Align Carbamoyl-phosphate synthase pyrimidine-specific large chain; Carbamoyl-phosphate synthetase ammonia chain; EC 6.3.5.5 (characterized)
to candidate WP_092483169.1 BM299_RS08945 carbamoyl-phosphate synthase large subunit
Query= SwissProt::P25994
(1071 letters)
>NCBI__GCF_900115975.1:WP_092483169.1
Length = 1070
Score = 1352 bits (3499), Expect = 0.0
Identities = 663/1051 (63%), Positives = 839/1051 (79%), Gaps = 3/1051 (0%)
Query: 1 MPKRVDINKILVIGSGPIIIGQAAEFDYAGTQACLALKEEGYEVILVNSNPATIMTDTEM 60
MP + + K+LV+GSGPIIIGQAAEFDYAGTQAC AL+EEG EV+L+NSNPATIMTD M
Sbjct: 1 MPIKKGLQKVLVVGSGPIIIGQAAEFDYAGTQACRALREEGLEVVLINSNPATIMTDANM 60
Query: 61 ADRVYIEPLTPEFLTRIIRKERPDAILPTLGGQTGLNLAVELSERGVLAECGVEVLGTKL 120
ADR+YIEP+TPEF+TR+I KE+PD LP+LGGQ GLN+A++LSE GVL + GV++LGT L
Sbjct: 61 ADRIYIEPITPEFVTRVIAKEKPDGFLPSLGGQVGLNMALQLSEMGVLEQYGVQLLGTPL 120
Query: 121 SAIQQAEDRDLFRTLMNELNEPVPESEIIHSLEEAEKFVSQIGFPVIVRPAYTLGGTGGG 180
AI++AEDR+ F+ M +NEPVPES I+ S++EA +F QIGFP++VRPAYTLGGTGGG
Sbjct: 121 DAIKRAEDREQFKDTMERINEPVPESTIVSSVDEAVEFAKQIGFPLVVRPAYTLGGTGGG 180
Query: 181 ICSNETELKEIVENGLKLSPVHQCLLEKSIAGYKEIEYEVMRDSQDHAIVVCNMENIDPV 240
+ N EL + GLK S +HQ L+E+S+ G+KEIE+EVMRD D+ I +C+MEN+DP+
Sbjct: 181 MVYNMNELIDTCTRGLKASIIHQALIERSVVGWKEIEFEVMRDGADNCITICSMENLDPM 240
Query: 241 GIHTGDSIVVAPSQTLSDREYQLLRNVSLKLIRALGIEGGCNVQLALDPDSFQYYIIEVN 300
GIHTGDSIVVAP+QTLSDREYQ+LR+ +LK+IRALG+EGGCN+Q ALDP+S+QYY+IEVN
Sbjct: 241 GIHTGDSIVVAPTQTLSDREYQMLRSAALKIIRALGVEGGCNIQYALDPNSYQYYVIEVN 300
Query: 301 PRVSRSSALASKATGYPIAKLAAKIAVGLSLDEMMNPVTGKTYAAFEPALDYVVSKIPRW 360
PRVSRSSALASKATGYPIAK+A+KIA+GL+LDE+ N VTGKTYA FEP++DY V K PRW
Sbjct: 301 PRVSRSSALASKATGYPIAKVASKIAIGLNLDEIKNAVTGKTYACFEPSIDYTVIKFPRW 360
Query: 361 PFDKFESANRKLGTQMKATGEVMAIGRTLEESLLKAVRSLEADVYHLELKDAADISDELL 420
PFDKF +A+R LGTQMKATGEVMAI RTLE +LLKAVRSLE V L ++DE +
Sbjct: 361 PFDKFAAADRTLGTQMKATGEVMAIDRTLEGALLKAVRSLEIGVPGLIYPGLERLTDEEI 420
Query: 421 EKRIKKAGDERLFYLAEAYRRGYTVEDLHEFSAIDVFFLHKLFGIVQFEKELKANAG--- 477
E+++ +A DERLF LAEA RRG E +H + +D FF+HK++ +VQ E L+ G
Sbjct: 421 EQKLARANDERLFVLAEALRRGMLFERIHNLTKMDYFFIHKIYNVVQLEDRLRREGGAAL 480
Query: 478 DTDVLRRAKELGFSDQYISREWKMKESELYSLRKQAGIAPVFKMVDTCAAEFESETPYFY 537
+LR AK++G +D Y+++ + E+ +LRK G+ PV+KMVDTCAAEFE+ TPY+Y
Sbjct: 481 TAGLLREAKQMGMADAYLAQAAGVTVQEVRTLRKAHGVEPVYKMVDTCAAEFEAVTPYYY 540
Query: 538 STYEEENESVVTDKKSVMVLGSGPIRIGQGVEFDYATVHSVWAIKQAGYEAIIVNNNPET 597
S Y+ E+E+ T + V+VLG GPIRIGQG+EFDY +VHS WA+K+ G EAII+NNNPET
Sbjct: 541 SCYDSEDEAEPTGNRKVVVLGGGPIRIGQGIEFDYCSVHSTWALKELGIEAIIINNNPET 600
Query: 598 VSTDFSISDKLYFEPLTIEDVMHIIDLEQPMGVVVQFGGQTAINLADELSARGVKILGTS 657
VSTDF +D+LYFEPL EDV++I++ E+P GV+VQFGGQT INLA L G+KILGTS
Sbjct: 601 VSTDFDTADRLYFEPLLPEDVLNILEKEKPEGVIVQFGGQTPINLAGHLDRAGIKILGTS 660
Query: 658 LEDLDRAEDRDKFEQALGELGVPQPLGKTATSVNQAVSIASDIGYPVLVRPSYVLGGRAM 717
++D+DRAEDR +F+ L +L +P+P G TATSV +A +I+ +IG+PVLVRPSYVLGGRAM
Sbjct: 661 MDDIDRAEDRKRFDAMLNDLDIPRPPGGTATSVAEAEAISRNIGFPVLVRPSYVLGGRAM 720
Query: 718 EIVYHEEELLHYMKNAVKINPQHPVLIDRYLTGKEIEVDAVSDGETVVIPGIMEHIERAG 777
EIVY+ E+L +YM+NAVK+ P+HPVL+D+Y G+EIEVDA++DGETV+IPGIM+H+ERAG
Sbjct: 721 EIVYNIEDLRNYMENAVKVTPEHPVLVDKYFLGEEIEVDAIADGETVLIPGIMKHVERAG 780
Query: 778 VHSGDSIAVYPPQSLTEDIKKKIEQYTIALAKGLNIVGLLNIQFVLSQGEVYVLEVNPRS 837
VHSGDSIAVYP L ++++I YT LA LN+ G++NIQ+VL G++YVLEVNPR+
Sbjct: 781 VHSGDSIAVYPANHLDRTVREQIVDYTTRLALELNVRGMINIQYVLYNGQIYVLEVNPRA 840
Query: 838 SRTVPFLSKITGIPMANLATKIILGQKLAAFGYTEGLQPEQQGVFVKAPVFSFAKLRRVD 897
SRTVP++SKITGIPM NLATKII+GQKL+ GY GL PE + V VKAPVFSFAKL +VD
Sbjct: 841 SRTVPYMSKITGIPMINLATKIIMGQKLSDMGYRGGLYPETKLVGVKAPVFSFAKLLQVD 900
Query: 898 ITLGPEMKSTGEVMGKDSTLEKALYKALIASGIQIPNYGSVLLTVADKDKEEGLAIAKRF 957
I+LGPEMKSTGEV+G D++ ALYKAL+ASG+ P G++L+TVADKDKEE L I K F
Sbjct: 901 ISLGPEMKSTGEVLGVDASYPVALYKALLASGVVFPRQGNILVTVADKDKEEALPIVKGF 960
Query: 958 HAIGYNILATEGTAGYLKEASIPAKVVGKIGQDGPNLLDVIRNGEAQFVINTLTKGKQPA 1017
+GYNI AT GTA YL+E + V K+ + P++ D++R G+ VINTLT+GK P
Sbjct: 961 AGLGYNIFATAGTARYLEEHGVAVTRVNKVREGSPHIDDLLRKGDIHLVINTLTRGKAPE 1020
Query: 1018 RDGFRIRRESVENGVACLTSLDTAEAILRVL 1048
RDGF IRR +VE V CLTSLDTA AIL VL
Sbjct: 1021 RDGFVIRRATVELAVPCLTSLDTARAILEVL 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: 2989
Number of extensions: 114
Number of successful extensions: 12
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: 1070
Length adjustment: 45
Effective length of query: 1026
Effective length of database: 1025
Effective search space: 1051650
Effective search space used: 1051650
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_092483169.1 BM299_RS08945 (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.19556.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 1562.1 0.0 0 1561.9 0.0 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092483169.1 BM299_RS08945 carbamoyl-phosphat
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900115975.1:WP_092483169.1 BM299_RS08945 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1561.9 0.0 0 0 3 1051 .. 4 1050 .. 2 1051 .. 1.00
Alignments for each domain:
== domain 1 score: 1561.9 bits; conditional E-value: 0
TIGR01369 3 redikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePlt 69
++ ++kvlv+GsGpi+igqAaEFDY+G+qa++al+eeg+evvL+nsn+At+mtd ++ad++YieP+t
lcl|NCBI__GCF_900115975.1:WP_092483169.1 4 KKGLQKVLVVGSGPIIIGQAAEFDYAGTQACRALREEGLEVVLINSNPATIMTDANMADRIYIEPIT 70
67899************************************************************** PP
TIGR01369 70 veavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealk 136
+e+v+++i kE+pD+ l++lGGq +Ln+a++l+e+GvLe+ygv+llGt+++aik+aedRe+Fk++++
lcl|NCBI__GCF_900115975.1:WP_092483169.1 71 PEFVTRVIAKEKPDGFLPSLGGQVGLNMALQLSEMGVLEQYGVQLLGTPLDAIKRAEDREQFKDTME 137
******************************************************************* PP
TIGR01369 137 eineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqv 203
ine+v++s+iv+sv+ea+e+a++ig+P++vR+a+tlgGtG+g+++n++el ++ ++lkas i+q
lcl|NCBI__GCF_900115975.1:WP_092483169.1 138 RINEPVPESTIVSSVDEAVEFAKQIGFPLVVRPAYTLGGTGGGMVYNMNELIDTCTRGLKASIIHQA 204
******************************************************************* PP
TIGR01369 204 lvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslki 270
l+e+s+ gwkEiE+Ev+RD +dnci++c++EnlDp+G+HtGdsivvaP+qtL+d+eyq+lR+a+lki
lcl|NCBI__GCF_900115975.1:WP_092483169.1 205 LIERSVVGWKEIEFEVMRDGADNCITICSMENLDPMGIHTGDSIVVAPTQTLSDREYQMLRSAALKI 271
******************************************************************* PP
TIGR01369 271 irelgvegecnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndv 337
ir+lgveg+cn+q+aldP+s++y+viEvnpRvsRssALAskAtGyPiAkva+k+a+G++Lde+kn v
lcl|NCBI__GCF_900115975.1:WP_092483169.1 272 IRALGVEGGCNIQYALDPNSYQYYVIEVNPRVSRSSALASKATGYPIAKVASKIAIGLNLDEIKNAV 338
******************************************************************* PP
TIGR01369 338 tketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekll 404
t++t+A+fEPs+DY v+k+Prw++dkf+ +dr+lgtqmk++GEvmai+rt+e al+ka+rsle+++
lcl|NCBI__GCF_900115975.1:WP_092483169.1 339 TGKTYACFEPSIDYTVIKFPRWPFDKFAAADRTLGTQMKATGEVMAIDRTLEGALLKAVRSLEIGVP 405
******************************************************************* PP
TIGR01369 405 glklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekel 471
gl + e +dee+e++l ++nd+Rlf++aealrrg+ e++++ltk+d ff++k+ ++v+le +l
lcl|NCBI__GCF_900115975.1:WP_092483169.1 406 GLIYPGLERLTDEEIEQKLARANDERLFVLAEALRRGMLFERIHNLTKMDYFFIHKIYNVVQLEDRL 472
******************************************************************* PP
TIGR01369 472 eeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYl 538
++e l++ ll++ak++G++d+ +a++++v+ +evr+lrk+ g+ pv+k+vDt+aaEfea tpY+
lcl|NCBI__GCF_900115975.1:WP_092483169.1 473 RREGGAALTAGLLREAKQMGMADAYLAQAAGVTVQEVRTLRKAHGVEPVYKMVDTCAAEFEAVTPYY 539
******************************************************************* PP
TIGR01369 539 YstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstDy 605
Ys y +e d++e t ++kv+vlG+GpiRigqg+EFDyc+vh+++al+e g+++i+in+nPEtvstD+
lcl|NCBI__GCF_900115975.1:WP_092483169.1 540 YSCYDSE-DEAEPTGNRKVVVLGGGPIRIGQGIEFDYCSVHSTWALKELGIEAIIINNNPETVSTDF 605
*******.999999999************************************************** PP
TIGR01369 606 diadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRek 672
d+adrLyFe+l edvl+i+ekek+egvivq+gGqt++nla +l++ag+kilGts+++idraEdR++
lcl|NCBI__GCF_900115975.1:WP_092483169.1 606 DTADRLYFEPLLPEDVLNILEKEKPEGVIVQFGGQTPINLAGHLDRAGIKILGTSMDDIDRAEDRKR 672
******************************************************************* PP
TIGR01369 673 FsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavev 739
F+++l++l+i++p g +atsv ea+ i ++ig+PvlvRpsyvlgGrameiv+n e+l++y+e+av+v
lcl|NCBI__GCF_900115975.1:WP_092483169.1 673 FDAMLNDLDIPRPPGGTATSVAEAEAISRNIGFPVLVRPSYVLGGRAMEIVYNIEDLRNYMENAVKV 739
******************************************************************* PP
TIGR01369 740 skekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkike 806
++e+Pvl+dky+ + E++vDa+adge+vli+gi++H+E+aGvHsGDs++v+p+++l++ v ++i +
lcl|NCBI__GCF_900115975.1:WP_092483169.1 740 TPEHPVLVDKYFL-GEEIEVDAIADGETVLIPGIMKHVERAGVHSGDSIAVYPANHLDRTVREQIVD 805
************9.***************************************************** PP
TIGR01369 807 ivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleele 873
+++++a el+v+G++niq+v+ ++++yv+Evn+RasRtvP++sk++g+p+++la+k+++g+kl++++
lcl|NCBI__GCF_900115975.1:WP_092483169.1 806 YTTRLALELNVRGMINIQYVLYNGQIYVLEVNPRASRTVPYMSKITGIPMINLATKIIMGQKLSDMG 872
******************************************************************* PP
TIGR01369 874 kgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkg 940
+ +++klv+vka+vfsf+kl +vd+ lgpemkstGEv g++ + al+kallas+ +++++g
lcl|NCBI__GCF_900115975.1:WP_092483169.1 873 YRGGLYPETKLVGVKAPVFSFAKLLQVDISLGPEMKSTGEVLGVDASYPVALYKALLASGVVFPRQG 939
*999*************************************************************** PP
TIGR01369 941 svllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaekilellkeeei 1007
++l++v+dkdkee+l+++k +a +g++++at+gta++lee+g+ ++ v+kv+e +++i +ll++++i
lcl|NCBI__GCF_900115975.1:WP_092483169.1 940 NILVTVADKDKEEALPIVKGFAGLGYNIFATAGTARYLEEHGVAVTRVNKVREGSPHIDDLLRKGDI 1006
******************************************************************* PP
TIGR01369 1008 elvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
+lvin+ +++k+ +++g++irr++ve +vp++t+l+ta+a+le+
lcl|NCBI__GCF_900115975.1:WP_092483169.1 1007 HLVINTLTRGKAPERDGFVIRRATVELAVPCLTSLDTARAILEV 1050
****************************************9987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1070 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: 00:00:00.09
# Mc/sec: 12.11
//
[ok]
This GapMind analysis is from Apr 10 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