Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_041098073.1 SUTH_RS06655 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000828635.1:WP_041098073.1
Length = 1081
Score = 1463 bits (3788), Expect = 0.0
Identities = 757/1087 (69%), Positives = 866/1087 (79%), Gaps = 21/1087 (1%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKR+DI SILI+GAGPI+IGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDP
Sbjct: 1 MPKRSDIHSILIIGAGPIIIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPGT 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
AD TYIEPI W V+ II KERPDAVLPTMGGQTALNCAL+L + GVLE++GV MIGA+
Sbjct: 61 ADVTYIEPITWRVLENIIAKERPDAVLPTMGGQTALNCALDLAKHGVLEKYGVEMIGASR 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
+AID AEDR +F AM +IGL +ARSGIAH+MEEA V +GFP IIRPSFTMGGSGGG
Sbjct: 121 EAIDMAEDREKFKQAMTRIGLGSARSGIAHSMEEAQQVQGAMGFPTIIRPSFTMGGSGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYN+EEF EIC RGL+ SPTKELLI+ESL+GWKEYEMEVVRD+ DNCIIVCSIEN D M
Sbjct: 181 IAYNQEEFAEICKRGLEASPTKELLIEESLLGWKEYEMEVVRDRKDNCIIVCSIENLDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPAQTLTD+EYQIMRNAS+AVLREIGV+TGGSNVQFA+NPK G ++VIEM
Sbjct: 241 GVHTGDSITVAPAQTLTDREYQIMRNASIAVLREIGVDTGGSNVQFAINPKTGAMVVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL NDITGG TPASFEPSIDYVVTK+P
Sbjct: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELKNDITGGATPASFEPSIDYVVTKVP 360
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
RF FEKF ANDRLTTQMKSVGEVMAIGR+ QES+QKALRGLEV GFD ++ D E
Sbjct: 361 RFAFEKFPQANDRLTTQMKSVGEVMAIGRSFQESMQKALRGLEVSVYGFD-EIEADREE- 418
Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
I REL G RIWY+A AFR G ++ F+LT ID WFLVQIE+++ E +
Sbjct: 419 ---INRELASPGPQRIWYLAQAFREGYTLQQAFDLTKIDPWFLVQIEDIITTEGWMRSQN 475
Query: 481 ITGLNADFLRQLKRKGFADARLAKLAGVR---------EAEIRKLRDQYDLHPVYKRVDT 531
+ L+A LR LKRKGF+D R+ L E +R+LR + PVYKRVDT
Sbjct: 476 LADLDAATLRNLKRKGFSDRRIGTLVSATHDPAAGASGETAVRELRHALGIRPVYKRVDT 535
Query: 532 CAAEFATDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALRE 591
CAAEF+T TAYMYSTYEEECEA P T ++KIMVLGGGPNRIGQGIEFDYCCVHA+LA+RE
Sbjct: 536 CAAEFSTSTAYMYSTYEEECEARP-TAKKKIMVLGGGPNRIGQGIEFDYCCVHAALAMRE 594
Query: 592 DGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLA 651
DGYETIMVNCNPETVSTDYDTSDRLYFEPVTLED+LEIV +E+P GVIVQ+GGQTPLK A
Sbjct: 595 DGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDILEIVHVEQPTGVIVQFGGQTPLKRA 654
Query: 652 RALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYP 711
R LEA GVP+IGTSPD ID AEDRERFQ + L LKQP N T A+ A EIGYP
Sbjct: 655 RELEANGVPIIGTSPDMIDAAEDRERFQKLLHDLGLKQPPNRTARTEPDAIRLAAEIGYP 714
Query: 712 LVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGE 771
LVVRPSYVLGGRAMEIV+++ DL RY + A+ VS +PVLLD FL+DA EVDVDA+ DG
Sbjct: 715 LVVRPSYVLGGRAMEIVHEQKDLERYMRDAIKVSFASPVLLDRFLNDATEVDVDALSDGT 774
Query: 772 MVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFA 831
VLIGGIMEHIEQAGVHSGDSACSLP +TLS+EIQD +R+Q + +A L V GLMNVQFA
Sbjct: 775 QVLIGGIMEHIEQAGVHSGDSACSLPPFTLSREIQDELRRQTEMMAKGLNVVGLMNVQFA 834
Query: 832 VKNN----EVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPY 887
++ + VY++EVNPRA+RTVPFVSKAT +PLAK+AAR MAG+SLA+QGVT E+IPPY
Sbjct: 835 IQGSGADAVVYVLEVNPRASRTVPFVSKATSLPLAKIAARCMAGRSLADQGVTGEIIPPY 894
Query: 888 YSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALL 947
+SVKE V PF KFPGVD +LGPEM+STGEVMGVGRTF EAF K+QL + + + K G+ +
Sbjct: 895 FSVKEAVFPFIKFPGVDTILGPEMKSTGEVMGVGRTFGEAFVKSQLAAGTRLPKSGKVFI 954
Query: 948 SVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKN 1007
SV+ D+ + VD+A +L + GF L AT GT + AGI +VNKV EGRPHI D IKN
Sbjct: 955 SVKPADRAKAVDVARELHELGFSLVATRGTGGAIEAAGIPVGMVNKVTEGRPHIVDMIKN 1014
Query: 1008 GEYTYIINTTSGRR-AIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQ 1066
GE I+NT +R AI DSR IR SAL KV TT+ G A + D E S+Q
Sbjct: 1015 GEIVLIVNTVEEKRTAIADSRSIRTSALGAKVTLFTTIEGARAACAGMRHDGLE-TYSLQ 1073
Query: 1067 EMHAQIK 1073
+HA++K
Sbjct: 1074 ALHAELK 1080
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: 3103
Number of extensions: 122
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: 1081
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1035
Effective search space: 1062945
Effective search space used: 1062945
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_041098073.1 SUTH_RS06655 (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.26144.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 1541.4 0.0 0 1541.3 0.0 1.0 1 lcl|NCBI__GCF_000828635.1:WP_041098073.1 SUTH_RS06655 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000828635.1:WP_041098073.1 SUTH_RS06655 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1541.3 0.0 0 0 1 1049 [. 2 1059 .. 2 1062 .. 0.98
Alignments for each domain:
== domain 1 score: 1541.3 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+di+++l+iG+Gpi+igqA+EFDYsG+qa+kal+eeg++v+Lvnsn+At+mtd+ ad +YieP
lcl|NCBI__GCF_000828635.1:WP_041098073.1 2 PKRSDIHSILIIGAGPIIIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPGTADVTYIEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
+t++++e+ii kErpDa+l+t+GGqtaLn+a++l ++GvLekygv+++G++ eai+ aedRekFk+a
lcl|NCBI__GCF_000828635.1:WP_041098073.1 69 ITWRVLENIIAKERPDAVLPTMGGQTALNCALDLAKHGVLEKYGVEMIGASREAIDMAEDREKFKQA 135
******************************************************************* PP
TIGR01369 135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201
++ i++ a+s i++s+eea++++ +g+P i+R++ft+gG+G+gia+n+ee+ e+++++l+asp+k
lcl|NCBI__GCF_000828635.1:WP_041098073.1 136 MTRIGLGSARSGIAHSMEEAQQVQGAMGFPTIIRPSFTMGGSGGGIAYNQEEFAEICKRGLEASPTK 202
******************************************************************* PP
TIGR01369 202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268
++l+e+sl gwkE+E+EvvRD+kdnciivc+iEnlDp+GvHtGdsi+vaP+qtLtd+eyq++R+as+
lcl|NCBI__GCF_000828635.1:WP_041098073.1 203 ELLIEESLLGWKEYEMEVVRDRKDNCIIVCSIENLDPMGVHTGDSITVAPAQTLTDREYQIMRNASI 269
******************************************************************* PP
TIGR01369 269 kiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelk 334
+++re+gv+++ +nvqfa++P++ +vviE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldelk
lcl|NCBI__GCF_000828635.1:WP_041098073.1 270 AVLREIGVDTGgSNVQFAINPKTGAMVVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELK 336
********9988******************************************************* PP
TIGR01369 335 ndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsle 400
nd+t+ t+AsfEPs+DYvv+k+Pr++++kf +++++l+tqmksvGEvmaigr+f+e++qkalr le
lcl|NCBI__GCF_000828635.1:WP_041098073.1 337 NDITGgATPASFEPSIDYVVTKVPRFAFEKFPQANDRLTTQMKSVGEVMAIGRSFQESMQKALRGLE 403
****878************************************************************ PP
TIGR01369 401 ekllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvel 467
+++g+++ + ++ee++++l +p ++R++++a+a+r+g+++++ ++ltkid +fl ++++++++
lcl|NCBI__GCF_000828635.1:WP_041098073.1 404 VSVYGFDEI---EADREEINRELASPGPQRIWYLAQAFREGYTLQQAFDLTKIDPWFLVQIEDIITT 467
*****9885...677888899********************************************** PP
TIGR01369 468 ekeleeeklkelkkellkkakklGfsdeqiaklvkvseae.........vrklrkelgivpvvkrvD 525
e +++++l +l++ +l+++k++Gfsd++i++lv+ +++ vr+lr++lgi pv+krvD
lcl|NCBI__GCF_000828635.1:WP_041098073.1 468 EGWMRSQNLADLDAATLRNLKRKGFSDRRIGTLVSATHDPaagasgetaVRELRHALGIRPVYKRVD 534
**********************************955544455566666****************** PP
TIGR01369 526 tvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagykti 592
t+aaEf+++t+Y+Ystyeee+ +++ t kkk++vlG+Gp+Rigqg+EFDyc+vha+la+re gy+ti
lcl|NCBI__GCF_000828635.1:WP_041098073.1 535 TCAAEFSTSTAYMYSTYEEEC-EARPTAKKKIMVLGGGPNRIGQGIEFDYCCVHAALAMREDGYETI 600
********************5.55566666************************************* PP
TIGR01369 593 linynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGt 659
++n+nPEtvstDyd++drLyFe++t+ed+l+i++ e+++gvivq+gGqt+l+ a+ele++gv+i+Gt
lcl|NCBI__GCF_000828635.1:WP_041098073.1 601 MVNCNPETVSTDYDTSDRLYFEPVTLEDILEIVHVEQPTGVIVQFGGQTPLKRARELEANGVPIIGT 667
******************************************************************* PP
TIGR01369 660 saesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameivene 726
s++ id aEdRe+F+kll++lg+kqp +++a++ +a ++a+eigyP++vRpsyvlgGrameiv+++
lcl|NCBI__GCF_000828635.1:WP_041098073.1 668 SPDMIDAAEDRERFQKLLHDLGLKQPPNRTARTEPDAIRLAAEIGYPLVVRPSYVLGGRAMEIVHEQ 734
******************************************************************* PP
TIGR01369 727 eeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlpp 793
++lery+++a++vs +Pvl+d++l+da+EvdvDa++dg++vli gi+eHiE+aGvHsGDs+++lpp
lcl|NCBI__GCF_000828635.1:WP_041098073.1 735 KDLERYMRDAIKVSFASPVLLDRFLNDATEVDVDALSDGTQVLIGGIMEHIEQAGVHSGDSACSLPP 801
******************************************************************* PP
TIGR01369 794 qklseevkkkikeivkkiakelkvkGllniqfvvkd....eevyviEvnvRasRtvPfvskalgvpl 856
+ls+e++++++++++ +ak l+v+Gl+n+qf++++ vyv+Evn+RasRtvPfvska+++pl
lcl|NCBI__GCF_000828635.1:WP_041098073.1 802 FTLSREIQDELRRQTEMMAKGLNVVGLMNVQFAIQGsgadAVVYVLEVNPRASRTVPFVSKATSLPL 868
**********************************864332569************************ PP
TIGR01369 857 vklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdlee 923
+k+a+++++g++l++ +gv+ e + +++vk+avf+f k+ gvd +lgpemkstGEvmg+gr++ e
lcl|NCBI__GCF_000828635.1:WP_041098073.1 869 AKIAARCMAGRSLAD--QGVTGEIIPPYFSVKEAVFPFIKFPGVDTILGPEMKSTGEVMGVGRTFGE 933
**************9..889*********************************************** PP
TIGR01369 924 allkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlk 990
a++k++la++++++k g+v++svk +d+ +++++a++l+e+g++++at+gt ++e agi + +v+k
lcl|NCBI__GCF_000828635.1:WP_041098073.1 934 AFVKSQLAAGTRLPKSGKVFISVKPADRAKAVDVARELHELGFSLVATRGTGGAIEAAGIPVGMVNK 1000
******************************************************************* PP
TIGR01369 991 vseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeall 1049
v+e +++i++++k++ei l++n+ ++k++a ++ +ir +a+ kv+l+t++e+a+a++
lcl|NCBI__GCF_000828635.1:WP_041098073.1 1001 VTEGRPHIVDMIKNGEIVLIVNTVEEKRTAIADSRSIRTSALGAKVTLFTTIEGARAAC 1059
*****************************************************999876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1081 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 0.03s 00:00:00.12 Elapsed: 00:00:00.12
# Mc/sec: 9.01
//
[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