Align Carbamoyl-phosphate synthase large chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase ammonia chain (uncharacterized)
to candidate Ga0059261_0007 Ga0059261_0007 carbamoyl-phosphate synthase, large subunit
Query= curated2:Q1D6Y8
(1083 letters)
>FitnessBrowser__Korea:Ga0059261_0007
Length = 1110
Score = 1262 bits (3266), Expect = 0.0
Identities = 661/1112 (59%), Positives = 811/1112 (72%), Gaps = 49/1112 (4%)
Query: 1 MPKRTDIRKVLVIGSGPIVIGQAVEFDYSGTQAIKALRDEGVEVVLLNSNPATVMTDPEF 60
MPKRTDI +LVIG+GPIVIGQA EFDYSGTQAIKAL++EG +VL+NSNPAT+MTDPE
Sbjct: 1 MPKRTDISSILVIGAGPIVIGQACEFDYSGTQAIKALKEEGYRIVLVNSNPATIMTDPEL 60
Query: 61 AHRTYIEPITVEAAERILASERPDSLLPTMGGQTALNLAKALAEQGILEKYGVRLIGASL 120
A TY+EPIT +I+ ERPD++LPTMGGQTALN A ALA G LEK+G +IGA
Sbjct: 61 ADATYVEPITPAVVAKIIEKERPDAVLPTMGGQTALNTALALANDGTLEKFGCIMIGADA 120
Query: 121 DAINKAEDRQLFKAAMQKIGVALPKSGYATTLDQAMSLVEDIGFPAIIRPSFTLGGTGGG 180
+AI+KAEDR FK AM KIG+ +S A + A++ +E +G PAIIRPSFT+GG+GGG
Sbjct: 121 EAIDKAEDRLKFKDAMTKIGLESARSAIAHSEADALAALEKVGLPAIIRPSFTMGGSGGG 180
Query: 181 IAYNREEFETICRSGLKASPTTTILVEESVLGWKEYELEVVRDTADNVIIVCSIENLDPM 240
IAYNREEF TI RSGL SPTT +L+EES+LGWKEYE+EVVRD DN II+CSIEN+D M
Sbjct: 181 IAYNREEFLTIVRSGLDLSPTTEVLIEESLLGWKEYEMEVVRDRNDNAIIICSIENIDAM 240
Query: 241 GVHTGDSITVAPAQTLTDREYQRMRQASLAIIREIGVETGGSNIQFGINPKDGRMVVIEM 300
G HTGDSITVAPA TLTD+EYQ MR AS+A++REIGVETGGSN+QF +NPKDGR++VIEM
Sbjct: 241 GTHTGDSITVAPALTLTDKEYQIMRNASIAVLREIGVETGGSNVQFAVNPKDGRLIVIEM 300
Query: 301 NPRVSRSSALASKATGYPIAKIAAKLALGYTLDELRNDITRDTPASFEPTLDYVVVKVPR 360
NPRVSRSSALASKATG+PIAK+AAKLA+GYTLDE+ NDIT TPASFEPT+DYVV K+PR
Sbjct: 301 NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEIENDITGATPASFEPTIDYVVTKIPR 360
Query: 361 FNFEKFPHADRTLTTSMRSVGEVMAIGRTFPEAYMKALRSMELGRVGLESPELPAEKEER 420
F FEKF A+ TL T+M+SVGEVMAIGR E+ KALR +E G G + + A
Sbjct: 361 FAFEKFKGAEATLGTAMKSVGEVMAIGRNIHESMQKALRGLETGLSGFNNVDHLAGAPRD 420
Query: 421 EKVLREALRIPRPERPWFVAQAFREGMTVEDVHALSAIDPWFLRYIQMLVNEAQSLQEYG 480
E + AL I P+R AQA REG TV +VHAL+ DPWFL + +V + G
Sbjct: 421 E--IEAALAIRSPDRLLIAAQALREGFTVAEVHALTKYDPWFLERMAEIVRAETEVATNG 478
Query: 481 RLDQLPDEV--LRQAKAHGFSDKYLGRLL-----------------------------GY 509
LP + +R+ K+ GFSDK L L G
Sbjct: 479 ----LPQDAAGMRKLKSMGFSDKRLAWLALQSANLREGAGAMARSSGLIGEVVKAMTGGV 534
Query: 510 PAEEVRAHRHARNIRPVYKRVDTCAAEFEAYTPYLYSTY------EEEDEAPPTDRQKVL 563
+VRAHRH +RPV+KR+DTCAAEF+A TPY+YSTY E E E+ +DR+K++
Sbjct: 535 TEADVRAHRHKLGVRPVFKRIDTCAAEFDAKTPYMYSTYEAPSFGEPECESQVSDRRKIV 594
Query: 564 ILGSGPIRIGQGIEFDYACVHAAFALREAGYETVMVNCNPETVSTDYDTSDRLYFEPLTI 623
ILG GP RIGQGIEFDY C HA FAL +AG+ET+MVNCNPETVSTDYDTSDRLYFEPLT
Sbjct: 595 ILGGGPNRIGQGIEFDYCCCHACFALSDAGFETIMVNCNPETVSTDYDTSDRLYFEPLTA 654
Query: 624 EDVLEVSQREKP----VGAIVQFGGQTPLRISVPLEKAGLPILGTSPDAIDRAEDRERFA 679
EDVLE+ E+ +G IVQFGGQTPL ++ LE AG+PILGTSPDAID AEDRERFA
Sbjct: 655 EDVLEILHVEQSKGELLGVIVQFGGQTPLNLARALEAAGIPILGTSPDAIDLAEDRERFA 714
Query: 680 ALIEKLGLKQPENGVARSHAEAFKVAERIGYPVMVRPSYVLGGRAMETVYDVASLERYMR 739
L+ KLGLKQP NG+ARS EA VAERIGYPV+ RPSYVLGGRAME V V L+ Y++
Sbjct: 715 DLVSKLGLKQPANGIARSREEAIAVAERIGYPVLTRPSYVLGGRAMEIVDTVEQLDHYIQ 774
Query: 740 EAVSASPEHPVLIDRFLKEAIEVDLDLVADRTGAVMIGGVLEHIQEAGVHSGDAAATLPP 799
AV S + PVLID++L++A+EVD+D +AD V++ GVL+HI+EAGVHSGD+A ++PP
Sbjct: 775 TAVQVSGDAPVLIDQYLRDAVEVDVDAIADGDD-VVVAGVLQHIEEAGVHSGDSACSIPP 833
Query: 800 HSLSPDLVERMKDQAIALARELGVVGLMNVQFAIQGKTIYILEVNPRASRTVPFISKATG 859
+SLS ++ ++ Q ALAR L V GLMN+QFA++ +Y++EVNPRASRTVPF++KA G
Sbjct: 834 YSLSAQIIAEIERQTEALARGLNVKGLMNIQFAVKDGEVYLIEVNPRASRTVPFVAKAIG 893
Query: 860 VAMAKIAALCMVGKTLKELGVTQEPEFKHVAVKESVFPFARFAGVDVILGPEMKSTGEVM 919
+AKIA+ M G+ LK+L + + +VAVKE+VFPF +F GVD +L PEMKSTGEVM
Sbjct: 894 APIAKIASRVMAGEKLKDLPKI-DRDIDYVAVKEAVFPFNKFPGVDPVLSPEMKSTGEVM 952
Query: 920 GLANDYASAFAKSQLAAGVKLPKSGKVFISVKDDDKPAVVDLARRLRSMGFSLVVTSGTH 979
G+ +D+ AFAKSQL AG+ LP G+VF+SVKD DKP V+ R L GFS+V T GT
Sbjct: 953 GIDSDFPIAFAKSQLGAGMTLPTEGRVFVSVKDGDKPVVLPGVRILVEQGFSIVATGGTA 1012
Query: 980 TYLATKGIEAQVVQKVTEGRPNIVDKIVDGEIVLVINTTFGKQEIADSFSIRRESLMHSV 1039
YL G+ + V KV +GRP+IVD+IVDG+I L+ NTT G Q + DS SIR +L +
Sbjct: 1013 DYLEANGVPVERVNKVAQGRPHIVDRIVDGDIALIFNTTEGWQSLKDSESIRASALSLKI 1072
Query: 1040 PYYTTVQAARMAVGALESLKCTELEVKPLQEY 1071
PY+TT A+ A A+ +L LEV+PLQ Y
Sbjct: 1073 PYFTTAPASVAAARAIAALAVQSLEVRPLQSY 1104
Lambda K H
0.318 0.135 0.380
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: 3070
Number of extensions: 143
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: 1083
Length of database: 1110
Length adjustment: 46
Effective length of query: 1037
Effective length of database: 1064
Effective search space: 1103368
Effective search space used: 1103368
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 Ga0059261_0007 Ga0059261_0007 (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.5471.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 1482.8 0.0 0 1482.1 0.0 1.3 1 lcl|FitnessBrowser__Korea:Ga0059261_0007 Ga0059261_0007 carbamoyl-phospha
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0007 Ga0059261_0007 carbamoyl-phosphate synthase, large subunit
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1482.1 0.0 0 0 1 1051 [. 2 1087 .. 2 1088 .. 0.96
Alignments for each domain:
== domain 1 score: 1482.1 bits; conditional E-value: 0
TIGR01369 1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYieP 67
pkr+di+++lviG+GpivigqA+EFDYsG+qa+kalkeeg+++vLvnsn+At+mtd+elad++Y+eP
lcl|FitnessBrowser__Korea:Ga0059261_0007 2 PKRTDISSILVIGAGPIVIGQACEFDYSGTQAIKALKEEGYRIVLVNSNPATIMTDPELADATYVEP 68
689**************************************************************** PP
TIGR01369 68 ltveavekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkea 134
+t+++v+kiiekErpDa+l+t+GGqtaLn a+ l + G Lek+g ++G++ eai+kaedR kFk+a
lcl|FitnessBrowser__Korea:Ga0059261_0007 69 ITPAVVAKIIEKERPDAVLPTMGGQTALNTALALANDGTLEKFGCIMIGADAEAIDKAEDRLKFKDA 135
******************************************************************* PP
TIGR01369 135 lkeineevakseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspik 201
+++i++e a+s+i++s+++al+a e++g+P i+R++ft+gG+G+gia+n+ee+ ++v+++l++sp++
lcl|FitnessBrowser__Korea:Ga0059261_0007 136 MTKIGLESARSAIAHSEADALAALEKVGLPAIIRPSFTMGGSGGGIAYNREEFLTIVRSGLDLSPTT 202
******************************************************************* PP
TIGR01369 202 qvlvekslagwkEiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdasl 268
+vl+e+sl gwkE+E+EvvRD++dn+ii+c+iEn+D++G HtGdsi+vaP+ tLtdkeyq++R+as+
lcl|FitnessBrowser__Korea:Ga0059261_0007 203 EVLIEESLLGWKEYEMEVVRDRNDNAIIICSIENIDAMGTHTGDSITVAPALTLTDKEYQIMRNASI 269
******************************************************************* PP
TIGR01369 269 kiirelgvege.cnvqfaldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelk 334
+++re+gve++ +nvqfa++P++ r++viE+npRvsRssALAskAtG+PiAkvaaklavGy+Lde++
lcl|FitnessBrowser__Korea:Ga0059261_0007 270 AVLREIGVETGgSNVQFAVNPKDGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEIE 336
*********988******************************************************* PP
TIGR01369 335 ndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrslee 401
nd+t+ t+AsfEP++DYvv+kiPr++++kf++++ +lgt mksvGEvmaigr+++e++qkalr le+
lcl|FitnessBrowser__Korea:Ga0059261_0007 337 NDITGATPASFEPTIDYVVTKIPRFAFEKFKGAEATLGTAMKSVGEVMAIGRNIHESMQKALRGLET 403
******************************************************************* PP
TIGR01369 402 kllglklkeke.aesdeeleealkkpndrRlfaiaealrrgvsveevyeltkidrffleklkklvel 467
+l+g++ ++ +++e+e al +++Rl++ a+alr+g++v ev+ ltk+d +fle+++++v++
lcl|FitnessBrowser__Korea:Ga0059261_0007 404 GLSGFNNVDHLaGAPRDEIEAALAIRSPDRLLIAAQALREGFTVAEVHALTKYDPWFLERMAEIVRA 470
****887666515678889999********************************************* PP
TIGR01369 468 ekeleeeklkelkkellkkakklGfsdeqiaklvk.......vseae.................... 507
e+e++++ l ++ ++k+k++Gfsd+++a l+ +
lcl|FitnessBrowser__Korea:Ga0059261_0007 471 ETEVATNGLP-QDAAGMRKLKSMGFSDKRLAWLALqsanlreG---Agamarssgligevvkamtgg 533
****977776.78999***************987744445550...055555555555555555566 PP
TIGR01369 508 .....vrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeee.....kddvevtekkkvlvlGsGp 564
vr+ r++lg+ pv+kr+Dt+aaEf+aktpY+Ystye+ + +++v++++k+++lG+Gp
lcl|FitnessBrowser__Korea:Ga0059261_0007 534 vteadVRAHRHKLGVRPVFKRIDTCAAEFDAKTPYMYSTYEAPsfgepECESQVSDRRKIVILGGGP 600
66666***********************************98766655678999999********** PP
TIGR01369 565 iRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekve 631
+Rigqg+EFDyc+ ha+ al++ag++ti++n+nPEtvstDyd++drLyFe+lt edvl+i++ e+ +
lcl|FitnessBrowser__Korea:Ga0059261_0007 601 NRIGQGIEFDYCCCHACFALSDAGFETIMVNCNPETVSTDYDTSDRLYFEPLTAEDVLEILHVEQSK 667
***************************************************************9987 PP
TIGR01369 632 ....gvivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsve 694
gvivq+gGqt+lnla++le+ag++ilGts+++id aEdRe+F+ l+ +lg+kqp++ +a+s e
lcl|FitnessBrowser__Korea:Ga0059261_0007 668 gellGVIVQFGGQTPLNLARALEAAGIPILGTSPDAIDLAEDRERFADLVSKLGLKQPANGIARSRE 734
44446************************************************************** PP
TIGR01369 695 eakeiakeigyPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDa 761
ea +a++igyPvl RpsyvlgGrameiv+ e+l +y+++av+vs ++Pvlid+yl davEvdvDa
lcl|FitnessBrowser__Korea:Ga0059261_0007 735 EAIAVAERIGYPVLTRPSYVLGGRAMEIVDTVEQLDHYIQTAVQVSGDAPVLIDQYLRDAVEVDVDA 801
******************************************************************* PP
TIGR01369 762 vadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvk 828
+adg++v++ag+l+HiEeaGvHsGDs++++pp +ls+++ +i+++++++a+ l+vkGl+niqf+vk
lcl|FitnessBrowser__Korea:Ga0059261_0007 802 IADGDDVVVAGVLQHIEEAGVHSGDSACSIPPYSLSAQIIAEIERQTEALARGLNVKGLMNIQFAVK 868
******************************************************************* PP
TIGR01369 829 deevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfs 895
d+evy+iEvn+RasRtvPfv+ka+g p++k+a +v++g+kl++l k + + ++vavk+avf+f+
lcl|FitnessBrowser__Korea:Ga0059261_0007 869 DGEVYLIEVNPRASRTVPFVAKAIGAPIAKIASRVMAGEKLKDLPK---IDRDIDYVAVKEAVFPFN 932
*******************************************887...788899************ PP
TIGR01369 896 klagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeellelakkla 962
k+ gvd+vl pemkstGEvmgi++d+ a++k++l ++++++++g+v++svkd dk +l+ ++ l+
lcl|FitnessBrowser__Korea:Ga0059261_0007 933 KFPGVDPVLSPEMKSTGEVMGIDSDFPIAFAKSQLGAGMTLPTEGRVFVSVKDGDKPVVLPGVRILV 999
******************************************************************* PP
TIGR01369 963 ekglkvyategtakvleeagikaevvlkvseeaekilellkeeeielvinltskkkkaaekgykirr 1029
e+g++++at gta++le +g+ +e v+kv + +++i++ + +++i l++n+t+ + ++ +++ +ir
lcl|FitnessBrowser__Korea:Ga0059261_0007 1000 EQGFSIVATGGTADYLEANGVPVERVNKVAQGRPHIVDRIVDGDIALIFNTTE-GWQSLKDSESIRA 1065
**************************************************997.77799999***** PP
TIGR01369 1030 eaveykvplvteletaeallea 1051
+a++ k+p++t++ + a+++a
lcl|FitnessBrowser__Korea:Ga0059261_0007 1066 SALSLKIPYFTTAPASVAAARA 1087
***********98877776665 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1052 nodes)
Target sequences: 1 (1110 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 0.02s 00:00:00.16 Elapsed: 00:00:00.16
# Mc/sec: 7.14
//
[ok]
This GapMind analysis is from Apr 09 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