Align Carbamoyl-phosphate synthase pyrimidine-specific large chain; Carbamoyl-phosphate synthetase ammonia chain; EC 6.3.5.5 (characterized)
to candidate WP_015738405.1 ADEG_RS01870 carbamoyl-phosphate synthase large subunit
Query= SwissProt::P25994
(1071 letters)
>NCBI__GCF_000024605.1:WP_015738405.1
Length = 1075
Score = 1318 bits (3411), Expect = 0.0
Identities = 655/1054 (62%), Positives = 831/1054 (78%), Gaps = 5/1054 (0%)
Query: 1 MPKRVDINKILVIGSGPIIIGQAAEFDYAGTQACLALKEEGYEVILVNSNPATIMTDTEM 60
MP+R D+ K++VIGSGPIIIGQAAEFDY+GTQAC AL+EEG EV+LVNSNPATIMTD M
Sbjct: 1 MPRRKDLKKVMVIGSGPIIIGQAAEFDYSGTQACRALREEGLEVVLVNSNPATIMTDPNM 60
Query: 61 ADRVYIEPLTPEFLTRIIRKERPDAILPTLGGQTGLNLAVELSERGVLAECGVEVLGTKL 120
ADRVYIEPLTPEF+ +++RKERPD +LPTLGGQ GLNLAVELS GVL E GVE+LGT L
Sbjct: 61 ADRVYIEPLTPEFVAKVLRKERPDGLLPTLGGQVGLNLAVELSRMGVLDELGVELLGTPL 120
Query: 121 SAIQQAEDRDLFRTLMNELNEPVPESEIIHSLEEAEKFVSQIGFPVIVRPAYTLGGTGGG 180
I++AEDR+LF+ M + EP+PES I+ LE+A F +IGFPV+VRPAYTLGGTGGG
Sbjct: 121 ETIEKAEDRELFKETMRAIGEPIPESRIVSRLEDAVSFAREIGFPVVVRPAYTLGGTGGG 180
Query: 181 ICSNETELKEIVENGLKLSPVHQCLLEKSIAGYKEIEYEVMRDSQDHAIVVCNMENIDPV 240
I NE EL EI GLK S + Q L+E+ ++G+KEIE+EVMRD D+ I VC MEN+DP+
Sbjct: 181 IARNEEELLEIAARGLKHSLIGQILVEQCVSGWKEIEFEVMRDGADNCITVCCMENLDPM 240
Query: 241 GIHTGDSIVVAPSQTLSDREYQLLRNVSLKLIRALGIEGGCNVQLALDPDSFQYYIIEVN 300
GIHTGDSIVVAPSQTL+D+EYQ+LR ++K+IRALGI GGCN+Q ALDP S +YY+IEVN
Sbjct: 241 GIHTGDSIVVAPSQTLTDKEYQMLRRAAIKIIRALGIRGGCNIQFALDPRSLRYYVIEVN 300
Query: 301 PRVSRSSALASKATGYPIAKLAAKIAVGLSLDEMMNPVTGKTYAAFEPALDYVVSKIPRW 360
PRVSRSSALASKATGYPIAK+AAKIAVGL LDE+ N VTGKT A FEP++DYVV K PRW
Sbjct: 301 PRVSRSSALASKATGYPIAKVAAKIAVGLRLDEIQNAVTGKTTACFEPSIDYVVVKFPRW 360
Query: 361 PFDKFESANRKLGTQMKATGEVMAIGRTLEESLLKAVRSLEADVYHLELKDAADISDELL 420
PFDKF ANR LGTQMK+TGEVMAIGRT EE+LLKAVRSLE ++ L L +A SD +
Sbjct: 361 PFDKFALANRVLGTQMKSTGEVMAIGRTFEEALLKAVRSLEIGLHGLVLPEAERFSDMEI 420
Query: 421 EKRIKKAGDERLFYLAEAYRRGYTVEDLHEFSAIDVFFLHKLFGIVQFEKELKANAG--- 477
E +++ DERLF +AEA RRGY V + SAID +FL ++ +V+FE+ L+ AG
Sbjct: 421 ESKLESPTDERLFVVAEALRRGYPVSKVASLSAIDPWFLERIKRLVEFEEALR-RAGKEL 479
Query: 478 DTDVLRRAKELGFSDQYISREWKMKESELYSLRKQAGIAPVFKMVDTCAAEFESETPYFY 537
D ++LR+AK LGFSD+ I+ + E + RK GI PV+KMVDTCAAEFE+ TPY+Y
Sbjct: 480 DPEILRQAKTLGFSDRTIAEFTGLPEDVVREKRKVWGIKPVYKMVDTCAAEFEAATPYYY 539
Query: 538 STYEEENESVVTDKKSVMVLGSGPIRIGQGVEFDYATVHSVWAIKQAGYEAIIVNNNPET 597
STYE+E+E+ + + V+VLGSGPIRIGQG+EFDY +VH VWA+++ G +AII+NNNPET
Sbjct: 540 STYEQEDEAPALEGRKVVVLGSGPIRIGQGIEFDYCSVHCVWALREEGIKAIIINNNPET 599
Query: 598 VSTDFSISDKLYFEPLTIEDVMHIIDLEQPMGVVVQFGGQTAINLADELSARGVKILGTS 657
VSTDF +D+LYFEPL EDV+++++ E+P GV+VQFGGQTAINLA L+A G KILGT+
Sbjct: 600 VSTDFDTADRLYFEPLVAEDVLNVLEKEKPEGVLVQFGGQTAINLAKPLAAAGFKILGTA 659
Query: 658 LEDLDRAEDRDKFEQALGELGVPQPLGKTATSVNQAVSIASDIGYPVLVRPSYVLGGRAM 717
+ED+DRAEDR+KF++ L +P+P G A S +A+++A +G+PVLVRPSYVLGGRAM
Sbjct: 660 VEDIDRAEDREKFDRVLEAENIPRPPGGAAKSPEEALAVAERVGFPVLVRPSYVLGGRAM 719
Query: 718 EIVYHEEELLHYMKNAVKINPQHPVLIDRYLTGKEIEVDAVSDGETVVIPGIMEHIERAG 777
EIVY+ EEL YM+ A +++P++PVL+D+Y+ GKE+EVDA+SDGE V+IPGIMEHIERAG
Sbjct: 720 EIVYNREELEEYMRFAARVSPEYPVLVDKYIFGKEVEVDAISDGEDVLIPGIMEHIERAG 779
Query: 778 VHSGDSIAVYPPQSLTEDIKKKIEQYTIALAKGLNIVGLLNIQFVL-SQGEVYVLEVNPR 836
+HSGDSIAVYPP++L ++ +++ YT ALA+ L + GLLNIQ+V+ ++G+VYVLEVNPR
Sbjct: 780 IHSGDSIAVYPPRTLNGEVVEQVVSYTTALARALRVRGLLNIQYVVDAEGKVYVLEVNPR 839
Query: 837 SSRTVPFLSKITGIPMANLATKIILGQKLAAFGYTEGLQPEQQGVFVKAPVFSFAKLRRV 896
+SRTVP+LSKITGIPM LA K+ILG+KL GY GL + +K PVFSFAKL V
Sbjct: 840 ASRTVPYLSKITGIPMIPLAVKVILGKKLKELGYGTGLYRGGRYFGIKVPVFSFAKLLDV 899
Query: 897 DITLGPEMKSTGEVMGKDSTLEKALYKALIASGIQIPNYGSVLLTVADKDKEEGLAIAKR 956
D++LGPEMKSTGEVMG ALYK +A+G P G+VL+TV+D+DKEE L + K
Sbjct: 900 DVSLGPEMKSTGEVMGVAEDFAAALYKGCVAAGYAFPEKGAVLVTVSDRDKEEALPLVKE 959
Query: 957 FHAIGYNILATEGTAGYLKEASIPAKVVGKIGQDGPNLLDVIRNGEAQFVINTLTKGKQP 1016
+G+ ILAT GTA L A +P + V K+ + PN++D++R G+ Q V+NTLTKG++P
Sbjct: 960 LARLGFKILATSGTARMLSAAGVPVETVKKLHEGSPNIIDLLRAGKIQMVLNTLTKGRRP 1019
Query: 1017 ARDGFRIRRESVENGVACLTSLDTAEAILRVLES 1050
R+GFRIRR +VE G+ C+TSLDT A++ V+ +
Sbjct: 1020 EREGFRIRRTAVELGIPCITSLDTMRAVVEVMRA 1053
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: 3024
Number of extensions: 111
Number of successful extensions: 13
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: 1075
Length adjustment: 45
Effective length of query: 1026
Effective length of database: 1030
Effective search space: 1056780
Effective search space used: 1056780
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_015738405.1 ADEG_RS01870 (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.12794.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 1604.3 0.0 0 1604.1 0.0 1.0 1 lcl|NCBI__GCF_000024605.1:WP_015738405.1 ADEG_RS01870 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015738405.1 ADEG_RS01870 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1604.1 0.0 0 0 1 1051 [. 2 1050 .. 2 1051 .. 0.99
Alignments for each domain:
== domain 1 score: 1604.1 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
p+r+d+kkv+viGsGpi+igqAaEFDYsG+qa++al+eeg+evvLvnsn+At+mtd+++ad+vYieP
lcl|NCBI__GCF_000024605.1:WP_015738405.1 2 PRRKDLKKVMVIGSGPIIIGQAAEFDYSGTQACRALREEGLEVVLVNSNPATIMTDPNMADRVYIEP 68
5799*************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
lt+e+v+k+++kErpD++l+tlGGq +Lnlavel+++GvL++ gv+llGt++e+i+kaedRe+Fke+
lcl|NCBI__GCF_000024605.1:WP_015738405.1 69 LTPEFVAKVLRKERPDGLLPTLGGQVGLNLAVELSRMGVLDELGVELLGTPLETIEKAEDRELFKET 135
******************************************************************* PP
TIGR01369 135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201
++ i+e++++s+iv++ e+a+++a+eig+Pv+vR+a+tlgGtG+gia+neeel e+++++lk+s i
lcl|NCBI__GCF_000024605.1:WP_015738405.1 136 MRAIGEPIPESRIVSRLEDAVSFAREIGFPVVVRPAYTLGGTGGGIARNEEELLEIAARGLKHSLIG 202
******************************************************************* PP
TIGR01369 202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268
q+lve+ + gwkEiE+Ev+RD +dnci+vc++EnlDp+G+HtGdsivvaPsqtLtdkeyq+lR a++
lcl|NCBI__GCF_000024605.1:WP_015738405.1 203 QILVEQCVSGWKEIEFEVMRDGADNCITVCCMENLDPMGIHTGDSIVVAPSQTLTDKEYQMLRRAAI 269
******************************************************************* PP
TIGR01369 269 kiirelgvegecnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkn 335
kiir+lg+ g+cn+qfaldP+s ry+viEvnpRvsRssALAskAtGyPiAkvaak+avG+ Lde++n
lcl|NCBI__GCF_000024605.1:WP_015738405.1 270 KIIRALGIRGGCNIQFALDPRSLRYYVIEVNPRVSRSSALASKATGYPIAKVAAKIAVGLRLDEIQN 336
******************************************************************* PP
TIGR01369 336 dvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleek 402
vt++t+A+fEPs+DYvvvk+Prw++dkf+ ++r lgtqmks+GEvmaigrtfeeal+ka+rsle++
lcl|NCBI__GCF_000024605.1:WP_015738405.1 337 AVTGKTTACFEPSIDYVVVKFPRWPFDKFALANRVLGTQMKSTGEVMAIGRTFEEALLKAVRSLEIG 403
******************************************************************* PP
TIGR01369 403 llglklkekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelek 469
l+gl l+e+e sd+e+e++l++p+d+Rlf++aealrrg+ v +v l+ id +fle++k+lve+e+
lcl|NCBI__GCF_000024605.1:WP_015738405.1 404 LHGLVLPEAERFSDMEIESKLESPTDERLFVVAEALRRGYPVSKVASLSAIDPWFLERIKRLVEFEE 470
******************************************************************* PP
TIGR01369 470 eleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktp 536
+l+ + kel+ e l++ak+lGfsd++ia++++ e+ vr+ rk gi pv+k+vDt+aaEfea+tp
lcl|NCBI__GCF_000024605.1:WP_015738405.1 471 ALR-RAGKELDPEILRQAKTLGFSDRTIAEFTGLPEDVVREKRKVWGIKPVYKMVDTCAAEFEAATP 536
**8.77888********************************************************** PP
TIGR01369 537 YlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPEtvst 603
Y+Ystye+e d+++ e +kv+vlGsGpiRigqg+EFDyc+vh+v+alre+g+k+i+in+nPEtvst
lcl|NCBI__GCF_000024605.1:WP_015738405.1 537 YYYSTYEQE-DEAPALEGRKVVVLGSGPIRIGQGIEFDYCSVHCVWALREEGIKAIIINNNPETVST 602
*********.99******************************************************* PP
TIGR01369 604 DydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGtsaesidraEdR 670
D+d+adrLyFe+l edvl+++ekek+egv+vq+gGqta+nlak l++ag kilGt +e+idraEdR
lcl|NCBI__GCF_000024605.1:WP_015738405.1 603 DFDTADRLYFEPLVAEDVLNVLEKEKPEGVLVQFGGQTAINLAKPLAAAGFKILGTAVEDIDRAEDR 669
******************************************************************* PP
TIGR01369 671 ekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeav 737
ekF+++l+ +i++p g +a+s eea +a+++g+PvlvRpsyvlgGrameiv+n+eele+y++ a+
lcl|NCBI__GCF_000024605.1:WP_015738405.1 670 EKFDRVLEAENIPRPPGGAAKSPEEALAVAERVGFPVLVRPSYVLGGRAMEIVYNREELEEYMRFAA 736
******************************************************************* PP
TIGR01369 738 evskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkki 804
+vs+e+Pvl+dky+ ++Ev+vDa++dge+vli+gi+eHiE+aG+HsGDs++v+pp++l+ ev++++
lcl|NCBI__GCF_000024605.1:WP_015738405.1 737 RVSPEYPVLVDKYIF-GKEVEVDAISDGEDVLIPGIMEHIERAGIHSGDSIAVYPPRTLNGEVVEQV 802
**************9.*************************************************** PP
TIGR01369 805 keivkkiakelkvkGllniqfvvkd.eevyviEvnvRasRtvPfvskalgvplvklavkvllgkkle 870
++++++a++l+v+Gllniq+vv+ ++vyv+Evn+RasRtvP++sk++g+p++ lavkv+lgkkl+
lcl|NCBI__GCF_000024605.1:WP_015738405.1 803 VSYTTALARALRVRGLLNIQYVVDAeGKVYVLEVNPRASRTVPYLSKITGIPMIPLAVKVILGKKLK 869
***********************9879**************************************** PP
TIGR01369 871 elekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakik 937
el++g +++++k++vfsf+kl +vdv lgpemkstGEvmg+++d++ al+k ++a+++ ++
lcl|NCBI__GCF_000024605.1:WP_015738405.1 870 ELGYGTGLYRGGRYFGIKVPVFSFAKLLDVDVSLGPEMKSTGEVMGVAEDFAAALYKGCVAAGYAFP 936
******************************************************************* PP
TIGR01369 938 kkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvseeaekilellke 1004
+kg vl++v+d+dkee+l+l+k+la++g+k++at+gta++l+ ag+ +e+v+k +e +++i++ll++
lcl|NCBI__GCF_000024605.1:WP_015738405.1 937 EKGAVLVTVSDRDKEEALPLVKELARLGFKILATSGTARMLSAAGVPVETVKKLHEGSPNIIDLLRA 1003
******************************************************************* PP
TIGR01369 1005 eeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
++i++v+n+ +k+++ +++g++irr+ave ++p++t+l+t++a++e+
lcl|NCBI__GCF_000024605.1:WP_015738405.1 1004 GKIQMVLNTLTKGRRPEREGFRIRRTAVELGIPCITSLDTMRAVVEV 1050
*******************************************9987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1075 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: 00:00:00.10
# Mc/sec: 10.75
//
[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