Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate CCNA_02994 CCNA_02994 carbamoyl-phosphate synthase large chain
Query= BRENDA::P00968
(1073 letters)
>FitnessBrowser__Caulo:CCNA_02994
Length = 1099
Score = 1269 bits (3283), Expect = 0.0
Identities = 675/1099 (61%), Positives = 812/1099 (73%), Gaps = 33/1099 (3%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDI SILI+GAGPIVIGQACEFDYSG QACKALR EGYR+ILVNSNPATIMTDP++
Sbjct: 1 MPKRTDISSILIIGAGPIVIGQACEFDYSGVQACKALRAEGYRIILVNSNPATIMTDPDV 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADATYIEPI E+V KIIEKERPDA+LPTMGGQTALN AL LE G L +FGV MIGA A
Sbjct: 61 ADATYIEPITPEMVAKIIEKERPDALLPTMGGQTALNTALALEADGTLAKFGVEMIGAKA 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
+ IDKAEDR++F AM K+GLE+ RS HT++EA+ VG P IIRPSFT+ G+GGG
Sbjct: 121 EVIDKAEDRQKFRDAMDKLGLESPRSRACHTLDEAMEGLEFVGLPAIIRPSFTLAGTGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYN EEF+EI RGLDLSPT E+L++ES++GWKEYEMEVVRDK DNCIIVCSIEN D M
Sbjct: 181 IAYNVEEFKEIVERGLDLSPTTEVLVEESVLGWKEYEMEVVRDKADNCIIVCSIENIDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPA TLTDKEYQ MR AS+AVLREIGVETGGSNVQFAVNP +GR++VIEM
Sbjct: 241 GVHTGDSITVAPALTLTDKEYQWMRAASIAVLREIGVETGGSNVQFAVNPADGRMVVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAKVAA+LAVGYTLDEL NDITGG TPASFEPSIDYVVTKIP
Sbjct: 301 NPRVSRSSALASKATGFPIAKVAARLAVGYTLDELKNDITGGATPASFEPSIDYVVTKIP 360
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPK--VSLDDP 418
RF FEK+ G+ LTT MKSVGEVMAIGRT +ES+QKALRGLE G +GFD DDP
Sbjct: 361 RFAFEKYPGSEPLLTTAMKSVGEVMAIGRTFKESVQKALRGLETGLSGFDEVEIAGADDP 420
Query: 419 E-ALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVA 477
+ + R L DR+ IA AFR GL+VD V + + WFL QI E+VR E V
Sbjct: 421 DNGKEAVIRALGVPTPDRLRVIAQAFRHGLTVDEVNAACSYEPWFLRQIAEIVRQEGWVK 480
Query: 478 EVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFA 537
G+ A R+LK +GF+DARLAKL E +R R ++ PV+KR+D+CA EF
Sbjct: 481 AGGLP-QTAQGFRELKAQGFSDARLAKLTASTEKAVRAARQALNVRPVFKRIDSCAGEFL 539
Query: 538 TDTAYMYSTYE-------EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALR 590
T YMYSTYE +CE++PS +K ++LGGGPNRIGQGIEFDYCC HA+ AL
Sbjct: 540 ASTPYMYSTYEFGALGQIPQCESDPSA-AKKAVILGGGPNRIGQGIEFDYCCCHAAFALD 598
Query: 591 EDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPK----GVIVQYGGQT 646
+ G E+IMVNCNPETVSTDYDTSDRLYFEP+T EDVLE++ +E K GVIVQ+GGQT
Sbjct: 599 QIGVESIMVNCNPETVSTDYDTSDRLYFEPLTAEDVLELLHVEMSKGTLAGVIVQFGGQT 658
Query: 647 PLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAK 706
PLKLA ALE AGVP++GTSPDAID AEDRERFQ + L + QP NA + + A +
Sbjct: 659 PLKLAHALEEAGVPILGTSPDAIDLAEDRERFQQLLNGLNIAQPENAIARSWDEARAEGD 718
Query: 707 EIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDA 766
+IG+P V+RPSYVLGGR MEI+ D + RY A +S + P+LLDH+L A EVDVDA
Sbjct: 719 KIGFPFVMRPSYVLGGRGMEIIRDHEAMERYIAGAGEISLEHPILLDHYLSRATEVDVDA 778
Query: 767 ICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLM 826
+CDG+ V + G++EHIE+AGVHSGDSACS+P ++L E + +++Q ++A L VRGLM
Sbjct: 779 LCDGKDVFVAGVLEHIEEAGVHSGDSACSMPPFSLKAETVEELKRQTVQMALALNVRGLM 838
Query: 827 NVQFAVK-----NNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTK 881
NVQFA++ N +Y++EVNPRA+RTVPFV+K G P+A +AA++MAG+SLA G+ K
Sbjct: 839 NVQFAIEEPHSDNPRIYVLEVNPRASRTVPFVAKTIGQPVAAIAAKIMAGESLASFGL-K 897
Query: 882 EVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVM----------GVGRTFAEAFAKA 931
+V + +VKE V PF +F GVD +LGPEMRSTGEVM G+G FA AFAK+
Sbjct: 898 DVPYDHIAVKEAVFPFARFAGVDTVLGPEMRSTGEVMGLDWKRDGETGMGPAFARAFAKS 957
Query: 932 QLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLV 991
QLG + G A +SV+E DK +V+ L GF++ +T GT L G+ V
Sbjct: 958 QLGGGVKLPTKGTAFVSVKESDKPWIVEPVKLLQAAGFKVLSTEGTQAYLAAQGVQVEHV 1017
Query: 992 NKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATA 1051
KV EGRPHI D +KNG + NTT G++A+EDS IRR+AL KV Y TT G A A
Sbjct: 1018 KKVLEGRPHIVDVMKNGGVQLVFNTTEGKQALEDSFEIRRTALMMKVPYYTTSAGALAAA 1077
Query: 1052 MALNADATEKVISVQEMHA 1070
A+ A A + + V+ + +
Sbjct: 1078 QAI-AGAPAEALDVRPLQS 1095
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: 3085
Number of extensions: 143
Number of successful extensions: 19
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: 1099
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1053
Effective search space: 1081431
Effective search space used: 1081431
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 CCNA_02994 CCNA_02994 (carbamoyl-phosphate synthase large chain)
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.2654.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 1439.4 0.0 0 1439.2 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_02994 CCNA_02994 carbamoyl-phosphate s
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02994 CCNA_02994 carbamoyl-phosphate synthase large chain
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1439.2 0.0 0 0 1 1051 [. 2 1079 .. 2 1080 .. 0.95
Alignments for each domain:
== domain 1 score: 1439.2 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71
pkr+di+++l+iG+GpivigqA+EFDYsG qa+kal+ eg++++Lvnsn+At+mtd+++ad++YieP+t+e
lcl|FitnessBrowser__Caulo:CCNA_02994 2 PKRTDISSILIIGAGPIVIGQACEFDYSGVQACKALRAEGYRIILVNSNPATIMTDPDVADATYIEPITPE 72
689******************************************************************** PP
TIGR01369 72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142
+v+kiiekErpDa+l+t+GGqtaLn a+ le G L+k+gv+++G+k e+i+kaedR+kF++a++++++e
lcl|FitnessBrowser__Caulo:CCNA_02994 73 MVAKIIEKERPDALLPTMGGQTALNTALALEADGTLAKFGVEMIGAKAEVIDKAEDRQKFRDAMDKLGLES 143
*********************************************************************** PP
TIGR01369 143 akseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwk 213
++s+++++ +ea+e e +g+P i+R++ftl+GtG+gia+n ee+ke+ve++l++sp+++vlve+s+ gwk
lcl|FitnessBrowser__Caulo:CCNA_02994 144 PRSRACHTLDEAMEGLEFVGLPAIIRPSFTLAGTGGGIAYNVEEFKEIVERGLDLSPTTEVLVEESVLGWK 214
*********************************************************************** PP
TIGR01369 214 EiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvq 283
E+E+EvvRD++dnciivc+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq +R as++++re+gve++ +nvq
lcl|FitnessBrowser__Caulo:CCNA_02994 215 EYEMEVVRDKADNCIIVCSIENIDPMGVHTGDSITVAPALTLTDKEYQWMRAASIAVLREIGVETGgSNVQ 285
****************************************************************988**** PP
TIGR01369 284 faldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.etvAsfEPslDYvv 353
fa++P + r+vviE+npRvsRssALAskAtG+PiAkvaa+lavGy+Ldelknd+t+ t+AsfEPs+DYvv
lcl|FitnessBrowser__Caulo:CCNA_02994 286 FAVNPADGRMVVIEMNPRVSRSSALASKATGFPIAKVAARLAVGYTLDELKNDITGgATPASFEPSIDYVV 356
*******************************************************878************* PP
TIGR01369 354 vkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkeke.....aesdeel 419
+kiPr++++k+ + + l+t mksvGEvmaigrtf+e++qkalr le++l+g+++ e + + +e++
lcl|FitnessBrowser__Caulo:CCNA_02994 357 TKIPRFAFEKYPGSEPLLTTAMKSVGEVMAIGRTFKESVQKALRGLETGLSGFDEVEIAgaddpDNGKEAV 427
****************************************************7665443100114556778 PP
TIGR01369 420 eealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakkl 490
+al p+++Rl +ia+a+r+g++v+ev+ ++ ++ +fl++++++v+ e ++ l +++ ++++k++
lcl|FitnessBrowser__Caulo:CCNA_02994 428 IRALGVPTPDRLRVIAQAFRHGLTVDEVNAACSYEPWFLRQIAEIVRQEGWVKAGGLP-QTAQGFRELKAQ 497
899999**********************************************977776.77899******* PP
TIGR01369 491 GfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeee......kddvevtekk 555
Gfsd+++akl+ ++e++vr++r++l++ pv+kr+D +a+Ef a+tpY+Ystye + +++ + k
lcl|FitnessBrowser__Caulo:CCNA_02994 498 GFSDARLAKLTASTEKAVRAARQALNVRPVFKRIDSCAGEFLASTPYMYSTYEFGalgqipQCESDPSAAK 568
****************************************************9765555555566667779 PP
TIGR01369 556 kvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiie 626
k ++lG+Gp+Rigqg+EFDyc+ ha+ al + g ++i++n+nPEtvstDyd++drLyFe+lt edvl++++
lcl|FitnessBrowser__Caulo:CCNA_02994 569 KAVILGGGPNRIGQGIEFDYCCCHAAFALDQIGVESIMVNCNPETVSTDYDTSDRLYFEPLTAEDVLELLH 639
*********************************************************************99 PP
TIGR01369 627 kekve....gvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsv 693
e + gvivq+gGqt+l+la++leeagv+ilGts+++id aEdRe+F++ll+ l+i qp++++a+s
lcl|FitnessBrowser__Caulo:CCNA_02994 640 VEMSKgtlaGVIVQFGGQTPLKLAHALEEAGVPILGTSPDAIDLAEDRERFQQLLNGLNIAQPENAIARSW 710
8865422228************************************************************* PP
TIGR01369 694 eeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavad 764
+ea+ ++ig+P ++RpsyvlgGr+mei++++e +ery+ a e+s e+P+l+d+yl+ a+EvdvDa++d
lcl|FitnessBrowser__Caulo:CCNA_02994 711 DEARAEGDKIGFPFVMRPSYVLGGRGMEIIRDHEAMERYIAGAGEISLEHPILLDHYLSRATEVDVDALCD 781
*********************************************************************** PP
TIGR01369 765 geevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkd.....e 830
g++v++ag+leHiEeaGvHsGDs++++pp +l++e+++++k+++ ++a +l+v+Gl+n+qf++++
lcl|FitnessBrowser__Caulo:CCNA_02994 782 GKDVFVAGVLEHIEEAGVHSGDSACSMPPFSLKAETVEELKRQTVQMALALNVRGLMNVQFAIEEphsdnP 852
**************************************************************986432224 PP
TIGR01369 831 evyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvd 901
++yv+Evn+RasRtvPfv+k++g p++++a+k+++g++l++ + k+ ++++avk+avf+f+++agvd
lcl|FitnessBrowser__Caulo:CCNA_02994 853 RIYVLEVNPRASRTVPFVAKTIGQPVAAIAAKIMAGESLASFGL---KDVPYDHIAVKEAVFPFARFAGVD 920
69***************************************886...99999******************* PP
TIGR01369 902 vvlgpemkstGEvmgigrd..........leeallkallaskakikkkgsvllsvkdkdkeellelakkla 962
vlgpem+stGEvmg++ + +++a++k++l + k+++kg++++svk++dk ++e +k l+
lcl|FitnessBrowser__Caulo:CCNA_02994 921 TVLGPEMRSTGEVMGLDWKrdgetgmgpaFARAFAKSQLGGGVKLPTKGTAFVSVKESDKPWIVEPVKLLQ 991
**************9763211222222226788889999999***************************** PP
TIGR01369 963 ekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreave 1033
++g+kv++tegt+++l+ +g+++e+v+kv e +++i++++k++ ++lv+n+t+ +k+a e+++ irr+a++
lcl|FitnessBrowser__Caulo:CCNA_02994 992 AAGFKVLSTEGTQAYLAAQGVQVEHVKKVLEGRPHIVDVMKNGGVQLVFNTTE-GKQALEDSFEIRRTALM 1061
**************************************************997.888999*********** PP
TIGR01369 1034 ykvplvteletaeallea 1051
+kvp+ t+ ++a a+++a
lcl|FitnessBrowser__Caulo:CCNA_02994 1062 MKVPYYTTSAGALAAAQA 1079
*********999988877 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1099 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: 00:00:00.11
# Mc/sec: 9.91
//
[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