Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_015930933.1 MNOD_RS20820 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000022085.1:WP_015930933.1
Length = 1157
Score = 1268 bits (3281), Expect = 0.0
Identities = 683/1143 (59%), Positives = 805/1143 (70%), Gaps = 90/1143 (7%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MPKRTDI SILI+GAGPIVIGQACEFDYSG QACKALR EGYR+ILVNSNPATIMTDPE+
Sbjct: 1 MPKRTDISSILIIGAGPIVIGQACEFDYSGTQACKALRAEGYRIILVNSNPATIMTDPEL 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADATY+EPI E+V KIIEKERPDA+LPTMGGQTALNCAL L+R GVL++FGV MIGATA
Sbjct: 61 ADATYVEPITPEIVAKIIEKERPDALLPTMGGQTALNCALSLKRMGVLDQFGVQMIGATA 120
Query: 121 DAIDKAEDRRRFDVAMKKIGL-----------------------------------ETAR 145
+AIDKAEDR F AM KIGL E +
Sbjct: 121 EAIDKAEDRHLFRDAMAKIGLETPRSALANASAAKKADREKYLEEIARIEAAHADPEARK 180
Query: 146 SGIA-------------------HTMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNRE 186
+ +A H + +AL A++G P IIRPSFT+GG+GGGIAYNRE
Sbjct: 181 AALAAFEKKWAAGEADRRKRYGEHALGQALIALAEIGLPAIIRPSFTLGGTGGGIAYNRE 240
Query: 187 EFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGD 246
EF +I RG+D SPT E+LI+ES++GWKEYEMEVVRDK DNCII+CSIEN D MG+HTGD
Sbjct: 241 EFLDIVERGIDASPTNEVLIEESVLGWKEYEMEVVRDKVDNCIIICSIENIDPMGVHTGD 300
Query: 247 SITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEMNPRVSR 306
SITVAPA TLTDKEYQ+MR+AS+AVLREIGVETGGSNVQFA++P GR++VIEMNPRVSR
Sbjct: 301 SITVAPALTLTDKEYQVMRDASIAVLREIGVETGGSNVQFAIDPATGRMVVIEMNPRVSR 360
Query: 307 SSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIPRFNFEK 366
SSALASKATGFPIAKVAAKLAVGYTLDE+ NDITGG TPASFEP+IDYVVTKIPRF FEK
Sbjct: 361 SSALASKATGFPIAKVAAKLAVGYTLDEIANDITGGATPASFEPTIDYVVTKIPRFAFEK 420
Query: 367 FAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFD--PKVSLDDPEALTKI 424
F GA LTT MKSVGE MAIGR ESLQKALR LE G TG D L + I
Sbjct: 421 FPGAEPTLTTSMKSVGEAMAIGRCFAESLQKALRSLETGLTGLDDIEIEGLGKGDDRNAI 480
Query: 425 RRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVGITGL 484
+ L DR+ +A A R G+S V ID WFL Q++ +V LE KV G+
Sbjct: 481 KAALGTPTPDRLLKVAQALRLGVSHAEVHASCRIDPWFLEQLQAIVDLEAKVRRFGLP-T 539
Query: 485 NADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMY 544
N RQLK GF+DARLA LAG EA +R R + PV+KR+DTCAAEFA+ TAYMY
Sbjct: 540 NPGAFRQLKAAGFSDARLAVLAGTDEAAVRAARRALAVRPVFKRIDTCAAEFASPTAYMY 599
Query: 545 STYEEEC------EANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIM 598
STY EA PS DR+K+++LGGGPNRIGQGIEFDYCC HA AL + GYETIM
Sbjct: 600 STYVAPFAGTLADEAQPS-DRKKVVILGGGPNRIGQGIEFDYCCCHACFALADAGYETIM 658
Query: 599 VNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKP----KGVIVQYGGQTPLKLARAL 654
VNCNPETVSTDYDTSDRLYFEP+T EDVLEI+ E+ GVIVQ+GGQTPLKLARAL
Sbjct: 659 VNCNPETVSTDYDTSDRLYFEPLTAEDVLEIIETERQAGTLHGVIVQFGGQTPLKLARAL 718
Query: 655 EAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVV 714
E AGVP++GTSPDAID AEDR++F+ +++L LKQP N ++E + A ++G P VV
Sbjct: 719 EEAGVPILGTSPDAIDLAEDRDQFKRLLDKLHLKQPKNGIAFSVEQSRLVAADLGLPFVV 778
Query: 715 RPSYVLGGRAMEIVYDEADLRRYFQTAV---------------------SVSNDAPVLLD 753
RPSYVLGGRAM I+ DEA Y + +V P+L D
Sbjct: 779 RPSYVLGGRAMAIIRDEAQFADYLLDTLPSLIPSDVKARYPNDKTGQINTVLGKNPLLFD 838
Query: 754 HFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQV 813
+L DA EVDVDA+ DG V I GIMEHIE+AG+HSGDSACSLP +LS E + QQ
Sbjct: 839 RYLTDATEVDVDAVADGRDVFIAGIMEHIEEAGIHSGDSACSLPPRSLSPETIAKLEQQT 898
Query: 814 QKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKS 873
+ LA L V GLMNVQ+A+K+ E+Y++EVNPRA+RTVPFV+K G P+AK+AARVMAG++
Sbjct: 899 RDLALALNVGGLMNVQYAIKDGEIYVLEVNPRASRTVPFVAKVIGEPIAKIAARVMAGEA 958
Query: 874 LAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQL 933
LA G+ + + P+ VKE V PF +FPGVD LLGPEMRSTGEV+G+ R+F AFAK+QL
Sbjct: 959 LASFGLKPKTL-PHIGVKEAVFPFARFPGVDVLLGPEMRSTGEVIGLDRSFGVAFAKSQL 1017
Query: 934 GSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNK 993
GS + + G +SVR+ DK R++ L + GF + AT GT L E G+ +NK
Sbjct: 1018 GSGNQVPSTGTLFVSVRDADKARILPAVRMLAELGFTILATGGTQRFLAENGVAATRINK 1077
Query: 994 VHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMA 1053
V EGRPH+ D IKNGE + NTT G A+ DSR +RR+AL +KV Y TTL G A A
Sbjct: 1078 VLEGRPHVVDAIKNGEIHLVFNTTEGAGALSDSRSLRRAALLHKVPYYTTLAGAMAAAEG 1137
Query: 1054 LNA 1056
+ A
Sbjct: 1138 IRA 1140
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: 3196
Number of extensions: 141
Number of successful extensions: 19
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 4
Length of query: 1073
Length of database: 1157
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1111
Effective search space: 1140997
Effective search space used: 1140997
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_015930933.1 MNOD_RS20820 (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.29721.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 1441.3 0.0 0 1188.7 0.0 2.4 2 lcl|NCBI__GCF_000022085.1:WP_015930933.1 MNOD_RS20820 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000022085.1:WP_015930933.1 MNOD_RS20820 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 249.9 0.0 2.1e-78 2.1e-78 1 152 [. 2 153 .. 2 168 .. 0.95
2 ! 1188.7 0.0 0 0 139 1050 .. 194 1136 .. 177 1138 .. 0.95
Alignments for each domain:
== domain 1 score: 249.9 bits; conditional E-value: 2.1e-78
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePlt 69
pkr+di+++l+iG+GpivigqA+EFDYsG+qa+kal+ eg++++Lvnsn+At+mtd+elad++Y+eP+t
lcl|NCBI__GCF_000022085.1:WP_015930933.1 2 PKRTDISSILIIGAGPIVIGQACEFDYSGTQACKALRAEGYRIILVNSNPATIMTDPELADATYVEPIT 70
689****************************************************************** PP
TIGR01369 70 veavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkei 138
+e+v+kiiekErpDa+l+t+GGqtaLn+a++l+++GvL+++gv+++G++ eai+kaedR++F++a+++i
lcl|NCBI__GCF_000022085.1:WP_015930933.1 71 PEIVAKIIEKERPDALLPTMGGQTALNCALSLKRMGVLDQFGVQMIGATAEAIDKAEDRHLFRDAMAKI 139
********************************************************************* PP
TIGR01369 139 neevakseivesve 152
++e+++s+ ++ +
lcl|NCBI__GCF_000022085.1:WP_015930933.1 140 GLETPRSALANASA 153
*******9987654 PP
== domain 2 score: 1188.7 bits; conditional E-value: 0
TIGR01369 139 neevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlv 205
+ + k+ + +al a +eig+P i+R++ftlgGtG+gia+n+ee+ +ve++++asp+++vl+
lcl|NCBI__GCF_000022085.1:WP_015930933.1 194 EADRRKRYGEHALGQALIALAEIGLPAIIRPSFTLGGTGGGIAYNREEFLDIVERGIDASPTNEVLI 260
5555566666778899999************************************************ PP
TIGR01369 206 ekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiir 272
e+s+ gwkE+E+EvvRD+ dncii+c+iEn+Dp+GvHtGdsi+vaP+ tLtdkeyq +Rdas++++r
lcl|NCBI__GCF_000022085.1:WP_015930933.1 261 EESVLGWKEYEMEVVRDKVDNCIIICSIENIDPMGVHTGDSITVAPALTLTDKEYQVMRDASIAVLR 327
******************************************************************* PP
TIGR01369 273 elgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvt 338
e+gve++ +nvqfa+dP + r+vviE+npRvsRssALAskAtG+PiAkvaaklavGy+Lde+ nd+t
lcl|NCBI__GCF_000022085.1:WP_015930933.1 328 EIGVETGgSNVQFAIDPATGRMVVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEIANDIT 394
*****988*********************************************************** PP
TIGR01369 339 k.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekll 404
+ t+AsfEP++DYvv+kiPr++++kf +++ +l+t+mksvGE maigr f e+lqkalrsle++l+
lcl|NCBI__GCF_000022085.1:WP_015930933.1 395 GgATPASFEPTIDYVVTKIPRFAFEKFPGAEPTLTTSMKSVGEAMAIGRCFAESLQKALRSLETGLT 461
878**************************************************************** PP
TIGR01369 405 g...lklkekea.esdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvel 467
g ++++ + ++++++ al +p+++Rl+ +a+alr gvs ev+ ++id +fle+l+ +v+l
lcl|NCBI__GCF_000022085.1:WP_015930933.1 462 GlddIEIEGLGKgDDRNAIKAALGTPTPDRLLKVAQALRLGVSHAEVHASCRIDPWFLEQLQAIVDL 528
*44444444444144566788999******************************************* PP
TIGR01369 468 ekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeak 534
e ++++ l ++ ++++k+ Gfsd+++a l++++ea+vr++r++l + pv+kr+Dt+aaEf +
lcl|NCBI__GCF_000022085.1:WP_015930933.1 529 EAKVRRFGLP-TNPGAFRQLKAAGFSDARLAVLAGTDEAAVRAARRALAVRPVFKRIDTCAAEFASP 594
*****88887.8999**************************************************** PP
TIGR01369 535 tpYlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktiliny 596
t+Y+Ysty + d+++ +++kkv++lG+Gp+Rigqg+EFDyc+ ha+ al +agy+ti++n+
lcl|NCBI__GCF_000022085.1:WP_015930933.1 595 TAYMYSTYVAPfagtlADEAQPSDRKKVVILGGGPNRIGQGIEFDYCCCHACFALADAGYETIMVNC 661
********987777778999999******************************************** PP
TIGR01369 597 nPEtvstDydiadrLyFeeltvedvldiiekek....vegvivqlgGqtalnlakeleeagvkilGt 659
nPEtvstDyd++drLyFe+lt edvl+iie+e+ +gvivq+gGqt+l+la++leeagv+ilGt
lcl|NCBI__GCF_000022085.1:WP_015930933.1 662 NPETVSTDYDTSDRLYFEPLTAEDVLEIIETERqagtLHGVIVQFGGQTPLKLARALEEAGVPILGT 728
*******************************983333478*************************** PP
TIGR01369 660 saesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameivene 726
s+++id aEdR++F++lld+l++kqpk+ +a sve+ + +a+++g+P +vRpsyvlgGram+i+++e
lcl|NCBI__GCF_000022085.1:WP_015930933.1 729 SPDAIDLAEDRDQFKRLLDKLHLKQPKNGIAFSVEQSRLVAADLGLPFVVRPSYVLGGRAMAIIRDE 795
******************************************************************* PP
TIGR01369 727 eeleryle.....................eavevskekPvlidkyledavEvdvDavadgeevliag 772
+++++yl ++++v ++P+l d+yl+da+EvdvDavadg +v+iag
lcl|NCBI__GCF_000022085.1:WP_015930933.1 796 AQFADYLLdtlpslipsdvkarypndktgQINTVLGKNPLLFDRYLTDATEVDVDAVADGRDVFIAG 862
*****9977788888888888888887777778889******************************* PP
TIGR01369 773 ileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnv 839
i+eHiEeaG+HsGDs+++lpp++ls e+ k++++++++a +l+v Gl+n+q+++kd+e+yv+Evn+
lcl|NCBI__GCF_000022085.1:WP_015930933.1 863 IMEHIEEAGIHSGDSACSLPPRSLSPETIAKLEQQTRDLALALNVGGLMNVQYAIKDGEIYVLEVNP 929
******************************************************************* PP
TIGR01369 840 RasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgp 906
RasRtvPfv+k++g p++k+a++v++g+ l++ + k k+ +++vk+avf+f+++ gvdv+lgp
lcl|NCBI__GCF_000022085.1:WP_015930933.1 930 RASRTVPFVAKVIGEPIAKIAARVMAGEALASFGL---KPKTLPHIGVKEAVFPFARFPGVDVLLGP 993
********************************886...99999************************ PP
TIGR01369 907 emkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyateg 973
em+stGEv+g++r++ a++k++l s++++++ g++++sv+d+dk ++l+++++lae+g++++at g
lcl|NCBI__GCF_000022085.1:WP_015930933.1 994 EMRSTGEVIGLDRSFGVAFAKSQLGSGNQVPSTGTLFVSVRDADKARILPAVRMLAELGFTILATGG 1060
******************************************************************* PP
TIGR01369 974 takvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvt 1040
t+++l+e+g+ a+ ++kv e ++++++++k++ei+lv+n+t+ ++ a +++ ++rr+a+ +kvp+ t
lcl|NCBI__GCF_000022085.1:WP_015930933.1 1061 TQRFLAENGVAATRINKVLEGRPHVVDAIKNGEIHLVFNTTE-GAGALSDSRSLRRAALLHKVPYYT 1126
***************************************987.899999****************** PP
TIGR01369 1041 eletaealle 1050
+l++a+a++e
lcl|NCBI__GCF_000022085.1:WP_015930933.1 1127 TLAGAMAAAE 1136
**99988765 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1157 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: 0.14u 0.03s 00:00:00.17 Elapsed: 00:00:00.16
# Mc/sec: 7.18
//
[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