Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate WP_015799094.1 AFER_RS08800 carbamoyl-phosphate synthase large subunit
Query= BRENDA::P00968
(1073 letters)
>NCBI__GCF_000023265.1:WP_015799094.1
Length = 1100
Score = 1048 bits (2709), Expect = 0.0
Identities = 573/1090 (52%), Positives = 740/1090 (67%), Gaps = 34/1090 (3%)
Query: 1 MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
MP+ ++S+L++G+GPIVIGQA EFDYSG QAC+ LREEG RVIL NSNPATIMTDPE
Sbjct: 1 MPRDPKVESVLVIGSGPIVIGQASEFDYSGVQACRVLREEGLRVILANSNPATIMTDPEF 60
Query: 61 ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
ADATYIEP+ EV+ +IIE ERPDAVLPT+GGQTALN A+EL+ GVLE GV M+GA
Sbjct: 61 ADATYIEPLTLEVLERIIEAERPDAVLPTLGGQTALNLAMELDASGVLERSGVRMLGARP 120
Query: 121 DAIDKAEDRRRFDVAMKKIGLETA-RSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGG 179
+I+ AE+R F + I + A R + ++EE VA ++G+P ++RPS+ +GG+G
Sbjct: 121 ASIELAENRDAFRQLLMSIDEQLAVRGRLVRSLEEGRDVADELGYPLMLRPSYILGGAGT 180
Query: 180 GIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDA 239
GIA + FE + GL SP E+L++ES+ GWKE+E+EV+RD NDNC++VCSIEN D
Sbjct: 181 GIATDPSSFEAMLRAGLIASPVGEVLVEESIAGWKEFELEVMRDANDNCVVVCSIENVDP 240
Query: 240 MGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIE 299
MG+HTGDSITVAPAQTLTD EYQ MR+ S +LR +GVETGGSNVQFAV P +GR++V+E
Sbjct: 241 MGVHTGDSITVAPAQTLTDLEYQRMRSLSFEILRRVGVETGGSNVQFAVEPTSGRMVVVE 300
Query: 300 MNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKI 359
MNPRVSRSSALASKATGFPIAK+A +LA+GYTLDE+MNDIT G TPASFEP++DYVV K+
Sbjct: 301 MNPRVSRSSALASKATGFPIAKIATRLAIGYTLDEIMNDIT-GVTPASFEPALDYVVVKV 359
Query: 360 PRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGF--DPKVSLDD 417
PR+ FEKF GA L T+M+SVGE MAIGR+ E+LQKALRG+E GF DP
Sbjct: 360 PRWVFEKFEGAEGILGTRMQSVGETMAIGRSFAEALQKALRGIERSRGGFGADPAEVTWQ 419
Query: 418 PEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVA 477
+ + + R++ + +A R G S++ V L+ ID WF+ ++ +V +
Sbjct: 420 AYSDDALATLVAVPTEQRVFAVGEALRRGWSIERVAELSRIDPWFIGEMAGIVARAADIR 479
Query: 478 EVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFA 537
+ L AD L LKR GF+D +LA L GV E +R+ R + VYK VDTCA EF
Sbjct: 480 GRDLASLGADELLDLKRWGFSDLQLAWLLGVDETAVREHRHTVGVRAVYKAVDTCAGEFP 539
Query: 538 TDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETI 597
T Y Y TYEEE E ++R ++++G GPNRIGQGIEFDYCCVHA+ ALRE G + I
Sbjct: 540 ARTPYYYGTYEEESE-TVGSNRPSVIIIGAGPNRIGQGIEFDYCCVHAAFALREAGVDAI 598
Query: 598 MVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIV----RIEKPKGVIVQYGGQTPLKLARA 653
MVN NPETVSTDYDTS RLY EP+ E VL+++ R+ +GVIV GGQTPLKLAR
Sbjct: 599 MVNSNPETVSTDYDTSSRLYVEPLVTEHVLDVIAEEQRLGSLQGVIVSLGGQTPLKLARD 658
Query: 654 LEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLV 713
++ + V+GTSPD+ID AEDR R+ ERL ++QP TVT++ A IG P++
Sbjct: 659 IDPS--LVLGTSPDSIDVAEDRRRWSALCERLGIRQPPGGTVTSLAEAEAVVAAIGLPVL 716
Query: 714 VRPSYVLGGRAMEIVYDEADLRRYFQTAV------SVSNDAPVLLDHFLDDAVEVDVDAI 767
VRPSYVLGGRAMEIVY E +LR F V ++S D P+L+D FL+ A+EVDVDA+
Sbjct: 717 VRPSYVLGGRAMEIVYSEDELRSAFSRLVDLAAEGAISQDRPILIDRFLEGAIEVDVDAV 776
Query: 768 CDGE-MVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLM 826
D E IG +MEH+E+AGVHSGDSAC++P +L+ + + Q + +A L V GL+
Sbjct: 777 RDREGACWIGAVMEHVEEAGVHSGDSACTIPPVSLAPALVAEIEAQTRAIADALDVVGLI 836
Query: 827 NVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAE---QGV-TKE 882
NVQFAV + V++IE NPRA+RTVPFV+KATGV L K+A R+M G +L + +G+
Sbjct: 837 NVQFAVADGTVFVIEANPRASRTVPFVAKATGVALVKIATRLMLGSTLRDLEREGLFVPR 896
Query: 883 VIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKH 942
+ Y +VKE VLPF +F G D +LGPEMRSTGEVMG+ RT AFAKAQL + + + +
Sbjct: 897 RVTSYVAVKEAVLPFGRFRGADSILGPEMRSTGEVMGIDRTMPMAFAKAQLAAGTRLPQQ 956
Query: 943 GRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGIN-PRLVNKV------- 994
G L++V + DKE +V +A +L+ GF+L AT GTA L G+ RLV KV
Sbjct: 957 GTVLVTVADRDKEALVPIAERLVAHGFDLAATEGTASWLQAHGVPVARLVAKVTEEEDLG 1016
Query: 995 ----HEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFAT 1050
EG +++GE IINT G D IR +AL+ K+ TTL A
Sbjct: 1017 ERAAPEGFVDAVRLVRSGEVALIINTPRGSGPRRDGYRIRTAALEAKIPLITTLEAARAA 1076
Query: 1051 AMALNADATE 1060
A+ A A +
Sbjct: 1077 VAAVEALARQ 1086
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: 2828
Number of extensions: 140
Number of successful extensions: 23
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: 1100
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1054
Effective search space: 1082458
Effective search space used: 1082458
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_015799094.1 AFER_RS08800 (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.16457.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 1383.1 0.0 0 1382.9 0.0 1.0 1 lcl|NCBI__GCF_000023265.1:WP_015799094.1 AFER_RS08800 carbamoyl-phosphate
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023265.1:WP_015799094.1 AFER_RS08800 carbamoyl-phosphate synthase large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1382.9 0.0 0 0 3 1051 .. 4 1079 .. 2 1080 .. 0.95
Alignments for each domain:
== domain 1 score: 1382.9 bits; conditional E-value: 0
TIGR01369 3 redikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePlt 69
+ ++++vlviGsGpivigqA+EFDYsG qa++ l+eeg++v+L nsn+At+mtd+e+ad++YiePlt
lcl|NCBI__GCF_000023265.1:WP_015799094.1 4 DPKVESVLVIGSGPIVIGQASEFDYSGVQACRVLREEGLRVILANSNPATIMTDPEFADATYIEPLT 70
67899************************************************************** PP
TIGR01369 70 veavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealk 136
e++e+iie ErpDa+l+tlGGqtaLnla+el+ +GvLe+ gv++lG++ +i+ ae+R++F+++l
lcl|NCBI__GCF_000023265.1:WP_015799094.1 71 LEVLERIIEAERPDAVLPTLGGQTALNLAMELDASGVLERSGVRMLGARPASIELAENRDAFRQLLM 137
******************************************************************* PP
TIGR01369 137 eineeva.kseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikq 202
i+e++a +++ v+s ee ++a+e+gyP+++R+++ lgG+G+gia++ + ++++ + +l asp+ +
lcl|NCBI__GCF_000023265.1:WP_015799094.1 138 SIDEQLAvRGRLVRSLEEGRDVADELGYPLMLRPSYILGGAGTGIATDPSSFEAMLRAGLIASPVGE 204
****98747899******************************************************* PP
TIGR01369 203 vlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslk 269
vlve+s+agwkE+E+Ev+RD++dnc++vc+iEn+Dp+GvHtGdsi+vaP+qtLtd eyq++R+ s++
lcl|NCBI__GCF_000023265.1:WP_015799094.1 205 VLVEESIAGWKEFELEVMRDANDNCVVVCSIENVDPMGVHTGDSITVAPAQTLTDLEYQRMRSLSFE 271
******************************************************************* PP
TIGR01369 270 iirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkn 335
i+r++gve++ +nvqfa++P+s r+vv+E+npRvsRssALAskAtG+PiAk+a++la+Gy+Lde++n
lcl|NCBI__GCF_000023265.1:WP_015799094.1 272 ILRRVGVETGgSNVQFAVEPTSGRMVVVEMNPRVSRSSALASKATGFPIAKIATRLAIGYTLDEIMN 338
********988******************************************************** PP
TIGR01369 336 dvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleek 402
d+t+ t+AsfEP+lDYvvvk+Prw ++kfe+++ lgt+m+svGE maigr+f ealqkalr +e +
lcl|NCBI__GCF_000023265.1:WP_015799094.1 339 DITGVTPASFEPALDYVVVKVPRWVFEKFEGAEGILGTRMQSVGETMAIGRSFAEALQKALRGIERS 405
******************************************************************* PP
TIGR01369 403 llglklkek....eaesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklv 465
g+ + + +a sd++l + + p+++R+fa+ ealrrg s+e+v el++id +f+ +++ +v
lcl|NCBI__GCF_000023265.1:WP_015799094.1 406 RGGFGADPAevtwQAYSDDALATLVAVPTEQRVFAVGEALRRGWSIERVAELSRIDPWFIGEMAGIV 472
99965543301114567788899999***************************************** PP
TIGR01369 466 elekeleeeklkelkkellkkakklGfsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfe 532
+ + +++ l l +++l +k+ Gfsd q+a l++v+e++vr+ r+++g+ v+k vDt+a+Ef+
lcl|NCBI__GCF_000023265.1:WP_015799094.1 473 ARAADIRGRDLASLGADELLDLKRWGFSDLQLAWLLGVDETAVREHRHTVGVRAVYKAVDTCAGEFP 539
******************************************************************* PP
TIGR01369 533 aktpYlYstyeeekddvevtekkkvlvlGsGpiRigqgvEFDycavhavlalreagyktilinynPE 599
a+tpY+Y tyeee ++ +++ +v+++G+Gp+Rigqg+EFDyc+vha+ alreag +i++n+nPE
lcl|NCBI__GCF_000023265.1:WP_015799094.1 540 ARTPYYYGTYEEE-SETVGSNRPSVIIIGAGPNRIGQGIEFDYCCVHAAFALREAGVDAIMVNSNPE 605
*************.777777788******************************************** PP
TIGR01369 600 tvstDydiadrLyFeeltvedvldiiekek....vegvivqlgGqtalnlakeleeagvkilGtsae 662
tvstDyd++ rLy e+l +e+vld+i +e+ +gviv+lgGqt+l+la++++ + +lGts++
lcl|NCBI__GCF_000023265.1:WP_015799094.1 606 TVSTDYDTSSRLYVEPLVTEHVLDVIAEEQrlgsLQGVIVSLGGQTPLKLARDIDPS--LVLGTSPD 670
**************************99974444699*****************987..58****** PP
TIGR01369 663 sidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeel 729
sid aEdR+++s+l+++lgi qp g ++ts+ ea+ +++ ig+PvlvRpsyvlgGrameiv++e+el
lcl|NCBI__GCF_000023265.1:WP_015799094.1 671 SIDVAEDRRRWSALCERLGIRQPPGGTVTSLAEAEAVVAAIGLPVLVRPSYVLGGRAMEIVYSEDEL 737
******************************************************************* PP
TIGR01369 730 eryle......eavevskekPvlidkyledavEvdvDavadge.evliagileHiEeaGvHsGDstl 789
++ ++ + ++s++ P+lid++le a+EvdvDav d e i +++eH+EeaGvHsGDs++
lcl|NCBI__GCF_000023265.1:WP_015799094.1 738 RSAFSrlvdlaAEGAISQDRPILIDRFLEGAIEVDVDAVRDREgACWIGAVMEHVEEAGVHSGDSAC 804
9987744443344579************************9772567889***************** PP
TIGR01369 790 vlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvpl 856
++pp +l ++ +i++++++ia +l+v+Gl+n+qf+v d++v viE+n+RasRtvPfv+ka+gv l
lcl|NCBI__GCF_000023265.1:WP_015799094.1 805 TIPPVSLAPALVAEIEAQTRAIADALDVVGLINVQFAVADGTVFVIEANPRASRTVPFVAKATGVAL 871
******************************************************************* PP
TIGR01369 857 vklavkvllgkkleele.kgv.kkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdl 921
vk+a++++lg++l++le +g+ + +++vavk+av++f +++g+d +lgpem+stGEvmgi+r++
lcl|NCBI__GCF_000023265.1:WP_015799094.1 872 VKIATRLMLGSTLRDLErEGLfVPRRVTSYVAVKEAVLPFGRFRGADSILGPEMRSTGEVMGIDRTM 938
*************99874344145667799************************************* PP
TIGR01369 922 eeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaev. 987
a++ka+la++++++++g+vl++v+d+dke+l+++a++l+++g+ + ategta+ l+ +g+ +
lcl|NCBI__GCF_000023265.1:WP_015799094.1 939 PMAFAKAQLAAGTRLPQQGTVLVTVADRDKEALVPIAERLVAHGFDLAATEGTASWLQAHGVPVARl 1005
**************************************************************98651 PP
TIGR01369 988 vlkvseea...........ekilellkeeeielvinltskkkkaaekgykirreaveykvplvtele 1043
v kv+ee+ +++ l++++e+ l+in+++ ++ +++gy+ir +a+e k+pl+t+le
lcl|NCBI__GCF_000023265.1:WP_015799094.1 1006 VAKVTEEEdlgeraapegfVDAVRLVRSGEVALIINTPR-GSGPRRDGYRIRTAALEAKIPLITTLE 1071
56666666899999997776677899**********996.999************************ PP
TIGR01369 1044 taeallea 1051
+a+a++ a
lcl|NCBI__GCF_000023265.1:WP_015799094.1 1072 AARAAVAA 1079
**998876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1100 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: 0.08u 0.03s 00:00:00.11 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