Citrus Sinensis ID: 010869

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------50
MHRASLVCSSYPVFLSPSSPRLPLSLPLQHQLPRSLPASFGVQLPSTSPQIYRHAVSLLHSSATQEIVETSASGLDFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVIEGSEEASSSASDASGRLVWIPFVEEIVPIVDMNGREMQITPPKGLLELNLRTDERSKKERRQLEWKERKKFQKRLIAAKKKLREMEQQHVFHGFRFGEKYQTSLLANHIVGINSKLLQQALQNIEIPSKRWNATELMNATKAELMISSLKISGEGSLGPCARAKKVVTNSSLQKKGNHLVSEGKKAMVLVVHNSEEGNECDPHSVVSESTANKSLALLQTLLSDDQRFVKIENRASMPLVLVLPALEMQMLEKLFLDNDHFAFDSKKVSNISESFL
cccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccEEEEEEEEcccccccEEEEEEcccccccccccccEEEEEEEEcccccEEEEEEEEEEEEccccEEEEEEcccccHHHHHHccccEEEEEccccccccccccccccccccEEEEccccEEEEEEEEEEccccccEEEEEEcccccccccccccccccccccccEEEEEcccccccEEEccccEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHcccHHHHHHHHHccccccccccccHHcHHHHHHHHHcEEEEccccccccccccccccccHHHHHHcccccccccEEEEEEEccccccccccccccccccccccHHHHHHHHHccccccEEEcccccccEEEEcccHHHHHHHHHHHccccccccccEEEEEEEccc
cccEEEEEcccccccccccccccccccccccccccccccccccccEEHcccccccccHHccccccccccccccccccEEEEEEEcccccEEEEEEEEccccHHHHccccccEEEEEcccccccEEEEEEEEcEEcccccEEEEEEcccccHHHHHHHcccEEEEcHHHccccccccEEEEEEEEEEEEEcccccEEEEEEEccccccccEEEEEcccccccccccccccccccccccccEEEcccHHHcccccccccEEEEccccccHHHcccccHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEccccccHHHHHHHHHHHccccHHHHHHHHHHcccccccccHHHHHHHcccccEEEEEEcccEHcccccccHHHHHHHHHHHHHHHHHHHcccEEEEEEEEccccccccccccccccccccHHHHHHHHHHcccccEEEEcccccccEEEEccHHHHHHHHHHHHHcccccccccEEEEEEEccc
mhraslvcssypvflspssprlplslplqhqlprslpasfgvqlpstspqIYRHAVSLLHSSATQEIVETsasgldfvdvGYVYSvhglqgeisvkpstdfpelrfttpgtrWLRQQVLGretirevklidgrehpgqkswiltfegidtveqarplvgstllaregdrpeledgefytrDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVnviegseeasssasdasgrlvwipfvEEIVpivdmngremqitppkgllelnlrtderSKKERRQLEWKERKKFQKRLIAAKKKLREMEQQHVFHGFRFGEKYQTSLLANHIVGINSKLLQQALQNieipskrwNATELMNATKAELMISSLkisgegslgpcarakkvvtnsslqkkgnHLVSEGKKAMVLVVHnseegnecdphsvvsesTANKSLALLQTLLsddqrfvkienrasmplvLVLPALEMQMLEKLFLdndhfafdskkvsnisesfl
MHRASLVCSSYPVFLSPSSPRLPLSLPLQHQLPRSLPASFGVQLPSTSPQIYRHAVSLLHSSATQEIVETSASGLDFVDVGYVYSVHGLQGeisvkpstdfpelrfttpgtrwlrqqvlgretirevklidgrehpgqksWILTFEGIDTVEQARPLVGstllaregdrpeledgefytrdlVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVIEGSEEAsssasdasgrlVWIPFVEEIVPIVdmngremqitppkgllelnlrtderskkerrqlewkerkKFQKRLIAAKKKLREMEQQHVFHGFRFGEKYQTSLLANHIVGINSKLLQQALQNIEIPSKRWNATELMNATKAELMISSLKISGEGSLGPCARAKKVvtnsslqkkgnhlvsEGKKAMVLVVHNSEEGNECDPHSVVSESTANKSLALLQTLLSDDQRFVKIENRASMPLVLVLPALEMQMLEKLFLDNDHfafdskkvsnisesfl
MHRASLVCSSYPVFlspssprlplslplqhqlprslpASFGVQLPSTSPQIYRHAVSLLHSSATQEIVETSASGLDFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVIegseeasssasdasgRLVWIPFVEEIVPIVDMNGREMQITPPKGLLELNLRTDERSKKERRQLEWKERKKFQKRLIAAKKKLREMEQQHVFHGFRFGEKYQTSLLANHIVGINSKLLQQALQNIEIPSKRWNATELMNATKAELMISSLKISGEGSLGPCARAKKVVTNSSLQKKGNHLVSEGKKAMVLVVHNSEEGNECDPHSVVSESTANKSLALLQTLLSDDQRFVKIENRASMPLVLVLPALEMQMLEKLFLDNDHFAFDSKKVSNISESFL
**********YPVF***********************************QIYRHAVSLLHSSATQEIVETSASGLDFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQKSWILTFEGIDTVEQARPLVGSTLLAR******LEDGEFYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVI**************GRLVWIPFVEEIVPIVDMNGRE**************************************LIA*******MEQQHVFHGFRFGEKYQTSLLANHIVGINSKLLQQALQNIEIPSKRWNATELMNATKAELMISSLKI***********************************MVLVV***********************LALLQTLLSDDQRFVKIENRASMPLVLVLPALEMQMLEKLFLDNDHFAF*************
*******CSSYPVFLSPSSPRL******************************************************FVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVIEG**********ASGRLVWIPFVEEIVPIVDMNGREMQITPPKGLL************************************REMEQQHVFHGFRFGEKYQTSLLANHIVGINSKLLQQA**********************************GSL**********TNSSLQKKGNHLVSEGKKAMVLVVHNSEEG****************SLALLQTLLSDDQRFVKIENRASMPLVLVLPALEMQMLEKLFLDNDHFAFDSKKVSNISESFL
********SSYPVFLSPSSPRLPLSLPLQHQLPRSLPASFGVQLPSTSPQIYRHAVSLLHSSATQEIVETSASGLDFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVIE************SGRLVWIPFVEEIVPIVDMNGREMQITPPKGLLELNLRTDERSKKERRQLEWKERKKFQKRLIAAKKKLREMEQQHVFHGFRFGEKYQTSLLANHIVGINSKLLQQALQNIEIPSKRWNATELMNATKAELMISSLKISGEGSLGPCARAKKVVTNSSLQKKGNHLVSEGKKAMVLVVHNSEE************STANKSLALLQTLLSDDQRFVKIENRASMPLVLVLPALEMQMLEKLFLDNDHFAFDSKKVSNISESFL
**RASLVCSSYPVFLSPSSPRLPLSLPLQHQLPRSLPASFGVQLPSTSPQIYRHAVSLLHSS***********GLDFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYS*******************GRLVWIPFVEEIVPIVDMNGREMQITPPKGLLELNLRTD*RSKKERRQLEWKERKKFQKRLIAAKKKLREMEQQHVFHGFRFGEKYQTSLLANHIVGINSKLLQQALQNIEIPSKRWNATELMNATKAELMISSLKISGEGSLGPCARAKKVVTNSSLQKKGNHLVSEGKKAMVLVVHNSE**************TANKSLALLQTLLSDDQRFVKIENRASMPLVLVLPALEMQMLEKLFLDNDHFAFDSKKVSNISES**
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MHRASLVCSSYPVFLSPSSPRLPLSLPLQHQLPRSLPASFGVQLPSTSPQIYRHAVSLLHSSATQEIVETSASGLDFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVIEGSEEASSSASDASGRLVWIPFVEEIVPIVDMNGREMQITPPKGLLELNLRTDERSKKERRQLEWKExxxxxxxxxxxxxxxxxxxxxHVFHGFRFGEKYQTSLLANHIVGINSKLLQQALQNIEIPSKRWNATELMNATKAELMISSLKISGEGSLGPCARAKKVVTNSSLQKKGNHLVSEGKKAMVLVVHNSEEGNECDPHSVVSESTANKSLALLQTLLSDDQRFVKIENRASMPLVLVLPALEMQMLEKLFLDNDHFAFDSKKVSNISESFL
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query498 2.2.26 [Sep-21-2011]
A5GI62175 Ribosome maturation facto yes no 0.343 0.977 0.415 3e-32
B7K5W1186 Ribosome maturation facto yes no 0.361 0.967 0.410 3e-32
B2J3X9235 Ribosome maturation facto yes no 0.383 0.812 0.369 5e-32
Q8YTB1246 Probable 16S rRNA-process yes no 0.373 0.756 0.381 1e-31
Q3ME71233 Probable 16S rRNA-process yes no 0.361 0.772 0.392 3e-31
Q7V4K0176 Ribosome maturation facto yes no 0.343 0.971 0.384 7e-31
A2CCX2176 Ribosome maturation facto yes no 0.343 0.971 0.379 1e-30
Q10VX5208 Ribosome maturation facto yes no 0.383 0.918 0.371 2e-30
B0JU07192 Ribosome maturation facto yes no 0.377 0.979 0.375 5e-29
A5GQ79175 Ribosome maturation facto yes no 0.343 0.977 0.386 5e-29
>sp|A5GI62|RIMM_SYNPW Ribosome maturation factor RimM OS=Synechococcus sp. (strain WH7803) GN=rimM PE=3 SV=1 Back     alignment and function desciption
 Score =  140 bits (352), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 81/195 (41%), Positives = 119/195 (61%), Gaps = 24/195 (12%)

Query: 76  DFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREH 135
           D++ VG V +V GL+GE+ V P++DFPE RFT PG+RWL+ +    +  RE++L  GR+ 
Sbjct: 5   DWLPVGKVVAVQGLKGELRVNPASDFPE-RFTEPGSRWLKAR---GQAPREIELTSGRQL 60

Query: 136 PGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGEL 195
           PG+  +++ F G+++ + A  LVG TL+    DRPEL +GEF+  DLVG+   +   G+ 
Sbjct: 61  PGKSVFVVRFAGVESRDAAEALVGQTLMVPADDRPELAEGEFHLLDLVGLEARLSADGDA 120

Query: 196 VGTVVNVFNSGANDLLHVMCYSSVNVIEGSEEASSSASDASGRLVWIPFVEEIVPIVDMN 255
           +GTV ++  SG NDLL         V+E  +          GR + IPFVE IVP V + 
Sbjct: 121 IGTVKDLI-SGGNDLL---------VLERPD----------GRTLMIPFVEAIVPDVHLE 160

Query: 256 GREMQITPPKGLLEL 270
              +++TPP GLLEL
Sbjct: 161 QGWLRLTPPPGLLEL 175
An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes.
Synechococcus sp. (strain WH7803) (taxid: 32051)
>sp|B7K5W1|RIMM_CYAP8 Ribosome maturation factor RimM OS=Cyanothece sp. (strain PCC 8801) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|B2J3X9|RIMM_NOSP7 Ribosome maturation factor RimM OS=Nostoc punctiforme (strain ATCC 29133 / PCC 73102) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|Q8YTB1|RIMM_NOSS1 Probable 16S rRNA-processing protein RimM OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|Q3ME71|RIMM_ANAVT Probable 16S rRNA-processing protein RimM OS=Anabaena variabilis (strain ATCC 29413 / PCC 7937) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|Q7V4K0|RIMM_PROMM Ribosome maturation factor RimM OS=Prochlorococcus marinus (strain MIT 9313) GN=rimM PE=3 SV=2 Back     alignment and function description
>sp|A2CCX2|RIMM_PROM3 Ribosome maturation factor RimM OS=Prochlorococcus marinus (strain MIT 9303) GN=rimM PE=3 SV=2 Back     alignment and function description
>sp|Q10VX5|RIMM_TRIEI Ribosome maturation factor RimM OS=Trichodesmium erythraeum (strain IMS101) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|B0JU07|RIMM_MICAN Ribosome maturation factor RimM OS=Microcystis aeruginosa (strain NIES-843) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|A5GQ79|RIMM_SYNR3 Ribosome maturation factor RimM OS=Synechococcus sp. (strain RCC307) GN=rimM PE=3 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query498
225463376 665 PREDICTED: uncharacterized protein LOC10 0.929 0.696 0.612 1e-157
255557441 631 conserved hypothetical protein [Ricinus 0.875 0.690 0.619 1e-149
224116700 673 predicted protein [Populus trichocarpa] 0.867 0.641 0.636 1e-147
357519207 667 Ribosome maturation factor rimM [Medicag 0.961 0.718 0.544 1e-139
42568351 653 RimM-like 16S rRNA processing protein [A 0.947 0.722 0.516 1e-137
84468326 669 hypothetical protein [Trifolium pratense 0.843 0.627 0.581 1e-135
449500620 1138 PREDICTED: uncharacterized LOC101214658 0.887 0.388 0.551 1e-129
297794617 654 16S rRNA processing protein RimM family 0.963 0.733 0.509 1e-126
449459390 846 PREDICTED: uncharacterized protein LOC10 0.761 0.447 0.588 1e-123
125553343 644 hypothetical protein OsI_21009 [Oryza sa 0.793 0.613 0.416 9e-89
>gi|225463376|ref|XP_002271571.1| PREDICTED: uncharacterized protein LOC100251997 [Vitis vinifera] gi|297740629|emb|CBI30811.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  561 bits (1445), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 286/467 (61%), Positives = 361/467 (77%), Gaps = 4/467 (0%)

Query: 24  LSLPLQHQLPRSLPASFGVQLPSTSPQIYRHAVSLLHSSATQEIVETSASGLDFVDVGYV 83
            +LP++ +  R + AS  V+LP T  + YRH +S LHS+AT+E++ETS    +FV+VGY+
Sbjct: 26  FALPVRGRPTRPVVAS--VRLPLTRLRNYRHTLSPLHSTATEEVLETSKVESEFVEVGYI 83

Query: 84  YSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQKSWIL 143
            SVHGLQGEI VKP+TDFPELRF  PG RWLRQQ  G+ETIREV+L++GR HPGQK+WIL
Sbjct: 84  SSVHGLQGEIRVKPNTDFPELRFAEPGIRWLRQQFSGKETIREVELVEGRGHPGQKTWIL 143

Query: 144 TFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTVVNVF 203
            F GIDTVE+A+ LVGS+LL RE DRPELE+GEFY+RDL+GMRV +KETGE VGTVVNVF
Sbjct: 144 KFGGIDTVEEAKQLVGSSLLVREDDRPELEEGEFYSRDLLGMRVTLKETGEPVGTVVNVF 203

Query: 204 NSGANDLLHVMCYSSVNVIEGSEEASSSASDASGRLVWIPFVEEIVPIVDMNGREMQITP 263
           ++GANDLL VM   SV   + +    S  +  SG LVW+PFVE IVP VDMN REMQITP
Sbjct: 204 STGANDLLQVMLDPSVKTPDHTGNPKSE-TGVSGPLVWVPFVEAIVPNVDMNKREMQITP 262

Query: 264 PKGLLELNLRTDERSKKERRQLEWKERKKFQKRLIAAKKKLREMEQQHVFHGFRFGEKYQ 323
           PKGLLELNLR+ ERSKKERRQLEWK+R+KFQ+RLIAAKKKL EMEQQHVFHGFRFG+K Q
Sbjct: 263 PKGLLELNLRSHERSKKERRQLEWKQRRKFQRRLIAAKKKLHEMEQQHVFHGFRFGQKAQ 322

Query: 324 TSLLANHIVGINSKLLQQALQNIEIPSKRWNATELMNATKAELMISSLKISGEGSLGPCA 383
            SLLA+ IVG+NSKLLQQALQNIE+ S+RW+++E ++    +L   +LK+S +    P +
Sbjct: 323 RSLLADQIVGVNSKLLQQALQNIELSSQRWSSSEFISTKLTKLGQRTLKVSKKCLTTPGS 382

Query: 384 RAKKVVTNSSLQKKGNHLVSEGKKAMVLVVHNSEEGNECDPHSVVSESTANKSLALLQTL 443
             +K+ +N  LQ+KG HL+S+GK A+VL V++SE+   C    +V   +A  S + LQTL
Sbjct: 383 E-EKLDSNFELQEKGLHLMSKGKMAIVLFVNDSEKHGRCSVPELVDSESAGNSTSFLQTL 441

Query: 444 LSDDQRFVKIENRASMPLVLVLPALEMQMLEKLFLDNDHFAFDSKKV 490
           LSDD+  +K E+R S+PL++V PA E+  LE LF ++DHFAFD KKV
Sbjct: 442 LSDDRISLKKEDRVSVPLIMVSPAHEVHSLENLFSNHDHFAFDPKKV 488

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255557441|ref|XP_002519751.1| conserved hypothetical protein [Ricinus communis] gi|223541168|gb|EEF42724.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|224116700|ref|XP_002331856.1| predicted protein [Populus trichocarpa] gi|222875374|gb|EEF12505.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|357519207|ref|XP_003629892.1| Ribosome maturation factor rimM [Medicago truncatula] gi|355523914|gb|AET04368.1| Ribosome maturation factor rimM [Medicago truncatula] Back     alignment and taxonomy information
>gi|42568351|ref|NP_568663.2| RimM-like 16S rRNA processing protein [Arabidopsis thaliana] gi|10177579|dbj|BAB10810.1| unnamed protein product [Arabidopsis thaliana] gi|332008000|gb|AED95383.1| RimM-like 16S rRNA processing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|84468326|dbj|BAE71246.1| hypothetical protein [Trifolium pratense] Back     alignment and taxonomy information
>gi|449500620|ref|XP_004161149.1| PREDICTED: uncharacterized LOC101214658 [Cucumis sativus] Back     alignment and taxonomy information
>gi|297794617|ref|XP_002865193.1| 16S rRNA processing protein RimM family [Arabidopsis lyrata subsp. lyrata] gi|297311028|gb|EFH41452.1| 16S rRNA processing protein RimM family [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|449459390|ref|XP_004147429.1| PREDICTED: uncharacterized protein LOC101214658 [Cucumis sativus] Back     alignment and taxonomy information
>gi|125553343|gb|EAY99052.1| hypothetical protein OsI_21009 [Oryza sativa Indica Group] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query498
TAIR|locus:2151461 653 AT5G46420 [Arabidopsis thalian 0.728 0.555 0.581 1.9e-110
UNIPROTKB|Q81WJ5171 rimM "Ribosome maturation fact 0.253 0.736 0.375 1.9e-18
TIGR_CMR|BA_3980171 BA_3980 "16S rRNA processing p 0.253 0.736 0.375 1.9e-18
UNIPROTKB|Q71YM3169 rimM "Ribosome maturation fact 0.253 0.745 0.345 2.1e-16
UNIPROTKB|P66653176 rimM "Ribosome maturation fact 0.261 0.738 0.333 2.1e-13
UNIPROTKB|Q47WU9176 rimM "Ribosome maturation fact 0.253 0.715 0.365 4e-13
TIGR_CMR|CPS_4068176 CPS_4068 "16S rRNA processing 0.253 0.715 0.365 4e-13
UNIPROTKB|Q5LNF0167 rimM "Ribosome maturation fact 0.255 0.760 0.309 3.2e-12
TIGR_CMR|SPO_3255167 SPO_3255 "16S rRNA processing 0.255 0.760 0.309 3.2e-12
UNIPROTKB|Q60BS2172 rimM "Ribosome maturation fact 0.263 0.761 0.381 1e-11
TAIR|locus:2151461 AT5G46420 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 1074 (383.1 bits), Expect = 1.9e-110, Sum P(2) = 1.9e-110
 Identities = 217/373 (58%), Positives = 279/373 (74%)

Query:    58 LLHSSATQEIVETSA-SGLDFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQ 116
             L  S+AT E VETS+ SGLD V+VG++  VHGLQGEI +KP+TDFP+LRF+ PG RWL+Q
Sbjct:    60 LTRSTATDEAVETSSNSGLDLVEVGFLSGVHGLQGEICIKPNTDFPDLRFSKPGRRWLKQ 119

Query:   117 QVLGRETIREVKLIDGREHPGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGE 176
             Q+LG++ I EV+L++GR HP QKSWIL F G+D V+Q R LVG+TLLA + DRPEL++GE
Sbjct:   120 QLLGQDKIDEVELVEGRPHPAQKSWILKFRGLDDVDQVRQLVGATLLAEDDDRPELDEGE 179

Query:   177 FYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVIXXXXXXXXXXXXXX 236
             FY+RDLVGMRV++KETG+LVGTV N+F++G NDLLHV+  SS+ V               
Sbjct:   180 FYSRDLVGMRVLLKETGQLVGTVANIFDNGGNDLLHVLLDSSMEVCNGNAKTN------- 232

Query:   237 XRLVWIPFVEEIVPIVDMNGREMQITPPKGLLELNLRTDERSKKERRQLEWKERKKFQKR 296
              +LVWIPFV+ IVP VD+  +EM ITPPKGLLE+N+R D+RSKKERRQLEWKERKK QKR
Sbjct:   233 -QLVWIPFVDAIVPDVDLERKEMYITPPKGLLEVNMRADDRSKKERRQLEWKERKKQQKR 291

Query:   297 LIAAKKKLREMEQQHVFHGFRFGEKYQTSLLANHIVGINSKLLQQALQNIEIPSKRWNAT 356
             LIAAKKKL EMEQ+HVF G RFGEK Q +LLA+HI+ +NS LLQ+ALQ+I+  SKRWN T
Sbjct:   292 LIAAKKKLCEMEQKHVFDGLRFGEKSQRNLLADHILNVNSTLLQKALQSIDTSSKRWNVT 351

Query:   357 ELMNATKAELMISSLKISGEGSLGPCARAKKVVTNSSLQKKGNHLVSEGKKAMVLVVHNS 416
             E +NA +A +   +L +S E  L   A  + +  N S  ++G +L SEGK ++ LV+++ 
Sbjct:   352 EEINALRARVSECNLSVSRE-CLSFDASKENMGDNFSFLQQGQNLFSEGKVSICLVLNDH 410

Query:   417 EEGNECDPHSVVS 429
             E       + VVS
Sbjct:   411 ENEEPEGENGVVS 423
GO:0005840 "ribosome" evidence=IEA
GO:0006364 "rRNA processing" evidence=IEA;ISS
GO:0008152 "metabolic process" evidence=IEA
GO:0009507 "chloroplast" evidence=ISM;IDA
GO:0016779 "nucleotidyltransferase activity" evidence=IEA
GO:0042254 "ribosome biogenesis" evidence=ISS
GO:0043022 "ribosome binding" evidence=IEA
GO:0000023 "maltose metabolic process" evidence=RCA
GO:0010267 "production of ta-siRNAs involved in RNA interference" evidence=RCA
GO:0019252 "starch biosynthetic process" evidence=RCA
GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA
GO:0043085 "positive regulation of catalytic activity" evidence=RCA
GO:0051607 "defense response to virus" evidence=RCA
UNIPROTKB|Q81WJ5 rimM "Ribosome maturation factor RimM" [Bacillus anthracis (taxid:1392)] Back     alignment and assigned GO terms
TIGR_CMR|BA_3980 BA_3980 "16S rRNA processing protein RimM" [Bacillus anthracis str. Ames (taxid:198094)] Back     alignment and assigned GO terms
UNIPROTKB|Q71YM3 rimM "Ribosome maturation factor RimM" [Listeria monocytogenes serotype 4b str. F2365 (taxid:265669)] Back     alignment and assigned GO terms
UNIPROTKB|P66653 rimM "Ribosome maturation factor RimM" [Mycobacterium tuberculosis (taxid:1773)] Back     alignment and assigned GO terms
UNIPROTKB|Q47WU9 rimM "Ribosome maturation factor RimM" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
TIGR_CMR|CPS_4068 CPS_4068 "16S rRNA processing protein RimM" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
UNIPROTKB|Q5LNF0 rimM "Ribosome maturation factor RimM" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
TIGR_CMR|SPO_3255 SPO_3255 "16S rRNA processing protein RimM" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
UNIPROTKB|Q60BS2 rimM "Ribosome maturation factor RimM" [Methylococcus capsulatus str. Bath (taxid:243233)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query498
PRK00122172 PRK00122, rimM, 16S rRNA-processing protein RimM; 5e-56
COG0806174 COG0806, RimM, RimM protein, required for 16S rRNA 4e-44
TIGR02273165 TIGR02273, 16S_RimM, 16S rRNA processing protein R 1e-42
pfam0178284 pfam01782, RimM, RimM N-terminal domain 6e-19
PRK14592165 PRK14592, rimM, 16S rRNA-processing protein RimM; 1e-18
PRK13828161 PRK13828, rimM, 16S rRNA-processing protein RimM; 8e-17
PRK13829162 PRK13829, rimM, 16S rRNA-processing protein RimM; 5e-12
PRK14590171 PRK14590, rimM, 16S rRNA-processing protein RimM; 7e-07
pfam0523978 pfam05239, PRC, PRC-barrel domain 1e-06
PRK14594166 PRK14594, rimM, 16S rRNA-processing protein RimM; 2e-06
PRK14593184 PRK14593, rimM, 16S rRNA-processing protein RimM; 0.002
>gnl|CDD|234650 PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information 
 Score =  184 bits (469), Expect = 5e-56
 Identities = 68/194 (35%), Positives = 95/194 (48%), Gaps = 27/194 (13%)

Query: 76  DFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREH 135
           D + VG + S HG++GE+ VK  TDFPE R    G   L +        +EV++  GR H
Sbjct: 6   DLLVVGKIVSAHGIKGEVKVKSFTDFPE-RIFDYGPWLLGKG----GEWQEVEIESGRFH 60

Query: 136 PGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGEL 195
            G    I+ FEG+D    A  L G  L       PELE+ E+Y  DL+G+ VV  E GE 
Sbjct: 61  KG--FLIVKFEGVDDRNAAEALKGCELFVPRSQLPELEEDEYYWHDLIGLEVVD-EDGEE 117

Query: 196 VGTVVNVFNSGANDLLHVMCYSSVNVIEGSEEASSSASDASGRLVWIPFVEEIVPIVDMN 255
           +G V ++  +GAND+L V                            IPFVEE+V  VD+ 
Sbjct: 118 LGKVTDILETGANDVLVV-------------------LKDKKEERLIPFVEEVVKEVDLE 158

Query: 256 GREMQITPPKGLLE 269
            + + +  P+GLL+
Sbjct: 159 AKRITVDWPEGLLD 172

Length = 172
>gnl|CDD|223877 COG0806, RimM, RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|233805 TIGR02273, 16S_RimM, 16S rRNA processing protein RimM Back     alignment and domain information
>gnl|CDD|216696 pfam01782, RimM, RimM N-terminal domain Back     alignment and domain information
>gnl|CDD|173056 PRK14592, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|184351 PRK13828, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|184352 PRK13829, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|173054 PRK14590, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|218519 pfam05239, PRC, PRC-barrel domain Back     alignment and domain information
>gnl|CDD|173058 PRK14594, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|237760 PRK14593, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 498
PRK00122172 rimM 16S rRNA-processing protein RimM; Provisional 100.0
COG0806174 RimM RimM protein, required for 16S rRNA processin 100.0
PRK14591169 rimM 16S rRNA-processing protein RimM; Provisional 100.0
PRK14590171 rimM 16S rRNA-processing protein RimM; Provisional 100.0
PRK14592165 rimM 16S rRNA-processing protein RimM; Provisional 100.0
PRK14593184 rimM 16S rRNA-processing protein RimM; Provisional 100.0
TIGR02273165 16S_RimM 16S rRNA processing protein RimM. This fa 100.0
PRK14594166 rimM 16S rRNA-processing protein RimM; Provisional 100.0
PLN02435 493 probable UDP-N-acetylglucosamine pyrophosphorylase 100.0
PRK13829162 rimM 16S rRNA-processing protein RimM; Provisional 100.0
PRK13828161 rimM 16S rRNA-processing protein RimM; Provisional 100.0
PLN02830 615 UDP-sugar pyrophosphorylase 100.0
KOG2388 477 consensus UDP-N-acetylglucosamine pyrophosphorylas 100.0
PTZ00339 482 UDP-N-acetylglucosamine pyrophosphorylase; Provisi 100.0
cd06424 315 UGGPase UGGPase catalyzes the synthesis of UDP-Glu 99.92
COG4284 472 UDP-glucose pyrophosphorylase [Carbohydrate transp 99.91
cd04193 323 UDPGlcNAc_PPase UDPGlcNAc pyrophosphorylase catala 99.89
cd00897 300 UGPase_euk Eukaryotic UGPase catalyses the synthes 99.82
PF0178284 RimM: RimM N-terminal domain; InterPro: IPR002676 99.8
PF01704 420 UDPGP: UTP--glucose-1-phosphate uridylyltransferas 99.8
PLN02474 469 UTP--glucose-1-phosphate uridylyltransferase 99.79
cd04180 266 UGPase_euk_like Eukaryotic UGPase-like includes UD 99.66
PF0523979 PRC: PRC-barrel domain; InterPro: IPR007903 The PR 98.8
cd00226246 PRCH Photosynthetic reaction center (RC) complex, 97.16
KOG2638 498 consensus UDP-glucose pyrophosphorylase [Carbohydr 97.03
COG187387 Protein implicated in RNA metabolism, contains PRC 93.94
KOG2388477 consensus UDP-N-acetylglucosamine pyrophosphorylas 93.92
PF01128 221 IspD: 2-C-methyl-D-erythritol 4-phosphate cytidyly 91.12
COG1213 239 Predicted sugar nucleotidyltransferases [Cell enve 89.23
PRK13385 230 2-C-methyl-D-erythritol 4-phosphate cytidylyltrans 88.74
TIGR02092 369 glgD glucose-1-phosphate adenylyltransferase, GlgD 88.74
TIGR01150252 puhA photosynthetic reaction center, subunit H, ba 88.17
COG2266177 GTP:adenosylcobinamide-phosphate guanylyltransfera 87.95
TIGR00454 183 conserved hypothetical protein TIGR00454. At this 87.77
PRK00560196 molybdopterin-guanine dinucleotide biosynthesis pr 87.73
PLN02728 252 2-C-methyl-D-erythritol 4-phosphate cytidylyltrans 87.41
TIGR0288876 spore_YlmC_YmxH sporulation protein, YlmC/YmxH fam 87.05
PF1310640 DUF3961: Domain of unknown function (DUF3961) 86.17
cd02509 274 GDP-M1P_Guanylyltransferase GDP-M1P_Guanylyltransf 85.63
PRK15480 292 glucose-1-phosphate thymidylyltransferase RfbA; Pr 85.37
COG0836 333 {ManC} Mannose-1-phosphate guanylyltransferase [Ce 84.24
cd04189 236 G1P_TT_long G1P_TT_long represents the long form o 84.12
COG2451100 Ribosomal protein L35AE/L33A [Translation, ribosom 83.77
COG1093269 SUI2 Translation initiation factor 2, alpha subuni 82.43
PRK0433787 50S ribosomal protein L35Ae; Validated 81.56
cd06422 221 NTP_transferase_like_1 NTP_transferase_like_1 is a 80.41
>PRK00122 rimM 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information 
Probab=100.00  E-value=4.2e-44  Score=337.07  Aligned_cols=170  Identities=40%  Similarity=0.655  Sum_probs=154.0

Q ss_pred             CCCCeEEEEEEeeeeeeeeeEEEEeccCCccccccCCCceEEEEeecCcceeEEEEEEEeEeecCCceEEEEecCCCCHH
Q 010869           73 SGLDFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQKSWILTFEGIDTVE  152 (498)
Q Consensus        73 ~~~e~v~IG~I~~~HGlkGevkV~~~tD~pe~~f~~~~~~~l~~~~~g~~~~~~v~v~~~R~~~~~~~~ivkf~GId~re  152 (498)
                      .+++++.||+|+++||+||||||+++||+|+ +|...+.+|+ .  .+ ...+++++++.|.++  +.++++|+||+|||
T Consensus         3 ~~~~~v~iG~i~~~hGlkGevkv~~~td~p~-~~~~~~~~~~-~--~~-~~~~~~~v~~~~~~~--~~~lvkf~gi~~~~   75 (172)
T PRK00122          3 KPEDLLVVGKIVSAHGIKGEVKVKSFTDFPE-RIFDYGPWLL-G--KG-GEWQEVEIESGRFHK--GFLIVKFEGVDDRN   75 (172)
T ss_pred             CccceEEEEEEECCCcccEEEEEEEecCCHH-HHcCcCcEEE-c--cC-CceEEEEEEEEEEEC--CEEEEEECCCCCHH
Confidence            4578999999999999999999999999999 6666777777 3  22 235678999999884  56999999999999


Q ss_pred             HHhcccCCeEEEeCCCCCCCCCCccchhccCCcEEEecCCCeEeEEEEEeccCCCceEEEEEeecccccccCccccccCc
Q 010869          153 QARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVIEGSEEASSSA  232 (498)
Q Consensus       153 ~Ae~L~G~~l~v~~~dlp~L~edEfY~~DLIGl~V~d~~~G~~LG~V~dV~~~ga~DlL~V~~~~~~~~~~~~~~~~~~~  232 (498)
                      +|++|+|+.||++++++|+|++|||||+|||||+|+| ++|..+|+|++|+++||||+|+|+.                 
T Consensus        76 ~Ae~l~g~~l~i~~~~lp~l~~~e~y~~dLiG~~V~d-~~g~~lG~V~~v~~~~a~dll~I~~-----------------  137 (172)
T PRK00122         76 AAEALKGCELFVPRSQLPELEEDEYYWHDLIGLEVVD-EDGEELGKVTDILETGANDVLVVLK-----------------  137 (172)
T ss_pred             HHHHhCCCEEEEEHHHCCCCCCCCEEHHHhCCcEEEe-CCCcEEEEEEEEccCCCceEEEEEC-----------------
Confidence            9999999999999999999999999999999999997 6788899999999999999999974                 


Q ss_pred             CCCCCcEEEEecccCccceeeCCCCEEEEeCCCCccc
Q 010869          233 SDASGRLVWIPFVEEIVPIVDMNGREMQITPPKGLLE  269 (498)
Q Consensus       233 ~~~~gkevLIPfv~e~V~~VDle~~~I~V~~peGLLe  269 (498)
                        .+++++||||+++||++||+++++|+|+||+||||
T Consensus       138 --~~~~e~liP~~~~~V~~iD~~~~~I~v~~p~gLld  172 (172)
T PRK00122        138 --DKKEERLIPFVEEVVKEVDLEAKRITVDWPEGLLD  172 (172)
T ss_pred             --CCCCEEEEecChhhCCEEECCCCEEEEeCCCcccC
Confidence              36789999999999999999999999999999986

>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>PRK14590 rimM 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>PRK14592 rimM 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>TIGR02273 16S_RimM 16S rRNA processing protein RimM Back     alignment and domain information
>PRK14594 rimM 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>PLN02435 probable UDP-N-acetylglucosamine pyrophosphorylase Back     alignment and domain information
>PRK13829 rimM 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>PRK13828 rimM 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>PLN02830 UDP-sugar pyrophosphorylase Back     alignment and domain information
>KOG2388 consensus UDP-N-acetylglucosamine pyrophosphorylase [Cell wall/membrane/envelope biogenesis] Back     alignment and domain information
>PTZ00339 UDP-N-acetylglucosamine pyrophosphorylase; Provisional Back     alignment and domain information
>cd06424 UGGPase UGGPase catalyzes the synthesis of UDP-Glucose/UDP-Galactose Back     alignment and domain information
>COG4284 UDP-glucose pyrophosphorylase [Carbohydrate transport and metabolism] Back     alignment and domain information
>cd04193 UDPGlcNAc_PPase UDPGlcNAc pyrophosphorylase catalayzes the synthesis of UDPGlcNAc Back     alignment and domain information
>cd00897 UGPase_euk Eukaryotic UGPase catalyses the synthesis of UDP-Glucose Back     alignment and domain information
>PF01782 RimM: RimM N-terminal domain; InterPro: IPR002676 The RimM protein is essential for efficient processing of 16S rRNA [] Back     alignment and domain information
>PF01704 UDPGP: UTP--glucose-1-phosphate uridylyltransferase; InterPro: IPR002618 This family consists of UTP--glucose-1-phosphate uridylyltransferases (2 Back     alignment and domain information
>PLN02474 UTP--glucose-1-phosphate uridylyltransferase Back     alignment and domain information
>cd04180 UGPase_euk_like Eukaryotic UGPase-like includes UDPase and UDPGlcNAc pyrophosphorylase enzymes Back     alignment and domain information
>PF05239 PRC: PRC-barrel domain; InterPro: IPR007903 The PRC-barrel is an all beta barrel domain found in photosynthetic reaction centre subunit H of the purple bacteria Back     alignment and domain information
>cd00226 PRCH Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase Back     alignment and domain information
>KOG2638 consensus UDP-glucose pyrophosphorylase [Carbohydrate transport and metabolism] Back     alignment and domain information
>COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only] Back     alignment and domain information
>KOG2388 consensus UDP-N-acetylglucosamine pyrophosphorylase [Cell wall/membrane/envelope biogenesis] Back     alignment and domain information
>PF01128 IspD: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; InterPro: IPR001228 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, a bacterial ispD protein, catalyzes the third step of the deoxyxylulose-5-phosphate pathway (DXP) of isoprenoid biosynthesis; the formation of 4-diphosphocytidyl-2C-methyl-D-erythritol from CTP and 2C-methyl-D-erythritol 4-phosphate [] Back     alignment and domain information
>COG1213 Predicted sugar nucleotidyltransferases [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>PRK13385 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; Provisional Back     alignment and domain information
>TIGR02092 glgD glucose-1-phosphate adenylyltransferase, GlgD subunit Back     alignment and domain information
>TIGR01150 puhA photosynthetic reaction center, subunit H, bacterial Back     alignment and domain information
>COG2266 GTP:adenosylcobinamide-phosphate guanylyltransferase [Coenzyme metabolism] Back     alignment and domain information
>TIGR00454 conserved hypothetical protein TIGR00454 Back     alignment and domain information
>PRK00560 molybdopterin-guanine dinucleotide biosynthesis protein A; Provisional Back     alignment and domain information
>PLN02728 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase Back     alignment and domain information
>TIGR02888 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family Back     alignment and domain information
>PF13106 DUF3961: Domain of unknown function (DUF3961) Back     alignment and domain information
>cd02509 GDP-M1P_Guanylyltransferase GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose Back     alignment and domain information
>PRK15480 glucose-1-phosphate thymidylyltransferase RfbA; Provisional Back     alignment and domain information
>COG0836 {ManC} Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>cd04189 G1P_TT_long G1P_TT_long represents the long form of glucose-1-phosphate thymidylyltransferase Back     alignment and domain information
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK04337 50S ribosomal protein L35Ae; Validated Back     alignment and domain information
>cd06422 NTP_transferase_like_1 NTP_transferase_like_1 is a member of the nucleotidyl transferase family Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query498
2f1l_A187 Crystal Structure Of A Putative 16s Ribosomal Rna P 8e-10
3h9n_A177 Crystal Structure Of The Ribosome Maturation Factor 2e-06
2dyi_A162 Crystal Structure Of 16s Ribosomal Rna Processing P 2e-04
>pdb|2F1L|A Chain A, Crystal Structure Of A Putative 16s Ribosomal Rna Processing Protein Rimm (Pa3744) From Pseudomonas Aeruginosa At 2.46 A Resolution Length = 187 Back     alignment and structure 
Iteration: 1

 Score = 62.0 bits (149), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 47/149 (31%), Positives = 78/149 (52%), Gaps = 15/149 (10%)
Query: 76  DFVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWL--RQQVLGRET-IREVKLIDG 132
           D V +G + SV+G++GE+ V          FT P    L  R+  L R+  IR+ +L+ G
Sbjct: 19  DLVVIGKIVSVYGIRGEVKV--------YSFTDPLDNLLDYRRWTLRRDGEIRQAELVRG 70
Query: 133 REHPGQKSWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKET 192
           R H   K      +G+D  E+AR   G  +     + P LE+GE+Y   L G++V+  + 
Sbjct: 71  RLH--GKVLAAKLKGLDDREEARTFTGYEICIPRSELPSLEEGEYYWHQLEGLKVI-DQG 127
Query: 193 GELVGTVVNVFNSGANDLLHVM-CYSSVN 220
            +L+G + ++  +GAND+  V  C  S++
Sbjct: 128 RQLLGVIDHLLETGANDVXVVKPCAGSLD 156
>pdb|3H9N|A Chain A, Crystal Structure Of The Ribosome Maturation Factor Rimm (Hi0203) From H.Influenzae. Northeast Structural Genomics Consortium Target Ir66 Length = 177 Back     alignment and structure
>pdb|2DYI|A Chain A, Crystal Structure Of 16s Ribosomal Rna Processing Protein Rimm From Thermus Thermophilus Hb8 Length = 162 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query498
3h9n_A177 Ribosome maturation factor RIMM; structural genomi 7e-47
2qgg_A182 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR 8e-45
2f1l_A187 16S rRNA processing protein; structural genomics, 1e-44
2dyi_A162 Probable 16S rRNA-processing protein RIMM; ribosom 2e-43
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-07
1jv1_A 505 Glcnac1P uridyltransferase isoform 1: AGX1; nucleo 2e-04
2yqc_A 486 UDP-N-acetylglucosamine pyrophosphorylase; uridine 2e-04
>3h9n_A Ribosome maturation factor RIMM; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Haemophilus influenzae} Length = 177 Back     alignment and structure
 Score =  159 bits (405), Expect = 7e-47
 Identities = 50/191 (26%), Positives = 92/191 (48%), Gaps = 23/191 (12%)

Query: 80  VGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQK 139
           VG + S +G++G + +  ST+  E  F      +L+ +       + ++L + R H    
Sbjct: 5   VGKLGSTYGIRGWLRIYSSTEQAESIFD-YQPWFLKIK----GEWQSIELENWRYH--NH 57

Query: 140 SWILTFEGIDTVEQARPLVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTV 199
             I+  +G+D  E A+ L    +       PELE+G++Y  DL+G  VV  E G  +GTV
Sbjct: 58  EIIVKLKGVDDREAAQILANVEIGVDLSVFPELEEGDYYWHDLIGCTVVNLE-GYTMGTV 116

Query: 200 VNVFNSGANDLLHVMCYSSVNVIEGSEEASSSASDASGRLVWIPFV-EEIVPIVDMNGRE 258
             +  +G+ND+L         V++ + + +        +   IPF+ E++V  VD+  + 
Sbjct: 117 TEMMETGSNDVL---------VVKANTKDAF-----GKQERLIPFLYEQVVKRVDLTTKT 162

Query: 259 MQITPPKGLLE 269
           +++    G LE
Sbjct: 163 IEVDWDAGFLE 173
>2qgg_A 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, structural genomics, PSI-2, protein structure initiative; 2.40A {Acinetobacter calcoaceticus} Length = 182 Back     alignment and structure
>2f1l_A 16S rRNA processing protein; structural genomics, joint CENT structural genomics, JCSG, protein structure initiative, PS unknown function; HET: UNL; 2.46A {Pseudomonas aeruginosa} SCOP: b.41.1.4 b.43.3.4 Length = 187 Back     alignment and structure
>2dyi_A Probable 16S rRNA-processing protein RIMM; ribosomal protein S19, PRC-barrel, STRU genomics, NPPSFA; 2.00A {Thermus thermophilus} PDB: 3a1p_A 2dog_A Length = 162 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1jv1_A Glcnac1P uridyltransferase isoform 1: AGX1; nucleotidyltransferase, alternative splicing; HET: UD1; 1.90A {Homo sapiens} SCOP: c.68.1.5 PDB: 1jv3_A* 1jvg_A* 1jvd_A* 1vm8_A* Length = 505 Back     alignment and structure
>2yqc_A UDP-N-acetylglucosamine pyrophosphorylase; uridine-diphospho-N- acetylglucosamine, N-acetylglucosamine-1-phosphate, transferase; 1.90A {Candida albicans} PDB: 2yqh_A* 2yqj_A* 2yqs_A* Length = 486 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query498
3h9n_A177 Ribosome maturation factor RIMM; structural genomi 100.0
2f1l_A187 16S rRNA processing protein; structural genomics, 100.0
2qgg_A182 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR 100.0
2dyi_A162 Probable 16S rRNA-processing protein RIMM; ribosom 100.0
2yqc_A 486 UDP-N-acetylglucosamine pyrophosphorylase; uridine 100.0
1jv1_A 505 Glcnac1P uridyltransferase isoform 1: AGX1; nucleo 100.0
3ogz_A 630 UDP-sugar pyrophosphorylase; LEFT handed beta heli 99.97
3r3i_A 528 UTP--glucose-1-phosphate uridylyltransferase; ross 99.94
3oc9_A 405 UDP-N-acetylglucosamine pyrophosphorylase; structu 99.92
3gue_A 484 UTP-glucose-1-phosphate uridylyltransferase 2; pho 99.87
2icy_A 469 Probable UTP-glucose-1-phosphate uridylyltransfera 99.77
2oeg_A 505 UTP-glucose-1-phosphate uridylyltransferase 2, put 99.75
2i5k_A 488 UTP--glucose-1-phosphate uridylyltransferase; LEFT 99.69
1eys_H259 Photosynthetic reaction center; membrane protein c 95.48
3htr_A120 Uncharacterized PRC-barrel domain protein; beta-ba 94.6
1pm3_A97 MTH1895; unknown function, structural genomics, PS 90.99
3st8_A 501 Bifunctional protein GLMU; acetyltransferase, pyro 90.38
3q80_A 231 2-C-methyl-D-erythritol 4-phosphate cytidyltransf; 89.17
1rzh_H260 Reaction center protein H chain; bacterial photosy 88.39
2qh5_A 308 PMI, ALGA, mannose-6-phosphate isomerase; structur 88.06
2wjn_H258 Reaction center protein H chain; bacteriochlorophy 87.7
2xwl_A 223 2-C-methyl-D-erythritol 4-phosphate cytidylyltran; 85.0
1fxo_A 293 Glucose-1-phosphate thymidylyltransferase; rhamnos 84.79
4ecm_A 269 Glucose-1-phosphate thymidylyltransferase; HET: DA 83.79
3f1c_A 246 Putative 2-C-methyl-D-erythritol 4-phosphate cytid 82.03
3d5n_A 197 Q97W15_sulso; NESG, SSR125, structural genomics, P 82.01
1vgw_A 231 4-diphosphocytidyl-2C-methyl-D-erythritol synthas; 81.05
1lvw_A 295 Glucose-1-phosphate thymidylyltransferase; protein 80.96
1h7e_A 245 3-deoxy-manno-octulosonate cytidylyltransferase; n 80.73
3rsb_A 196 Adenosylcobinamide-phosphate guanylyltransferase; 80.54
>3h9n_A Ribosome maturation factor RIMM; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.70A {Haemophilus influenzae} Back     alignment and structure
Probab=100.00  E-value=2.7e-46  Score=352.33  Aligned_cols=172  Identities=28%  Similarity=0.426  Sum_probs=155.3

Q ss_pred             eEEEEEEeeeeeeeeeEEEEeccCCccccccCCCceEEEEeecCcceeEEEEEEEeEeecCCceEEEEecCCCCHHHHhc
Q 010869           77 FVDVGYVYSVHGLQGEISVKPSTDFPELRFTTPGTRWLRQQVLGRETIREVKLIDGREHPGQKSWILTFEGIDTVEQARP  156 (498)
Q Consensus        77 ~v~IG~I~~~HGlkGevkV~~~tD~pe~~f~~~~~~~l~~~~~g~~~~~~v~v~~~R~~~~~~~~ivkf~GId~re~Ae~  156 (498)
                      +|.||+|+++||+||||||+++||+|+ +|..++.+|+..  .+  .+++++|+++|.|+  +.+++||+||+|||+|++
T Consensus         2 ~v~vG~I~~~hGikGevkv~~~Td~pe-~~~~~~~~~l~~--~~--~~~~~~v~~~r~~~--~~~lvkf~gi~dr~~Ae~   74 (177)
T 3h9n_A            2 IEVVGKLGSTYGIRGWLRIYSSTEQAE-SIFDYQPWFLKI--KG--EWQSIELENWRYHN--HEIIVKLKGVDDREAAQI   74 (177)
T ss_dssp             EEEEEEEEEECSSSSCEEEEECSSSSG-GGGGCCSEEEEE--TT--EEEEECEEEEEESS--SCEEEEESSCCSHHHHHT
T ss_pred             EEEEEEEeCCCccCEEEEEEECCCCHH-HhcCCCEEEEec--CC--eEEEEEEEEEEEeC--CEEEEEEcCCCCHHHHHH
Confidence            689999999999999999999999999 777788888865  33  45789999999984  679999999999999999


Q ss_pred             ccCCeEEEeCCCCCCCCCCccchhccCCcEEEecCCCeEeEEEEEeccCCCceEEEEEeecccccccCccccccCcCCCC
Q 010869          157 LVGSTLLAREGDRPELEDGEFYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVIEGSEEASSSASDAS  236 (498)
Q Consensus       157 L~G~~l~v~~~dlp~L~edEfY~~DLIGl~V~d~~~G~~LG~V~dV~~~ga~DlL~V~~~~~~~~~~~~~~~~~~~~~~~  236 (498)
                      |+|+.|||+++++|+|++|||||+|||||+|++ ++|+.||+|++|+++||||||+|+....              ...+
T Consensus        75 L~G~~l~v~~~~lp~l~edE~Y~~dLiGl~V~~-~~g~~lG~V~~v~~~gandvl~V~~~~~--------------~~~~  139 (177)
T 3h9n_A           75 LANVEIGVDLSVFPELEEGDYYWHDLIGCTVVN-LEGYTMGTVTEMMETGSNDVLVVKANTK--------------DAFG  139 (177)
T ss_dssp             TTTCEEEEECCCCCCCSSSCGGGGGTTTCEEEE-TTCCEEEEEEEEEESSSCEEEEEECCTT--------------CTTC
T ss_pred             hcCCEEEEEHHHCCCCCCCCCCHHHhcCCEEEe-CCCCEEEEEEEEeeCCCcEEEEEEeccc--------------cCCC
Confidence            999999999999999999999999999999997 5788999999999999999999986210              0125


Q ss_pred             CcEEEEecc-cCccceeeCCCCEEEEeCCCCcccc
Q 010869          237 GRLVWIPFV-EEIVPIVDMNGREMQITPPKGLLEL  270 (498)
Q Consensus       237 gkevLIPfv-~e~V~~VDle~~~I~V~~peGLLeL  270 (498)
                      ++++||||+ ++||++||+++|+|+|+||+||||.
T Consensus       140 ~~e~LIP~v~~~~V~~VDl~~~~I~v~~p~glle~  174 (177)
T 3h9n_A          140 KQERLIPFLYEQVVKRVDLTTKTIEVDWDAGFLEH  174 (177)
T ss_dssp             CSEEEEECCBTTTEEEEEGGGTEEEECCCSSTTCC
T ss_pred             CcEEEeeccchheEEEEeCCCCEEEEECCcchhhc
Confidence            789999999 9999999999999999999999985
>2f1l_A 16S rRNA processing protein; structural genomics, joint CENT structural genomics, JCSG, protein structure initiative, PS unknown function; HET: UNL; 2.46A {Pseudomonas aeruginosa} SCOP: b.41.1.4 b.43.3.4 Back     alignment and structure
>2qgg_A 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73, structural genomics, PSI-2, protein structure initiative; 2.40A {Acinetobacter calcoaceticus} Back     alignment and structure
>2dyi_A Probable 16S rRNA-processing protein RIMM; ribosomal protein S19, PRC-barrel, STRU genomics, NPPSFA; 2.00A {Thermus thermophilus} PDB: 3a1p_A 2dog_A Back     alignment and structure
>2yqc_A UDP-N-acetylglucosamine pyrophosphorylase; uridine-diphospho-N- acetylglucosamine, N-acetylglucosamine-1-phosphate, transferase; 1.90A {Candida albicans} PDB: 2yqh_A* 2yqj_A* 2yqs_A* Back     alignment and structure
>1jv1_A Glcnac1P uridyltransferase isoform 1: AGX1; nucleotidyltransferase, alternative splicing; HET: UD1; 1.90A {Homo sapiens} SCOP: c.68.1.5 PDB: 1jv3_A* 1jvg_A* 1jvd_A* 1vm8_A* Back     alignment and structure
>3ogz_A UDP-sugar pyrophosphorylase; LEFT handed beta helix, rossmann fold, UDP sugar pyrophospho transferase; 2.03A {Leishmania major} PDB: 3oh3_A* 3oh1_A* 3oh0_A* 3oh2_A* 3oh4_A* Back     alignment and structure
>3r3i_A UTP--glucose-1-phosphate uridylyltransferase; rossmann fold, beta barrel, nucleotidyltransferase; 3.57A {Homo sapiens} PDB: 3r2w_A Back     alignment and structure
>3oc9_A UDP-N-acetylglucosamine pyrophosphorylase; structural genomics, seattle structural genomics center for infectious disease, ssgcid; 1.80A {Entamoeba histolytica} Back     alignment and structure
>3gue_A UTP-glucose-1-phosphate uridylyltransferase 2; phosphatase, UDP, structural GE structural genomics consortium, SGC; HET: UPG PG4; 1.92A {Trypanosoma brucei} Back     alignment and structure
>2oeg_A UTP-glucose-1-phosphate uridylyltransferase 2, putative; rossmann-fold, beta-helix, pyrophosphorylase; HET: UPG; 2.30A {Leishmania major} PDB: 2oef_A* Back     alignment and structure
>2i5k_A UTP--glucose-1-phosphate uridylyltransferase; LEFT-handed beta-helix, SGC domain; 3.10A {Saccharomyces cerevisiae} Back     alignment and structure
>1eys_H Photosynthetic reaction center; membrane protein complex, electron transport; HET: BGL BCL BPH MQ8 HEM CRT LDA PEF; 2.20A {Thermochromatium tepidum} SCOP: b.41.1.1 f.23.10.1 Back     alignment and structure
>3htr_A Uncharacterized PRC-barrel domain protein; beta-barrel, photo-reaction-center domain, structural genomics, PSI-2; HET: MSE; 2.06A {Rhodopseudomonas palustris} Back     alignment and structure
>1pm3_A MTH1895; unknown function, structural genomics, PSI, protein structure initiative; 3.15A {Methanothermobacterthermautotrophicus} SCOP: b.41.1.2 Back     alignment and structure
>3st8_A Bifunctional protein GLMU; acetyltransferase, pyrophosphorylase, rossmann fold, LEFT-handed-beta-helix, cell shape; HET: COA GP1 UD1; 1.98A {Mycobacterium tuberculosis} PDB: 3spt_A* 3foq_A 3dk5_A 3d8v_A 3d98_A* 3dj4_A 2qkx_A* Back     alignment and structure
>3q80_A 2-C-methyl-D-erythritol 4-phosphate cytidyltransf; TB structural genomics consortium, TBSGC, rossman fold; HET: CDM; 2.00A {Mycobacterium tuberculosis} SCOP: c.68.1.0 PDB: 3q7u_A* 3okr_A 2xwn_A* Back     alignment and structure
>1rzh_H Reaction center protein H chain; bacterial photosynthesis, proton TR pathway, revertant, integral membrane protein, photosynthes; HET: BCL BPH U10 HTO SPO LDA CDL; 1.80A {Rhodobacter sphaeroides} SCOP: b.41.1.1 f.23.10.1 PDB: 1e14_H* 1f6n_H* 1fnp_H* 1fnq_H* 1jgw_H* 1jgx_H* 1jgy_H* 1jgz_H* 1jh0_H* 1k6l_H* 1k6n_H* 1kby_H* 1l9b_H* 1l9j_H* 1m3x_H* 1mps_H* 1pcr_H* 1e6d_H* 1rg5_H* 1rgn_H* ... Back     alignment and structure
>2qh5_A PMI, ALGA, mannose-6-phosphate isomerase; structural genomics, PSI, protein structure initi nysgrc; 2.30A {Helicobacter pylori} Back     alignment and structure
>2wjn_H Reaction center protein H chain; bacteriochlorophyll, lipidic-sponge phase, photosynthesis, R center, electron transport, cell membrane; HET: HEM FME BCB BPB MPG MQ7 NS5; 1.86A {Rhodopseudomonas viridis} PDB: 1prc_H* 1r2c_H* 1vrn_H* 1dxr_H* 2jbl_H* 2prc_H* 2i5n_H* 2wjm_H* 2x5u_H* 2x5v_H* 3d38_H* 3prc_H* 3t6e_H* 4ac5_H* 5prc_H* 6prc_H* 7prc_H* 3t6d_H* 3g7f_H* Back     alignment and structure
>2xwl_A 2-C-methyl-D-erythritol 4-phosphate cytidylyltran; transferase, MEP pathway; HET: CTP; 1.49A {Mycobacterium smegmatis} PDB: 2xwm_A* Back     alignment and structure
>1fxo_A Glucose-1-phosphate thymidylyltransferase; rhamnose, nucleotidyltransferase, pyrophosphorylase, allostery; HET: TMP; 1.66A {Pseudomonas aeruginosa} SCOP: c.68.1.6 PDB: 1fzw_A 1g0r_A* 1g1l_A* 1g23_A* 1g2v_A* 1g3l_A* 1h5r_A* 1h5s_C* 1h5t_A* 1h5s_D* 1h5s_A* 1h5r_B* 1h5s_B* 1h5t_B* 1iim_A* 1iin_A* 3pkp_A* 3pkq_A* 1mp5_A* 1mp3_A* ... Back     alignment and structure
>4ecm_A Glucose-1-phosphate thymidylyltransferase; HET: DAU; 2.30A {Bacillus anthracis} PDB: 3hl3_A* Back     alignment and structure
>3f1c_A Putative 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2; structural genomics, PSI-2, protein structure initiative; 2.30A {Listeria monocytogenes str} SCOP: c.68.1.0 Back     alignment and structure
>3d5n_A Q97W15_sulso; NESG, SSR125, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; 2.80A {Sulfolobus solfataricus} Back     alignment and structure
>1vgw_A 4-diphosphocytidyl-2C-methyl-D-erythritol synthas; structural genomics, transferase; 2.35A {Neisseria gonorrhoeae} SCOP: c.68.1.13 PDB: 1vgz_A Back     alignment and structure
>1lvw_A Glucose-1-phosphate thymidylyltransferase; protein nucleotide complex, nucleotide binding fold; HET: TYD; 1.70A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: c.68.1.6 Back     alignment and structure
>1h7e_A 3-deoxy-manno-octulosonate cytidylyltransferase; nucleotidyltransferase, CMP-KDO synthetase, nucleoside monophosphate glycosides; 1.83A {Escherichia coli} SCOP: c.68.1.13 PDB: 1gqc_A* 1gq9_A 1h6j_A 1h7f_A* 1h7g_A* 1h7h_A* 1h7t_A* Back     alignment and structure
>3rsb_A Adenosylcobinamide-phosphate guanylyltransferase; pyrophosphorylase binding motif, pyrophosphorylase; HET: GTP; 2.80A {Methanocaldococcus jannaschii} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 498
d2f1la175 b.41.1.4 (A:101-175) 16S rRNA processing protein R 1e-15
d2f1la289 b.43.3.4 (A:7-95) 16S rRNA processing protein RimM 4e-15
d1jv1a_ 501 c.68.1.5 (A:) UDP-N-acetylglucosamine pyrophosphor 5e-13
>d2f1la1 b.41.1.4 (A:101-175) 16S rRNA processing protein RimM, C-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 75 Back     information, alignment and structure

class: All beta proteins
fold: PRC-barrel domain
superfamily: PRC-barrel domain
family: RimM C-terminal domain-like
domain: 16S rRNA processing protein RimM, C-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 69.7 bits (171), Expect = 1e-15
 Identities = 17/90 (18%), Positives = 40/90 (44%), Gaps = 16/90 (17%)

Query: 177 FYTRDLVGMRVVMKETGELVGTVVNVFNSGANDLLHVMCYSSVNVIEGSEEASSSASDAS 236
           +Y   L G++V+  +  +L+G + ++  +GAND++         V++    +        
Sbjct: 1   YYWHQLEGLKVI-DQGRQLLGVIDHLLETGANDVM---------VVKPCAGSL------D 44

Query: 237 GRLVWIPFVEEIVPIVDMNGREMQITPPKG 266
            R   +P+  + V  +D+   EM++     
Sbjct: 45  DRERLLPYTGQCVLSIDLAAGEMRVDWDAD 74
>d2f1la2 b.43.3.4 (A:7-95) 16S rRNA processing protein RimM, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Length = 89 Back     information, alignment and structure
>d1jv1a_ c.68.1.5 (A:) UDP-N-acetylglucosamine pyrophosphorylase {Human (Homo sapiens), AGX1 [TaxId: 9606]} Length = 501 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query498
d1jv1a_ 501 UDP-N-acetylglucosamine pyrophosphorylase {Human ( 100.0
d2icya2 378 UDP-glucose pyrophosphorylase 2 (UDPGP 2) {Thale c 99.85
d2f1la289 16S rRNA processing protein RimM, N-terminal domai 99.83
d2f1la175 16S rRNA processing protein RimM, C-terminal domai 99.81
d1eysh1201 Photosynthetic reaction centre {Thermochromatium t 96.82
d2i5nh1222 Photosynthetic reaction centre {Rhodopseudomonas v 95.28
d1rzhh1213 Photosynthetic reaction centre {Rhodobacter sphaer 93.86
d1pm3a_78 MTH1895 {Archaeon Methanobacterium thermoautotroph 93.26
d1lvwa_ 295 RmlA (RfbA) {Archaeon Methanobacterium thermoautot 92.51
d1w77a1 226 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) 92.34
d1i52a_ 225 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) 88.47
d1w55a1 205 IspD/IspF bifunctional enzyme, CDP-me synthase dom 87.83
d1e5ka_188 Molybdenum cofactor biosynthesis protein MobA {Esc 86.16
d1vgwa_ 226 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) 85.97
d1fxoa_ 292 RmlA (RfbA) {Pseudomonas aeruginosa [TaxId: 287]} 85.84
d1sqra_87 Ribosomal protein L35ae {Pyrococcus furiosus [TaxI 84.8
d1vpaa_ 221 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) 84.56
d2cu2a2 268 Putative mannose-1-phosphate guanylyl transferase 84.33
d2oi6a2 248 N-acetylglucosamine 1-phosphate uridyltransferase 83.71
d1mc3a_ 291 RffH {Escherichia coli [TaxId: 562]} 82.68
>d1jv1a_ c.68.1.5 (A:) UDP-N-acetylglucosamine pyrophosphorylase {Human (Homo sapiens), AGX1 [TaxId: 9606]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Nucleotide-diphospho-sugar transferases
superfamily: Nucleotide-diphospho-sugar transferases
family: UDP-glucose pyrophosphorylase
domain: UDP-N-acetylglucosamine pyrophosphorylase
species: Human (Homo sapiens), AGX1 [TaxId: 9606]

Probab=100.00  E-value=2.6e-41  Score=360.01  Aligned_cols=191  Identities=14%  Similarity=0.158  Sum_probs=154.1

Q ss_pred             HHHHHHHHHHHcCCcccccccccCCHHHHHHHHHHHhcCCHHHHHHHHHhccccccccchhhhhchhhhhhhhhcccCCC
Q 010869          296 RLIAAKKKLREMEQQHVFHGFRFGEKYQTSLLANHIVGINSKLLQQALQNIEIPSKRWNATELMNATKAELMISSLKISG  375 (498)
Q Consensus       296 ~~~~lk~~L~~~gQ~Hlf~fw~~L~~~er~~L~~qL~~id~~~l~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~piP~  375 (498)
                      .+++++++|+++||+|||+||++|+++||++|++||.+||+..+++.++.+......+.       ......+.+.|+|+
T Consensus         2 ~~~~l~~~L~~~gQ~HLl~~~~~l~~~ek~~L~~qL~~id~~~l~~~~~~a~~~~~~~~-------~~~~~~~~~~p~p~   74 (501)
T d1jv1a_           2 NINDLKLTLSKAGQEHLLRFWNELEEAQQVELYAELQAMNFEELNFFFQKAIEGFNQSS-------HQKNVDARMEPVPR   74 (501)
T ss_dssp             CHHHHHHHHHHTTCGGGGTTGGGSCHHHHHHHHHHHHTCCHHHHHHHHHHHHHCC------------------CCBCCCG
T ss_pred             CHHHHHHHHHHhCcHHHHhhhhhCCHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhhcc-------cccCccccccCCCh
Confidence            36789999999999999999999999999999999999999999888886544322111       11112344667887


Q ss_pred             CCCCCC-CCchhhcccchHHHHHHhhhhccCcEEEEEecCCCCCCCccc-CCCC-cc-cCCCcchHHHHHHHHHHHHHHH
Q 010869          376 EGSLGP-CARAKKVVTNSSLQKKGNHLVSEGKKAMVLVVHNSEEGNECD-PHSV-VS-ESTANKSLALLQTLLSDDQRFV  451 (498)
Q Consensus       376 e~~~~~-~~~~~~~~~~~~~~~~Gl~~Is~GkVavlLlAGGqg~rlG~~-p~~l-~s-~~~~kslfql~aerI~~lq~La  451 (498)
                      + .+.. ..+.+.+.   +|+++|+++|++||||||+||||+|||+||+ |+++ |. +.+++|+||+++++|+++|++|
T Consensus        75 ~-~~~~~~~~~~~~~---~~~~~G~~~i~~gkvavvllaGG~GTRLG~~~pK~~~~v~~~~~ksllql~~e~i~~l~~~a  150 (501)
T d1jv1a_          75 E-VLGSATRDQDQLQ---AWESEGLFQISQNKVAVLLLAGGQGTRLGVAYPKGMYDVGLPSRKTLFQIQAERILKLQQVA  150 (501)
T ss_dssp             G-GEEETTTTGGGHH---HHHHHHHHHHHTTCEEEEEECCCCCCTTSCSSCGGGCCCCCTTCCCHHHHHHHHHHHHHHHH
T ss_pred             h-hhcccccChHHHH---HHHHhhHHHHhcCCEEEEEECCCccccCCCCCCceeeeeccCCCCcHHHHHHHHHHHHHHHH
Confidence            6 2221 22333444   7999999999999999999999999999998 6442 21 2347999999999999999998


Q ss_pred             hh--cCCccceEEEeCCccchHHHHHhhHhCCCCccCCCcEEEEecCC
Q 010869          452 KI--ENRASMPLVLVLPALEMQMLEKLFLDNDHFAFDSKKVSNISESF  497 (498)
Q Consensus       452 ~~--~~~~~IPwyIMTS~~T~~~T~~fF~~n~yFGL~~~qV~fF~Q~~  497 (498)
                      ..  +.++.||||||||..|++.|++||++|+||||+++||+||+|+.
T Consensus       151 ~~~~~~~~~iPl~IMtS~~T~~~t~~~l~~~~~FGl~~~~v~~f~Q~~  198 (501)
T d1jv1a_         151 EKYYGNKCIIPWYIMTSGRTMESTKEFFTKHKYFGLKKENVIFFQQGM  198 (501)
T ss_dssp             HHHHSSCCCCCEEEEECTTTHHHHHHHHHHTGGGGSCGGGEEEEECCE
T ss_pred             HHhcCCCCCceEEEECChhHhHHHHHHHHhccccCCCcCceEEEEecC
Confidence            54  67889999999999999999999999999999999999999975
>d2icya2 c.68.1.5 (A:6-383) UDP-glucose pyrophosphorylase 2 (UDPGP 2) {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d2f1la2 b.43.3.4 (A:7-95) 16S rRNA processing protein RimM, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d2f1la1 b.41.1.4 (A:101-175) 16S rRNA processing protein RimM, C-terminal domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1eysh1 b.41.1.1 (H:59-259) Photosynthetic reaction centre {Thermochromatium tepidum [TaxId: 1050]} Back     information, alignment and structure
>d2i5nh1 b.41.1.1 (H:37-258) Photosynthetic reaction centre {Rhodopseudomonas viridis [TaxId: 1079]} Back     information, alignment and structure
>d1rzhh1 b.41.1.1 (H:36-248) Photosynthetic reaction centre {Rhodobacter sphaeroides [TaxId: 1063]} Back     information, alignment and structure
>d1pm3a_ b.41.1.2 (A:) MTH1895 {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1lvwa_ c.68.1.6 (A:) RmlA (RfbA) {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Back     information, alignment and structure
>d1w77a1 c.68.1.13 (A:75-300) 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP) {Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702]} Back     information, alignment and structure
>d1i52a_ c.68.1.13 (A:) 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1w55a1 c.68.1.13 (A:3-207) IspD/IspF bifunctional enzyme, CDP-me synthase domain {Campylobacter jejuni [TaxId: 197]} Back     information, alignment and structure
>d1e5ka_ c.68.1.8 (A:) Molybdenum cofactor biosynthesis protein MobA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vgwa_ c.68.1.13 (A:) 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP) {Neisseria gonorrhoeae [TaxId: 485]} Back     information, alignment and structure
>d1fxoa_ c.68.1.6 (A:) RmlA (RfbA) {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1sqra_ b.43.3.3 (A:) Ribosomal protein L35ae {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1vpaa_ c.68.1.13 (A:) 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP) {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2cu2a2 c.68.1.20 (A:1-268) Putative mannose-1-phosphate guanylyl transferase (GDP)/mannose-6-phosphate isomerase TTHA1750 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2oi6a2 c.68.1.5 (A:4-251) N-acetylglucosamine 1-phosphate uridyltransferase GlmU, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1mc3a_ c.68.1.6 (A:) RffH {Escherichia coli [TaxId: 562]} Back     information, alignment and structure