+nsn+At+mtd+++ad++Y+eP+++
NCBI__GCF_900142125.1:WP_072910070.1 2 PKRTDIKKILIIGAGPIIIGQACEFDYSGTQACKALKEEGYEVVLLNSNPATIMTDPDFADRTYVEPVNPV 72
689******************************************************************** PP
TIGR01369 72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142
++++iiekE+pDa+l+tlGGqtaLn av + e+G+Lek+gv+l+G+++ ikkaedR +Fk+a+++i++ v
NCBI__GCF_900142125.1:WP_072910070.1 73 VLSRIIEKEKPDALLPTLGGQTALNTAVAVAEAGILEKHGVELIGARLGPIKKAEDRTLFKQAMEKIGVAV 143
*********************************************************************** PP
TIGR01369 143 akseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwk 213
++s ++s +ea+e+++++g+P i+R++ftlgGtG+gia+n ee ++++ +++asp+++vlve+s+ gwk
NCBI__GCF_900142125.1:WP_072910070.1 144 PRSGLAHSYKEAMEVIDHVGFPAIIRPSFTLGGTGGGIAYNLEEYERMAIAGIEASPTNEVLVEESVIGWK 214
*********************************************************************** PP
TIGR01369 214 EiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvq 283
E+E+Ev+RD +dn++i+c+iEn+D++GvHtGdsi+vaP+qtLtdkeyq+lRdaslkiire+gv+++ +n+q
NCBI__GCF_900142125.1:WP_072910070.1 215 EYELEVMRDMADNVVIICSIENFDAMGVHTGDSITVAPAQTLTDKEYQILRDASLKIIREIGVDTGgSNIQ 285
***************************************************************9988**** PP
TIGR01369 284 faldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvv 354
f+++P++ r+vviE+npRvsRssALAskAtG+PiAk+aakl+vGy Lde++nd+t+et AsfEP++DYvv+
NCBI__GCF_900142125.1:WP_072910070.1 286 FGVNPKDGRLVVIEMNPRVSRSSALASKATGFPIAKIAAKLSVGYRLDEIPNDITRETLASFEPTIDYVVT 356
*********************************************************************** PP
TIGR01369 355 kiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklk..........ekeaes 415
k+Pr+ ++kf +++ +l+tqmksvGE m+igrtf+e+lqkalrs+e++ +g++++ + ++ +
NCBI__GCF_900142125.1:WP_072910070.1 357 KVPRFTFEKFPQAEAHLTTQMKSVGEAMSIGRTFKESLQKALRSMEIGSHGFESRlfekpgdyrrTLTQGE 427
***************************************************76651111111111234566 PP
TIGR01369 416 deeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleee.klk....elkk 481
+el+++l+ pn +R++ + +a+r+g+s++e+y+lt id +fl+++++++e+e+ l ++ kl +
NCBI__GCF_900142125.1:WP_072910070.1 428 LDELRTNLRVPNCDRMWHLGDAIRAGFSIDEIYQLTGIDPWFLRNIEQIIEMESLLVTQkKLMaagdQQFV 498
7888999**********************************************998776333233325567 PP
TIGR01369 482 ellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevt 552
+ll++ak++Gfsd+++a l++v+e++vr+lr+++++ pv+krvDt+ aEfea tpYlYstye+e ++e t
NCBI__GCF_900142125.1:WP_072910070.1 499 DLLRNAKQYGFSDKRLAFLWEVTEKDVRELRQKYEVRPVYKRVDTCGAEFEAFTPYLYSTYETE-CEAEPT 568
99**************************************************************.677778 PP
TIGR01369 553 ekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvld 623
+k+k+++lG+Gp+Rigqg+EFDyc+vh+v al +ag++ti++n+nPEtvstDyd++drLyFe+lt+edvl+
NCBI__GCF_900142125.1:WP_072910070.1 569 DKRKIMILGGGPNRIGQGIEFDYCCVHGVFALTDAGFETIMVNCNPETVSTDYDTSDRLYFEPLTLEDVLE 639
888******************************************************************** PP
TIGR01369 624 iiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsve 694
i+ +ek+egvivq+gGqt+l+la ele+agv+i+Gts+++idraEdRe+F++ll++l++kqp++ +a+s +
NCBI__GCF_900142125.1:WP_072910070.1 640 IVATEKPEGVIVQYGGQTPLKLAVELEKAGVPIIGTSPDAIDRAEDRERFQALLHKLNLKQPENGIARSFD 710
*********************************************************************** PP
TIGR01369 695 eakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadg 765
ea++ia +igyPv+vRpsyvlgGrameiv++ e+l+ry++ av++s+e+P+lidk+l+da+E+dvDa+adg
NCBI__GCF_900142125.1:WP_072910070.1 711 EAEKIAGRIGYPVVVRPSYVLGGRAMEIVYDIEQLRRYMKFAVQASPEHPILIDKFLQDAIEIDVDALADG 781
*********************************************************************** PP
TIGR01369 766 eevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviE 836
+ev+i gi++HiEeaG+HsGDs++ lpp +l +e+ +i++++ ++a elkv+Gl+niqf+vk++++y+iE
NCBI__GCF_900142125.1:WP_072910070.1 782 TEVVIGGIMQHIEEAGIHSGDSACALPPYSLPDEIIAEIRRQTIALALELKVVGLMNIQFAVKGGTIYLIE 852
*********************************************************************** PP
TIGR01369 837 vnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpe 907
vn+RasRtvPfvska+g +l+++a+kv++g++l+e +gv + +++v+vk+avf+f k+ gvd +lgpe
NCBI__GCF_900142125.1:WP_072910070.1 853 VNPRASRTVPFVSKATGRQLAQIAAKVMAGQSLAE--QGVAGDIIPEHVSVKEAVFPFVKFPGVDTLLGPE 921
***********************************..7899****************************** PP
TIGR01369 908 mkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvl 978
mkstGEvmgi+ d+ +a++ka+l ++ k+++ g++++svkd+dke+++e + kla++g+k++at+gtak+l
NCBI__GCF_900142125.1:WP_072910070.1 922 MKSTGEVMGIDMDFGKAFAKAQLGAGVKLPTSGKIFISVKDSDKEHIVEPVLKLANAGFKIMATAGTAKYL 992
*********************************************************************** PP
TIGR01369 979 eeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeall 1049
+e+g+ +e+v+kv+e ++++++++k++ei +v+n+t +++++ ++++irr+a++++++++t++++++a++
NCBI__GCF_900142125.1:WP_072910070.1 993 NEHGVITEHVNKVKEGRPHCVDAIKSREICMVFNTTL-GAQSVADSFSIRRSALMQEIAYFTTVAGIKAVT 1062
**********************************886.88899999******************9999875 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1085 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 27.31
//
[ok]
This GapMind analysis is from Jul 25 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