Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_012758395.1 RLEG_RS14680 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000023185.1:WP_012758395.1
Length = 1162
Score = 1254 bits (3245), Expect = 0.0
Identities = 680/1149 (59%), Positives = 815/1149 (70%), Gaps = 96/1149 (8%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKR DIKSILI+GAGPIVIGQACEFDYSG QACKAL+EEGYRVILVNSNPATIMTDP +
Sbjct: 1 MPKRQDIKSILIIGAGPIVIGQACEFDYSGTQACKALKEEGYRVILVNSNPATIMTDPGL 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADATY+EPI EVV KII KERPDA+LPTMGGQTALN AL L+R GVL+ + V MIGA
Sbjct: 61 ADATYVEPITPEVVAKIIAKERPDALLPTMGGQTALNTALSLKRMGVLDRYNVEMIGAKP 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETARSGIAHT----------------------------- 151
AID AEDR F AM +IGLET RS +A+
Sbjct: 121 AAIDMAEDRALFREAMARIGLETPRSMLANATDIKDLDRKTHEAERIKLRESLSGSDLDK 180
Query: 152 --------------------MEEALAVAAD----VGFPCIIRPSFTMGGSGGGIAYNREE 187
M A+A+AA VG P IIRPSFT+GG+GGGIAYNR E
Sbjct: 181 ALDELENQWNLGESDRKQRYMSHAMAIAAQAIDHVGLPAIIRPSFTLGGTGGGIAYNRSE 240
Query: 188 FEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGDS 247
F EI GLD SPT E+L++ES++GWKEYEMEVVRDK DNCII+CSIEN D MG+HTGDS
Sbjct: 241 FFEIVGGGLDASPTTEVLVEESVLGWKEYEMEVVRDKADNCIIICSIENIDPMGVHTGDS 300
Query: 248 ITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEMNPRVSRS 307
ITVAPA TLTDKEYQIMRNAS+AVLREIGVETGGSNVQFAVNPK+GRL+VIEMNPRVSRS
Sbjct: 301 ITVAPALTLTDKEYQIMRNASIAVLREIGVETGGSNVQFAVNPKDGRLVVIEMNPRVSRS 360
Query: 308 SALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIPRFNFEKF 367
SALASKATGFPIAK+AAKLA+GYTLDEL NDITGG TPASFEPSIDYVVTKIPRF FEKF
Sbjct: 361 SALASKATGFPIAKIAAKLAIGYTLDELDNDITGGATPASFEPSIDYVVTKIPRFAFEKF 420
Query: 368 AGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSL----DDPEALTK 423
GA+ LTT MKSVGEVMAIGRT ESLQKALRGLE G TG D ++ + + +
Sbjct: 421 PGASPVLTTAMKSVGEVMAIGRTFAESLQKALRGLETGLTGLD-EIEIPGFEEGESSQNA 479
Query: 424 IRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVGITG 483
IR + DR+ +A A R G+S V ID WF+ +++ +V +E ++ E G+
Sbjct: 480 IRAAIGTPTPDRLRMVAQALRQGMSEAEVHEGCKIDPWFIAELKAIVEMEARIREHGLP- 538
Query: 484 LNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYM 543
+A LR LK GF+DARLA L G R E+ + R++ ++ PV+KR+DTCAAEFA+ TAYM
Sbjct: 539 QDATNLRMLKAMGFSDARLATLTGKRPKEVAEFRNKLNVRPVFKRIDTCAAEFASPTAYM 598
Query: 544 YSTYE------EECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETI 597
YSTYE EA S DR+K+++LGGGPNRIGQGIEFDYCC HA+ AL++ GYE I
Sbjct: 599 YSTYETPFVGAARSEAEVS-DRKKVVILGGGPNRIGQGIEFDYCCCHAAFALKDAGYEAI 657
Query: 598 MVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPK----GVIVQYGGQTPLKLARA 653
M+NCNPETVSTDYDTSDRLYFEP+T EDV+EI+R E+ K GVIVQ+GGQTPLKLA A
Sbjct: 658 MINCNPETVSTDYDTSDRLYFEPLTAEDVIEILRAEQEKGEVVGVIVQFGGQTPLKLAEA 717
Query: 654 LEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLV 713
LE G+P++GT+PD ID AEDR+RFQ + +L L QP N ++E A A EIG+PLV
Sbjct: 718 LEKNGIPILGTAPDMIDLAEDRDRFQKLLMKLDLNQPNNGIAYSVEQARMVATEIGFPLV 777
Query: 714 VRPSYVLGGRAMEIVYDEADLRRYFQTAV---------------------SVSNDAPVLL 752
VRPSYVLGGRAM+I++ E L+ Y V ++ P+L
Sbjct: 778 VRPSYVLGGRAMQILHSEGQLQSYLLDTVPELVPEDIKQRYPNDKTGQINTLLGKNPLLF 837
Query: 753 DHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQ 812
D +L A+EVDVD + DG V + GIMEHIE+AG+HSGDSACSLP TLS E+ D + +Q
Sbjct: 838 DSYLSHAIEVDVDCLSDGTDVYVAGIMEHIEEAGIHSGDSACSLPPRTLSNEMLDELERQ 897
Query: 813 VQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGK 872
+ +A L V GLMNVQFA+K++ VY++EVNPRA+RTVPFV+K G P+AK+AARVMAG+
Sbjct: 898 AKAMAKALNVGGLMNVQFAIKDDVVYVLEVNPRASRTVPFVAKTIGAPIAKIAARVMAGE 957
Query: 873 SL-AEQGVTKEVIPP----YYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEA 927
L A E P + +VKE V PF +FPGVD LLGPEMRSTGEV+G+ FA A
Sbjct: 958 KLDATFAAYGEKPDPRKLKHIAVKEAVFPFARFPGVDTLLGPEMRSTGEVIGLDTDFALA 1017
Query: 928 FAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGIN 987
FAK+QLG+ + + G +SVR+ DK RV+ L++QGF++ AT GTA LGE GI
Sbjct: 1018 FAKSQLGAGVELPRDGTVFVSVRDADKPRVLPAIHILVEQGFKVLATGGTARFLGENGIT 1077
Query: 988 PRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGG 1047
+NKV EGRPHI+D I+N + +INTT G +AI DS+ +RR+ L KV Y TT+ G
Sbjct: 1078 ATKINKVLEGRPHIEDAIRNRQVQLVINTTDGNKAISDSKSLRRATLMQKVPYYTTMAGA 1137
Query: 1048 FATAMALNA 1056
A A A+ A
Sbjct: 1138 EAAAQAIKA 1146
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: 3247
Number of extensions: 161
Number of successful extensions: 20
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 5
Number of HSP's successfully gapped: 4
Length of query: 1073
Length of database: 1162
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1116
Effective search space: 1146132
Effective search space used: 1146132
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_012758395.1 RLEG_RS14680 (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.23116.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 1454.1 0.0 0 1207.7 0.0 2.5 2 lcl|NCBI__GCF_000023185.1:WP_012758395.1 RLEG_RS14680 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023185.1:WP_012758395.1 RLEG_RS14680 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 243.5 0.0 1.8e-76 1.8e-76 1 151 [. 2 152 .. 2 167 .. 0.97
2 ! 1207.7 0.0 0 0 142 1051 .. 196 1143 .. 178 1144 .. 0.95
Alignments for each domain:
== domain 1 score: 243.5 bits; conditional E-value: 1.8e-76
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePlt 69
pkr+dik++l+iG+GpivigqA+EFDYsG+qa+kalkeeg++v+Lvnsn+At+mtd+ lad++Y+eP+t
lcl|NCBI__GCF_000023185.1:WP_012758395.1 2 PKRQDIKSILIIGAGPIVIGQACEFDYSGTQACKALKEEGYRVILVNSNPATIMTDPGLADATYVEPIT 70
689****************************************************************** PP
TIGR01369 70 veavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkei 138
+e+v+kii kErpDa+l+t+GGqtaLn a++l+++GvL++y+v+++G+k ai+ aedR +F+ea++ i
lcl|NCBI__GCF_000023185.1:WP_012758395.1 71 PEVVAKIIAKERPDALLPTMGGQTALNTALSLKRMGVLDRYNVEMIGAKPAAIDMAEDRALFREAMARI 139
********************************************************************* PP
TIGR01369 139 neevakseivesv 151
++e+++s ++ +
lcl|NCBI__GCF_000023185.1:WP_012758395.1 140 GLETPRSMLANAT 152
*******998765 PP
== domain 2 score: 1207.7 bits; conditional E-value: 0
TIGR01369 142 vakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlveks 208
++ + + ++ a +a++++g+P i+R++ftlgGtG+gia+n++e+ e+v +l+asp+++vlve+s
lcl|NCBI__GCF_000023185.1:WP_012758395.1 196 RKQRYMSHAMAIAAQAIDHVGLPAIIRPSFTLGGTGGGIAYNRSEFFEIVGGGLDASPTTEVLVEES 262
5677889999********************************************************* PP
TIGR01369 209 lagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelg 275
+ gwkE+E+EvvRD++dncii+c+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq++R+as++++re+g
lcl|NCBI__GCF_000023185.1:WP_012758395.1 263 VLGWKEYEMEVVRDKADNCIIICSIENIDPMGVHTGDSITVAPALTLTDKEYQIMRNASIAVLREIG 329
******************************************************************* PP
TIGR01369 276 vege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtk.e 340
ve++ +nvqfa++P++ r+vviE+npRvsRssALAskAtG+PiAk+aakla+Gy+Ldel nd+t+
lcl|NCBI__GCF_000023185.1:WP_012758395.1 330 VETGgSNVQFAVNPKDGRLVVIEMNPRVSRSSALASKATGFPIAKIAAKLAIGYTLDELDNDITGgA 396
**988***********************************************************878 PP
TIGR01369 341 tvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllg.. 405
t+AsfEPs+DYvv+kiPr++++kf +++ l+t mksvGEvmaigrtf e+lqkalr le++l+g
lcl|NCBI__GCF_000023185.1:WP_012758395.1 397 TPASFEPSIDYVVTKIPRFAFEKFPGASPVLTTAMKSVGEVMAIGRTFAESLQKALRGLETGLTGld 463
*****************************************************************44 PP
TIGR01369 406 .lklk..ekeaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelek 469
++++ e+ + s+++++ a+ +p+++Rl ++a+alr+g+s ev+e +kid +f+ +lk +ve+e
lcl|NCBI__GCF_000023185.1:WP_012758395.1 464 eIEIPgfEEGESSQNAIRAAIGTPTPDRLRMVAQALRQGMSEAEVHEGCKIDPWFIAELKAIVEMEA 530
43333113455677888999*********************************************** PP
TIGR01369 470 eleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktp 536
+++e+ l ++ +l+ +k++Gfsd+++a+l++++ +ev + r++l++ pv+kr+Dt+aaEf + t+
lcl|NCBI__GCF_000023185.1:WP_012758395.1 531 RIREHGLP-QDATNLRMLKAMGFSDARLATLTGKRPKEVAEFRNKLNVRPVFKRIDTCAAEFASPTA 596
***88887.7999****************************************************** PP
TIGR01369 537 YlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynP 598
Y+Ystye+ + ++ev+++kkv++lG+Gp+Rigqg+EFDyc+ ha+ al++agy++i+in+nP
lcl|NCBI__GCF_000023185.1:WP_012758395.1 597 YMYSTYETPfvgaaRSEAEVSDRKKVVILGGGPNRIGQGIEFDYCCCHAAFALKDAGYEAIMINCNP 663
******9877777799*************************************************** PP
TIGR01369 599 EtvstDydiadrLyFeeltvedvldiiekek....vegvivqlgGqtalnlakeleeagvkilGtsa 661
EtvstDyd++drLyFe+lt edv++i++ e+ v gvivq+gGqt+l+la++le++g++ilGt +
lcl|NCBI__GCF_000023185.1:WP_012758395.1 664 ETVSTDYDTSDRLYFEPLTAEDVIEILRAEQekgeVVGVIVQFGGQTPLKLAEALEKNGIPILGTAP 730
**************************998872233568***************************** PP
TIGR01369 662 esidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneee 728
+ id aEdR++F+kll +l+++qp++ +a sve+a+ +a+eig+P++vRpsyvlgGram+i+++e +
lcl|NCBI__GCF_000023185.1:WP_012758395.1 731 DMIDLAEDRDRFQKLLMKLDLNQPNNGIAYSVEQARMVATEIGFPLVVRPSYVLGGRAMQILHSEGQ 797
******************************************************************* PP
TIGR01369 729 leryle.....................eavevskekPvlidkyledavEvdvDavadgeevliagil 774
l++yl +++++ ++P+l d yl++a+EvdvD ++dg++v++agi+
lcl|NCBI__GCF_000023185.1:WP_012758395.1 798 LQSYLLdtvpelvpedikqrypndktgQINTLLGKNPLLFDSYLSHAIEVDVDCLSDGTDVYVAGIM 864
****9767788888888888877766556667789******************************** PP
TIGR01369 775 eHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRa 841
eHiEeaG+HsGDs+++lpp++ls+e+++++++++k++ak+l+v Gl+n+qf++kd+ vyv+Evn+Ra
lcl|NCBI__GCF_000023185.1:WP_012758395.1 865 EHIEEAGIHSGDSACSLPPRTLSNEMLDELERQAKAMAKALNVGGLMNVQFAIKDDVVYVLEVNPRA 931
******************************************************************* PP
TIGR01369 842 sRtvPfvskalgvplvklavkvllgkkleelekgvkke...kksklvavkaavfsfsklagvdvvlg 905
sRtvPfv+k++g p++k+a++v++g+kl + + ++ k k++avk+avf+f+++ gvd +lg
lcl|NCBI__GCF_000023185.1:WP_012758395.1 932 SRTVPFVAKTIGAPIAKIAARVMAGEKLDATFAAYGEKpdpRKLKHIAVKEAVFPFARFPGVDTLLG 998
****************************998766555511156799********************* PP
TIGR01369 906 pemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyate 972
pem+stGEv+g+++d++ a++k++l ++ +++++g+v++sv+d+dk ++l++++ l+e+g+kv+at
lcl|NCBI__GCF_000023185.1:WP_012758395.1 999 PEMRSTGEVIGLDTDFALAFAKSQLGAGVELPRDGTVFVSVRDADKPRVLPAIHILVEQGFKVLATG 1065
******************************************************************* PP
TIGR01369 973 gtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplv 1039
gta++l e+gi+a++++kv e +++i +++++++++lvin+t+ ++ka ++++++rr+++++kvp+
lcl|NCBI__GCF_000023185.1:WP_012758395.1 1066 GTARFLGENGITATKINKVLEGRPHIEDAIRNRQVQLVINTTD-GNKAISDSKSLRRATLMQKVPYY 1131
****************************************998.88899999*************** PP
TIGR01369 1040 teletaeallea 1051
t++++aea+++a
lcl|NCBI__GCF_000023185.1:WP_012758395.1 1132 TTMAGAEAAAQA 1143
*******99987 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1162 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: 0.19u 0.03s 00:00:00.22 Elapsed: 00:00:00.21
# Mc/sec: 5.60
//
[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