Align Carbamoyl-phosphate synthase pyrimidine-specific large chain; Carbamoyl-phosphate synthetase ammonia chain; EC 6.3.5.5 (characterized)
to candidate WP_012102719.1 CKL_RS11625 carbamoyl-phosphate synthase (glutamine-hydrolyzing) large subunit
Query= SwissProt::P25994
(1071 letters)
>NCBI__GCF_000016505.1:WP_012102719.1
Length = 1072
Score = 1165 bits (3013), Expect = 0.0
Identities = 568/1042 (54%), Positives = 780/1042 (74%), Gaps = 5/1042 (0%)
Query: 1 MPKRVDINKILVIGSGPIIIGQAAEFDYAGTQACLALKEEGYEVILVNSNPATIMTDTEM 60
MP R ++ K+L+IGSGPIIIGQAAEFDY+GTQAC A+K+EG E +LVNSNPATIMTD +
Sbjct: 1 MPLRENLKKVLIIGSGPIIIGQAAEFDYSGTQACEAIKKEGIETVLVNSNPATIMTDKNI 60
Query: 61 ADRVYIEPLTPEFLTRIIRKERPDAILPTLGGQTGLNLAVELSERGVLAECGVEVLGTKL 120
A + Y+EPLT E L II++ERPD +L GGQT LNLA+EL + G+L + VE+LG K
Sbjct: 61 AHKTYVEPLTVESLEAIIKRERPDGVLAGFGGQTALNLAMELGKLGILKKYNVELLGIKT 120
Query: 121 SAIQQAEDRDLFRTLMNELNEPVPESEIIHSLEEAEKFVSQIGFPVIVRPAYTLGGTGGG 180
+I+ AEDR+ F+ LM E+ EP+ S I LE+ + F+ ++ P+I+RPAYTLGGTGGG
Sbjct: 121 ESIKNAEDRESFKNLMEEIEEPIALSTIATDLEQCKSFLDKVSLPIIIRPAYTLGGTGGG 180
Query: 181 ICSNETELKEIVENGLKLSPVHQCLLEKSIAGYKEIEYEVMRDSQDHAIVVCNMENIDPV 240
I N E EI +NGL+ SP++Q LLE+S+AG+KE+EYE+MRD +D+ +VVCNMEN+DPV
Sbjct: 181 IADNYEEYLEICKNGLEESPINQILLEQSLAGWKELEYEIMRDKKDNCMVVCNMENLDPV 240
Query: 241 GIHTGDSIVVAPSQTLSDREYQLLRNVSLKLIRALGIEGGCNVQLALDPDSFQYYIIEVN 300
GIHTGDSIVVAPSQTL+DREYQ+LR S+K+IR L IEGGCN+Q AL+P +Y +IEVN
Sbjct: 241 GIHTGDSIVVAPSQTLTDREYQMLRRSSIKIIRKLKIEGGCNIQFALNPSGNEYMVIEVN 300
Query: 301 PRVSRSSALASKATGYPIAKLAAKIAVGLSLDEMMNPVTGKTYAAFEPALDYVVSKIPRW 360
PRVSRSSALASKA GYPIAK+AAKIA+G +LDE+ N VTG + A FEPALDY V K+P+W
Sbjct: 301 PRVSRSSALASKAAGYPIAKIAAKIALGYTLDELKNYVTGNSSALFEPALDYCVVKMPKW 360
Query: 361 PFDKFESANRKLGTQMKATGEVMAIGRTLEESLLKAVRSLEADVYHLELKDAADISDELL 420
PFDKF++ANR L TQMKATGEVMAI R+ E +LLKAV SLE + L+L D++ +
Sbjct: 361 PFDKFKTANRTLKTQMKATGEVMAIDRSFESALLKAVISLEGKIVGLKLDKFEDMNLSQI 420
Query: 421 EKRIKKAGDERLFYLAEAYRRGYTVEDLHEFSAIDVFFLHKLFGIVQFEKELKANAGDTD 480
++KK DERLF LAEA R+G +V++L+E + ID +F++ + I+ E +L +N + D
Sbjct: 421 IDKLKKEDDERLFALAEALRKGISVDELYEITKIDKWFIYGVKNIIDMENKLVSNVPNVD 480
Query: 481 VLRRAKELGFSDQYISREWKMKESELYSLRKQAGIAPVFKMVDTCAAEFESETPYFYSTY 540
++ +A+ +GF+D+YI MK +L LR+ GI V+KMVDTC+ EFE++T Y+YS Y
Sbjct: 481 IIHQAELMGFTDEYICNLMGMKLEDLKQLREVNGIRVVYKMVDTCSGEFEAKTSYYYSCY 540
Query: 541 EEENESVVTDKKSVMVLGSGPIRIGQGVEFDYATVHSVWAIKQAGYEAIIVNNNPETVST 600
+ EN++V++D K ++V+GSGPIRIGQG+EFDY V+ VWAIK+AGYEAII+NNNPETVST
Sbjct: 541 DLENDNVISDNKKILVIGSGPIRIGQGIEFDYCCVNGVWAIKKAGYEAIIINNNPETVST 600
Query: 601 DFSISDKLYFEPLTIEDVMHIIDLEQPMGVVVQFGGQTAINLADELSARGVKILGTSLED 660
DF ISDKLYF+PL I+DVM++I+ E+ GV+VQFGGQTA+NL+ +L+ RGV +LGTS E
Sbjct: 601 DFDISDKLYFDPLYIDDVMNVINEEKVDGVIVQFGGQTALNLSKKLNDRGVNLLGTSFES 660
Query: 661 LDRAEDRDKFEQALGELGVPQPLGKTATSVNQAVSIASDIGYPVLVRPSYVLGGRAMEIV 720
+D AEDR+KF L +L + P+G + TS+ +A + S+IGYPV+VRPSYV+GGRAM++V
Sbjct: 661 IDLAEDREKFRILLKKLNINSPIGGSVTSLKEAYKLVSEIGYPVIVRPSYVIGGRAMKVV 720
Query: 721 YHEEELLHYMKNAVKINPQHPVLIDRYLTGKEIEVDAVSDGETVVIPGIMEHIERAGVHS 780
Y+ EEL Y+K AV ++ +HPVL+D+Y+ G+EIEVDA+SDG+ ++IPGIMEH+ER GVHS
Sbjct: 721 YNPEELERYLKEAVNLSKEHPVLVDKYILGREIEVDAISDGQDLIIPGIMEHVERTGVHS 780
Query: 781 GDSIAVYPPQSLTEDIKKKIEQYTIALAKGLNIVGLLNIQFVLSQGEVYVLEVNPRSSRT 840
GDSIA+YP L E + ++IE+YT+ +A+ LN+ GLLN+Q+ ++YV+EVNPR+SRT
Sbjct: 781 GDSIAIYPASDLPEKVCQRIEEYTVNIARELNVKGLLNVQYAFDGDKIYVIEVNPRASRT 840
Query: 841 VPFLSKITGIPMANLATKIILGQKLAAFGYTEGLQPEQQGVFVKAPVFSFAKLRRVDITL 900
VP LSK+T +PM +A +++LG+K+ F Y + + VK PVFS KL VD+ L
Sbjct: 841 VPILSKVTDVPMVEIAVEVMLGKKIKEFNYKQDMYKYSNIFAVKMPVFSSKKLPGVDVAL 900
Query: 901 GPEMKSTGEVMGKDSTLEKALYKALIASGIQIPNYGSVLLTVADKDKEEGLAIAKRFHAI 960
GPEMKSTGEV+G D +KA+YKA A+G++I G++ + + D+DK L + K+++++
Sbjct: 901 GPEMKSTGEVLGVDYDKDKAIYKAFKAAGVEIFKKGNLYVCINDRDKCSSLEVIKKYNSL 960
Query: 961 GYNILATEGTAGYLKEASIPAKVVGKIGQDGPNLLDVIRNGEAQFVINTLTKGKQPARDG 1020
+NI+A+ GT +LKE I + + + I+ + VIN T+G R+G
Sbjct: 961 NFNIIASSGTFKFLKENGIKCSKLSI-----EDAISYIKEDKIDIVINIPTQGYDGTREG 1015
Query: 1021 FRIRRESVENGVACLTSLDTAE 1042
F++R ++ + T +DTA+
Sbjct: 1016 FKLRHMALAHDKVVFTCIDTAD 1037
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: 2874
Number of extensions: 112
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: 1072
Length adjustment: 45
Effective length of query: 1026
Effective length of database: 1027
Effective search space: 1053702
Effective search space used: 1053702
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_012102719.1 CKL_RS11625 (carbamoyl-phosphate synthase (glutamine-hydrolyzing) 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.30583.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 1523.4 9.5 0 1523.3 9.5 1.0 1 lcl|NCBI__GCF_000016505.1:WP_012102719.1 CKL_RS11625 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012102719.1 CKL_RS11625 carbamoyl-phosphate synthase (glutamine-hydrolyzing) large subu
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1523.3 9.5 0 0 2 1051 .. 3 1042 .. 2 1043 .. 0.99
Alignments for each domain:
== domain 1 score: 1523.3 bits; conditional E-value: 0
TIGR01369 2 kredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePl 68
re++kkvl+iGsGpi+igqAaEFDYsG+qa+ a+k+egie+vLvnsn+At+mtd+++a+k+Y+ePl
lcl|NCBI__GCF_000016505.1:WP_012102719.1 3 LRENLKKVLIIGSGPIIIGQAAEFDYSGTQACEAIKKEGIETVLVNSNPATIMTDKNIAHKTYVEPL 69
5899*************************************************************** PP
TIGR01369 69 tveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkeal 135
tve++e ii++ErpD++l+++GGqtaLnla+el + G+L+ky+v+llG+k e+ik+aedRe Fk+++
lcl|NCBI__GCF_000016505.1:WP_012102719.1 70 TVESLEAIIKRERPDGVLAGFGGQTALNLAMELGKLGILKKYNVELLGIKTESIKNAEDRESFKNLM 136
******************************************************************* PP
TIGR01369 136 keineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikq 202
+ei+e++a s+i+++ e++ ++ +++ +P+i+R+a+tlgGtG+gia+n ee e+++++l+ spi+q
lcl|NCBI__GCF_000016505.1:WP_012102719.1 137 EEIEEPIALSTIATDLEQCKSFLDKVSLPIIIRPAYTLGGTGGGIADNYEEYLEICKNGLEESPINQ 203
******************************************************************* PP
TIGR01369 203 vlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslk 269
+l+e+slagwkE+EyE++RD+kdnc++vcn+EnlDp+G+HtGdsivvaPsqtLtd+eyq+lR +s+k
lcl|NCBI__GCF_000016505.1:WP_012102719.1 204 ILLEQSLAGWKELEYEIMRDKKDNCMVVCNMENLDPVGIHTGDSIVVAPSQTLTDREYQMLRRSSIK 270
******************************************************************* PP
TIGR01369 270 iirelgvegecnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelknd 336
iir+l++eg+cn+qfal+P+ ++y+viEvnpRvsRssALAskA+GyPiAk+aak+a+Gy+Ldelkn
lcl|NCBI__GCF_000016505.1:WP_012102719.1 271 IIRKLKIEGGCNIQFALNPSGNEYMVIEVNPRVSRSSALASKAAGYPIAKIAAKIALGYTLDELKNY 337
******************************************************************* PP
TIGR01369 337 vtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekl 403
vt++++A fEP+lDY+vvk+P+w++dkf++++r+l tqmk++GEvmai+r+fe+al+ka+ sle k+
lcl|NCBI__GCF_000016505.1:WP_012102719.1 338 VTGNSSALFEPALDYCVVKMPKWPFDKFKTANRTLKTQMKATGEVMAIDRSFESALLKAVISLEGKI 404
******************************************************************* PP
TIGR01369 404 lglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklveleke 470
+glkl++ e ++ +++ ++lkk +d+Rlfa+aealr+g+sv+e+ye+tkid++f++ +k+++++e++
lcl|NCBI__GCF_000016505.1:WP_012102719.1 405 VGLKLDKFEDMNLSQIIDKLKKEDDERLFALAEALRKGISVDELYEITKIDKWFIYGVKNIIDMENK 471
******************************************************************* PP
TIGR01369 471 leeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpY 537
l ++ + + +++a +Gf+de i +l++++ +++++lr+ +gi v+k+vDt+++Efeakt+Y
lcl|NCBI__GCF_000016505.1:WP_012102719.1 472 LVSNVP---NVDIIHQAELMGFTDEYICNLMGMKLEDLKQLREVNGIRVVYKMVDTCSGEFEAKTSY 535
*85444...589******************************************************* PP
TIGR01369 538 lYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvstD 604
+Ys y e +d+ ++++kk+lv+GsGpiRigqg+EFDyc+v++v+a+++agy++i+in+nPEtvstD
lcl|NCBI__GCF_000016505.1:WP_012102719.1 536 YYSCYDLE-NDNVISDNKKILVIGSGPIRIGQGIEFDYCCVNGVWAIKKAGYEAIIINNNPETVSTD 601
********.999999999************************************************* PP
TIGR01369 605 ydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdRe 671
+di+d+LyF++l+++dv+++i++ekv+gvivq+gGqtalnl+k+l+++gv++lGts+esid aEdRe
lcl|NCBI__GCF_000016505.1:WP_012102719.1 602 FDISDKLYFDPLYIDDVMNVINEEKVDGVIVQFGGQTALNLSKKLNDRGVNLLGTSFESIDLAEDRE 668
******************************************************************* PP
TIGR01369 672 kFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeave 738
kF ll++l+i+ p g ++ts++ea+++++eigyPv+vRpsyv+gGram++v+n eeleryl+eav+
lcl|NCBI__GCF_000016505.1:WP_012102719.1 669 KFRILLKKLNINSPIGGSVTSLKEAYKLVSEIGYPVIVRPSYVIGGRAMKVVYNPEELERYLKEAVN 735
******************************************************************* PP
TIGR01369 739 vskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkik 805
+ske+Pvl+dky+ + E++vDa++dg++++i+gi+eH+E++GvHsGDs++++p+++l e+v ++i+
lcl|NCBI__GCF_000016505.1:WP_012102719.1 736 LSKEHPVLVDKYIL-GREIEVDAISDGQDLIIPGIMEHVERTGVHSGDSIAIYPASDLPEKVCQRIE 801
*************9.**************************************************** PP
TIGR01369 806 eivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleel 872
e++ +ia+el+vkGlln+q++ +++++yviEvn+RasRtvP++sk+++vp+v++av+v+lgkk++e
lcl|NCBI__GCF_000016505.1:WP_012102719.1 802 EYTVNIARELNVKGLLNVQYAFDGDKIYVIEVNPRASRTVPILSKVTDVPMVEIAVEVMLGKKIKEF 868
******************************************************************* PP
TIGR01369 873 ekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkk 939
++ k s+++avk++vfs +kl gvdv lgpemkstGEv g+++d+++a++ka++a++ +i kk
lcl|NCBI__GCF_000016505.1:WP_012102719.1 869 NYKQDMYKYSNIFAVKMPVFSSKKLPGVDVALGPEMKSTGEVLGVDYDKDKAIYKAFKAAGVEIFKK 935
**9999999********************************************************** PP
TIGR01369 940 gsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaekilellkeee 1006
g++++ ++d+dk + le++kk++++ ++++a++gt k+l+e+gik++++ e++++ +ke++
lcl|NCBI__GCF_000016505.1:WP_012102719.1 936 GNLYVCINDRDKCSSLEVIKKYNSLNFNIIASSGTFKFLKENGIKCSKLS-----IEDAISYIKEDK 997
***********************************************887.....4567889***** PP
TIGR01369 1007 ielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
i++vin+++++ + +++g+k+r+ a+ ++ ++t+++ta +++ a
lcl|NCBI__GCF_000016505.1:WP_012102719.1 998 IDIVINIPTQGYDGTREGFKLRHMALAHDKVVFTCIDTADVYADA 1042
**************************************9998876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1072 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: 00:00:00.08
# Mc/sec: 13.04
//
[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