Align Carbamoyl-phosphate synthase pyrimidine-specific large chain; Carbamoyl-phosphate synthetase ammonia chain; EC 6.3.5.5 (characterized)
to candidate WP_011159606.1 TX73_RS20760 carbamoyl-phosphate synthase large subunit
Query= SwissProt::P25994
(1071 letters)
>NCBI__GCF_000195775.1:WP_011159606.1
Length = 1109
Score = 967 bits (2499), Expect = 0.0
Identities = 526/1089 (48%), Positives = 729/1089 (66%), Gaps = 51/1089 (4%)
Query: 1 MPKRVDINKILVIGSGPIIIGQAAEFDYAGTQACLALKEEGYEVILVNSNPATIMTDTEM 60
MPKR DI+ IL+IG+GPI+IGQA EFDY+GTQA ALK+EGY V+LVNSNPATIMTD E+
Sbjct: 1 MPKRTDISTILIIGAGPIVIGQACEFDYSGTQAVKALKQEGYRVVLVNSNPATIMTDPEL 60
Query: 61 ADRVYIEPLTPEFLTRIIRKER-----PDAILPTLGGQTGLNLAVELSERGVLAECGVEV 115
AD YIEP+TPE + +II KER A+LPT+GGQT LN A+ L + G L + VE+
Sbjct: 61 ADATYIEPITPEIVAKIIEKERYVIPGGFALLPTMGGQTALNCALSLRKLGTLEKFDVEM 120
Query: 116 LGTKLSAIQQAEDRDLFRTLMNELNEPVPESEIIHSLEEAEKFVSQIGFPVIVRPAYTLG 175
+G AI +AEDR+ FR M ++ P S + SL +A + + +IGFP ++RP++T+G
Sbjct: 121 IGATADAIDKAEDRERFREAMTKIGLETPNSRQVKSLPDALRALDEIGFPALIRPSFTMG 180
Query: 176 GTGGGICSNETELKEIVENGLKLSPVHQCLLEKSIAGYKEIEYEVMRDSQDHAIVVCNME 235
GTGGGI + E EIVE G+ SP ++ L+E+SI G+KE E EV+RD D+ I+VC++E
Sbjct: 181 GTGGGIAYTKAEFIEIVERGIDASPTNEVLIEESILGWKEYEMEVVRDKHDNCIIVCSIE 240
Query: 236 NIDPVGIHTGDSIVVAPSQTLSDREYQLLRNVSLKLIRALGIE-GGCNVQLALDPDSFQY 294
N+DP+G+HTGDSI VAP+ TL+D+EYQ++R+ SL ++R +G+E GG NVQ A++PD +
Sbjct: 241 NLDPMGVHTGDSITVAPALTLTDKEYQIMRDASLAVLREIGVETGGSNVQFAVNPDDGRL 300
Query: 295 YIIEVNPRVSRSSALASKATGYPIAKLAAKIAVGLSLDEMMNPVT-GKTYAAFEPALDYV 353
+IE+NPRVSRSSALASKATG+PIAK+AAK+AVG SLDE+ N +T G T A+FEP +DYV
Sbjct: 301 VVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYSLDEIANDITGGATPASFEPTIDYV 360
Query: 354 VSKIPRWPFDKFESANRKLGTQMKATGEVMAIGRTLEESLLKAVRSLEADVYHLELKDAA 413
V+KIPR+ F+KF A+ L T MK+ GEVMAIGRT +ESL KA+R LE+ + L+ +
Sbjct: 361 VTKIPRFAFEKFPGASPTLTTAMKSVGEVMAIGRTFQESLQKALRGLESGLTGLDEIEID 420
Query: 414 DISDELLEKRIKKA----GDERLFYLAEAYRRGYTVEDLHEFSAIDVFFLHKLFGIVQFE 469
+ + I+ A RL +A+A R G++ E++ ID +FL +L GIV E
Sbjct: 421 GLGRGDDKNAIRAALGTPTPSRLLQVAQAMRLGWSNEEIFNSCKIDPWFLAQLRGIVDME 480
Query: 470 KELKANAGDTD---VLRRAKELGFSDQYISREWKMKESELYSLRKQAGIAPVFKMVDTCA 526
++ AG D +R K +GFSD ++ E+E+ + R+ G+ PVFK +DTCA
Sbjct: 481 ARVR-EAGLPDHAFGMRTLKAMGFSDARLAVLADTTEAEVKAKRRALGVRPVFKRIDTCA 539
Query: 527 AEFESETPYFYSTYEE------ENESVVTDKKSVMVLGSGPIRIGQGVEFDYATVHSVWA 580
AEF S T Y YSTYE +ES +DK+ V++LG GP RIGQG+EFDY H+ +A
Sbjct: 540 AEFASPTAYMYSTYESPFAGPASDESRPSDKQKVIILGGGPNRIGQGIEFDYCCCHACFA 599
Query: 581 IKQAGYEAIIVNNNPETVSTDFSISDKLYFEPLTIEDVMHIIDLEQP----MGVVVQFGG 636
+ AGYE+I+VN NPETVSTD+ +D+LYFEPLT EDV+ IID E+ GV+VQFGG
Sbjct: 600 LHDAGYESIMVNCNPETVSTDYDTADRLYFEPLTGEDVLEIIDTERSNGTLRGVIVQFGG 659
Query: 637 QTAINLADELSARGVKILGTSLEDLDRAEDRDKFEQALGELGVPQPLGKTATSVNQAVSI 696
QT + LA L A V ILGTS + +D AEDRD+F++ L +L + QP A SV QA +
Sbjct: 660 QTPLKLARALEAADVPILGTSPDAIDLAEDRDRFKRILDKLRLKQPKNGIAYSVEQARLV 719
Query: 697 ASDIGYPVLVRPSYVLGGRAMEIVYHEEELLHYMKNAV------------------KINP 738
A+++G P++VRPSYVLGGRAM+I+ + +L Y+ + +IN
Sbjct: 720 AAELGLPLVVRPSYVLGGRAMQIIREDNQLSDYLLGTLPELVPGDVKARYPNDKTGQINT 779
Query: 739 ---QHPVLIDRYLT-GKEIEVDAVSDGETVVIPGIMEHIERAGVHSGDSIAVYPPQSLTE 794
+P+L DRYL+ E++VD +SDG+ I GIMEHIE AG+HSGDS PP SL+
Sbjct: 780 VLGTNPLLFDRYLSDATEVDVDCLSDGKDTFIVGIMEHIEEAGIHSGDSACSLPPHSLSA 839
Query: 795 DIKKKIEQYTIALAKGLNIVGLLNIQFVLSQGEVYVLEVNPRSSRTVPFLSKITGIPMAN 854
+ ++E+ T LA GL++VGL+N+Q+ + GE+YVLEVNPR+SRTVPF++K+ G+P+A
Sbjct: 840 ETIAELERQTRELALGLDVVGLMNVQYAIKDGEIYVLEVNPRASRTVPFVAKVIGMPVAK 899
Query: 855 LATKIILGQKLAAFGYTEGLQPEQQGVFVKAPVFSFAKLRRVDITLGPEMKSTGEVMGKD 914
LA +I+ G+K+A G + V VK VF FA+ VD LGPEM+STGEVMG D
Sbjct: 900 LAARIMAGEKIADLGLK---KRNLDHVGVKESVFPFARFPGVDTVLGPEMRSTGEVMGID 956
Query: 915 STLEKALYKALIASGIQIPNYGSVLLTVADKDKEEGLAIAKRFHAIGYNILATEGTAGYL 974
+ E A K+ + G ++P G+V ++V + DK + K H++G+ ++AT GT YL
Sbjct: 957 RSFEIAFAKSQLGGGTRVPRKGTVFVSVRESDKARIVDAVKLLHSVGFKVIATSGTQRYL 1016
Query: 975 KEASIPAKVVGKIGQDGPNLLDVIRNGEAQFVINTLTKGKQPARDGFRIRRESVENGVAC 1034
+ +PA+ V K+ + P+++D I NGE Q V NT T+G Q D +RR ++ + V
Sbjct: 1017 SDHGVPAEKVNKVLEGRPHIVDAIMNGEVQLVFNT-TEGPQALADSRSLRRAALLHKVPY 1075
Query: 1035 LTSLDTAEA 1043
T+L A A
Sbjct: 1076 YTTLSGAVA 1084
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: 2843
Number of extensions: 132
Number of successful extensions: 20
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: 1109
Length adjustment: 46
Effective length of query: 1025
Effective length of database: 1063
Effective search space: 1089575
Effective search space used: 1089575
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_011159606.1 TX73_RS20760 (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.15702.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 1459.0 0.0 0 1458.2 0.0 1.3 1 lcl|NCBI__GCF_000195775.1:WP_011159606.1 TX73_RS20760 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195775.1:WP_011159606.1 TX73_RS20760 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1458.2 0.0 0 0 1 1049 [. 2 1086 .. 2 1089 .. 0.96
Alignments for each domain:
== domain 1 score: 1458.2 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+di+++l+iG+GpivigqA+EFDYsG+qa+kalk+eg++vvLvnsn+At+mtd+elad++YieP
lcl|NCBI__GCF_000195775.1:WP_011159606.1 2 PKRTDISTILIIGAGPIVIGQACEFDYSGTQAVKALKQEGYRVVLVNSNPATIMTDPELADATYIEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekEr...pD..ailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRe 129
+t+e+v+kiiekEr p a+l+t+GGqtaLn+a++l++ G Lek++v+++G++ +ai+kaedRe
lcl|NCBI__GCF_000195775.1:WP_011159606.1 69 ITPEIVAKIIEKERyviPGgfALLPTMGGQTALNCALSLRKLGTLEKFDVEMIGATADAIDKAEDRE 135
**************544224489******************************************** PP
TIGR01369 130 kFkealkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalk 196
+F+ea+++i++e+++s+ v+s +al+a +eig+P ++R++ft+gGtG+gia++++e+ e+ve++++
lcl|NCBI__GCF_000195775.1:WP_011159606.1 136 RFREAMTKIGLETPNSRQVKSLPDALRALDEIGFPALIRPSFTMGGTGGGIAYTKAEFIEIVERGID 202
******************************************************************* PP
TIGR01369 197 aspikqvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqll 263
asp+++vl+e+s+ gwkE+E+EvvRD++dnciivc+iEnlDp+GvHtGdsi+vaP+ tLtdkeyq++
lcl|NCBI__GCF_000195775.1:WP_011159606.1 203 ASPTNEVLIEESILGWKEYEMEVVRDKHDNCIIVCSIENLDPMGVHTGDSITVAPALTLTDKEYQIM 269
******************************************************************* PP
TIGR01369 264 Rdaslkiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGys 329
Rdasl+++re+gve++ +nvqfa++P++ r+vviE+npRvsRssALAskAtG+PiAkvaaklavGys
lcl|NCBI__GCF_000195775.1:WP_011159606.1 270 RDASLAVLREIGVETGgSNVQFAVNPDDGRLVVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYS 336
**************988************************************************** PP
TIGR01369 330 Ldelkndvtk.etvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqka 395
Lde+ nd+t+ t+AsfEP++DYvv+kiPr++++kf +++ +l+t mksvGEvmaigrtf+e+lqka
lcl|NCBI__GCF_000195775.1:WP_011159606.1 337 LDEIANDITGgATPASFEPTIDYVVTKIPRFAFEKFPGASPTLTTAMKSVGEVMAIGRTFQESLQKA 403
*********878******************************************************* PP
TIGR01369 396 lrsleekllglklkeke....aesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffl 458
lr le++l+gl++ e ++++++ al +p+++Rl+ +a+a+r g s ee+++ +kid +fl
lcl|NCBI__GCF_000195775.1:WP_011159606.1 404 LRGLESGLTGLDEIEIDglgrGDDKNAIRAALGTPTPSRLLQVAQAMRLGWSNEEIFNSCKIDPWFL 470
**********66554331111345667788999********************************** PP
TIGR01369 459 eklkklvelekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvD 525
+l+ +v++e +++e l + + ++++k++Gfsd+++a l++++eaev++ r++lg+ pv+kr+D
lcl|NCBI__GCF_000195775.1:WP_011159606.1 471 AQLRGIVDMEARVREAGLPDH-AFGMRTLKAMGFSDARLAVLADTTEAEVKAKRRALGVRPVFKRID 536
**************9988855.5679***************************************** PP
TIGR01369 526 tvaaEfeaktpYlYstyeee.....kddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalrea 587
t+aaEf + t+Y+Ystye+ +d+++ ++k+kv++lG+Gp+Rigqg+EFDyc+ ha+ al++a
lcl|NCBI__GCF_000195775.1:WP_011159606.1 537 TCAAEFASPTAYMYSTYESPfagpaSDESRPSDKQKVIILGGGPNRIGQGIEFDYCCCHACFALHDA 603
******************9777776899999999********************************* PP
TIGR01369 588 gyktilinynPEtvstDydiadrLyFeeltvedvldiiekekv....egvivqlgGqtalnlakele 650
gy++i++n+nPEtvstDyd+adrLyFe+lt edvl+ii++e+ +gvivq+gGqt+l+la++le
lcl|NCBI__GCF_000195775.1:WP_011159606.1 604 GYESIMVNCNPETVSTDYDTADRLYFEPLTGEDVLEIIDTERSngtlRGVIVQFGGQTPLKLARALE 670
****************************************986222268****************** PP
TIGR01369 651 eagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgG 717
+a v+ilGts+++id aEdR++F+++ld+l +kqpk+ +a sve+a+ +a+e+g+P++vRpsyvlgG
lcl|NCBI__GCF_000195775.1:WP_011159606.1 671 AADVPILGTSPDAIDLAEDRDRFKRILDKLRLKQPKNGIAYSVEQARLVAAELGLPLVVRPSYVLGG 737
******************************************************************* PP
TIGR01369 718 rameiveneeeleryle.....................eavevskekPvlidkyledavEvdvDava 763
ram+i++++++l++yl ++++v ++P+l d+yl+da+EvdvD ++
lcl|NCBI__GCF_000195775.1:WP_011159606.1 738 RAMQIIREDNQLSDYLLgtlpelvpgdvkarypndktgQINTVLGTNPLLFDRYLSDATEVDVDCLS 804
***************9778888999999898888877777788899********************* PP
TIGR01369 764 dgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkde 830
dg++ +i+gi+eHiEeaG+HsGDs+++lpp++ls+e+ +++++++++a l+v+Gl+n+q+++kd+
lcl|NCBI__GCF_000195775.1:WP_011159606.1 805 DGKDTFIVGIMEHIEEAGIHSGDSACSLPPHSLSAETIAELERQTRELALGLDVVGLMNVQYAIKDG 871
******************************************************************* PP
TIGR01369 831 evyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfskl 897
e+yv+Evn+RasRtvPfv+k++g+p++kla+++++g+k+++l+ k+ + ++v+vk++vf+f+++
lcl|NCBI__GCF_000195775.1:WP_011159606.1 872 EIYVLEVNPRASRTVPFVAKVIGMPVAKLAARIMAGEKIADLGL---KKRNLDHVGVKESVFPFARF 935
*****************************************876...88899*************** PP
TIGR01369 898 agvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakklaek 964
gvd vlgpem+stGEvmgi+r++e a++k++l ++++++kg+v++sv+++dk ++++++k l++
lcl|NCBI__GCF_000195775.1:WP_011159606.1 936 PGVDTVLGPEMRSTGEVMGIDRSFEIAFAKSQLGGGTRVPRKGTVFVSVRESDKARIVDAVKLLHSV 1002
******************************************************************* PP
TIGR01369 965 glkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirrea 1031
g+kv+at+gt+++l+++g+ ae+v+kv e +++i+++++++e++lv+n+t+ + +a ++ ++rr+a
lcl|NCBI__GCF_000195775.1:WP_011159606.1 1003 GFKVIATSGTQRYLSDHGVPAEKVNKVLEGRPHIVDAIMNGEVQLVFNTTE-GPQALADSRSLRRAA 1068
************************************************997.88889999******* PP
TIGR01369 1032 veykvplvteletaeall 1049
+ +kvp+ t+l++a a++
lcl|NCBI__GCF_000195775.1:WP_011159606.1 1069 LLHKVPYYTTLSGAVAAA 1086
***********9988776 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1109 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: 0.18u 0.04s 00:00:00.22 Elapsed: 00:00:00.20
# Mc/sec: 5.62
//
[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