Align Carbamoyl-phosphate synthase pyrimidine-specific large chain; Carbamoyl-phosphate synthetase ammonia chain; EC 6.3.5.5 (characterized)
to candidate WP_017751024.1 PN53_RS06640 carbamoyl-phosphate synthase large subunit
Query= SwissProt::P25994
(1071 letters)
>NCBI__GCF_000816635.1:WP_017751024.1
Length = 1068
Score = 1192 bits (3084), Expect = 0.0
Identities = 597/1051 (56%), Positives = 789/1051 (75%), Gaps = 4/1051 (0%)
Query: 1 MPKRVDINKILVIGSGPIIIGQAAEFDYAGTQACLALKEEGYEVILVNSNPATIMTDTEM 60
MP +I K+LVIGSGPIIIGQAAEFDY+GTQAC +L+EEG EV+L+NSNPATIMTD E+
Sbjct: 1 MPLNKNIKKVLVIGSGPIIIGQAAEFDYSGTQACESLREEGIEVVLINSNPATIMTDREI 60
Query: 61 ADRVYIEPLTPEFLTRIIRKERPDAILPTLGGQTGLNLAVELSERGVLAECGVEVLGTKL 120
AD+VYIEPLT EF+ ++I++ERPD++L +GGQT LNL VEL E+ +L + V ++GT +
Sbjct: 61 ADKVYIEPLTVEFVEKVIKEERPDSLLAGMGGQTALNLTVELHEKKILQKYNVNIIGTSI 120
Query: 121 SAIQQAEDRDLFRTLMNELNEPVPESEIIHSLEEAEKFVSQIGFPVIVRPAYTLGGTGGG 180
AI++ EDR+LFR M ++ +PV +S II +E KF +IG+PVIVRPAYTLGGTGGG
Sbjct: 121 EAIEKGEDRELFRDTMQKIGQPVVDSAIITDMESGRKFAKKIGYPVIVRPAYTLGGTGGG 180
Query: 181 ICSNETELKEIVENGLKLSPVHQCLLEKSIAGYKEIEYEVMRDSQDHAIVVCNMENIDPV 240
I ++E EL I+E+GL+LS +HQ LLE+SI G+KEIEYEVMRDS + I VCNMENIDPV
Sbjct: 181 IANDEYELNTILESGLELSSIHQVLLERSIKGWKEIEYEVMRDSFGNCITVCNMENIDPV 240
Query: 241 GIHTGDSIVVAPSQTLSDREYQLLRNVSLKLIRALGIEGGCNVQLALDPDSFQYYIIEVN 300
GIHTGDSIV APSQTLSD+EYQ+LR+ S+ +I +GIEGGCNVQLAL+P+SF+Y +IE+N
Sbjct: 241 GIHTGDSIVTAPSQTLSDKEYQMLRSASIDIINEVGIEGGCNVQLALNPNSFEYAVIEIN 300
Query: 301 PRVSRSSALASKATGYPIAKLAAKIAVGLSLDEMMNPVTGKTYAAFEPALDYVVSKIPRW 360
PRVSRSSALASKATGYPIAK+AAKIA+G LDE+ N VT KT+A FEP+LDYVV KIP+W
Sbjct: 301 PRVSRSSALASKATGYPIAKVAAKIALGYGLDEIENAVTKKTFACFEPSLDYVVVKIPKW 360
Query: 361 PFDKFESANRKLGTQMKATGEVMAIGRTLEESLLKAVRSLEADVYHLELKDAADISDELL 420
PFDKF++A+R+LGT+M ATGE+MAIG E +LLK +RSLE Y L+ + + E L
Sbjct: 361 PFDKFQNADRELGTKMMATGEIMAIGSNFEAALLKGIRSLEIGAYSLDYEKFKNSGLEDL 420
Query: 421 EKRIKKAGDERLFYLAEAYRRGYTVEDLHEFSAIDVFFLHKLFGIVQFEKELKANA---G 477
+ I A DER+F LAE RRGY VE L E + ID FF++KL I+ E++LK +
Sbjct: 421 KNIIIYADDERIFALAEMLRRGYRVEKLSEITGIDKFFIYKLKWIIDQEEKLKNSTIDDL 480
Query: 478 DTDVLRRAKELGFSDQYISREWKMKESELYSLRKQAGIAPVFKMVDTCAAEFESETPYFY 537
D D LR K+ GFSD+ ++ K+ E+Y LR I P +KMVDTC EFE+ +PY+Y
Sbjct: 481 DKDWLRMLKKKGFSDKGMADMLKISPDEIYKLRIIWNIRPAYKMVDTCGGEFEALSPYYY 540
Query: 538 STYEEENESVVTDKKSVMVLGSGPIRIGQGVEFDYATVHSVWAIKQAGYEAIIVNNNPET 597
STYEE +E V++ K V+V+GSGPIRIGQG+EFDYA+VH + +++ G E IIVNNNPET
Sbjct: 541 STYEEHDEVNVSENKKVVVIGSGPIRIGQGIEFDYASVHCIKILRKLGIETIIVNNNPET 600
Query: 598 VSTDFSISDKLYFEPLTIEDVMHIIDLEQPMGVVVQFGGQTAINLADELSARGVKILGTS 657
VSTDF ISDKLYFEP+T E+V++IID E+P GV++QFGG+TAI LA+ L + + LGT+
Sbjct: 601 VSTDFDISDKLYFEPITEEEVLNIIDKEKPYGVILQFGGETAIKLAEFLKEKNIVTLGTT 660
Query: 658 LEDLDRAEDRDKFEQALGELGVPQPLGKTATSVNQAVSIASDIGYPVLVRPSYVLGGRAM 717
+ +D AEDR+KF+ L L + +P GK S+ + A +G+PVLVRPSYVLGG+ M
Sbjct: 661 ADQIDMAEDREKFDDLLERLDISRPKGKGIWSIEDGLKEAKRVGFPVLVRPSYVLGGQGM 720
Query: 718 EIVYHEEELLHYMKNAVKINPQHPVLIDRYLTGKEIEVDAVSDGETVVIPGIMEHIERAG 777
EI Y+E+EL +Y+ A + ++P+LID+YL G+EIEVDA+ DGE V+IPGIMEH+ERAG
Sbjct: 721 EITYNEDELTYYLSKAFVKDKKNPILIDKYLMGREIEVDAICDGEDVLIPGIMEHLERAG 780
Query: 778 VHSGDSIAVYPPQSLTEDIKKKIEQYTIALAKGLNIVGLLNIQFVLSQGEVYVLEVNPRS 837
VHSGDSI +YP Q++ +D+K +I YT LA G+ I G++NIQF+ +GE+YV+EVNPR+
Sbjct: 781 VHSGDSITMYPTQNVDDDMKSRILDYTKKLALGIGIHGMINIQFIEYRGELYVIEVNPRA 840
Query: 838 SRTVPFLSKITGIPMANLATKIILGQKLAAFGYTEGLQPEQQGVFVKAPVFSFAKLRRVD 897
SRTVP++SK++ +P+ ++ATK++LGQKL GY G+ E V VK PVFS KL V+
Sbjct: 841 SRTVPYISKVSNVPIVDIATKVMLGQKLKEIGYGVGISKEPDIVAVKVPVFSTQKLPNVE 900
Query: 898 ITLGPEMKSTGEVMGKDSTLEKALYKALIASGIQIPN-YGSVLLTVADKDKEEGLAIAKR 956
++LGPEM+STGEV+G TL +ALYK +AS + N ++L T++D DKEE L IAK
Sbjct: 901 VSLGPEMRSTGEVLGVGKTLTEALYKGFVASKMFSYNKIDTILATISDHDKEEFLPIAKE 960
Query: 957 FHAIGYNILATEGTAGYLKEASIPAKVVGKIGQDGPNLLDVIRNGEAQFVINTLTKGKQP 1016
+ +G AT+ T+ L + I K V K+ ++ PN++D+I+N E V+NT TKG
Sbjct: 961 INKLGIKFAATKNTSKLLMDNGIEVKEVRKVNEERPNIIDIIKNEEVDLVVNTPTKGNDS 1020
Query: 1017 ARDGFRIRRESVENGVACLTSLDTAEAILRV 1047
RDGF IRR ++E + +TSLDT +A+ V
Sbjct: 1021 TRDGFHIRRAAIERNIEVITSLDTFKAMAYV 1051
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: 2954
Number of extensions: 125
Number of successful extensions: 14
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: 1068
Length adjustment: 45
Effective length of query: 1026
Effective length of database: 1023
Effective search space: 1049598
Effective search space used: 1049598
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_017751024.1 PN53_RS06640 (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.4191157.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 1538.5 8.5 0 1538.3 8.5 1.0 1 NCBI__GCF_000816635.1:WP_017751024.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000816635.1:WP_017751024.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1538.3 8.5 0 0 3 1049 .. 4 1049 .. 2 1052 .. 0.99
Alignments for each domain:
== domain 1 score: 1538.3 bits; conditional E-value: 0
TIGR01369 3 redikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveav 73
+++ikkvlviGsGpi+igqAaEFDYsG+qa+ +l+eegievvL+nsn+At+mtd+e+adkvYiePltve+v
NCBI__GCF_000816635.1:WP_017751024.1 4 NKNIKKVLVIGSGPIIIGQAAEFDYSGTQACESLREEGIEVVLINSNPATIMTDREIADKVYIEPLTVEFV 74
689******************************************************************** PP
TIGR01369 74 ekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevak 144
ek+i++ErpD++l+++GGqtaLnl+vel+ek +L+ky+v+++Gt++eai+k+edRe+F++++++i+++v +
NCBI__GCF_000816635.1:WP_017751024.1 75 EKVIKEERPDSLLAGMGGQTALNLTVELHEKKILQKYNVNIIGTSIEAIEKGEDRELFRDTMQKIGQPVVD 145
*********************************************************************** PP
TIGR01369 145 seivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEi 215
s+i++++e ++a++igyPvivR+a+tlgGtG+gia++e el+++ e++l++s+i+qvl+e+s++gwkEi
NCBI__GCF_000816635.1:WP_017751024.1 146 SAIITDMESGRKFAKKIGYPVIVRPAYTLGGTGGGIANDEYELNTILESGLELSSIHQVLLERSIKGWKEI 216
*********************************************************************** PP
TIGR01369 216 EyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvegecnvqfal 286
EyEv+RDs++nci+vcn+En+Dp+G+HtGdsiv aPsqtL+dkeyq+lR+as+ ii+e+g+eg+cnvq al
NCBI__GCF_000816635.1:WP_017751024.1 217 EYEVMRDSFGNCITVCNMENIDPVGIHTGDSIVTAPSQTLSDKEYQMLRSASIDIINEVGIEGGCNVQLAL 287
*********************************************************************** PP
TIGR01369 287 dPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvkiP 357
+P+s +y viE+npRvsRssALAskAtGyPiAkvaak+a+Gy+Lde++n vtk+t+A+fEPslDYvvvkiP
NCBI__GCF_000816635.1:WP_017751024.1 288 NPNSFEYAVIEINPRVSRSSALASKATGYPIAKVAAKIALGYGLDEIENAVTKKTFACFEPSLDYVVVKIP 358
*********************************************************************** PP
TIGR01369 358 rwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklkekeaesdeeleealkkpnd 428
+w++dkf+++dr+lgt+m+++GE+maig +fe+al+k++rsle+++++l+ ++ ++ e+l++ + +++d
NCBI__GCF_000816635.1:WP_017751024.1 359 KWPFDKFQNADRELGTKMMATGEIMAIGSNFEAALLKGIRSLEIGAYSLDYEKFKNSGLEDLKNIIIYADD 429
*********************************************************************** PP
TIGR01369 429 rRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleeeklkelkkellkkakklGfsdeqiak 499
+R+fa+ae lrrg+ ve++ e+t id+ff++klk +++ e++l+++++++l+k+ l+ +kk+Gfsd+ +a
NCBI__GCF_000816635.1:WP_017751024.1 430 ERIFALAEMLRRGYRVEKLSEITGIDKFFIYKLKWIIDQEEKLKNSTIDDLDKDWLRMLKKKGFSDKGMAD 500
*********************************************************************** PP
TIGR01369 500 lvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGsGpiRigqg 570
++k s +e+ klr +i p++k+vDt+ +Efea pY+Ystyee+ d+v+v+e+kkv+v+GsGpiRigqg
NCBI__GCF_000816635.1:WP_017751024.1 501 MLKISPDEIYKLRIIWNIRPAYKMVDTCGGEFEALSPYYYSTYEEH-DEVNVSENKKVVVIGSGPIRIGQG 570
********************************************99.************************ PP
TIGR01369 571 vEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqt 641
+EFDy++vh+++ lr+ g++ti++n+nPEtvstD+di+d+LyFe++t e+vl+ii+kek+ gvi+q+gG t
NCBI__GCF_000816635.1:WP_017751024.1 571 IEFDYASVHCIKILRKLGIETIIVNNNPETVSTDFDISDKLYFEPITEEEVLNIIDKEKPYGVILQFGGET 641
*********************************************************************** PP
TIGR01369 642 alnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRps 712
a++la+ l+e+++ lGt+a++id+aEdRekF+ ll++l+i++pkgk + s+e+ + ak++g+PvlvRps
NCBI__GCF_000816635.1:WP_017751024.1 642 AIKLAEFLKEKNIVTLGTTADQIDMAEDREKFDDLLERLDISRPKGKGIWSIEDGLKEAKRVGFPVLVRPS 712
*********************************************************************** PP
TIGR01369 713 yvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvH 783
yvlgG++mei +ne+el+ yl++a+ k++P+lidkyl + E++vDa++dge+vli+gi+eH+E+aGvH
NCBI__GCF_000816635.1:WP_017751024.1 713 YVLGGQGMEITYNEDELTYYLSKAFVKDKKNPILIDKYLM-GREIEVDAICDGEDVLIPGIMEHLERAGVH 782
****************************************.****************************** PP
TIGR01369 784 sGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgv 854
sGDs++++p+q++++++k++i +++kk+a + ++G++niqf+ +e+yviEvn+RasRtvP++sk+ +v
NCBI__GCF_000816635.1:WP_017751024.1 783 SGDSITMYPTQNVDDDMKSRILDYTKKLALGIGIHGMINIQFIEYRGELYVIEVNPRASRTVPYISKVSNV 853
*********************************************************************** PP
TIGR01369 855 plvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeal 925
p+v++a+kv+lg+kl+e ++gv +k++++vavk++vfs +kl +v+v lgpem+stGEv g+g++l+eal
NCBI__GCF_000816635.1:WP_017751024.1 854 PIVDIATKVMLGQKLKEIGYGVGISKEPDIVAVKVPVFSTQKLPNVEVSLGPEMRSTGEVLGVGKTLTEAL 924
*********************************************************************** PP
TIGR01369 926 lkallask.akikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseea 995
+k ++ask + ++k +++l +++d+dkee+l++ak+++++g+k at++t+k l ++gi+++ v+kv+ee+
NCBI__GCF_000816635.1:WP_017751024.1 925 YKGFVASKmFSYNKIDTILATISDHDKEEFLPIAKEINKLGIKFAATKNTSKLLMDNGIEVKEVRKVNEER 995
****999868889999******************************************************* PP
TIGR01369 996 ekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeall 1049
++i++++k+ee++lv+n+++k+++++++g++irr+a+e++++++t+l+t++a++
NCBI__GCF_000816635.1:WP_017751024.1 996 PNIIDIIKNEEVDLVVNTPTKGNDSTRDGFHIRRAAIERNIEVITSLDTFKAMA 1049
*************************************************99986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1068 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 29.49
//
[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