Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_012972888.1 AZL_RS01400 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000010725.1:WP_012972888.1
Length = 1081
Score = 1281 bits (3315), Expect = 0.0
Identities = 676/1066 (63%), Positives = 806/1066 (75%), Gaps = 14/1066 (1%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDIKSI I+GAGPIVIGQACEFDYSG QACKALREEGYRVILVNSNPATIMTDP +
Sbjct: 1 MPKRTDIKSICIIGAGPIVIGQACEFDYSGVQACKALREEGYRVILVNSNPATIMTDPGL 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADATYIEPI VV KI+EKERPDA+LPTMGGQTALN A+ L G LE GV MIGA
Sbjct: 61 ADATYIEPITPAVVAKILEKERPDALLPTMGGQTALNTAMALSDDGTLERLGVEMIGAKR 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
D I KAEDR F AM K+GLE+ +S + T+ EA+ VG P IIRPSFT+ G+GGG
Sbjct: 121 DVIAKAEDRILFRDAMDKLGLESPKSRMVRTLTEAMDALEFVGLPAIIRPSFTLAGTGGG 180
Query: 181 IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
IAYNR EFE+I GL SP E+LI+ES++GWKEYEMEVVRD DNCII+C+IEN D M
Sbjct: 181 IAYNRAEFEDIVRGGLRASPVGEVLIEESVLGWKEYEMEVVRDGADNCIIICAIENIDPM 240
Query: 241 GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
G+HTGDSITVAP+ TLTDKEYQIMR+AS+AVLREIGV+TGGSNVQFAVNP NGRLIVIEM
Sbjct: 241 GVHTGDSITVAPSLTLTDKEYQIMRDASIAVLREIGVDTGGSNVQFAVNPANGRLIVIEM 300
Query: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
NPRVSRSSALASKATGFPIAK+AAKLAVGY LDEL NDIT G TPASFEP+IDYVVTK+P
Sbjct: 301 NPRVSRSSALASKATGFPIAKIAAKLAVGYRLDELTNDIT-GTTPASFEPTIDYVVTKMP 359
Query: 361 RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
RF FEKF G+ LTT MKSVGE M+IGRT QES+QKALR +E G TGF+ D
Sbjct: 360 RFTFEKFKGSEPLLTTSMKSVGEAMSIGRTFQESVQKALRSMETGLTGFNEVKIGDGNPD 419
Query: 421 LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
T IR L DR+ IA AFR G +V+ V ++ D WFL QI+ +V E + G
Sbjct: 420 RTAIRGALATPTPDRLLVIAQAFRHGFTVEEVQAVSKYDPWFLEQIKAIVDREAAIRADG 479
Query: 481 ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
+ A +L+ LK+ GF+DARLA+LA EA + R + + PVYKR+DTCAAEFA+ T
Sbjct: 480 LPTDKAGWLK-LKQMGFSDARLAELAKTSEAAVATARREAGVTPVYKRIDTCAAEFASAT 538
Query: 541 AYMYSTY------EEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGY 594
YMYSTY E ECEA+P TD+ K+++LGGGPNRIGQGIEFDYCCVHA AL+E G
Sbjct: 539 PYMYSTYETDGTGEAECEADP-TDKRKVVILGGGPNRIGQGIEFDYCCVHAVYALQEAGI 597
Query: 595 ETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGV----IVQYGGQTPLKL 650
ETIMVNCNPETVSTDYDT+DRLYFEP+T EDV+E+VR+E+ G IVQ+GGQTPLKL
Sbjct: 598 ETIMVNCNPETVSTDYDTADRLYFEPLTAEDVVELVRVEQRNGTVLGCIVQFGGQTPLKL 657
Query: 651 ARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGY 710
A ALEAAG+P++GTSPDAID AEDRERFQ + L LKQPAN ++E A A IG+
Sbjct: 658 AAALEAAGIPILGTSPDAIDLAEDRERFQKLLHELALKQPANGLARSLEEAEAVASRIGF 717
Query: 711 PLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDG 770
P+V+RPSYVLGGRAMEIV+D A L+RY TAV VS PVL+D +L DA+EVDVD +CDG
Sbjct: 718 PVVIRPSYVLGGRAMEIVHDMAGLQRYMGTAVQVSGKNPVLIDSYLQDAIEVDVDVVCDG 777
Query: 771 EMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQF 830
E V + G+MEHIE+AG+HSGDSAC+LP Y+L E + +Q LA L+V GLMNVQF
Sbjct: 778 ETVYVAGVMEHIEEAGIHSGDSACALPPYSLPAETIAEINRQSDALARALKVVGLMNVQF 837
Query: 831 AVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSV 890
AV+ VY++EVNPRA+RTVPFV+KATG +AK+AARVMAG++L+ + PP+ +V
Sbjct: 838 AVQAGTVYILEVNPRASRTVPFVAKATGTAIAKIAARVMAGEALSSFTLNGP-NPPHTAV 896
Query: 891 KEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVR 950
KE V PF +FPGVD +LGPEM+STGEVMG+ FA AFAKAQLG+ T+ G +SV+
Sbjct: 897 KEAVFPFARFPGVDIVLGPEMKSTGEVMGLDHNFALAFAKAQLGAGVTLPVKGCVFVSVK 956
Query: 951 EGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEY 1010
+ DK + ++ KL + GF + AT GTA VL +AG+ +VNKV EG+PHI D + NG+
Sbjct: 957 DHDKPALAIISKKLHEMGFRILATSGTAKVLKDAGVEAEVVNKVVEGKPHIVDAMINGDV 1016
Query: 1011 TYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNA 1056
+INTT G +A+ DS +RR+AL Y + Y TT+ G A A+ A
Sbjct: 1017 HLVINTTEGAQALSDSFSLRRTALTYNIPYYTTVAGARAAVEAIAA 1062
Lambda K H
0.318 0.135 0.383
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: 3060
Number of extensions: 130
Number of successful extensions: 17
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: 1073
Length of database: 1081
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1035
Effective search space: 1062945
Effective search space used: 1062945
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 (21.7 bits)
S2: 58 (26.9 bits)
Align candidate WP_012972888.1 AZL_RS01400 (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.5706.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 1505.1 0.0 0 1504.9 0.0 1.0 1 lcl|NCBI__GCF_000010725.1:WP_012972888.1 AZL_RS01400 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000010725.1:WP_012972888.1 AZL_RS01400 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1504.9 0.0 0 0 1 1051 [. 2 1059 .. 2 1060 .. 0.97
Alignments for each domain:
== domain 1 score: 1504.9 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+dik++ +iG+GpivigqA+EFDYsG qa+kal+eeg++v+Lvnsn+At+mtd+ lad++YieP
lcl|NCBI__GCF_000010725.1:WP_012972888.1 2 PKRTDIKSICIIGAGPIVIGQACEFDYSGVQACKALREEGYRVILVNSNPATIMTDPGLADATYIEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
+t+++v+ki+ekErpDa+l+t+GGqtaLn a+ l++ G Le+ gv+++G+k ++i+kaedR +F++a
lcl|NCBI__GCF_000010725.1:WP_012972888.1 69 ITPAVVAKILEKERPDALLPTMGGQTALNTAMALSDDGTLERLGVEMIGAKRDVIAKAEDRILFRDA 135
******************************************************************* PP
TIGR01369 135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201
++++++e +ks++v++ +ea++a e +g+P i+R++ftl+GtG+gia+n++e++ +v+ +l+asp+
lcl|NCBI__GCF_000010725.1:WP_012972888.1 136 MDKLGLESPKSRMVRTLTEAMDALEFVGLPAIIRPSFTLAGTGGGIAYNRAEFEDIVRGGLRASPVG 202
******************************************************************* PP
TIGR01369 202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268
+vl+e+s+ gwkE+E+EvvRD +dncii+c+iEn+Dp+GvHtGdsi+vaPs tLtdkeyq++Rdas+
lcl|NCBI__GCF_000010725.1:WP_012972888.1 203 EVLIEESVLGWKEYEMEVVRDGADNCIIICAIENIDPMGVHTGDSITVAPSLTLTDKEYQIMRDASI 269
******************************************************************* PP
TIGR01369 269 kiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelk 334
+++re+gv+++ +nvqfa++P + r++viE+npRvsRssALAskAtG+PiAk+aaklavGy Ldel+
lcl|NCBI__GCF_000010725.1:WP_012972888.1 270 AVLREIGVDTGgSNVQFAVNPANGRLIVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYRLDELT 336
********9988******************************************************* PP
TIGR01369 335 ndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrslee 401
nd+t++t+AsfEP++DYvv+k+Pr+ ++kf++ + l+t+mksvGE m+igrtf+e++qkalrs+e+
lcl|NCBI__GCF_000010725.1:WP_012972888.1 337 NDITGTTPASFEPTIDYVVTKMPRFTFEKFKGSEPLLTTSMKSVGEAMSIGRTFQESVQKALRSMET 403
******************************************************************* PP
TIGR01369 402 kllglklkeke..aesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklve 466
+l+g+++ + + ++++++ al +p+++Rl++ia+a+r+g++veev ++k+d +fle++k +v+
lcl|NCBI__GCF_000010725.1:WP_012972888.1 404 GLTGFNEVKIGdgNPDRTAIRGALATPTPDRLLVIAQAFRHGFTVEEVQAVSKYDPWFLEQIKAIVD 470
****8876544114456778899******************************************** PP
TIGR01369 467 lekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfea 533
e +++ l ++k + k+k++Gfsd+++a+l+k+sea+v ++r+e+g++pv+kr+Dt+aaEf +
lcl|NCBI__GCF_000010725.1:WP_012972888.1 471 REAAIRADGLP-TDKAGWLKLKQMGFSDARLAELAKTSEAAVATARREAGVTPVYKRIDTCAAEFAS 536
*****977776.8999999************************************************ PP
TIGR01369 534 ktpYlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilin 595
+tpY+Ystye++ + +++ t+k+kv++lG+Gp+Rigqg+EFDyc+vhav al+eag++ti++n
lcl|NCBI__GCF_000010725.1:WP_012972888.1 537 ATPYMYSTYETDgtgeaECEADPTDKRKVVILGGGPNRIGQGIEFDYCCVHAVYALQEAGIETIMVN 603
**********98766555567778899**************************************** PP
TIGR01369 596 ynPEtvstDydiadrLyFeeltvedvldiiekekve....gvivqlgGqtalnlakeleeagvkilG 658
+nPEtvstDyd+adrLyFe+lt edv+++++ e+ + g+ivq+gGqt+l+la +le+ag++ilG
lcl|NCBI__GCF_000010725.1:WP_012972888.1 604 CNPETVSTDYDTADRLYFEPLTAEDVVELVRVEQRNgtvlGCIVQFGGQTPLKLAAALEAAGIPILG 670
*******************************998662222689************************ PP
TIGR01369 659 tsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiven 725
ts+++id aEdRe+F+kll+el +kqp++ a+s+eea+ +a++ig+Pv++RpsyvlgGrameiv++
lcl|NCBI__GCF_000010725.1:WP_012972888.1 671 TSPDAIDLAEDRERFQKLLHELALKQPANGLARSLEEAEAVASRIGFPVVIRPSYVLGGRAMEIVHD 737
******************************************************************* PP
TIGR01369 726 eeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlp 792
++ l+ry+ +av+vs ++Pvlid yl+da+EvdvD+v+dge+v++ag++eHiEeaG+HsGDs++ lp
lcl|NCBI__GCF_000010725.1:WP_012972888.1 738 MAGLQRYMGTAVQVSGKNPVLIDSYLQDAIEVDVDVVCDGETVYVAGVMEHIEEAGIHSGDSACALP 804
******************************************************************* PP
TIGR01369 793 pqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvkl 859
p +l +e+ +i+++++++a++lkv+Gl+n+qf+v+ ++vy++Evn+RasRtvPfv+ka+g ++k+
lcl|NCBI__GCF_000010725.1:WP_012972888.1 805 PYSLPAETIAEINRQSDALARALKVVGLMNVQFAVQAGTVYILEVNPRASRTVPFVAKATGTAIAKI 871
******************************************************************* PP
TIGR01369 860 avkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeall 926
a++v++g+ l++ + + +++ + avk+avf+f+++ gvd+vlgpemkstGEvmg++++++ a++
lcl|NCBI__GCF_000010725.1:WP_012972888.1 872 AARVMAGEALSSFTL---NGPNPPHTAVKEAVFPFARFPGVDIVLGPEMKSTGEVMGLDHNFALAFA 935
************775...899999******************************************* PP
TIGR01369 927 kallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevvlkvse 993
ka+l ++ +++ kg v++svkd+dk +l + kkl+e+g++++at+gtakvl++ag++aevv+kv e
lcl|NCBI__GCF_000010725.1:WP_012972888.1 936 KAQLGAGVTLPVKGCVFVSVKDHDKPALAIISKKLHEMGFRILATSGTAKVLKDAGVEAEVVNKVVE 1002
******************************************************************* PP
TIGR01369 994 eaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaeallea 1051
+++i++++ +++++lvin+t+ +++a ++++++rr+a++y++p+ t++++a+a++ea
lcl|NCBI__GCF_000010725.1:WP_012972888.1 1003 GKPHIVDAMINGDVHLVINTTE-GAQALSDSFSLRRTALTYNIPYYTTVAGARAAVEA 1059
*******************997.8889999***********************99987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1081 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: 12.28
//
[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