Psyllid ID: psy3773

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-------500-------510-------520-------530-------540-------550-------560-------570-------58
MEKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKFAMLNPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINMNSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATRHGFLLFWISIKLLSNDHNYTTIASGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYLSATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD
ccccHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEccccEEEEcccccHHHHHHHHHHHHHccccccccccccccccccccccccccccEEEEEEEcccEEEEEEEEcccccccccccccccccHHHHHHHHHHHHHcccccccccEEEEEEcccHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHcccccccccccEEEEEEEEcccccccccccEEEEccccccccccEEEEccccEEEcccccccccccccHHHHHccEEEccccccHHHHHHHHccccccccccEEEEEEEEEEccEEEEEEccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEccccccccccHHHHHHHHHHHccccccccccccccccccEEEEEEEEEcccccEEEEEEEcccccHHHHHcccccccccccccccccEEEEcccccccEEEEEcccccHHHHHHHcccEEEEEccccccccccccEEEEEccccEEEEcccccccHHHHHHcccccEEEEEEEcccHHHHccccccccccccccHHHHHccccccccEEEEccc
ccccHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEEEccEEEEEcccccHHHHHHHHHHHHcccccccccHHEEcccccccccccccccEEEEEEEccccEEEEEEEEcccccHcHHHHHHccccccHHHHHHHHcccccccccccEEEEEEccccHHHHHHHHHHHHHccccHHHHHHcccccHHHHHHHHHHHHHHHcccccccccccEEEEEEEEEccccccccccEEEEccccccccEEEEEcccccccccccccccccccHcHHHHHHHHEHHHHHHcHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHcHEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEEEEEccccccHcHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccHcHHHEHHEEEEEcccccHEEEHHHHcccccccEEEEEEcccccHHHHHHHccEEEEEEcccccHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccEEEEcHHHHHHcEEEHHHHHHHHHHHHHHEEEEEEEcc
MEKGIAAKDAIAQILINSRmcakekrpicqdtgIVNVFLKIGMnvrfkgfngsihDVINegvrrgytnpnnilrasivsdphfirkntqdntpavinmelvpgnfldikiaskgggsenktkfamlnpsdsLVDWIMKtvptmgagwcppgilgigiggtPEKAMLMAKKVLMQDINmnsiikngpknkIEELRLELFNKINSlgigaqgmgglsTVLDVKImmypthaaskpvaiipncaatrHGFLLFWISIKLlsndhnyttiaSGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGylsatdsrnsrdgrfierigfynplaskkeKKFKILLNRFTYWkqvgaktsltVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARkiwffdpnslklFSIKILNKKNHGNYVLANLYGITDRNLATKLQGYYLKISindfpkllssdtfyWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD
MEKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASkgggsenkTKFAMLNPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINMNSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATRHGFLLFWISIKLLSNDHNYTTIASGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYLSATDSRNSRDGRFIERigfynplaskkekKFKILLNRFTYWKQVGAKTSLTVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD
MEKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKFAMLNPSDSLVDWIMKTVPTMGAGWCPPgilgigiggTPEKAMLMAKKVLMQDINMNSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATRHGFLLFWISIKLLSNDHNYTTIASGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLViigilfsipiiifgsKLVLILIEKFssiiilcsillgylsATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQsstkiictkkykkkyGILIPfikifiknvdiikkkiivdWD
*******KDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIAS**********FAMLNPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINMNSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATRHGFLLFWISIKLLSNDHNYTTIASGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYLSATD*****DGRFIERIGFYN**********KILLNRFTYWKQVGAKTSLTVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDW*
*E*GIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKFAMLNPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINMNSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATRHGFLLFWISIKLLSNDHN************AIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYL***********************************************TSLTVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNS***********KNHGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSS***********KYGILIPFIKIFIKNVDIIKKKIIVDWD
MEKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKFAMLNPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINMNSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATRHGFLLFWISIKLLSNDHNYTTIASGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYLSATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD
****IAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKFAMLNPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINMNSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATRHGFLLFWISIKLLSNDHNYTTIASGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYLSAT****SRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
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MEKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKFAMLNPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINMNSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATRHGFLLFWISIKLLSNDHNYTTIASGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYLSATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD
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 ?
Query578 2.2.26 [Sep-21-2011]
Q0KD80222 Ribosome maturation facto no N/A 0.290 0.756 0.354 7e-29
B3R397207 Ribosome maturation facto no N/A 0.290 0.811 0.354 2e-28
Q46Y83221 Ribosome maturation facto no N/A 0.290 0.760 0.326 1e-27
B1YV58225 Ribosome maturation facto no N/A 0.370 0.951 0.310 4e-27
Q0BH68226 Ribosome maturation facto no N/A 0.370 0.946 0.310 5e-27
Q1LQE1220 Ribosome maturation facto no N/A 0.299 0.786 0.335 1e-26
Q58690285 Putative fumarate hydrata yes N/A 0.413 0.838 0.366 1e-25
A9ADT0223 Ribosome maturation facto no N/A 0.295 0.766 0.327 3e-25
Q39ID5225 Ribosome maturation facto no N/A 0.370 0.951 0.281 5e-25
A4JCJ8225 Ribosome maturation facto no N/A 0.295 0.76 0.333 5e-25
>sp|Q0KD80|RIMM_CUPNH Ribosome maturation factor RimM OS=Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) GN=rimM PE=3 SV=1 Back     alignment and function desciption
 Score =  129 bits (324), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 66/186 (35%), Positives = 93/186 (50%), Gaps = 18/186 (9%)

Query: 402 DHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFS----------I 451
           + L+ +G +  AYGI GWI +    DD +   +AR+ W   P    L +          +
Sbjct: 41  EDLVEVGYIGAAYGIRGWIKVLPHADDASALLHARRWWLLAPPQAGLVAADASRAQPVCV 100

Query: 452 KILNKKNHGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVE 511
           KI   + H   V+A   G+ DRNLA  L+G  + I   DFP     D FYW +LI C V 
Sbjct: 101 KIAQSREHSGTVVAQASGVADRNLAEALKGRRVWIRRADFPAP-EEDEFYWVDLIGCTVS 159

Query: 512 NIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKK 571
           N  G+LLG V+ +I N  H IL       ++ C     K    LIPF+  F+++VD   K
Sbjct: 160 NEQGELLGEVSGLIDNGAHQIL-------QVACVLPDGKAGERLIPFVDAFLRSVDTAGK 212

Query: 572 KIIVDW 577
           +I+VDW
Sbjct: 213 RIVVDW 218
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.
Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (taxid: 381666)
>sp|B3R397|RIMM_CUPTR Ribosome maturation factor RimM OS=Cupriavidus taiwanensis (strain R1 / LMG 19424) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|Q46Y83|RIMM_CUPPJ Ribosome maturation factor RimM OS=Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|B1YV58|RIMM_BURA4 Ribosome maturation factor RimM OS=Burkholderia ambifaria (strain MC40-6) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|Q0BH68|RIMM_BURCM Ribosome maturation factor RimM OS=Burkholderia ambifaria (strain ATCC BAA-244 / AMMD) GN=rimM PE=3 SV=2 Back     alignment and function description
>sp|Q1LQE1|RIMM_RALME Ribosome maturation factor RimM OS=Ralstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|Q58690|FUMA_METJA Putative fumarate hydratase subunit alpha OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=MJ1294 PE=3 SV=1 Back     alignment and function description
>sp|A9ADT0|RIMM_BURM1 Ribosome maturation factor RimM OS=Burkholderia multivorans (strain ATCC 17616 / 249) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|Q39ID5|RIMM_BURS3 Ribosome maturation factor RimM OS=Burkholderia sp. (strain 383) GN=rimM PE=3 SV=1 Back     alignment and function description
>sp|A4JCJ8|RIMM_BURVG Ribosome maturation factor RimM OS=Burkholderia vietnamiensis (strain G4 / LMG 22486) 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 ?
Query578
340788535518 fumarate hydratase class I, aerobic [Col 0.430 0.480 0.787 1e-119
409405380513 fumarate hydratase [Herbaspirillum sp. G 0.430 0.485 0.779 1e-118
415942121513 Fumarate hydratase protein [Herbaspirill 0.430 0.485 0.779 1e-118
300310873513 fumarate hydratase [Herbaspirillum serop 0.430 0.485 0.779 1e-118
399019450513 hydro-lyase, Fe-S type, tartrate/fumarat 0.432 0.487 0.768 1e-116
398835699513 hydro-lyase, Fe-S type, tartrate/fumarat 0.430 0.485 0.767 1e-116
152980967512 fumarate hydratase, class I [Janthinobac 0.430 0.486 0.751 1e-114
134094155512 fumarase A [Herminiimonas arsenicoxydans 0.430 0.486 0.751 1e-113
395761117513 fumarate hydratase [Janthinobacterium li 0.430 0.485 0.759 1e-113
445495265509 fumarate hydratase class I [Janthinobact 0.430 0.489 0.742 1e-112
>gi|340788535|ref|YP_004754000.1| fumarate hydratase class I, aerobic [Collimonas fungivorans Ter331] gi|340553802|gb|AEK63177.1| Fumarate hydratase class I, aerobic [Collimonas fungivorans Ter331] Back     alignment and taxonomy information
 Score =  434 bits (1117), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 196/249 (78%), Positives = 228/249 (91%)

Query: 2   EKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEG 61
           E+  AAKDAIAQIL NSRMCA+ KRPICQDTGIVNVFLKIGM+VRF+GF GSI D +NEG
Sbjct: 45  EQSPAAKDAIAQILTNSRMCAEGKRPICQDTGIVNVFLKIGMDVRFEGFKGSITDAVNEG 104

Query: 62  VRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKT 121
           VRRGY NP+N+LRASIV+DP F RKNT+DNTPAV++MELVPGN +D++IA+KGGGSENKT
Sbjct: 105 VRRGYLNPDNMLRASIVADPQFERKNTKDNTPAVVHMELVPGNTVDVQIAAKGGGSENKT 164

Query: 122 KFAMLNPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINMNSI 181
           KF MLNPSDSLVDW+MKTVPTMGAGWCPPG+LGIGIGGT E+AMLMAK+VLM+DI+M  +
Sbjct: 165 KFVMLNPSDSLVDWVMKTVPTMGAGWCPPGMLGIGIGGTAERAMLMAKQVLMEDIDMYDL 224

Query: 182 IKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCA 241
           +K GP+NK EELR+ELF K+N+LGIGAQG+GGL+TVLDVKIMM+PTHAASKPVA+IPNCA
Sbjct: 225 LKRGPQNKTEELRIELFQKVNALGIGAQGLGGLTTVLDVKIMMHPTHAASKPVAMIPNCA 284

Query: 242 ATRHGFLLF 250
           ATRHG  + 
Sbjct: 285 ATRHGHFVL 293

Source: Collimonas fungivorans Ter331

Species: Collimonas fungivorans

Genus: Collimonas

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria
>gi|409405380|ref|ZP_11253842.1| fumarate hydratase [Herbaspirillum sp. GW103] gi|386433929|gb|EIJ46754.1| fumarate hydratase [Herbaspirillum sp. GW103] Back     alignment and taxonomy information
>gi|415942121|ref|ZP_11555849.1| Fumarate hydratase protein [Herbaspirillum frisingense GSF30] gi|407758908|gb|EKF68672.1| Fumarate hydratase protein [Herbaspirillum frisingense GSF30] Back     alignment and taxonomy information
>gi|300310873|ref|YP_003774965.1| fumarate hydratase [Herbaspirillum seropedicae SmR1] gi|124483326|emb|CAM32536.1| Fumarate hydratase protein [Herbaspirillum seropedicae] gi|300073658|gb|ADJ63057.1| fumarate hydratase protein [Herbaspirillum seropedicae SmR1] Back     alignment and taxonomy information
>gi|399019450|ref|ZP_10721598.1| hydro-lyase, Fe-S type, tartrate/fumarate subfamily [Herbaspirillum sp. CF444] gi|398098060|gb|EJL88353.1| hydro-lyase, Fe-S type, tartrate/fumarate subfamily [Herbaspirillum sp. CF444] Back     alignment and taxonomy information
>gi|398835699|ref|ZP_10593058.1| hydro-lyase, Fe-S type, tartrate/fumarate subfamily [Herbaspirillum sp. YR522] gi|398215504|gb|EJN02066.1| hydro-lyase, Fe-S type, tartrate/fumarate subfamily [Herbaspirillum sp. YR522] Back     alignment and taxonomy information
>gi|152980967|ref|YP_001352570.1| fumarate hydratase, class I [Janthinobacterium sp. Marseille] gi|151281044|gb|ABR89454.1| fumarate hydratase, class I [Janthinobacterium sp. Marseille] Back     alignment and taxonomy information
>gi|134094155|ref|YP_001099230.1| fumarase A [Herminiimonas arsenicoxydans] gi|133738058|emb|CAL61103.1| putative fumarate hydratase class I, aerobic (Fumarase) (FumA-like) [Herminiimonas arsenicoxydans] Back     alignment and taxonomy information
>gi|395761117|ref|ZP_10441786.1| fumarate hydratase [Janthinobacterium lividum PAMC 25724] Back     alignment and taxonomy information
>gi|445495265|ref|ZP_21462309.1| fumarate hydratase class I [Janthinobacterium sp. HH01] gi|444791426|gb|ELX12973.1| fumarate hydratase class I [Janthinobacterium sp. HH01] 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 ?
Query578
TIGR_CMR|CPS_3613507 CPS_3613 "putative fumarate hy 0.422 0.481 0.622 2.9e-80
UNIPROTKB|Q9KSF2505 VC1304 "Fumarate hydratase, cl 0.422 0.483 0.598 3.8e-78
TIGR_CMR|VC_1304505 VC_1304 "fumarate hydratase, c 0.422 0.483 0.598 3.8e-78
TIGR_CMR|SO_2222516 SO_2222 "fumarate hydratase, c 0.422 0.472 0.590 7.9e-78
TIGR_CMR|SPO_1498502 SPO_1498 "fumarate hydratase, 0.420 0.484 0.520 2.9e-71
TIGR_CMR|CHY_1375280 CHY_1375 "fumarate hydratase, 0.404 0.835 0.429 1e-45
TIGR_CMR|DET_0453280 DET_0453 "fumarate hydratase, 0.399 0.825 0.405 1.5e-42
TIGR_CMR|CHY_0061281 CHY_0061 "fumarate hydratase, 0.406 0.836 0.421 5.2e-42
UNIPROTKB|P05847303 ttdA "L-tartrate dehydratase, 0.401 0.765 0.273 3e-18
TIGR_CMR|GSU_0994541 GSU_0994 "fumarate hydratase, 0.401 0.428 0.304 1.2e-15
TIGR_CMR|CPS_3613 CPS_3613 "putative fumarate hydratase, class I" [Colwellia psychrerythraea 34H (taxid:167879)] Back     alignment and assigned GO terms
 Score = 806 (288.8 bits), Expect = 2.9e-80, P = 2.9e-80
 Identities = 152/244 (62%), Positives = 192/244 (78%)

Query:     2 EKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEG 61
             E+  AAKDAIAQILINSRM A+ KRPICQDTGIV  F+K+GM V++   + ++  +++EG
Sbjct:    39 EESTAAKDAIAQILINSRMSAQGKRPICQDTGIVTCFVKVGMEVQWDKTDMTVQQMVDEG 98

Query:    62 VRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKT 121
              RR Y NP+N LRASIV DP   R NT+DNTPAV+++++VPG  L+I IA+KGGGSENKT
Sbjct:    99 TRRAYLNPDNPLRASIVKDPAGKRINTKDNTPAVVHIDMVPGAGLEIMIAAKGGGSENKT 158

Query:   122 KFAMLNPSDSLVDWIMKTVPTMGAGWCPPXXXXXXXXXTPEKAMLMAKKVLMQDINMNSI 181
             K AMLNPSDS+ DW++KT+PTMGAGWCPP         T EKA ++AK+ LM  +N+  +
Sbjct:   159 KMAMLNPSDSIADWVVKTLPTMGAGWCPPGMLGIGIGGTAEKAGVLAKESLMDPVNIQDL 218

Query:   182 IKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCA 241
             I+ GP+N  EELRLE+F ++N LGIGAQG+GGL+TV+DVKI   PTHAASKPV +IPNCA
Sbjct:   219 IERGPQNAEEELRLEIFERVNKLGIGAQGLGGLTTVVDVKINSVPTHAASKPVVMIPNCA 278

Query:   242 ATRH 245
             ATRH
Sbjct:   279 ATRH 282
GO:0004333 "fumarate hydratase activity" evidence=ISS
GO:0006099 "tricarboxylic acid cycle" evidence=ISS
UNIPROTKB|Q9KSF2 VC1304 "Fumarate hydratase, class I, putative" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)] Back     alignment and assigned GO terms
TIGR_CMR|VC_1304 VC_1304 "fumarate hydratase, class I, putative" [Vibrio cholerae O1 biovar El Tor (taxid:686)] Back     alignment and assigned GO terms
TIGR_CMR|SO_2222 SO_2222 "fumarate hydratase, class I, anaerobic, putative" [Shewanella oneidensis MR-1 (taxid:211586)] Back     alignment and assigned GO terms
TIGR_CMR|SPO_1498 SPO_1498 "fumarate hydratase, class I, putative" [Ruegeria pomeroyi DSS-3 (taxid:246200)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_1375 CHY_1375 "fumarate hydratase, alpha subunit" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
TIGR_CMR|DET_0453 DET_0453 "fumarate hydratase, alpha subunit, putative" [Dehalococcoides ethenogenes 195 (taxid:243164)] Back     alignment and assigned GO terms
TIGR_CMR|CHY_0061 CHY_0061 "fumarate hydratase, alpha subunit" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)] Back     alignment and assigned GO terms
UNIPROTKB|P05847 ttdA "L-tartrate dehydratase, alpha subunit" [Escherichia coli K-12 (taxid:83333)] Back     alignment and assigned GO terms
TIGR_CMR|GSU_0994 GSU_0994 "fumarate hydratase, class I" [Geobacter sulfurreducens PCA (taxid:243231)] 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 EFICAz Software ?

Prediction LevelEC numberConfidence of Prediction
3rd Layer4.2.1LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query578
pfam05681271 pfam05681, Fumerase, Fumarate hydratase (Fumerase) 1e-125
COG1951297 COG1951, TtdA, Tartrate dehydratase alpha subunit/ 1e-109
PRK06246280 PRK06246, PRK06246, fumarate hydratase; Provisiona 9e-87
TIGR00722273 TIGR00722, ttdA_fumA_fumB, hydro-lyases, Fe-S type 2e-60
PRK00122172 PRK00122, rimM, 16S rRNA-processing protein RimM; 1e-35
TIGR02273165 TIGR02273, 16S_RimM, 16S rRNA processing protein R 1e-34
COG0806174 COG0806, RimM, RimM protein, required for 16S rRNA 5e-31
PRK15389536 PRK15389, PRK15389, fumarate hydratase; Provisiona 7e-26
TIGR03717176 TIGR03717, R_switched_YjbE, integral membrane prot 2e-25
PTZ00226570 PTZ00226, PTZ00226, fumarate hydratase; Provisiona 3e-25
PLN00133576 PLN00133, PLN00133, class I-fumerate hydratase; Pr 8e-23
PRK08230299 PRK08230, PRK08230, tartrate dehydratase subunit a 2e-22
PRK15391548 PRK15391, PRK15391, fumarate hydratase FumB; Provi 5e-20
PRK0004075 PRK00040, rpsP, 30S ribosomal protein S16; Reviewe 4e-19
PRK15390548 PRK15390, PRK15390, fumarate hydratase FumA; Provi 5e-19
PRK15392550 PRK15392, PRK15392, putative fumarate hydratase; P 2e-18
pfam0088661 pfam00886, Ribosomal_S16, Ribosomal protein S16 3e-16
pfam03741184 pfam03741, TerC, Integral membrane protein TerC fa 7e-16
COG022887 COG0228, RpsP, Ribosomal protein S16 [Translation, 2e-14
COG0861254 COG0861, TerC, Membrane protein TerC, possibly inv 2e-14
PRK14523137 PRK14523, rpsP, 30S ribosomal protein S16; Provisi 2e-13
pfam0178284 pfam01782, RimM, RimM N-terminal domain 9e-12
TIGR0000278 TIGR00002, S16, ribosomal protein S16 4e-11
PRK1452588 PRK14525, rpsP, 30S ribosomal protein S16; Provisi 8e-11
PRK14590171 PRK14590, rimM, 16S rRNA-processing protein RimM; 1e-10
PRK14592165 PRK14592, rimM, 16S rRNA-processing protein RimM; 2e-08
PRK14591169 PRK14591, rimM, 16S rRNA-processing protein RimM; 9e-07
PRK14520155 PRK14520, rpsP, 30S ribosomal protein S16; Provisi 3e-06
PRK14521186 PRK14521, rpsP, 30S ribosomal protein S16; Provisi 4e-06
PRK1452494 PRK14524, rpsP, 30S ribosomal protein S16; Provisi 6e-06
CHL0000582 CHL00005, rps16, ribosomal protein S16 9e-06
PRK13828161 PRK13828, rimM, 16S rRNA-processing protein RimM; 5e-04
pfam0523978 pfam05239, PRC, PRC-barrel domain 8e-04
PRK14522116 PRK14522, rpsP, 30S ribosomal protein S16; Provisi 0.003
>gnl|CDD|218689 pfam05681, Fumerase, Fumarate hydratase (Fumerase) Back     alignment and domain information 
 Score =  369 bits (951), Expect = e-125
 Identities = 129/248 (52%), Positives = 165/248 (66%), Gaps = 14/248 (5%)

Query: 2   EKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEG 61
           E+   AK  +AQIL N+ + A+ KRPICQDTG   VF+KIG  V      G + + INEG
Sbjct: 31  EESPLAKFVLAQILENAEIAAEGKRPICQDTGTAVVFVKIGQEVPI---EGDLEEAINEG 87

Query: 62  VRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKT 121
           VRR YT     LR S+V+DP   RKNT DNTPAVI++E+VPG+ L+I +A+KGGGSENK+
Sbjct: 88  VRRAYTEGP--LRPSVVADP-LERKNTGDNTPAVIHIEIVPGDELEITVAAKGGGSENKS 144

Query: 122 KFAMLNPSD---SLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINM 178
           K AMLNPSD    +  ++++TV   G   CPPG++G+GIGGT EKA L+AKK L++ ++ 
Sbjct: 145 KLAMLNPSDGIEGIKKFVLETVKEAGPNACPPGVVGVGIGGTSEKAALLAKKALLRPVDE 204

Query: 179 NSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIP 238
            +     P  +  EL  EL  KIN LGIG QG+GG +T LDVKI   P H AS PVA+  
Sbjct: 205 RN-----PDPRDAELEEELLEKINKLGIGPQGLGGKTTALDVKIERAPRHIASLPVAVNV 259

Query: 239 NCAATRHG 246
           NC A RH 
Sbjct: 260 NCWADRHA 267

This family consists of several bacterial fumarate hydratase proteins FumA and FumB. Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth. Three fumarases, FumA, FumB, and FumC, have been reported in E. coli. fumA and fumB genes are homologous and encode products of identical sizes which form thermolabile dimers of Mr 120,000. FumA and FumB are class I enzymes and are members of the iron-dependent hydrolases, which include aconitase and malate hydratase. The active FumA contains a 4Fe-4S centre, and it can be inactivated upon oxidation to give a 3Fe-4S centre. Length = 271
>gnl|CDD|224862 COG1951, TtdA, Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|180486 PRK06246, PRK06246, fumarate hydratase; Provisional Back     alignment and domain information
>gnl|CDD|233103 TIGR00722, ttdA_fumA_fumB, hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha region Back     alignment and domain information
>gnl|CDD|234650 PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|233805 TIGR02273, 16S_RimM, 16S rRNA processing protein RimM Back     alignment and domain information
>gnl|CDD|223877 COG0806, RimM, RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|237955 PRK15389, PRK15389, fumarate hydratase; Provisional Back     alignment and domain information
>gnl|CDD|163429 TIGR03717, R_switched_YjbE, integral membrane protein, YjbE family Back     alignment and domain information
>gnl|CDD|240319 PTZ00226, PTZ00226, fumarate hydratase; Provisional Back     alignment and domain information
>gnl|CDD|215068 PLN00133, PLN00133, class I-fumerate hydratase; Provisional Back     alignment and domain information
>gnl|CDD|181309 PRK08230, PRK08230, tartrate dehydratase subunit alpha; Validated Back     alignment and domain information
>gnl|CDD|185289 PRK15391, PRK15391, fumarate hydratase FumB; Provisional Back     alignment and domain information
>gnl|CDD|234588 PRK00040, rpsP, 30S ribosomal protein S16; Reviewed Back     alignment and domain information
>gnl|CDD|185288 PRK15390, PRK15390, fumarate hydratase FumA; Provisional Back     alignment and domain information
>gnl|CDD|185290 PRK15392, PRK15392, putative fumarate hydratase; Provisional Back     alignment and domain information
>gnl|CDD|216173 pfam00886, Ribosomal_S16, Ribosomal protein S16 Back     alignment and domain information
>gnl|CDD|217707 pfam03741, TerC, Integral membrane protein TerC family Back     alignment and domain information
>gnl|CDD|223306 COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|223930 COG0861, TerC, Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism] Back     alignment and domain information
>gnl|CDD|172989 PRK14523, rpsP, 30S ribosomal protein S16; Provisional Back     alignment and domain information
>gnl|CDD|216696 pfam01782, RimM, RimM N-terminal domain Back     alignment and domain information
>gnl|CDD|129114 TIGR00002, S16, ribosomal protein S16 Back     alignment and domain information
>gnl|CDD|172991 PRK14525, rpsP, 30S ribosomal protein S16; Provisional Back     alignment and domain information
>gnl|CDD|173054 PRK14590, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|173056 PRK14592, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|173055 PRK14591, rimM, 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>gnl|CDD|184724 PRK14520, rpsP, 30S ribosomal protein S16; Provisional Back     alignment and domain information
>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional Back     alignment and domain information
>gnl|CDD|172990 PRK14524, rpsP, 30S ribosomal protein S16; Provisional Back     alignment and domain information
>gnl|CDD|176950 CHL00005, rps16, ribosomal protein S16 Back     alignment and domain information
>gnl|CDD|184351 PRK13828, 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|172988 PRK14522, rpsP, 30S ribosomal protein S16; 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 578
PRK06246280 fumarate hydratase; Provisional 100.0
TIGR00722273 ttdA_fumA_fumB hydro-lyases, Fe-S type, tartrate/f 100.0
PRK08230299 tartrate dehydratase subunit alpha; Validated 100.0
PF05681271 Fumerase: Fumarate hydratase (Fumerase); InterPro: 100.0
COG1951297 TtdA Tartrate dehydratase alpha subunit/Fumarate h 100.0
PRK15389536 fumarate hydratase; Provisional 100.0
PRK15392550 putative fumarate hydratase; Provisional 100.0
PLN00133576 class I-fumerate hydratase; Provisional 100.0
PTZ00226570 fumarate hydratase; Provisional 100.0
PRK15390548 fumarate hydratase FumA; Provisional 100.0
PRK15391548 fumarate hydratase FumB; Provisional 100.0
PRK14591169 rimM 16S rRNA-processing protein RimM; Provisional 100.0
COG0806174 RimM RimM protein, required for 16S rRNA processin 100.0
PRK00122172 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
TIGR02273165 16S_RimM 16S rRNA processing protein RimM. This fa 100.0
PRK14594166 rimM 16S rRNA-processing protein RimM; Provisional 100.0
PRK14593184 rimM 16S rRNA-processing protein RimM; Provisional 100.0
PRK13829162 rimM 16S rRNA-processing protein RimM; Provisional 100.0
PRK13828161 rimM 16S rRNA-processing protein RimM; Provisional 100.0
TIGR03716215 R_switched_YkoY integral membrane protein, YkoY fa 99.91
PF03741183 TerC: Integral membrane protein TerC family; Inter 99.91
TIGR03717176 R_switched_YjbE integral membrane protein, YjbE fa 99.9
COG0861254 TerC Membrane protein TerC, possibly involved in t 99.89
PF0178284 RimM: RimM N-terminal domain; InterPro: IPR002676 99.81
PRK0004075 rpsP 30S ribosomal protein S16; Reviewed 99.68
TIGR0000278 S16 ribosomal protein S16. This model describes ri 99.67
PRK1452588 rpsP 30S ribosomal protein S16; Provisional 99.65
PRK1452494 rpsP 30S ribosomal protein S16; Provisional 99.65
CHL0000582 rps16 ribosomal protein S16 99.65
PRK14523137 rpsP 30S ribosomal protein S16; Provisional 99.64
COG022887 RpsP Ribosomal protein S16 [Translation, ribosomal 99.63
PRK14520155 rpsP 30S ribosomal protein S16; Provisional 99.62
PRK14521186 rpsP 30S ribosomal protein S16; Provisional 99.61
TIGR03718302 R_switched_Alx integral membrane protein, TerC fam 99.59
KOG3419|consensus112 99.59
PRK14522116 rpsP 30S ribosomal protein S16; Provisional 99.57
PF0088662 Ribosomal_S16: Ribosomal protein S16; InterPro: IP 99.52
PF0523979 PRC: PRC-barrel domain; InterPro: IPR007903 The PR 98.4
PRK14013338 hypothetical protein; Provisional 98.32
PF03741183 TerC: Integral membrane protein TerC family; Inter 96.96
TIGR03717176 R_switched_YjbE integral membrane protein, YjbE fa 96.85
cd00226246 PRCH Photosynthetic reaction center (RC) complex, 96.36
TIGR03716215 R_switched_YkoY integral membrane protein, YkoY fa 95.14
TIGR03718302 R_switched_Alx integral membrane protein, TerC fam 94.58
COG0861254 TerC Membrane protein TerC, possibly involved in t 93.21
COG187387 Protein implicated in RNA metabolism, contains PRC 92.96
COG2451100 Ribosomal protein L35AE/L33A [Translation, ribosom 85.65
>PRK06246 fumarate hydratase; Provisional Back     alignment and domain information 
Probab=100.00  E-value=2.7e-86  Score=671.91  Aligned_cols=240  Identities=48%  Similarity=0.823  Sum_probs=234.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHhhcCCCcccccCCceEEEEEeCceeeecCCCccHHHHHHHHHHHhhcCCCCCCcCCCCCC
Q psy3773           1 MEKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNILRASIVSD   80 (578)
Q Consensus         1 ~E~~~~ak~~l~~il~N~~iA~~~~~P~CQDTG~~~~fv~~G~~~~~~g~~~~l~~~i~~gv~~a~~~~~~~lR~s~v~~   80 (578)
                      +|+||++|++|++||+|+++|++.++|+|||||+|+||+++|+++++.|  ++++++|+|||++||+  ++|||+|+|+|
T Consensus        38 ~E~s~~ak~~l~~ileN~~iA~~~~~P~CQDTG~~~~fv~iG~~v~~~~--~~l~~ai~egv~~a~~--~~pLR~s~V~~  113 (280)
T PRK06246         38 KEESPIGKEILKAILENAEIAKEEQVPLCQDTGMAVVFVEIGQDVHIEG--GDLEDAINEGVRKGYE--EGYLRKSVVAD  113 (280)
T ss_pred             hccChhHHHHHHHHHHHHHHHhcCCCccccCCCcEEEEEEeCCCcccCC--ccHHHHHHHHHHHHhc--cCCCchhccCC
Confidence            5999999999999999999999999999999999999999999999985  4799999999999999  89999999988


Q ss_pred             CccCccCCCCCCceEEEEEeeCCcEEEEEEEecCCCCcccccccccCCch---hHHHHHHHHhhccCCCCCCCceeEEEE
Q psy3773          81 PHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKFAMLNPSD---SLVDWIMKTVPTMGAGWCPPGILGIGI  157 (578)
Q Consensus        81 p~~~r~ntg~n~p~~i~~~~v~gd~~~i~~~~KGgGsen~s~~~~l~p~~---~v~~~v~~~v~~~G~~~CpP~~vgvGi  157 (578)
                      |+ +|+|||||||++||+++++||+++|+++||||||||+|+++||+|++   ||++||+|+|.++|+|||||++|||||
T Consensus       114 pl-~r~NtgdNtpa~i~~~~v~gd~~~i~~~~KGgGSEn~s~l~ml~P~~g~e~i~~fvle~v~~aG~~~CPP~~vGVGI  192 (280)
T PRK06246        114 PL-TRKNTGDNTPAVIHTEIVPGDKLKITVAPKGGGSENMSALKMLKPADGLEGIKKFVLETVKEAGGNPCPPIIVGVGI  192 (280)
T ss_pred             cc-cCccCCCCccceEEEEEecCCEEEEEEEecCCccccHhhhcccCcchhHHHHHHHHHHHHHHcCCCCCCCCeEEEEe
Confidence            95 99999999999999999999999999999999999999999999985   899999999999999999999999999


Q ss_pred             cCCHHHHHHHHHHHhccccccccccccCCChhhHHHHHHHHHHHHHhcchHHHHHHHHHHhhhhhccccccccCCceEEe
Q psy3773         158 GGTPEKAMLMAKKVLMQDINMNSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAII  237 (578)
Q Consensus       158 Ggt~~~a~~laK~al~r~~~~~~~~~~~~~~~~~~Le~el~~~~n~lGiGa~glgg~~t~l~v~i~~~p~h~a~~pvav~  237 (578)
                      |||+|+|++|||+||+|++|     ++||||++++||+||++++|++|||||||||.+|+++|||+.+|+|+|++|||||
T Consensus       193 GGt~d~a~~laK~Allr~i~-----~~n~~~~~a~lE~eLl~~iN~lGIGp~GlGG~tTal~V~Ie~~p~H~AslPVaV~  267 (280)
T PRK06246        193 GGTFDKAAKLAKKALLRPIG-----ERNPDPEIAALEEELLEEINKLGIGPMGLGGKTTALDVKIETYPCHIASLPVAVN  267 (280)
T ss_pred             CCCHHHHHHHHHHHhcCccc-----CCCCChHHHHHHHHHHHHHHhcCcCCCccCCceEEEEEEEeecCCcccCCceEEE
Confidence            99999999999999999999     9999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccccceEEE
Q psy3773         238 PNCAATRHGFLLF  250 (578)
Q Consensus       238 ~~C~~~R~g~~li  250 (578)
                      +|||++||+.+.|
T Consensus       268 ~~C~a~R~~~v~i  280 (280)
T PRK06246        268 IQCHAARHAEVVL  280 (280)
T ss_pred             cccchhhCceEeC
Confidence            9999999998764

>TIGR00722 ttdA_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha region Back     alignment and domain information
>PRK08230 tartrate dehydratase subunit alpha; Validated Back     alignment and domain information
>PF05681 Fumerase: Fumarate hydratase (Fumerase); InterPro: IPR004646 This entry represents various Fe-S type hydro-lyases, including the alpha subunit from both L-tartrate dehydratase (TtdA; 4 Back     alignment and domain information
>COG1951 TtdA Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain [Energy production and conversion] Back     alignment and domain information
>PRK15389 fumarate hydratase; Provisional Back     alignment and domain information
>PRK15392 putative fumarate hydratase; Provisional Back     alignment and domain information
>PLN00133 class I-fumerate hydratase; Provisional Back     alignment and domain information
>PTZ00226 fumarate hydratase; Provisional Back     alignment and domain information
>PRK15390 fumarate hydratase FumA; Provisional Back     alignment and domain information
>PRK15391 fumarate hydratase FumB; Provisional Back     alignment and domain information
>PRK14591 rimM 16S rRNA-processing protein RimM; Provisional Back     alignment and domain information
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK00122 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
>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
>PRK14593 rimM 16S rRNA-processing protein RimM; Provisional 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
>TIGR03716 R_switched_YkoY integral membrane protein, YkoY family Back     alignment and domain information
>PF03741 TerC: Integral membrane protein TerC family; InterPro: IPR005496 A family containining a number of integral membrane proteins is named after TerC protein Back     alignment and domain information
>TIGR03717 R_switched_YjbE integral membrane protein, YjbE family Back     alignment and domain information
>COG0861 TerC Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism] 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
>PRK00040 rpsP 30S ribosomal protein S16; Reviewed Back     alignment and domain information
>TIGR00002 S16 ribosomal protein S16 Back     alignment and domain information
>PRK14525 rpsP 30S ribosomal protein S16; Provisional Back     alignment and domain information
>PRK14524 rpsP 30S ribosomal protein S16; Provisional Back     alignment and domain information
>CHL00005 rps16 ribosomal protein S16 Back     alignment and domain information
>PRK14523 rpsP 30S ribosomal protein S16; Provisional Back     alignment and domain information
>COG0228 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK14520 rpsP 30S ribosomal protein S16; Provisional Back     alignment and domain information
>PRK14521 rpsP 30S ribosomal protein S16; Provisional Back     alignment and domain information
>TIGR03718 R_switched_Alx integral membrane protein, TerC family Back     alignment and domain information
>KOG3419|consensus Back     alignment and domain information
>PRK14522 rpsP 30S ribosomal protein S16; Provisional Back     alignment and domain information
>PF00886 Ribosomal_S16: Ribosomal protein S16; InterPro: IPR000307 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms 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
>PRK14013 hypothetical protein; Provisional Back     alignment and domain information
>PF03741 TerC: Integral membrane protein TerC family; InterPro: IPR005496 A family containining a number of integral membrane proteins is named after TerC protein Back     alignment and domain information
>TIGR03717 R_switched_YjbE integral membrane protein, YjbE family 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
>TIGR03716 R_switched_YkoY integral membrane protein, YkoY family Back     alignment and domain information
>TIGR03718 R_switched_Alx integral membrane protein, TerC family Back     alignment and domain information
>COG0861 TerC Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion 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
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis] 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 ?
Query578
3h9n_A177 Crystal Structure Of The Ribosome Maturation Factor 2e-10
2gy9_P78 Structure Of The 30s Subunit Of A Pre-Translocation 5e-10
1p6g_P82 Real Space Refined Coordinates Of The 30s Subunit F 5e-10
3fih_P80 Ternary Complex-Bound E.Coli 70s Ribosome. This Ent 5e-10
1pns_P83 Crystal Structure Of A Streptomycin Dependent Ribos 8e-06
1jgo_S91 Crystal Structure Of The Ribosome At 5.5 A Resoluti 8e-06
3fic_P84 T. Thermophilus 70s Ribosome In Complex With Mrna, 8e-06
1emw_A88 Solution Structure Of The Ribosomal Protein S16 Fro 8e-06
2f1l_A187 Crystal Structure Of A Putative 16s Ribosomal Rna P 2e-05
>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 
Iteration: 1

 Score = 63.9 bits (154), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/134 (30%), Positives = 69/134 (51%), Gaps = 5/134 (3%)
Query: 403 HLITIGVVLRAYGIFGWILIKLFLDD-KNIFFYARKIWFFDPNSLKLFSIKILNKKNHGN 461
           H+  +G +   YGI GW+ I    +  ++IF Y  + WF      +  SI++ N + H +
Sbjct: 1   HIEVVGKLGSTYGIRGWLRIYSSTEQAESIFDY--QPWFLKIKG-EWQSIELENWRYHNH 57
Query: 462 YVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTV 521
            ++  L G+ DR  A  L    + + ++ FP+L   D +YW +LI C V N+ G   GTV
Sbjct: 58  EIIVKLKGVDDREAAQILANVEIGVDLSVFPELEEGD-YYWHDLIGCTVVNLEGYTXGTV 116
Query: 522 TEIIQNKVHSILRI 535
           TE  +   + +L +
Sbjct: 117 TEXXETGSNDVLVV 130
>pdb|2GY9|P Chain P, Structure Of The 30s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 78 Back     alignment and structure
>pdb|1P6G|P Chain P, Real Space Refined Coordinates Of The 30s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 82 Back     alignment and structure
>pdb|3FIH|P Chain P, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 30s Subunit, Trnas And The Ternary Complex. Length = 80 Back     alignment and structure
>pdb|1PNS|P Chain P, Crystal Structure Of A Streptomycin Dependent Ribosome From E. Coli, 30s Subunit Of 70s Ribosome. This File, 1pns, Contains The 30s Subunit, Two Trnas, And One Mrna Molecule. The 50s Ribosomal Subunit Is In File 1pnu. Length = 83 Back     alignment and structure
>pdb|3FIC|P Chain P, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 30s Subunit And The Ligands Length = 84 Back     alignment and structure
>pdb|1EMW|A Chain A, Solution Structure Of The Ribosomal Protein S16 From Thermus Thermophilus Length = 88 Back     alignment and structure
>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

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query578
2f1l_A187 16S rRNA processing protein; structural genomics, 4e-39
3h9n_A177 Ribosome maturation factor RIMM; structural genomi 6e-38
2qgg_A182 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR 2e-37
2dyi_A162 Probable 16S rRNA-processing protein RIMM; ribosom 8e-31
3r8n_P82 30S ribosomal protein S16; protein biosynthesis, R 2e-21
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-16
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-08
3pys_P83 30S ribosomal protein S16; ribosome, IGR, IRES, PS 9e-15
3bn0_A112 30S ribosomal protein S16; ribonucleoprotein, ribo 4e-13
3bbn_P88 Ribosomal protein S16; small ribosomal subunit, sp 2e-12
>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
 Score =  140 bits (356), Expect = 4e-39
 Identities = 39/177 (22%), Positives = 78/177 (44%), Gaps = 10/177 (5%)

Query: 402 DHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGN 461
           D L+ IG ++  YGI G + +  F D  +     R+         ++   +++  + HG 
Sbjct: 18  DDLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDG--EIRQAELVRGRLHGK 75

Query: 462 YVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTV 521
            + A L G+ DR  A    GY + I  ++ P L     +YW  L    V +   +LLG +
Sbjct: 76  VLAAKLKGLDDREEARTFTGYEICIPRSELPSL-EEGEYYWHQLEGLKVIDQGRQLLGVI 134

Query: 522 TEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD 578
             +++   + ++ +     K        ++   L+P+    + ++D+   ++ VDWD
Sbjct: 135 DHLLETGANDVMVV-----KPCAGSLDDRE--RLLPYTGQCVLSIDLAAGEMRVDWD 184
>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
>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
>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
>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
>3pys_P 30S ribosomal protein S16; ribosome, IGR, IRES, PSIV, CRPV; 3.40A {Thermus thermophilus} PDB: 1pnx_P 1voq_P 1vos_P 1vov_P 1vox_P 1voz_P 1pns_P 3ms0_P 3mr8_P 3pyq_P 3pyn_P 3pyu_P 3fic_P* 1emw_A 1fjg_P* 1hnw_P* 1hnx_P* 1hnz_P* 1hr0_P 1i94_P* ... Length = 83 Back     alignment and structure
>3bn0_A 30S ribosomal protein S16; ribonucleoprotein, ribosome; 2.00A {Aquifex aeolicus} SCOP: d.27.1.1 Length = 112 Back     alignment and structure
>3bbn_P Ribosomal protein S16; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 88 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query578
2f1l_A187 16S rRNA processing protein; structural genomics, 100.0
3h9n_A177 Ribosome maturation factor RIMM; structural genomi 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
3r8n_P82 30S ribosomal protein S16; protein biosynthesis, R 99.7
3pys_P83 30S ribosomal protein S16; ribosome, IGR, IRES, PS 99.69
3bbn_P88 Ribosomal protein S16; small ribosomal subunit, sp 99.66
3bn0_A112 30S ribosomal protein S16; ribonucleoprotein, ribo 99.61
1eys_H259 Photosynthetic reaction center; membrane protein c 95.44
3htr_A120 Uncharacterized PRC-barrel domain protein; beta-ba 94.31
1pm3_A97 MTH1895; unknown function, structural genomics, PS 87.07
1rzh_H260 Reaction center protein H chain; bacterial photosy 82.8
2wjn_H258 Reaction center protein H chain; bacteriochlorophy 82.58
>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
Probab=100.00  E-value=5.1e-43  Score=338.83  Aligned_cols=169  Identities=22%  Similarity=0.445  Sum_probs=147.6

Q ss_pred             chhhheeeeeecccccccccEEEEEccCchhhhccCcEEEEEcCCCCeeEEEEEEEEEEeCCEEEEEecCCCCHHHHHhh
Q psy3773         400 TVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLANLYGITDRNLATKL  479 (578)
Q Consensus       400 tv~~ll~iG~I~~~hGlkGevkv~~~td~p~~f~~~~~v~l~~~~~~~~~~~~ve~~r~~~~~~ivkfegIddre~Ae~L  479 (578)
                      ..++++.+|+|+++||+||||||+|+||+|++|...+.+|+...  ...++++|+++|.|++.+++||+||+|||+||+|
T Consensus        16 ~~~~~v~VG~I~~~hGikGeVkV~~~Td~pe~~~~~~~~~l~~~--~~~~~~~v~~~r~~~~~~ivkf~gi~dr~~Ae~L   93 (187)
T 2f1l_A           16 PADDLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRD--GEIRQAELVRGRLHGKVLAAKLKGLDDREEARTF   93 (187)
T ss_dssp             ---CEEEEEEEEEEETTTTEEEEEECSSSGGGGGGCCEEEEEET--TEEEEEEEEEEEEETTEEEEEETTCCSHHHHHTT
T ss_pred             CCCCEEEEEEEeCCEeeCEEEEEEECCCCHHHhccCCEEEEecC--CcEEEEEEEEEEEECCEEEEEEeCCCCHHHHHHh
Confidence            45789999999999999999999999999999999888887532  3567999999999999999999999999999999


Q ss_pred             cCCEEEEeCCCCCCCCCCCcchhhhccCcEEEecCCcEeEEEEEeccCCCceEEEEEeCCccceehhccCCCcEEEeecc
Q psy3773         480 QGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFI  559 (578)
Q Consensus       480 ~G~~l~v~~~dlp~lL~edEfY~~DLIG~~V~d~~g~~LG~V~dV~~~ga~dllvV~~~~~~~~~~~~~~~~ke~LIPfv  559 (578)
                      +|++||++++++|++ ++|||||+|||||+|+|++|+.+|+|++|+++||||+|+|+..++.       ...+|+||||+
T Consensus        94 ~G~~l~v~r~~lp~l-~edEfY~~DLIGl~V~~~~g~~lG~V~~v~~~ganDvlvV~~~~g~-------~~~ke~LIPfv  165 (187)
T 2f1l_A           94 TGYEICIPRSELPSL-EEGEYYWHQLEGLKVIDQGRQLLGVIDHLLETGANDVMVVKPCAGS-------LDDRERLLPYT  165 (187)
T ss_dssp             TTCEEEEEGGGSCC------CCHHHHTTCEEEETTSCEEEEEEEEECCSSSCEEEEECCTTS-------SSSCCEEEECS
T ss_pred             CCCEEEEEHHHCCCC-CCCCEeHHHcCCeEEEeCCCCEEEEEEEEccCCCcEEEEEEeCCCC-------CCCcEEEEech
Confidence            999999999999995 9999999999999999999999999999999999999999864100       00179999999


Q ss_pred             cccceeeecCCCEEEEeCC
Q psy3773         560 KIFIKNVDIIKKKIIVDWD  578 (578)
Q Consensus       560 ~~fV~~VDle~k~I~V~l~  578 (578)
                      ++||++||+++|+|+|+||
T Consensus       166 ~~~V~~VDle~~~I~V~~p  184 (187)
T 2f1l_A          166 GQCVLSIDLAAGEMRVDWD  184 (187)
T ss_dssp             TTTEEEEETTTTEEEECCC
T ss_pred             HHhcCEEeCCCCEEEEeCC
Confidence            9999999999999999997
>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
>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
>3pys_P 30S ribosomal protein S16; ribosome, IGR, IRES, PSIV, CRPV; 3.40A {Thermus thermophilus} PDB: 1pnx_P 1voq_P 1vos_P 1vov_P 1vox_P 1voz_P 1pns_P 3ms0_P 3mr8_P 3pyq_P 3pyn_P 3pyu_P 3fic_P* 1emw_A 1fjg_P* 1hnw_P* 1hnx_P* 1hnz_P* 1hr0_P 1i94_P* ... Back     alignment and structure
>3bbn_P Ribosomal protein S16; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>3bn0_A 30S ribosomal protein S16; ribonucleoprotein, ribosome; 2.00A {Aquifex aeolicus} SCOP: d.27.1.1 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
>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
>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

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 578
d2f1la175 b.41.1.4 (A:101-175) 16S rRNA processing protein R 2e-16
d2gy9p178 d.27.1.1 (P:1-78) Ribosomal protein S16 {Escherich 5e-15
d2uubp183 d.27.1.1 (P:1-83) Ribosomal protein S16 {Thermus t 1e-12
d2f1la289 b.43.3.4 (A:7-95) 16S rRNA processing protein RimM 3e-12
d3bn0a1101 d.27.1.1 (A:2-102) Ribosomal protein S16 {Aquifex 7e-12
>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 = 71.6 bits (176), Expect = 2e-16
 Identities = 14/79 (17%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 500 FYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFI 559
           +YW  L    V +   +LLG +  +++   + ++ +                   L+P+ 
Sbjct: 1   YYWHQLEGLKVIDQGRQLLGVIDHLLETGANDVMVVK-------PCAGSLDDRERLLPYT 53

Query: 560 KIFIKNVDIIKKKIIVDWD 578
              + ++D+   ++ VDWD
Sbjct: 54  GQCVLSIDLAAGEMRVDWD 72
>d2gy9p1 d.27.1.1 (P:1-78) Ribosomal protein S16 {Escherichia coli [TaxId: 562]} Length = 78 Back     information, alignment and structure
>d2uubp1 d.27.1.1 (P:1-83) Ribosomal protein S16 {Thermus thermophilus [TaxId: 274]} Length = 83 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]} Length = 89 Back     information, alignment and structure
>d3bn0a1 d.27.1.1 (A:2-102) Ribosomal protein S16 {Aquifex aeolicus [TaxId: 63363]} Length = 101 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 ?
Query578
d2f1la289 16S rRNA processing protein RimM, N-terminal domai 99.82
d2f1la175 16S rRNA processing protein RimM, C-terminal domai 99.78
d2gy9p178 Ribosomal protein S16 {Escherichia coli [TaxId: 56 99.66
d2uubp183 Ribosomal protein S16 {Thermus thermophilus [TaxId 99.63
d3bn0a1101 Ribosomal protein S16 {Aquifex aeolicus [TaxId: 63 99.54
d1eysh1201 Photosynthetic reaction centre {Thermochromatium t 96.18
d2i5nh1222 Photosynthetic reaction centre {Rhodopseudomonas v 93.67
d1rzhh1213 Photosynthetic reaction centre {Rhodobacter sphaer 91.87
d1pm3a_78 MTH1895 {Archaeon Methanobacterium thermoautotroph 91.07
>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
class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: RimM N-terminal domain-like
domain: 16S rRNA processing protein RimM, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.82  E-value=2e-20  Score=157.34  Aligned_cols=89  Identities=25%  Similarity=0.418  Sum_probs=82.9

Q ss_pred             hheeeeeecccccccccEEEEEccCchhhhccCcEEEEEcCCCCeeEEEEEEEEEEeCCEEEEEecCCCCHHHHHhhcCC
Q psy3773         403 HLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLANLYGITDRNLATKLQGY  482 (578)
Q Consensus       403 ~ll~iG~I~~~hGlkGevkv~~~td~p~~f~~~~~v~l~~~~~~~~~~~~ve~~r~~~~~~ivkfegIddre~Ae~L~G~  482 (578)
                      |++.+|+|++|||+|||||++++||+|+.|...+.+|+...  ....++.+++.+.+++.++++|+||+|||+|++|+|+
T Consensus         1 d~i~iGki~~~hGlkG~vki~~~t~~~~~~~~~~~~~~~~~--~~~~~~~i~~~~~~~~~~~vk~~~i~~r~~Ae~l~g~   78 (89)
T d2f1la2           1 DLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRD--GEIRQAELVRGRLHGKVLAAKLKGLDDREEARTFTGY   78 (89)
T ss_dssp             CEEEEEEEEEEETTTTEEEEEECSSSGGGGGGCCEEEEEET--TEEEEEEEEEEEEETTEEEEEETTCCSHHHHHTTTTC
T ss_pred             CEEEEEEEeCCEeeeEEEEEEECCCCHHHHhCCCeEEEecC--CeEEEEEEEEEEecccEEEEEEcCCCCHHHHHHhCCC
Confidence            58899999999999999999999999999999998888654  3578999999999999999999999999999999999


Q ss_pred             EEEEeCCCCCC
Q psy3773         483 YLKISINDFPK  493 (578)
Q Consensus       483 ~l~v~~~dlp~  493 (578)
                      +||+++++||.
T Consensus        79 ~i~i~~~~LPs   89 (89)
T d2f1la2          79 EICIPRSELPS   89 (89)
T ss_dssp             EEEEEGGGSCC
T ss_pred             EEEEEHHHCCC
Confidence            99999999983
>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
>d2gy9p1 d.27.1.1 (P:1-78) Ribosomal protein S16 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2uubp1 d.27.1.1 (P:1-83) Ribosomal protein S16 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d3bn0a1 d.27.1.1 (A:2-102) Ribosomal protein S16 {Aquifex aeolicus [TaxId: 63363]} 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