Align Carbamoyl-phosphate synthase pyrimidine-specific large chain; Carbamoyl-phosphate synthetase ammonia chain; EC 6.3.5.5 (characterized)
to candidate WP_078430316.1 BK574_RS23585 carbamoyl phosphate synthase large subunit
Query= SwissProt::P25994
(1071 letters)
>NCBI__GCF_002019605.1:WP_078430316.1
Length = 1058
Score = 1057 bits (2734), Expect = 0.0
Identities = 537/974 (55%), Positives = 711/974 (72%), Gaps = 11/974 (1%)
Query: 1 MPKRVDINKILVIGSGPIIIGQAAEFDYAGTQACLALKEEGYEVILVNSNPATIMTDTEM 60
MP+ I+ +LVIGSGPI+IGQAAEFDYAGTQACLALKEEG VILVN+NPAT+MTD
Sbjct: 1 MPRITSISSVLVIGSGPIVIGQAAEFDYAGTQACLALKEEGIRVILVNNNPATVMTDEAC 60
Query: 61 ADRVYIEPLTPEFLTRIIRKERPDAILPTLGGQTGLNLAVELSERGVLAECGVEVLGTKL 120
AD VY EPLT E + +II+KE+PD +L TLGGQTGLNLA L + +L + V +LGT +
Sbjct: 61 ADVVYFEPLTVESIEKIIQKEQPDGLLATLGGQTGLNLAFALHKANILDKYNVHLLGTPI 120
Query: 121 SAIQQAEDRDLFRTLMNELNEPVPESEIIHSLEEAEKFVSQIGFPVIVRPAYTLGGTGGG 180
+I + EDR+ FR LMNELNEPVPES+I+ + E A KF + +G+P+I+RPAYTLGG GGG
Sbjct: 121 ESIMKGEDREEFRDLMNELNEPVPESQIVSTEEAAVKFANSVGYPIIIRPAYTLGGAGGG 180
Query: 181 ICSNETELKEIVENGLKLSPVHQCLLEKSIAGYKEIEYEVMRDSQDHAIVVCNMENIDPV 240
I +E EL+ IV+ GL SP+ QCL+E+SIAG+KEIEYEVMRD+ D I VCNMENIDPV
Sbjct: 181 IADDEKELRYIVKGGLAQSPITQCLIERSIAGFKEIEYEVMRDANDTCITVCNMENIDPV 240
Query: 241 GIHTGDSIVVAPSQTLSDREYQLLRNVSLKLIRALGIEGGCNVQLALDPDSFQYYIIEVN 300
GIHTGDSIVVAPSQTL+D EYQ+LR+ S+K+IRALGI GGCN+Q ALDP+S QYY+IEVN
Sbjct: 241 GIHTGDSIVVAPSQTLTDVEYQMLRSASVKIIRALGIVGGCNIQFALDPNSKQYYLIEVN 300
Query: 301 PRVSRSSALASKATGYPIAKLAAKIAVGLSLDEMMNPVTGKTYAAFEPALDYVVSKIPRW 360
PRVSRSSALASKATGYPIA++AAK+++G L E++NPVTG TYA+FEPALDYVV K PRW
Sbjct: 301 PRVSRSSALASKATGYPIARMAAKLSIGYHLHELLNPVTGHTYASFEPALDYVVVKFPRW 360
Query: 361 PFDKFESANRKLGTQMKATGEVMAIGRTLEESLLKAVRSLEADVYHLELKDAADISDELL 420
PFDKF A+RKLGTQMKATGEVMAI R LE + KAVRSLE L DE L
Sbjct: 361 PFDKFTQADRKLGTQMKATGEVMAIERNLESGIQKAVRSLEIKTDGLSFPALKKWGDEEL 420
Query: 421 EKRIKKAGDERLFYLAEAYRRGYTVEDLHEFSAIDVFFLHKLFGIVQFEKELKANA---- 476
+ +KKA D R F + E RRG TV+ +HE + I++FFL+ ++ E+E+ ++
Sbjct: 421 WEVVKKADDRRFFAILELLRRGITVDTIHEETMINLFFLYSFKHLIDLEQEITNSSLELV 480
Query: 477 GDTDVLRRAKELGFSDQYISREWKMKESELYSLRKQAGIAPVFKMVDTCAAEFESETPYF 536
+ D++ + K GFSDQ+IS+ W + ++ RK GI P +KMVDTCAAEF + T Y+
Sbjct: 481 SEADLI-KYKRFGFSDQWISQVWNVSLHDVREKRKAYGILPSYKMVDTCAAEFTANTAYY 539
Query: 537 YSTYEEENE-SVVTDKKSVMVLGSGPIRIGQGVEFDYATVHSVWAIKQAGYEAIIVNNNP 595
YS++ E++ V ++KK ++++GSGPIRIGQG+EFDY +VH ++K+ GYEAII+NNNP
Sbjct: 540 YSSWHGEHDVDVSSNKKKILIVGSGPIRIGQGIEFDYCSVHGAISLKKLGYEAIIMNNNP 599
Query: 596 ETVSTDFSISDKLYFEPLTIEDVMHIIDLEQPMGVVVQFGGQTAINLADELSARGVKILG 655
ETVSTD+ ++D+LYFEPLT+EDV+++++LEQ GV+VQ GGQTAI+L L GV++ G
Sbjct: 600 ETVSTDYEMADRLYFEPLTVEDVLNVVELEQIEGVIVQLGGQTAISLVQGLEEAGVRLYG 659
Query: 656 TSLEDLDRAEDRDKFEQALGELGVPQPLGKTATSVNQAVSIASDIGYPVLVRPSYVLGGR 715
T+++ +D+ EDR +F + + VP G T V A IGYPVL+RPSYV+GG+
Sbjct: 660 TTMDTIDQLEDRGRFYDFMKSVNVPHIPGVTVYDEVGLVEQAEKIGYPVLLRPSYVIGGQ 719
Query: 716 AMEIVYHEEELLHYMKNAVKINPQHPVLIDRYLTGKEIEVDAVSDGETVVIPGIMEHIER 775
M I+ EE++ Y+ N + + P+LID Y G EIEVDA++DGE ++IPG+ EHIE+
Sbjct: 720 GMVIITSREEMVDYVNNQDQ-SIVFPILIDAYYPGVEIEVDALTDGEDILIPGMFEHIEK 778
Query: 776 AGVHSGDSIAVYPPQSLTEDIKKKIEQYTIALAKGLNIVGLLNIQFVLSQGEVYVLEVNP 835
AGVHSGDS+AV PP SL E++K+ + +YT +AKG++ G+ NIQFVL ++YV+E+NP
Sbjct: 779 AGVHSGDSMAVTPPFSLKEEVKQTVYEYTNKIAKGMDFKGIFNIQFVLYNHQLYVIEINP 838
Query: 836 RSSRTVPFLSKITGIPMANLATKIILGQKLAAFGYTEGLQPEQQGVFVKAPVFSFAKLRR 895
R+SRTVP LSK+TG+ M +++LGQ L G G PE VKAP+FS++KL
Sbjct: 839 RASRTVPILSKVTGLNMVETTVQLLLGQSLRNLGLPTGHLPETNYYTVKAPIFSYSKLAG 898
Query: 896 VDITLGPEMKSTGEVMGKDSTLEKALYKALIASGIQIP----NYGSVLLTVADKDKEEGL 951
+D L EMKSTGE++ +T+E A+ KA S QIP G + + +A+++ E
Sbjct: 899 LDPILEAEMKSTGELISIGNTVEDAMKKAFAWSEGQIPPLYRQKGLIFVNIAEEELAEFR 958
Query: 952 AIAKRFHAIGYNIL 965
+ K+ +G+ I+
Sbjct: 959 PLVKKMSELGFTIV 972
Lambda K H
0.316 0.135 0.377
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: 2763
Number of extensions: 109
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: 1071
Length of database: 1058
Length adjustment: 45
Effective length of query: 1026
Effective length of database: 1013
Effective search space: 1039338
Effective search space used: 1039338
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 (21.6 bits)
S2: 58 (26.9 bits)
Align candidate WP_078430316.1 BK574_RS23585 (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.3409651.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 1477.5 0.2 0 1477.3 0.2 1.1 1 NCBI__GCF_002019605.1:WP_078430316.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002019605.1:WP_078430316.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1477.3 0.2 0 0 3 1050 .. 4 1035 .. 2 1037 .. 0.97
Alignments for each domain:
== domain 1 score: 1477.3 bits; conditional E-value: 0
TIGR01369 3 redikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveav 73
++i++vlviGsGpivigqAaEFDY+G+qa++alkeegi+v+Lvn+n+Atvmtde++ad vY+ePltve++
NCBI__GCF_002019605.1:WP_078430316.1 4 ITSISSVLVIGSGPIVIGQAAEFDYAGTQACLALKEEGIRVILVNNNPATVMTDEACADVVYFEPLTVESI 74
5789******************************************************************* PP
TIGR01369 74 ekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevak 144
ekii+kE+pD++l+tlGGqt+Lnla l+++ +L+ky+v+llGt++e+i+k+edRe+F+++++e+ne+v++
NCBI__GCF_002019605.1:WP_078430316.1 75 EKIIQKEQPDGLLATLGGQTGLNLAFALHKANILDKYNVHLLGTPIESIMKGEDREEFRDLMNELNEPVPE 145
*********************************************************************** PP
TIGR01369 145 seivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEi 215
s+iv+++e a+++a+++gyP+i+R+a+tlgG+G+gia++e+el+ +v+ +l++spi+q+l+e+s+ag+kEi
NCBI__GCF_002019605.1:WP_078430316.1 146 SQIVSTEEAAVKFANSVGYPIIIRPAYTLGGAGGGIADDEKELRYIVKGGLAQSPITQCLIERSIAGFKEI 216
*********************************************************************** PP
TIGR01369 216 EyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvegecnvqfal 286
EyEv+RD++d+ci+vcn+En+Dp+G+HtGdsivvaPsqtLtd eyq+lR+as+kiir+lg++g+cn+qfal
NCBI__GCF_002019605.1:WP_078430316.1 217 EYEVMRDANDTCITVCNMENIDPVGIHTGDSIVVAPSQTLTDVEYQMLRSASVKIIRALGIVGGCNIQFAL 287
*********************************************************************** PP
TIGR01369 287 dPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvkiP 357
dP+sk+y++iEvnpRvsRssALAskAtGyPiA++aakl++Gy+L+el n+vt++t+AsfEP+lDYvvvk+P
NCBI__GCF_002019605.1:WP_078430316.1 288 DPNSKQYYLIEVNPRVSRSSALASKATGYPIARMAAKLSIGYHLHELLNPVTGHTYASFEPALDYVVVKFP 358
*********************************************************************** PP
TIGR01369 358 rwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkekeaesdeeleealkkpnd 428
rw++dkf+++drklgtqmk++GEvmai+r++e+++qka+rsle+k+ gl+ + +++ deel+e +kk++d
NCBI__GCF_002019605.1:WP_078430316.1 359 RWPFDKFTQADRKLGTQMKATGEVMAIERNLESGIQKAVRSLEIKTDGLSFPALKKWGDEELWEVVKKADD 429
*********************************************************************** PP
TIGR01369 429 rRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiak 499
rR+fai+e+lrrg++v++++e t i+ ffl+++k+l++le+e+++++l+ +++ l k+k+ Gfsd++i++
NCBI__GCF_002019605.1:WP_078430316.1 430 RRFFAILELLRRGITVDTIHEETMINLFFLYSFKHLIDLEQEITNSSLELVSEADLIKYKRFGFSDQWISQ 500
*********************************************************************** PP
TIGR01369 500 lvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvev.tekkkvlvlGsGpiRigq 569
+++vs ++vr+ rk++gi+p++k+vDt+aaEf a+t+Y+Ys++++e +dv+v ++kkk+l++GsGpiRigq
NCBI__GCF_002019605.1:WP_078430316.1 501 VWNVSLHDVREKRKAYGILPSYKMVDTCAAEFTANTAYYYSSWHGE-HDVDVsSNKKKILIVGSGPIRIGQ 570
**********************************************.6666515569************** PP
TIGR01369 570 gvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGq 640
g+EFDyc+vh++ +l++ gy++i++n+nPEtvstDy++adrLyFe+ltvedvl+++e e++egvivqlgGq
NCBI__GCF_002019605.1:WP_078430316.1 571 GIEFDYCSVHGAISLKKLGYEAIIMNNNPETVSTDYEMADRLYFEPLTVEDVLNVVELEQIEGVIVQLGGQ 641
*********************************************************************** PP
TIGR01369 641 talnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRp 711
ta++l++ leeagv++ Gt++++id++EdR +F+ ++++++++++ g ++ + ++e a++igyPvl+Rp
NCBI__GCF_002019605.1:WP_078430316.1 642 TAISLVQGLEEAGVRLYGTTMDTIDQLEDRGRFYDFMKSVNVPHIPGVTVYDEVGLVEQAEKIGYPVLLRP 712
*********************************************************************** PP
TIGR01369 712 syvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGv 782
syv+gG++m i++++ee+ +y++++ + s P+lid y+ +vE++vDa++dge++li+g++eHiE+aGv
NCBI__GCF_002019605.1:WP_078430316.1 713 SYVIGGQGMVIITSREEMVDYVNNQ-DQSIVFPILIDAYYP-GVEIEVDALTDGEDILIPGMFEHIEKAGV 781
**********************998.68999**********.***************************** PP
TIGR01369 783 HsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalg 853
HsGDs++v+pp +l+eevk+++ e+++kiak +++kG++niqfv+ ++++yviE+n+RasRtvP++sk++g
NCBI__GCF_002019605.1:WP_078430316.1 782 HSGDSMAVTPPFSLKEEVKQTVYEYTNKIAKGMDFKGIFNIQFVLYNHQLYVIEINPRASRTVPILSKVTG 852
*********************************************************************** PP
TIGR01369 854 vplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleea 924
+++v+++v++llg++l++l+ + +++++++vka+ fs+sklag+d++l++emkstGE+++ig+++e+a
NCBI__GCF_002019605.1:WP_078430316.1 853 LNMVETTVQLLLGQSLRNLGLPTGHLPETNYYTVKAPIFSYSKLAGLDPILEAEMKSTGELISIGNTVEDA 923
********************999************************************************ PP
TIGR01369 925 llkallask....akikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkv 991
+ ka+++s+ +++kg +++ +++++ e+ +l+kk+ e+g+++++++++ l++
NCBI__GCF_002019605.1:WP_078430316.1 924 MKKAFAWSEgqipPLYRQKGLIFVNIAEEELAEFRPLVKKMSELGFTIVEENQL---LSD----------- 980
*******99543334579*******************************99944...222........... PP
TIGR01369 992 seeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaealle 1050
++ ++ e++ +e++ + i++++k+ k+ ++ r++a++++v+++te++t +++l+
NCBI__GCF_002019605.1:WP_078430316.1 981 -SRPLTFNEWIDQEDAVAYISIPKKGYKTWKE---QRQQALKNRVTVITEMTTLSMMLN 1035
.22346889**************999877765...9*****************999986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1058 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 52.65
//
[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