Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_011383145.1 AMB_RS03605 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000009985.1:WP_011383145.1
Length = 1085
Score = 1293 bits (3347), Expect = 0.0
Identities = 672/1071 (62%), Positives = 820/1071 (76%), Gaps = 20/1071 (1%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDIKSILI+GAGPIVIGQACEFDYSG QACKAL++EGYRVILVNSNPATIMTDP +
Sbjct: 1 MPKRTDIKSILIIGAGPIVIGQACEFDYSGVQACKALKDEGYRVILVNSNPATIMTDPGL 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADATYIEPI E+V KIIEKERPDA+LPTMGGQTALN A++L G+LE+FGV MI A
Sbjct: 61 ADATYIEPITPEIVAKIIEKERPDALLPTMGGQTALNTAMKLADMGILEKFGVEMIAAKR 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
D I KAEDR F AM KIGLE+ +S + T++EA VG P IIRPSFT+ G+GGG
Sbjct: 121 DVIAKAEDRLLFRDAMDKIGLESPKSRMVKTLQEAREALDFVGLPAIIRPSFTLAGTGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYN E+E I + GL SP E+L++ES++GWKEYEMEVVRDK DNCII+CSIEN D M
Sbjct: 181 IAYNVAEYEHIVSGGLAASPVHEVLVEESVLGWKEYEMEVVRDKKDNCIIICSIENVDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAPA TLTDKEYQIMRNAS+AVLREIGV+TGGSNVQFAVNPK+GR+ VIEM
Sbjct: 241 GVHTGDSITVAPALTLTDKEYQIMRNASLAVLREIGVDTGGSNVQFAVNPKDGRMTVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL NDIT G TPASFEP+IDYVVTKIP
Sbjct: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELTNDIT-GCTPASFEPTIDYVVTKIP 359
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFD----PKVSLD 416
RF FEKF GA+ LTT MKSVGE MAIGRT QESLQK LR +E G TG D P
Sbjct: 360 RFTFEKFPGADPNLTTSMKSVGEAMAIGRTFQESLQKGLRSMETGLTGLDEVEIPGAGAG 419
Query: 417 DPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKV 476
D + ++ L DR+ IA AFR GL++D V D+WFL Q++ +V E ++
Sbjct: 420 DMK--DAVKSALAQPRHDRLLVIAQAFRFGLTIDEVHAACFYDKWFLAQLKGIVDAEAEI 477
Query: 477 AEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEF 536
G+ ++A L +LK+ GF+D RLAKL+G E R+ ++ PV+KR+DTCAAEF
Sbjct: 478 RAKGLP-IDAPGLLRLKKMGFSDQRLAKLSGKSLVETAFRREVLNVKPVFKRIDTCAAEF 536
Query: 537 ATDTAYMYSTYE------EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALR 590
+ TAYMYS YE ECE++PS DR+K+++LGGGPNRIGQGIEFDYCCVHA+ AL
Sbjct: 537 PSSTAYMYSCYEGDGVNPPECESDPS-DRDKVIILGGGPNRIGQGIEFDYCCVHAAYALD 595
Query: 591 EDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIE----KPKGVIVQYGGQT 646
E G ETIMVNCNPETVSTDYDTSDRLYFEP+T E V+++VR E K G IVQ+GGQT
Sbjct: 596 EAGKETIMVNCNPETVSTDYDTSDRLYFEPLTAETVIDLVRKEQSNGKVLGCIVQFGGQT 655
Query: 647 PLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAK 706
PLKLA ALE AG+P++GTSPD+ID AEDRERFQ + +L LKQPAN T ++E A++ A+
Sbjct: 656 PLKLAHALEQAGIPILGTSPDSIDLAEDRERFQKMLHQLGLKQPANGTARSLEEAIKVAE 715
Query: 707 EIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDA 766
+IGYP+V+RPS+VLGGRAM+IVYD L RY AV VS D PVL+D++L DA+EVDVDA
Sbjct: 716 KIGYPVVIRPSFVLGGRAMQIVYDHEALERYMVEAVKVSGDDPVLIDYYLKDAIEVDVDA 775
Query: 767 ICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLM 826
+CDG V + GIM+HIE+AG+HSGDSACSLP Y+L + + +Q +A L V GLM
Sbjct: 776 LCDGNQVYVAGIMQHIEEAGIHSGDSACSLPPYSLDKATIAELERQTAAMAKALNVVGLM 835
Query: 827 NVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPP 886
N Q+A+K+ ++Y++EVNPRA+RTVPFV+KATGVP+AK+AARVMAG++LA G++
Sbjct: 836 NCQYAIKDGDIYILEVNPRASRTVPFVAKATGVPIAKIAARVMAGETLASFGLSTRPELK 895
Query: 887 YYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRAL 946
+ +VKE V PF +FPGVD LLGPEM+STGEVMG+ FA AFAK+QLG+ + + G A
Sbjct: 896 HVAVKEAVFPFARFPGVDILLGPEMKSTGEVMGIDSDFARAFAKSQLGAGTNLPTEGGAF 955
Query: 947 LSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGI-NPRLVNKVHEGRPHIQDRI 1005
+SVR+GDK +V++A +LL+ GF++ AT GTA L + G+ +VNKV EGRPH D +
Sbjct: 956 ISVRDGDKPAMVEIARRLLEMGFKVMATDGTAFYLKDRGVTGVTIVNKVLEGRPHCVDAM 1015
Query: 1006 KNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNA 1056
NG+ ++NTT G +A++DS IRR+AL + + TT+ G A A+ A
Sbjct: 1016 MNGQVQLVVNTTEGSQAVKDSFSIRRTALTNNIPHYTTVAGARAAVEAIEA 1066
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: 3035
Number of extensions: 123
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: 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_011383145.1 AMB_RS03605 (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.15382.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 1506.3 0.0 0 1506.1 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011383145.1 AMB_RS03605 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383145.1 AMB_RS03605 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1506.1 0.0 0 0 1 1051 [. 2 1063 .. 2 1064 .. 0.97
Alignments for each domain:
== domain 1 score: 1506.1 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+dik++l+iG+GpivigqA+EFDYsG qa+kalk+eg++v+Lvnsn+At+mtd+ lad++YieP
lcl|NCBI__GCF_000009985.1:WP_011383145.1 2 PKRTDIKSILIIGAGPIVIGQACEFDYSGVQACKALKDEGYRVILVNSNPATIMTDPGLADATYIEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
+t+e+v+kiiekErpDa+l+t+GGqtaLn a++l ++G+Lek+gv+++ +k ++i+kaedR +F++a
lcl|NCBI__GCF_000009985.1:WP_011383145.1 69 ITPEIVAKIIEKERPDALLPTMGGQTALNTAMKLADMGILEKFGVEMIAAKRDVIAKAEDRLLFRDA 135
******************************************************************* PP
TIGR01369 135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201
+++i++e +ks++v++ +ea ea + +g+P i+R++ftl+GtG+gia+n +e +++v+ +l+asp++
lcl|NCBI__GCF_000009985.1:WP_011383145.1 136 MDKIGLESPKSRMVKTLQEAREALDFVGLPAIIRPSFTLAGTGGGIAYNVAEYEHIVSGGLAASPVH 202
******************************************************************* PP
TIGR01369 202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268
+vlve+s+ gwkE+E+EvvRD+kdncii+c+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++R+asl
lcl|NCBI__GCF_000009985.1:WP_011383145.1 203 EVLVEESVLGWKEYEMEVVRDKKDNCIIICSIENVDPMGVHTGDSITVAPALTLTDKEYQIMRNASL 269
******************************************************************* PP
TIGR01369 269 kiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelk 334
+++re+gv+++ +nvqfa++P++ r++viE+npRvsRssALAskAtG+PiAkvaaklavGy+Ldel+
lcl|NCBI__GCF_000009985.1:WP_011383145.1 270 AVLREIGVDTGgSNVQFAVNPKDGRMTVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELT 336
********9988******************************************************* PP
TIGR01369 335 ndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrslee 401
nd+t+ t+AsfEP++DYvv+kiPr+ ++kf ++d +l+t+mksvGE maigrtf+e+lqk+lrs+e+
lcl|NCBI__GCF_000009985.1:WP_011383145.1 337 NDITGCTPASFEPTIDYVVTKIPRFTFEKFPGADPNLTTSMKSVGEAMAIGRTFQESLQKGLRSMET 403
******************************************************************* PP
TIGR01369 402 kllg...lklkek.eaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkkl 464
+l+g ++++ + + +++++++al +p ++Rl++ia+a+r g++++ev+ ++ +d++fl +lk +
lcl|NCBI__GCF_000009985.1:WP_011383145.1 404 GLTGldeVEIPGAgAGDMKDAVKSALAQPRHDRLLVIAQAFRFGLTIDEVHAACFYDKWFLAQLKGI 470
****4443444441445667788999***************************************** PP
TIGR01369 465 velekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEf 531
v++e e++ + l +++ l ++kk+Gfsd+++akl ++s e r+ l++ pv+kr+Dt+aaEf
lcl|NCBI__GCF_000009985.1:WP_011383145.1 471 VDAEAEIRAKGLP-IDAPGLLRLKKMGFSDQRLAKLSGKSLVETAFRREVLNVKPVFKRIDTCAAEF 536
*******966655.9**************************************************** PP
TIGR01369 532 eaktpYlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktil 593
+++t+Y+Ys ye++ + +++ ++++kv++lG+Gp+Rigqg+EFDyc+vha+ al eag++ti+
lcl|NCBI__GCF_000009985.1:WP_011383145.1 537 PSSTAYMYSCYEGDgvnppECESDPSDRDKVIILGGGPNRIGQGIEFDYCCVHAAYALDEAGKETIM 603
************99777766677788889************************************** PP
TIGR01369 594 inynPEtvstDydiadrLyFeeltvedvldiiekekve....gvivqlgGqtalnlakeleeagvki 656
+n+nPEtvstDyd++drLyFe+lt e+v+d+++ke+ + g+ivq+gGqt+l+la++le+ag++i
lcl|NCBI__GCF_000009985.1:WP_011383145.1 604 VNCNPETVSTDYDTSDRLYFEPLTAETVIDLVRKEQSNgkvlGCIVQFGGQTPLKLAHALEQAGIPI 670
***********************************866223379*********************** PP
TIGR01369 657 lGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiv 723
lGts++sid aEdRe+F+k+l++lg+kqp++ +a+s+eea ++a++igyPv++Rps+vlgGram+iv
lcl|NCBI__GCF_000009985.1:WP_011383145.1 671 LGTSPDSIDLAEDRERFQKMLHQLGLKQPANGTARSLEEAIKVAEKIGYPVVIRPSFVLGGRAMQIV 737
******************************************************************* PP
TIGR01369 724 eneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlv 790
+++e lery+ eav+vs + Pvlid yl+da+EvdvDa++dg++v++agi++HiEeaG+HsGDs+++
lcl|NCBI__GCF_000009985.1:WP_011383145.1 738 YDHEALERYMVEAVKVSGDDPVLIDYYLKDAIEVDVDALCDGNQVYVAGIMQHIEEAGIHSGDSACS 804
******************************************************************* PP
TIGR01369 791 lppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplv 857
lpp +l++ + +++++++++ak+l+v+Gl+n q+++kd+++y++Evn+RasRtvPfv+ka+gvp++
lcl|NCBI__GCF_000009985.1:WP_011383145.1 805 LPPYSLDKATIAELERQTAAMAKALNVVGLMNCQYAIKDGDIYILEVNPRASRTVPFVAKATGVPIA 871
******************************************************************* PP
TIGR01369 858 klavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleea 924
k+a++v++g++l++ g++++++ k+vavk+avf+f+++ gvd++lgpemkstGEvmgi++d+++a
lcl|NCBI__GCF_000009985.1:WP_011383145.1 872 KIAARVMAGETLAS--FGLSTRPELKHVAVKEAVFPFARFPGVDILLGPEMKSTGEVMGIDSDFARA 936
**************..56799********************************************** PP
TIGR01369 925 llkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagik.aevvlk 990
++k++l ++++++++g +++sv+d dk +++e+a++l e+g+kv+at+gta +l+++g++ ++ v+k
lcl|NCBI__GCF_000009985.1:WP_011383145.1 937 FAKSQLGAGTNLPTEGGAFISVRDGDKPAMVEIARRLLEMGFKVMATDGTAFYLKDRGVTgVTIVNK 1003
*********************************************************9973678899 PP
TIGR01369 991 vseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
v e ++++++++++++++lv+n+t+ +++a++++++irr+a+++++p+ t++++a+a++ea
lcl|NCBI__GCF_000009985.1:WP_011383145.1 1004 VLEGRPHCVDAMMNGQVQLVVNTTE-GSQAVKDSFSIRRTALTNNIPHYTTVAGARAAVEA 1063
9*********************997.8889999***********************99987 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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.09
# Mc/sec: 11.80
//
[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