Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate AZOBR_RS12895 AZOBR_RS12895 carbamoyl phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>FitnessBrowser__azobra:AZOBR_RS12895
Length = 1083
Score = 1273 bits (3294), Expect = 0.0
Identities = 677/1068 (63%), Positives = 800/1068 (74%), Gaps = 16/1068 (1%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDIKSI I+GAGPIVIGQACEFDYSG QACKALREEG+RVILVNSNPATIMTDP +
Sbjct: 1 MPKRTDIKSICIIGAGPIVIGQACEFDYSGVQACKALREEGFRVILVNSNPATIMTDPGL 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADATYIEPI VV KI+EKERPDA+LPTMGGQTALN A+ L G LE GV MIGA
Sbjct: 61 ADATYIEPITPAVVAKILEKERPDALLPTMGGQTALNTAMALSDDGTLERLGVEMIGAKR 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
D I KAEDR F AM K+GLE+ RS + M+EA VG P IIRPSFT+ G+GGG
Sbjct: 121 DVIAKAEDRILFRDAMDKLGLESPRSRLVRNMQEATEALEFVGLPAIIRPSFTLAGTGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYNR EFE+I GL SP E+LI+ES++GWKEYEMEVVRDK DNCIIVC+IEN D M
Sbjct: 181 IAYNRAEFEDIVRGGLRASPVGEVLIEESVLGWKEYEMEVVRDKADNCIIVCAIENIDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAP+ TLTDKEYQIMRNAS+AVLREIGVETGGSNVQFAVNP NGRLIVIEM
Sbjct: 241 GVHTGDSITVAPSLTLTDKEYQIMRNASIAVLREIGVETGGSNVQFAVNPANGRLIVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAK+AAKLA+GYTLDEL NDIT G TPASFEP+IDYVVTK+P
Sbjct: 301 NPRVSRSSALASKATGFPIAKIAAKLAIGYTLDELTNDIT-GTTPASFEPTIDYVVTKMP 359
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGF-DPKVSLDDPE 419
RF FEKFAG LTT MKSVGE M+IGRT QES+QKALR +E G TGF + ++ D
Sbjct: 360 RFTFEKFAGTEPLLTTSMKSVGEAMSIGRTFQESVQKALRSMETGLTGFNEVRIGDSDTP 419
Query: 420 ALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEV 479
IR L DR+ IA AFR G +V V ++ D WFL QI+ +V E+ +
Sbjct: 420 DAAAIRGALARPTPDRLLVIAQAFRHGFTVAEVQQVSKYDPWFLEQIKAIVDREQAIRSG 479
Query: 480 GITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATD 539
G+ A + + LK+ GF+DARLA+LAG E E + R + PV+KR+DTCAAEFA+
Sbjct: 480 GLPTDKAGW-QSLKQMGFSDARLAELAGKSEGEAAEARRAAGVTPVFKRIDTCAAEFASR 538
Query: 540 TAYMYSTYE------EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDG 593
T YMYSTYE ECE++P T+++K+++LGGGPNRIGQGIEFDYCCVHA ALRE G
Sbjct: 539 TPYMYSTYETDGTGAAECESDP-TEKKKVVILGGGPNRIGQGIEFDYCCVHAVYALREAG 597
Query: 594 YETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGV----IVQYGGQTPLK 649
ETIMVNCNPETVSTDYDT+DRLYFEP+T EDV+E+VR+E+ G IVQ+GGQTPLK
Sbjct: 598 IETIMVNCNPETVSTDYDTADRLYFEPLTAEDVIELVRVEQRNGTVLGCIVQFGGQTPLK 657
Query: 650 LARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIG 709
LA ALE AG+P++GTSPDAID AEDRERFQ + +L L QPAN ++E A A IG
Sbjct: 658 LADALEKAGIPILGTSPDAIDLAEDRERFQKLLHQLDLLQPANGLARSLEEAETVAARIG 717
Query: 710 YPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICD 769
+P+V+RPSYVLGGRAMEIV+D A L+RY AV VS PVL+D +L DA+EVDVD + D
Sbjct: 718 FPVVIRPSYVLGGRAMEIVHDMAGLKRYMGNAVKVSGKNPVLIDSYLQDAIEVDVDVVAD 777
Query: 770 GE-MVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNV 828
V I GIMEHIE+AG+HSGDSAC+LP Y+L E + +Q + LA L V GLMNV
Sbjct: 778 ATGQVYIAGIMEHIEEAGIHSGDSACALPPYSLPAETIAEIGRQGEALARALHVVGLMNV 837
Query: 829 QFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYY 888
QFAVK+ VY++EVNPRA+RTVPFV+KATG +AKVAARVMAG+ LA+ + PP+
Sbjct: 838 QFAVKDGTVYILEVNPRASRTVPFVAKATGTAIAKVAARVMAGEKLADFTLNGPT-PPHT 896
Query: 889 SVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLS 948
+VKE V PF +FPGVD +LGPEM+STGEVMG+ FA AFAK+QLG+ T+ G +S
Sbjct: 897 AVKEAVFPFARFPGVDIVLGPEMKSTGEVMGLDHNFALAFAKSQLGAGVTLPVQGTVFIS 956
Query: 949 VREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNG 1008
V+E DK V + KL GF + AT GTA L +AG+ +NKV EG+PHI D + NG
Sbjct: 957 VKERDKPSAVQIGQKLHAMGFRVLATTGTAAALRQAGVPAESINKVVEGQPHIVDAMING 1016
Query: 1009 EYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNA 1056
E +INTT G +A+ DS +RR+AL Y + Y TT+ G A A+ A
Sbjct: 1017 EVHLVINTTDGAQALSDSFSLRRTALTYNLPYYTTMAGARAAVEAIAA 1064
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: 3118
Number of extensions: 127
Number of successful extensions: 18
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: 1083
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1037
Effective search space: 1064999
Effective search space used: 1064999
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 AZOBR_RS12895 AZOBR_RS12895 (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.28973.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 1490.5 0.0 0 1490.4 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS12895 AZOBR_RS12895 carbamoyl phosphat
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS12895 AZOBR_RS12895 carbamoyl phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1490.4 0.0 0 0 1 1051 [. 2 1061 .. 2 1062 .. 0.98
Alignments for each domain:
== domain 1 score: 1490.4 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+dik++ +iG+GpivigqA+EFDYsG qa+kal+eeg++v+Lvnsn+At+mtd+ lad++YieP
lcl|FitnessBrowser__azobra:AZOBR_RS12895 2 PKRTDIKSICIIGAGPIVIGQACEFDYSGVQACKALREEGFRVILVNSNPATIMTDPGLADATYIEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
+t+++v+ki+ekErpDa+l+t+GGqtaLn a+ l++ G Le+ gv+++G+k ++i+kaedR +F++a
lcl|FitnessBrowser__azobra:AZOBR_RS12895 69 ITPAVVAKILEKERPDALLPTMGGQTALNTAMALSDDGTLERLGVEMIGAKRDVIAKAEDRILFRDA 135
******************************************************************* PP
TIGR01369 135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201
++++++e ++s+ v++++ea+ea e +g+P i+R++ftl+GtG+gia+n++e++ +v+ +l+asp+
lcl|FitnessBrowser__azobra:AZOBR_RS12895 136 MDKLGLESPRSRLVRNMQEATEALEFVGLPAIIRPSFTLAGTGGGIAYNRAEFEDIVRGGLRASPVG 202
******************************************************************* PP
TIGR01369 202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268
+vl+e+s+ gwkE+E+EvvRD++dnciivc+iEn+Dp+GvHtGdsi+vaPs tLtdkeyq++R+as+
lcl|FitnessBrowser__azobra:AZOBR_RS12895 203 EVLIEESVLGWKEYEMEVVRDKADNCIIVCAIENIDPMGVHTGDSITVAPSLTLTDKEYQIMRNASI 269
******************************************************************* PP
TIGR01369 269 kiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelk 334
+++re+gve++ +nvqfa++P + r++viE+npRvsRssALAskAtG+PiAk+aakla+Gy+Ldel+
lcl|FitnessBrowser__azobra:AZOBR_RS12895 270 AVLREIGVETGgSNVQFAVNPANGRLIVIEMNPRVSRSSALASKATGFPIAKIAAKLAIGYTLDELT 336
*********988******************************************************* PP
TIGR01369 335 ndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrslee 401
nd+t++t+AsfEP++DYvv+k+Pr+ ++kf++++ l+t+mksvGE m+igrtf+e++qkalrs+e+
lcl|FitnessBrowser__azobra:AZOBR_RS12895 337 NDITGTTPASFEPTIDYVVTKMPRFTFEKFAGTEPLLTTSMKSVGEAMSIGRTFQESVQKALRSMET 403
******************************************************************* PP
TIGR01369 402 kllg...lklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklv 465
+l+g +++ ++ + + +++ al +p+++Rl++ia+a+r+g++v ev +++k+d +fle++k +v
lcl|FitnessBrowser__azobra:AZOBR_RS12895 404 GLTGfneVRIGDSDTPDAAAIRGALARPTPDRLLVIAQAFRHGFTVAEVQQVSKYDPWFLEQIKAIV 470
****5444566777778888999******************************************** PP
TIGR01369 466 elekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfe 532
+ e+++++ l ++k ++++k++Gfsd+++a+l+++se e ++r+++g++pv+kr+Dt+aaEf
lcl|FitnessBrowser__azobra:AZOBR_RS12895 471 DREQAIRSGGLP-TDKAGWQSLKQMGFSDARLAELAGKSEGEAAEARRAAGVTPVFKRIDTCAAEFA 536
******977776.9999************************************************** PP
TIGR01369 533 aktpYlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktili 594
++tpY+Ystye++ + +++ tekkkv++lG+Gp+Rigqg+EFDyc+vhav alreag++ti++
lcl|FitnessBrowser__azobra:AZOBR_RS12895 537 SRTPYMYSTYETDgtgaaECESDPTEKKKVVILGGGPNRIGQGIEFDYCCVHAVYALREAGIETIMV 603
***********99777655677788999*************************************** PP
TIGR01369 595 nynPEtvstDydiadrLyFeeltvedvldiiekekve....gvivqlgGqtalnlakeleeagvkil 657
n+nPEtvstDyd+adrLyFe+lt edv+++++ e+ + g+ivq+gGqt+l+la++le+ag++il
lcl|FitnessBrowser__azobra:AZOBR_RS12895 604 NCNPETVSTDYDTADRLYFEPLTAEDVIELVRVEQRNgtvlGCIVQFGGQTPLKLADALEKAGIPIL 670
********************************998662222689*********************** PP
TIGR01369 658 GtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameive 724
Gts+++id aEdRe+F+kll++l++ qp++ a+s+eea+++a++ig+Pv++RpsyvlgGrameiv+
lcl|FitnessBrowser__azobra:AZOBR_RS12895 671 GTSPDAIDLAEDRERFQKLLHQLDLLQPANGLARSLEEAETVAARIGFPVVIRPSYVLGGRAMEIVH 737
******************************************************************* PP
TIGR01369 725 neeeleryleeavevskekPvlidkyledavEvdvDavadg.eevliagileHiEeaGvHsGDstlv 790
+++ l+ry+ +av+vs ++Pvlid yl+da+EvdvD+vad ++v+iagi+eHiEeaG+HsGDs++
lcl|FitnessBrowser__azobra:AZOBR_RS12895 738 DMAGLKRYMGNAVKVSGKNPVLIDSYLQDAIEVDVDVVADAtGQVYIAGIMEHIEEAGIHSGDSACA 804
***************************************96369*********************** PP
TIGR01369 791 lppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplv 857
lpp +l +e+ +i ++ +++a++l+v+Gl+n+qf+vkd++vy++Evn+RasRtvPfv+ka+g ++
lcl|FitnessBrowser__azobra:AZOBR_RS12895 805 LPPYSLPAETIAEIGRQGEALARALHVVGLMNVQFAVKDGTVYILEVNPRASRTVPFVAKATGTAIA 871
******************************************************************* PP
TIGR01369 858 klavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleea 924
k+a++v++g+kl++ + + +++ + avk+avf+f+++ gvd+vlgpemkstGEvmg++++++ a
lcl|FitnessBrowser__azobra:AZOBR_RS12895 872 KVAARVMAGEKLADFTL---NGPTPPHTAVKEAVFPFARFPGVDIVLGPEMKSTGEVMGLDHNFALA 935
**************775...899999***************************************** PP
TIGR01369 925 llkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkv 991
++k++l ++ +++ +g+v++svk++dk +++++ +kl+++g++v+at+gta++l++ag+ ae ++kv
lcl|FitnessBrowser__azobra:AZOBR_RS12895 936 FAKSQLGAGVTLPVQGTVFISVKERDKPSAVQIGQKLHAMGFRVLATTGTAAALRQAGVPAESINKV 1002
******************************************************************* PP
TIGR01369 992 seeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
e +++i++++ ++e++lvin+t+ +++a ++++++rr+a++y++p+ t++++a+a++ea
lcl|FitnessBrowser__azobra:AZOBR_RS12895 1003 VEGQPHIVDAMINGEVHLVINTTD-GAQALSDSFSLRRTALTYNLPYYTTMAGARAAVEA 1061
*********************997.8889999***********************99987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1083 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: 00:00:00.08
# Mc/sec: 12.68
//
[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