Psyllid ID: psy6417

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190----
Protein Sequence
MLEYNLTDATALVQKNIEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYNWDVKRRNQLKMGLEKSNRLRQMTRPVYLSSTRFESKSTNNIYEIDFTLGDPEASNKPAEDLKNPFQKEKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCIMF
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHHccEEEEEEcccccEEEEEEcccEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHcccccEEEEcccccccccccEEEEEcccccccccccccccccccccccccEEEEccccccccccHHHHHHHHcccccccEEEEc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEEcccHEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccEEEHHHHHEEcHcHHHHHHHHHHHHccccccEcccEEEEEEEEEEccccccHHHccccccccccccccHHHccccccccccEEEEEEEccccccHHHHHHHHcccccccEEEEEc
Coil and Loop (DISEMBL)
MLEYNLTDATALVQKNIEAakknssipptdkvCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYNWDVKRRNQLKMGLEKsnrlrqmtrpvylsstrfeskstnniyeidftlgdpeasnkpaedlknpfqkEKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCIMF
Flexible Loop (DISEMBL)
MLEYNLTDATALVQKNIeaakknssipptDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMArvynwdvkrrnqlkmgleksnrlrqmtrpvylsstrfeskstnniYEIDftlgdpeasnkpaedlknpfqkEKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCIMF
Low Complexity Region (SEG)
MLEYNLTDATALVQKNIEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYNWDVKRRNQLKMGLEKSNRLRQMTRPVYLSSTRFESKSTNNIYEIDFTLGDPEASNKPAEDLKNPFQKEKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCIMF
Disordered region (IsUnstruct)
****************************TDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYNWDVKRRNQL******************************NIYEIDFTL******************KEKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCIM*
Disordered Region (DISOPRED)
*LEYNLTDATALVQKNIEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYNWD***********************VYLSSTRFE*****************************PFQKEKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCIMF
Disordered Region (DISEMBL)
MLEYNLTDATALVQKNIEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYNWDVKRRNQLKMGLEKSNRLRQMTRPVYLSSTRFESKSTNNIYEIDFTLGDPEASNKPAEDLKNPFQKEKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCIMF
Disordered Region (DISPRO)
MLEYNLTDATALVQKNIEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYNWDVKRRNQLKMGL*KSNRLRQMTRPVYLSSTRFESKSTNNIYEIDFTLGDPEASNKPAEDLKNPFQKEKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCIMF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLEYNLTDATALVQKNIEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNxxxxxxxxxxxxxxxxxxxxxFTTTEVNMARVYNWDVKRRNQLKMGLEKSNRLRQMTRPVYLSSTRFESKSTNNIYEIDFTLGDPEASNKPAEDLKNPFQKEKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCIMF
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	194	2.2.26 [Sep-21-2011]
Q5RCG9	197	Prefoldin subunit 3 OS=Po	yes	N/A	0.386	0.380	0.76	5e-30
P61759	196	Prefoldin subunit 3 OS=Mu	yes	N/A	0.386	0.382	0.76	5e-30
Q2TBX2	197	Prefoldin subunit 3 OS=Bo	yes	N/A	0.386	0.380	0.76	1e-29
P61758	197	Prefoldin subunit 3 OS=Ho	yes	N/A	0.386	0.380	0.746	1e-29
Q9VGP6	185	Probable prefoldin subuni	yes	N/A	0.365	0.383	0.676	3e-22
P57741	195	Probable prefoldin subuni	yes	N/A	0.407	0.405	0.556	1e-19
P48363	199	Prefoldin subunit 3 OS=Sa	yes	N/A	0.541	0.527	0.390	1e-15
Q10143	169	Probable prefoldin subuni	yes	N/A	0.402	0.461	0.487	3e-14
Q54LS2	195	Probable prefoldin subuni	yes	N/A	0.438	0.435	0.4	8e-14
O18054	185	Probable prefoldin subuni	yes	N/A	0.376	0.394	0.410	1e-11

>sp|Q5RCG9|PFD3_PONAB Prefoldin subunit 3 OS=Pongo abelii GN=VBP1 PE=2 SV=1

 Score =  130 bits (327), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 57/75 (76%), Positives = 67/75 (89%)

Query: 24  SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
           +S+PPTDKVCLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct: 115 ASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLSTATKNLDSLEEDLDFLRDQFTTTEV 174

Query: 84  NMARVYNWDVKRRNQ 98
           NMARVYNWDVKRRN+
Sbjct: 175 NMARVYNWDVKRRNK 189

Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.
Pongo abelii (taxid: 9601)

>sp|P61759|PFD3_MOUSE Prefoldin subunit 3 OS=Mus musculus GN=Vbp1 PE=2 SV=2

 Score =  130 bits (327), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 57/75 (76%), Positives = 67/75 (89%)

Query: 24  SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
           +S+PPTDKVCLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct: 114 ASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLSTATKNLDSLEEDLDFLRDQFTTTEV 173

Query: 84  NMARVYNWDVKRRNQ 98
           NMARVYNWDVKRRN+
Sbjct: 174 NMARVYNWDVKRRNK 188

Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Mus musculus (taxid: 10090)

>sp|Q2TBX2|PFD3_BOVIN Prefoldin subunit 3 OS=Bos taurus GN=VBP1 PE=2 SV=1

 Score =  129 bits (324), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 57/75 (76%), Positives = 67/75 (89%)

Query: 24  SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
           +S+PPTDKVCLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct: 115 ASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLLTATKNLDSLEEDLDFLRDQFTTTEV 174

Query: 84  NMARVYNWDVKRRNQ 98
           NMARVYNWDVKRRN+
Sbjct: 175 NMARVYNWDVKRRNK 189

Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Bos taurus (taxid: 9913)

>sp|P61758|PFD3_HUMAN Prefoldin subunit 3 OS=Homo sapiens GN=VBP1 PE=1 SV=3

 Score =  129 bits (324), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 56/75 (74%), Positives = 67/75 (89%)

Query: 24  SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
           +S+PPTDK+CLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct: 115 ASVPPTDKMCLWLGANVMLEYDIDEAQALLEKNLSTATKNLDSLEEDLDFLRDQFTTTEV 174

Query: 84  NMARVYNWDVKRRNQ 98
           NMARVYNWDVKRRN+
Sbjct: 175 NMARVYNWDVKRRNK 189

Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Homo sapiens (taxid: 9606)

>sp|Q9VGP6|PFD3_DROME Probable prefoldin subunit 3 OS=Drosophila melanogaster GN=CG6719 PE=3 SV=2

 Score =  105 bits (261), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 48/71 (67%), Positives = 56/71 (78%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           +PPT  V LWLGA+VMLEY L +A AL+ +NI +A  NL  +EHD DFLRDQ TTTEVNM
Sbjct: 103 VPPTKTVYLWLGASVMLEYPLDEAEALLNQNITSAVGNLKSVEHDQDFLRDQITTTEVNM 162

Query: 86  ARVYNWDVKRR 96
           ARVYNW VK+R
Sbjct: 163 ARVYNWGVKKR 173

Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Drosophila melanogaster (taxid: 7227)

>sp|P57741|PFD3_ARATH Probable prefoldin subunit 3 OS=Arabidopsis thaliana GN=At5g49510 PE=2 SV=1

 Score = 95.9 bits (237), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 44/79 (55%), Positives = 56/79 (70%)

Query: 18  EAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQ 77
           E     + I  TD VCLWLGANVMLEY+  +A+AL++ N+E AK +L  +  DL FLRDQ
Sbjct: 102 EGIYSRACIEDTDSVCLWLGANVMLEYSCEEASALLKNNLENAKASLEVLVADLQFLRDQ 161

Query: 78  FTTTEVNMARVYNWDVKRR 96
            T T+V +ARVYNWDV +R
Sbjct: 162 VTVTQVTIARVYNWDVHQR 180

Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Arabidopsis thaliana (taxid: 3702)

>sp|P48363|PFD3_YEAST Prefoldin subunit 3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PAC10 PE=1 SV=1

 Score = 82.8 bits (203), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 43/110 (39%), Positives = 68/110 (61%), Gaps = 5/110 (4%)

Query: 1   MLEYNLTDATALVQKNIEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAA 60
           +L Y L D T   +  ++  +  + +    KV LWLGA+VMLEY + +A  L++K +  +
Sbjct: 94  LLHYQLND-TLYTKAQVDIPEDRADL----KVGLWLGADVMLEYPIDEAIELLKKKLADS 148

Query: 61  KKNLSYIEHDLDFLRDQFTTTEVNMARVYNWDVKRRNQLKMGLEKSNRLR 110
           +++L+    D++FLR+  TT EVN AR+YNWDV+RR  LK   E +  L+
Sbjct: 149 EQSLTVSTEDVEFLRENITTMEVNCARLYNWDVQRRQDLKQAQEGTKNLK 198

Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q10143|PFD3_SCHPO Probable prefoldin subunit 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC3H8.07c PE=3 SV=1

 Score = 78.6 bits (192), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 52/78 (66%)

Query: 24  SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
           + +   D V LWLGANVMLEY + +A AL+ + + +A++ L   + DL+FLR Q TT EV
Sbjct: 92  AEVEAKDNVYLWLGANVMLEYTVEEAEALLTQKLNSAEETLKACKEDLEFLRAQVTTMEV 151

Query: 84  NMARVYNWDVKRRNQLKM 101
           N ARVYN+ V  R + KM
Sbjct: 152 NTARVYNYTVLLRKKTKM 169

Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q54LS2|PFD3_DICDI Probable prefoldin subunit 3 OS=Dictyostelium discoideum GN=pfdn3 PE=3 SV=1

 Score = 76.6 bits (187), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 56/85 (65%)

Query: 18  EAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQ 77
           E    ++ +     + LWLGANVMLEY+  +A  +++KN +   + LS    DL F++DQ
Sbjct: 103 EGVYSSAQVNEPKSIYLWLGANVMLEYSFEEAREVLRKNKDTVDRQLSESIQDLGFVKDQ 162

Query: 78  FTTTEVNMARVYNWDVKRRNQLKMG 102
            TTT+VN++RVYN+D+ ++ +LK+ 
Sbjct: 163 ITTTDVNVSRVYNYDIIQKRKLKLS 187

Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Dictyostelium discoideum (taxid: 44689)

>sp|O18054|PFD3_CAEEL Probable prefoldin subunit 3 OS=Caenorhabditis elegans GN=pfd-3 PE=3 SV=1

 Score = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 52/73 (71%)

Query: 24  SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
           +++   +KV +WLGANVM+EY+L +A  L+ KN  + +K +  + ++L +++DQ TTTEV
Sbjct: 102 ATVQKPEKVSIWLGANVMVEYDLENARKLLDKNRGSVQKVVDELTNELSYIKDQITTTEV 161

Query: 84  NMARVYNWDVKRR 96
           NM+ + N+ V +R
Sbjct: 162 NMSHIVNFGVNKR 174

Binds specifically to cytosolic chaperonin (c-CPN) and transfers target proteins to it. Binds to nascent polypeptide chain and promotes folding in an environment in which there are many competing pathways for nonnative proteins.

Caenorhabditis elegans (taxid: 6239)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	194
383856573	190	PREDICTED: prefoldin subunit 3-like [Meg	0.386	0.394	0.8	3e-30
340708751	190	PREDICTED: prefoldin subunit 3-like isof	0.386	0.394	0.786	5e-30
156554938	192	PREDICTED: prefoldin subunit 3-like [Nas	0.365	0.369	0.859	7e-30
380011378	190	PREDICTED: prefoldin subunit 3-like [Api	0.386	0.394	0.786	7e-30
350427777	190	PREDICTED: prefoldin subunit 3-like [Bom	0.386	0.394	0.786	7e-30
66500931	190	PREDICTED: prefoldin subunit 3-like [Api	0.386	0.394	0.786	7e-30
146285349	187	putative prefoldin [Lygus lineolaris]	0.396	0.411	0.766	1e-29
307198408	352	Prefoldin subunit 3 [Harpegnathos saltat	0.386	0.213	0.773	3e-29
307172404	188	Prefoldin subunit 3 [Camponotus floridan	0.386	0.398	0.786	3e-29
332023712	187	Prefoldin subunit 3 [Acromyrmex echinati	0.386	0.401	0.773	4e-29

>gi|383856573|ref|XP_003703782.1| PREDICTED: prefoldin subunit 3-like [Megachile rotundata]

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 60/75 (80%), Positives = 67/75 (89%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           IPPTDKVCLWLGANVMLEY L DA  ++ KNIEAAK+NLSY+EHDLDF+RDQFTTTEVNM
Sbjct: 114 IPPTDKVCLWLGANVMLEYTLDDAQEMLTKNIEAAKRNLSYVEHDLDFVRDQFTTTEVNM 173

Query: 86  ARVYNWDVKRRNQLK 100
           AR+YNW+VKRR   K
Sbjct: 174 ARIYNWEVKRRQAAK 188

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340708751|ref|XP_003392985.1| PREDICTED: prefoldin subunit 3-like isoform 1 [Bombus terrestris] gi|340708753|ref|XP_003392986.1| PREDICTED: prefoldin subunit 3-like isoform 2 [Bombus terrestris]

 Score =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 59/75 (78%), Positives = 66/75 (88%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           IPPTDKVCLWLGANVMLEY L DA  ++ KNIEAAK+NL Y+EHDLDF+RDQFTTTEVNM
Sbjct: 114 IPPTDKVCLWLGANVMLEYTLDDAQEMLTKNIEAAKRNLGYVEHDLDFVRDQFTTTEVNM 173

Query: 86  ARVYNWDVKRRNQLK 100
           AR+YNW+VKRR   K
Sbjct: 174 ARIYNWEVKRRQAAK 188

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156554938|ref|XP_001599491.1| PREDICTED: prefoldin subunit 3-like [Nasonia vitripennis]

 Score =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 61/71 (85%), Positives = 65/71 (91%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           I PTDKVCLWLGANVMLEY L DA  L+ KNI+AAKKNL+YIEHDLDF+RDQFTTTEVNM
Sbjct: 116 IAPTDKVCLWLGANVMLEYTLDDAQELLTKNIQAAKKNLAYIEHDLDFVRDQFTTTEVNM 175

Query: 86  ARVYNWDVKRR 96
           ARVYNWDVKRR
Sbjct: 176 ARVYNWDVKRR 186

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380011378|ref|XP_003689784.1| PREDICTED: prefoldin subunit 3-like [Apis florea]

 Score =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 59/75 (78%), Positives = 66/75 (88%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           IPPTDKVCLWLGANVMLEY L DA  ++ KNIEAAK+NL Y+EHDLDF+RDQFTTTEVNM
Sbjct: 114 IPPTDKVCLWLGANVMLEYTLDDAQEMLTKNIEAAKRNLGYVEHDLDFVRDQFTTTEVNM 173

Query: 86  ARVYNWDVKRRNQLK 100
           AR+YNW+VKRR   K
Sbjct: 174 ARIYNWEVKRRQAAK 188

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350427777|ref|XP_003494878.1| PREDICTED: prefoldin subunit 3-like [Bombus impatiens]

 Score =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 59/75 (78%), Positives = 66/75 (88%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           IPPTDKVCLWLGANVMLEY L DA  ++ KNIEAAK+NL Y+EHDLDF+RDQFTTTEVNM
Sbjct: 114 IPPTDKVCLWLGANVMLEYTLDDAQEMLTKNIEAAKRNLGYVEHDLDFVRDQFTTTEVNM 173

Query: 86  ARVYNWDVKRRNQLK 100
           AR+YNW+VKRR   K
Sbjct: 174 ARIYNWEVKRRQAAK 188

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66500931|ref|XP_624282.1| PREDICTED: prefoldin subunit 3-like [Apis mellifera]

 Score =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 59/75 (78%), Positives = 66/75 (88%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           IPPTDKVCLWLGANVMLEY L DA  ++ KNIEAAK+NL Y+EHDLDF+RDQFTTTEVNM
Sbjct: 114 IPPTDKVCLWLGANVMLEYTLDDAQEMLTKNIEAAKRNLGYVEHDLDFVRDQFTTTEVNM 173

Query: 86  ARVYNWDVKRRNQLK 100
           AR+YNW+VKRR   K
Sbjct: 174 ARIYNWEVKRRQAAK 188

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|146285349|gb|ABQ18252.1| putative prefoldin [Lygus lineolaris]

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 59/77 (76%), Positives = 69/77 (89%)

Query: 24  SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
           +S+PPTDKVCLWLGANVMLEY L DA  L+ KN+EAAK++LS++EHDLDFLRDQFTTTEV
Sbjct: 110 ASVPPTDKVCLWLGANVMLEYTLEDAMKLLNKNMEAAKEHLSFVEHDLDFLRDQFTTTEV 169

Query: 84  NMARVYNWDVKRRNQLK 100
           NMARVYNW+VK+R   K
Sbjct: 170 NMARVYNWNVKKRQAAK 186

Source: Lygus lineolaris

Species: Lygus lineolaris

Genus: Lygus

Family: Miridae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307198408|gb|EFN79350.1| Prefoldin subunit 3 [Harpegnathos saltator]

 Score =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 58/75 (77%), Positives = 65/75 (86%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           IPPTDKVCLWLGANVMLEY L DA  ++ KNIEAAK+NL Y+EHDLDF+RDQFTT EVNM
Sbjct: 276 IPPTDKVCLWLGANVMLEYTLDDAQEMLTKNIEAAKRNLGYVEHDLDFVRDQFTTMEVNM 335

Query: 86  ARVYNWDVKRRNQLK 100
           AR+YNW+VKRR   K
Sbjct: 336 ARIYNWEVKRRQAAK 350

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307172404|gb|EFN63866.1| Prefoldin subunit 3 [Camponotus floridanus]

 Score =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 59/75 (78%), Positives = 65/75 (86%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           IPPTDKVCLWLGANVMLEY L DA  ++ KNIEAAKKNL Y+EHDLDF+RDQFTT EVNM
Sbjct: 112 IPPTDKVCLWLGANVMLEYTLDDAQEVLTKNIEAAKKNLGYVEHDLDFVRDQFTTMEVNM 171

Query: 86  ARVYNWDVKRRNQLK 100
           AR+YNW+VKRR   K
Sbjct: 172 ARIYNWEVKRRQAAK 186

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332023712|gb|EGI63936.1| Prefoldin subunit 3 [Acromyrmex echinatior]

 Score =  133 bits (334), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 58/75 (77%), Positives = 65/75 (86%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           IPPTDKVCLWLGANVMLEY L DA  ++ KNIEAAKKNL Y+EHDLDF+RDQ+TT EVNM
Sbjct: 111 IPPTDKVCLWLGANVMLEYTLDDAQEVLTKNIEAAKKNLGYVEHDLDFVRDQYTTVEVNM 170

Query: 86  ARVYNWDVKRRNQLK 100
           AR+YNW+VKRR   K
Sbjct: 171 ARIYNWEVKRRQAAK 185

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	194
UNIPROTKB|F6XQ49	197	VBP1 "Uncharacterized protein"	0.386	0.380	0.76	1.9e-28
UNIPROTKB|K7GNY9	197	VBP1 "Uncharacterized protein"	0.386	0.380	0.76	1.9e-28
MGI|MGI:1333804	196	Vbp1 "von Hippel-Lindau bindin	0.386	0.382	0.76	1.9e-28
UNIPROTKB|E1BXR1	200	VBP1 "Uncharacterized protein"	0.386	0.375	0.746	3.9e-28
UNIPROTKB|G5E5K1	197	VBP1 "Prefoldin subunit 3" [Bo	0.386	0.380	0.76	3.9e-28
UNIPROTKB|Q2TBX2	197	VBP1 "Prefoldin subunit 3" [Bo	0.386	0.380	0.76	3.9e-28
UNIPROTKB|F5H2A7	192	VBP1 "Prefoldin subunit 3" [Ho	0.386	0.390	0.746	3.9e-28
UNIPROTKB|P61758	197	VBP1 "Prefoldin subunit 3" [Ho	0.386	0.380	0.746	3.9e-28
UNIPROTKB|F1RZQ7	197	VBP1 "Uncharacterized protein"	0.386	0.380	0.746	8.2e-28
ZFIN|ZDB-GENE-050522-494	236	vbp1 "von Hippel-Lindau bindin	0.386	0.317	0.733	3.5e-27

UNIPROTKB|F6XQ49 VBP1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 317 (116.6 bits), Expect = 1.9e-28, P = 1.9e-28
 Identities = 57/75 (76%), Positives = 67/75 (89%)

Query:    24 SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
             +S+PPTDKVCLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct:   115 ASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLSTATKNLDSLEEDLDFLRDQFTTTEV 174

Query:    84 NMARVYNWDVKRRNQ 98
             NMARVYNWDVKRRN+
Sbjct:   175 NMARVYNWDVKRRNK 189

GO:0051082 "unfolded protein binding" evidence=IEA

GO:0016272 "prefoldin complex" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

UNIPROTKB|K7GNY9 VBP1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 317 (116.6 bits), Expect = 1.9e-28, P = 1.9e-28
 Identities = 57/75 (76%), Positives = 67/75 (89%)

Query:    24 SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
             +S+PPTDKVCLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct:   115 ASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLSTATKNLDSLEEDLDFLRDQFTTTEV 174

Query:    84 NMARVYNWDVKRRNQ 98
             NMARVYNWDVKRRN+
Sbjct:   175 NMARVYNWDVKRRNK 189

GO:0051082 "unfolded protein binding" evidence=IEA

GO:0016272 "prefoldin complex" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

MGI|MGI:1333804 Vbp1 "von Hippel-Lindau binding protein 1" [Mus musculus (taxid:10090)]

 Score = 317 (116.6 bits), Expect = 1.9e-28, P = 1.9e-28
 Identities = 57/75 (76%), Positives = 67/75 (89%)

Query:    24 SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
             +S+PPTDKVCLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct:   114 ASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLSTATKNLDSLEEDLDFLRDQFTTTEV 173

Query:    84 NMARVYNWDVKRRNQ 98
             NMARVYNWDVKRRN+
Sbjct:   174 NMARVYNWDVKRRNK 188

GO:0005634 "nucleus" evidence=TAS

GO:0005737 "cytoplasm" evidence=TAS

GO:0006457 "protein folding" evidence=IEA

GO:0016272 "prefoldin complex" evidence=IEA

GO:0051082 "unfolded protein binding" evidence=IEA

UNIPROTKB|E1BXR1 VBP1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 56/75 (74%), Positives = 67/75 (89%)

Query:    24 SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
             +S+PPTDKVCLWLGANVMLEY++ +A AL++KN+  A +NL  +E DLDFLRDQFTTTEV
Sbjct:   118 ASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLSTATRNLDSLEEDLDFLRDQFTTTEV 177

Query:    84 NMARVYNWDVKRRNQ 98
             NMARVYNWDVKRRN+
Sbjct:   178 NMARVYNWDVKRRNK 192

GO:0006457 "protein folding" evidence=IEA

GO:0016272 "prefoldin complex" evidence=IEA

GO:0051082 "unfolded protein binding" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

UNIPROTKB|G5E5K1 VBP1 "Prefoldin subunit 3" [Bos taurus (taxid:9913)]

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 57/75 (76%), Positives = 67/75 (89%)

Query:    24 SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
             +S+PPTDKVCLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct:   115 ASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLLTATKNLDSLEEDLDFLRDQFTTTEV 174

Query:    84 NMARVYNWDVKRRNQ 98
             NMARVYNWDVKRRN+
Sbjct:   175 NMARVYNWDVKRRNK 189

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

GO:0051082 "unfolded protein binding" evidence=IEA

GO:0016272 "prefoldin complex" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

UNIPROTKB|Q2TBX2 VBP1 "Prefoldin subunit 3" [Bos taurus (taxid:9913)]

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 57/75 (76%), Positives = 67/75 (89%)

Query:    24 SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
             +S+PPTDKVCLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct:   115 ASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLLTATKNLDSLEEDLDFLRDQFTTTEV 174

Query:    84 NMARVYNWDVKRRNQ 98
             NMARVYNWDVKRRN+
Sbjct:   175 NMARVYNWDVKRRNK 189

GO:0051086 "chaperone mediated protein folding independent of cofactor" evidence=TAS

GO:0006457 "protein folding" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0005634 "nucleus" evidence=IEA

GO:0051082 "unfolded protein binding" evidence=IEA

GO:0016272 "prefoldin complex" evidence=IEA

UNIPROTKB|F5H2A7 VBP1 "Prefoldin subunit 3" [Homo sapiens (taxid:9606)]

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 56/75 (74%), Positives = 67/75 (89%)

Query:    24 SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
             +S+PPTDK+CLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct:   110 ASVPPTDKMCLWLGANVMLEYDIDEAQALLEKNLSTATKNLDSLEEDLDFLRDQFTTTEV 169

Query:    84 NMARVYNWDVKRRNQ 98
             NMARVYNWDVKRRN+
Sbjct:   170 NMARVYNWDVKRRNK 184

GO:0006457 "protein folding" evidence=IEA

GO:0016272 "prefoldin complex" evidence=IEA

GO:0051082 "unfolded protein binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

UNIPROTKB|P61758 VBP1 "Prefoldin subunit 3" [Homo sapiens (taxid:9606)]

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 56/75 (74%), Positives = 67/75 (89%)

Query:    24 SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
             +S+PPTDK+CLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTEV
Sbjct:   115 ASVPPTDKMCLWLGANVMLEYDIDEAQALLEKNLSTATKNLDSLEEDLDFLRDQFTTTEV 174

Query:    84 NMARVYNWDVKRRNQ 98
             NMARVYNWDVKRRN+
Sbjct:   175 NMARVYNWDVKRRNK 189

GO:0016272 "prefoldin complex" evidence=IEA

GO:0051082 "unfolded protein binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006457 "protein folding" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0051084 "'de novo' posttranslational protein folding" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

UNIPROTKB|F1RZQ7 VBP1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 311 (114.5 bits), Expect = 8.2e-28, P = 8.2e-28
 Identities = 56/75 (74%), Positives = 66/75 (88%)

Query:    24 SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
             +S+PPTDKVCLWLGANVMLEY++ +A AL++KN+  A KNL  +E DLDFLRDQFTTTE 
Sbjct:   115 ASVPPTDKVCLWLGANVMLEYDIDEAQALLEKNLSTATKNLDSLEEDLDFLRDQFTTTEQ 174

Query:    84 NMARVYNWDVKRRNQ 98
             NMARVYNWDVKRRN+
Sbjct:   175 NMARVYNWDVKRRNK 189

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

GO:0051082 "unfolded protein binding" evidence=IEA

GO:0016272 "prefoldin complex" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

ZFIN|ZDB-GENE-050522-494 vbp1 "von Hippel-Lindau binding protein 1" [Danio rerio (taxid:7955)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 55/75 (73%), Positives = 66/75 (88%)

Query:    24 SSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV 83
             +S+PPTDKVCLWLGANVMLEY++  A AL++KN+  A +NL  +E DLDFLRDQFTTTEV
Sbjct:   152 ASVPPTDKVCLWLGANVMLEYDIDAAQALLEKNLATASRNLDSLEEDLDFLRDQFTTTEV 211

Query:    84 NMARVYNWDVKRRNQ 98
             NMARVYNWDVKRR++
Sbjct:   212 NMARVYNWDVKRRSK 226

GO:0006457 "protein folding" evidence=IEA

GO:0016272 "prefoldin complex" evidence=IEA

GO:0051082 "unfolded protein binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P57741	PFD3_ARATH	No assigned EC number	0.5569	0.4072	0.4051	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	194
pfam02996	120	pfam02996, Prefoldin, Prefoldin subunit	9e-18
cd00584	129	cd00584, Prefoldin_alpha, Prefoldin alpha subunit;	8e-13
cd00890	129	cd00890, Prefoldin, Prefoldin is a hexameric molec	6e-11
PRK00391	79	PRK00391, rpsR, 30S ribosomal protein S18; Reviewe	2e-04
COG0238	75	COG0238, RpsR, Ribosomal protein S18 [Translation,	3e-04

>gnl|CDD|202504 pfam02996, Prefoldin, Prefoldin subunit

 Score = 75.0 bits (185), Expect = 9e-18
 Identities = 25/66 (37%), Positives = 39/66 (59%)

Query: 26  IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNM 85
           +  TDKV + LGA   +E +L +A   ++K IE  +K L  +E +L+ L+DQ TT E N+
Sbjct: 55  VIDTDKVLVDLGAGYYVEKSLEEAIEFLKKRIEELEKQLEKLEEELEKLKDQITTLEANL 114

Query: 86  ARVYNW 91
            +V   
Sbjct: 115 QQVQQK 120

This family comprises of several prefoldin subunits. The biogenesis of the cytoskeletal proteins actin and tubulin involves interaction of nascent chains of each of the two proteins with the oligomeric protein prefoldin (PFD) and their subsequent transfer to the cytosolic chaperonin CCT (chaperonin containing TCP-1). Electron microscopy shows that eukaryotic PFD, which has a similar structure to its archaeal counterpart, interacts with unfolded actin along the tips of its projecting arms. In its PFD-bound state, actin seems to acquire a conformation similar to that adopted when it is bound to CCT. Length = 120

>gnl|CDD|238327 cd00584, Prefoldin_alpha, Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly

 Score = 62.2 bits (152), Expect = 8e-13
 Identities = 19/66 (28%), Positives = 32/66 (48%)

Query: 25  SIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVN 84
            +  TDKV + LG    +E +L +A   + K IE   K +  ++ +L  L+DQ  T E  
Sbjct: 64  KVKDTDKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEAE 123

Query: 85  MARVYN 90
           +  +  
Sbjct: 124 LQELQQ 129

The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. Length = 129

>gnl|CDD|238453 cd00890, Prefoldin, Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly

 Score = 57.0 bits (138), Expect = 6e-11
 Identities = 18/66 (27%), Positives = 35/66 (53%)

Query: 25  SIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVN 84
            +   DKV + LG  V +E +L +A   ++K +E  +K +  +E  L+ L+DQ T  +  
Sbjct: 64  EVKDDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEE 123

Query: 85  MARVYN 90
           + ++  
Sbjct: 124 LQQLQQ 129

The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. Length = 129

>gnl|CDD|178997 PRK00391, rpsR, 30S ribosomal protein S18; Reviewed

 Score = 37.9 bits (89), Expect = 2e-04
 Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 1/34 (2%)

Query: 152 KNPFQKEKVVCILCKMKIK-PDYKNIKLLSQFVS 184
           +  F + K VC  C  KI+  DYK+++LL +F+S
Sbjct: 7   RRRFFRRKKVCRFCAEKIEYIDYKDVELLKKFIS 40

Length = 79

>gnl|CDD|223316 COG0238, RpsR, Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 1/34 (2%)

Query: 152 KNPFQKEKVVCILCKMKIKP-DYKNIKLLSQFVS 184
           + PF + + VC      I+  DYK+++LL +F+S
Sbjct: 8   RAPFFRRRKVCRFTAEGIEEIDYKDVELLKRFIS 41

Length = 75

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	194
KOG3313|consensus	187		100.0
TIGR00293	126	prefoldin, archaeal alpha subunit/eukaryotic subun	99.56
PRK03947	140	prefoldin subunit alpha; Reviewed	99.48
cd00584	129	Prefoldin_alpha Prefoldin alpha subunit; Prefoldin	99.47
PF02996	120	Prefoldin: Prefoldin subunit; InterPro: IPR004127	99.42
cd00890	129	Prefoldin Prefoldin is a hexameric molecular chape	99.31
PRK00391	79	rpsR 30S ribosomal protein S18; Reviewed	99.18
TIGR00165	70	S18 ribosomal protein S18. This ribosomal small su	99.09
COG0238	75	RpsR Ribosomal protein S18 [Translation, ribosomal	99.03
PRK13401	82	30S ribosomal protein S18; Provisional	98.95
PRK13400	147	30S ribosomal protein S18; Provisional	98.94
CHL00077	86	rps18 ribosomal protein S18	98.71
KOG3162|consensus	159		98.7
PF01084	54	Ribosomal_S18: Ribosomal protein S18; InterPro: IP	98.5
KOG4021|consensus	239		98.22
PRK14011	144	prefoldin subunit alpha; Provisional	97.56
COG1730	145	GIM5 Predicted prefoldin, molecular chaperone impl	97.05
PRK01203	130	prefoldin subunit alpha; Provisional	96.53
cd00632	105	Prefoldin_beta Prefoldin beta; Prefoldin is a hexa	94.1
KOG3047|consensus	157		92.6
TIGR02338	110	gimC_beta prefoldin, beta subunit, archaeal. Chape	92.31
PF01920	106	Prefoldin_2: Prefoldin subunit; InterPro: IPR00277	92.28

>KOG3313|consensus

Probab=100.00  E-value=2.3e-42  Score=289.41  Aligned_cols=87  Identities=62%  Similarity=0.963  Sum_probs=84.4

Q ss_pred             cccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeEEeeeeeehhhHHhh
Q psy6417          17 IEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYNWDVKRR   96 (194)
Q Consensus        17 ~d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtEVN~ARvYNwdV~rr   96 (194)
                      +|+||+||+|||+++|||||||||||||++|||++||++||.+|+++++.+++||+|||||||||||||||||||||++|
T Consensus        97 sd~vy~ka~V~~~~kV~LWLGAnVMlEY~leEAeaLLkknl~sa~k~l~~~~~DldfLrdQvTTtEVN~ArvYNw~V~~R  176 (187)
T KOG3313|consen   97 SDGVYTKASVPPTDKVYLWLGANVMLEYDLEEAEALLKKNLTSAVKSLDVLEEDLDFLRDQVTTTEVNMARVYNWDVKKR  176 (187)
T ss_pred             cccceeeeecCCcCeEEEEecceeEEEecHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhceeeeeeeeeeeechHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhcc
Q psy6417          97 NQLKMGL  103 (194)
Q Consensus        97 r~~k~~~  103 (194)
                      |+.+...
T Consensus       177 ~~~~~t~  183 (187)
T KOG3313|consen  177 RAAKATN  183 (187)
T ss_pred             HHHhhcc
Confidence            9887654

>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5

Probab=99.56  E-value=6.8e-15  Score=112.89  Aligned_cols=65  Identities=20%  Similarity=0.265  Sum_probs=62.4

Q ss_pred             cccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccee
Q psy6417          17 IEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTT   81 (194)
Q Consensus        17 ~d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTt   81 (194)
                      ..++|.+|.|+++++|++|||+|+|+|++++||+++|+++++.+.++++.+++++.|+++|++..
T Consensus        55 g~~~~v~~~v~~~~~v~v~iG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~i  119 (126)
T TIGR00293        55 GAGSFVKAKVKDTDKVLVSIGSGYYVEKDAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQL  119 (126)
T ss_pred             CCCeEEEEEeCCCCEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999999999999999999999999999999999999999874

This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.

>PRK03947 prefoldin subunit alpha; Reviewed

Probab=99.48  E-value=1e-13  Score=108.49  Aligned_cols=65  Identities=25%  Similarity=0.288  Sum_probs=62.0

Q ss_pred             cccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccee
Q psy6417          17 IEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTT   81 (194)
Q Consensus        17 ~d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTt   81 (194)
                      ..++|.+|.|+++++|++|||+|||+||+++||+++|+++++.+.++++.+++++.++++|+.-.
T Consensus        63 g~~~yv~~~v~~~~kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~  127 (140)
T PRK03947         63 GAGSFVKAKVKDKDKVIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQL  127 (140)
T ss_pred             CCCcEEEEEecCCCeEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56899999999999999999999999999999999999999999999999999999999998644

>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly

Probab=99.47  E-value=5.3e-14  Score=108.32  Aligned_cols=73  Identities=26%  Similarity=0.393  Sum_probs=70.2

Q ss_pred             ccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeEEeeeeeeh
Q psy6417          18 EAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYN   90 (194)
Q Consensus        18 d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtEVN~ARvYN   90 (194)
                      .++|.+|.|+++++|++|+|+|+|+|++++||+++|+++++..+++++.+++++..+++|++.++.+++++|.
T Consensus        57 ~~~~~~~~i~~~~~v~v~iG~g~~vE~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~~l~~~~~  129 (129)
T cd00584          57 AGVFVKAKVKDTDKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEAELQELQQ  129 (129)
T ss_pred             CCeEEeEEeCCCCEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            3789999999999999999999999999999999999999999999999999999999999999999998763

The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.

>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits

Probab=99.42  E-value=2e-13  Score=102.83  Aligned_cols=74  Identities=28%  Similarity=0.420  Sum_probs=71.1

Q ss_pred             ccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeEEeeeeeehh
Q psy6417          18 EAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYNW   91 (194)
Q Consensus        18 d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtEVN~ARvYNw   91 (194)
                      .++|.+|.|+++++|.+|||+|+++|.+++||+++|+++++..+..++.+.+++..++++++.++-.++++|+|
T Consensus        47 ~~~~v~g~i~~~~~vlV~lG~~~~vE~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~  120 (120)
T PF02996_consen   47 SGVFVPGKIPDTDKVLVSLGAGYYVEMSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQQLYQQ  120 (120)
T ss_dssp             TTEEEEEE-SSTTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCEEEEEeeCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999987

Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.

>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly

Probab=99.31  E-value=2.4e-12  Score=97.39  Aligned_cols=74  Identities=24%  Similarity=0.362  Sum_probs=70.6

Q ss_pred             cccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeEEeeeeeeh
Q psy6417          17 IEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVYN   90 (194)
Q Consensus        17 ~d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtEVN~ARvYN   90 (194)
                      ..++|.+|.|+++++|++|+|+|+++|++++||+++|+++++..+++++.++++++.+++|++.++.+|+++|+
T Consensus        56 g~~~~~~~~i~~~~~v~v~iG~~~~ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~~~~  129 (129)
T cd00890          56 GAGLFVKAEVKDDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEELQQLQQ  129 (129)
T ss_pred             CCceEEEEEECCCCEEEEEecCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            45899999999999999999999999999999999999999999999999999999999999999999888763

The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.

>PRK00391 rpsR 30S ribosomal protein S18; Reviewed

Probab=99.18  E-value=1.5e-11  Score=91.79  Aligned_cols=41  Identities=37%  Similarity=0.717  Sum_probs=36.1

Q ss_pred             cCCCcccCCceeeecCCCC-CCCCCCHHHHHhhccCCccceee
Q psy6417         151 LKNPFQKEKVVCILCKMKI-KPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       151 ~~~Py~k~~k~C~lC~~~i-~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      ..+++.++++.|+||..++ .||||||+||+||||+ +|+|+.
T Consensus         6 ~~~~~~~r~k~c~~c~~~~~~iDYKnv~lL~~Fis~-~GkIlp   47 (79)
T PRK00391          6 ARRRFFRRKKVCRFCAEKIEYIDYKDVELLKKFISE-RGKILP   47 (79)
T ss_pred             cccccCCCCCCCcccCCCCCcCCccCHHHHHHhcCC-CceEcC
Confidence            4566778889999999886 6999999999999999 799984

>TIGR00165 S18 ribosomal protein S18

Probab=99.09  E-value=5.7e-11  Score=86.96  Aligned_cols=37  Identities=30%  Similarity=0.536  Sum_probs=32.2

Q ss_pred             cccCCceeeecCCCC-CCCCCCHHHHHhhccCCccceee
Q psy6417         155 FQKEKVVCILCKMKI-KPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       155 y~k~~k~C~lC~~~i-~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      |.++++.||+|..++ .||||||+||+||||++ |+|+.
T Consensus         1 ~~~r~k~c~~~~~~~~~iDYKnv~lL~~Fis~~-GkIlp   38 (70)
T TIGR00165         1 YFRRKKYCRFTAEGIQFIDYKDLDLLKKFISER-GKILP   38 (70)
T ss_pred             CCCCCCCCCccCCCCCcCCccCHHHHHHhcCCC-CeEcC
Confidence            556778999999765 69999999999999995 99974

This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically.

>COG0238 RpsR Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]

Probab=99.03  E-value=1.2e-10  Score=86.71  Aligned_cols=40  Identities=33%  Similarity=0.698  Sum_probs=35.4

Q ss_pred             CCCcccCCceeeecCCCC-CCCCCCHHHHHhhccCCccceee
Q psy6417         152 KNPFQKEKVVCILCKMKI-KPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       152 ~~Py~k~~k~C~lC~~~i-~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      .+|+++++|.|+||..++ .|||||+++|++|||+ +|+|..
T Consensus         8 r~~~~rrrk~c~~~~~~~~~iDYKd~~~L~rfise-~GKI~p   48 (75)
T COG0238           8 RAPFFRRRKVCRFTAEGIEEIDYKDVELLKRFISE-RGKILP   48 (75)
T ss_pred             cccccccccccccccccCCccCccCHHHHHHHhcc-cCcccc
Confidence            456888999999999987 5999999999999999 699963

>PRK13401 30S ribosomal protein S18; Provisional

Probab=98.95  E-value=4.3e-10  Score=84.84  Aligned_cols=35  Identities=29%  Similarity=0.461  Sum_probs=30.9

Q ss_pred             cCCceeeecCCCC-CCCCCCHHHHHhhccCCccceee
Q psy6417         157 KEKVVCILCKMKI-KPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       157 k~~k~C~lC~~~i-~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      ++++.|+||..++ .||||||+||+||||+ +|+|+.
T Consensus        11 ~r~k~c~~~~~~~~~iDYKnv~lL~~Fis~-~GkIlp   46 (82)
T PRK13401         11 TKAKKNLLDSLGIESVDYKDTALLRTFISD-RGKIRS   46 (82)
T ss_pred             CCCCCCCcccCCCCcCCccCHHHHHHhcCC-CccCcC
Confidence            3457999999887 5999999999999999 899974

>PRK13400 30S ribosomal protein S18; Provisional

Probab=98.94  E-value=6.9e-10  Score=91.29  Aligned_cols=43  Identities=21%  Similarity=0.560  Sum_probs=36.5

Q ss_pred             cccCCCcccCCceeeecCCCC-CCCCCCHHHHHhhccCCccceee
Q psy6417         149 EDLKNPFQKEKVVCILCKMKI-KPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       149 ~~~~~Py~k~~k~C~lC~~~i-~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      -...+.|++++|.|+||..++ .||||||+||++|||+ +|+|+.
T Consensus        12 ~~gr~~~~~RrK~C~~c~~~~~~IDYKNv~lL~~FISe-~GKIlP   55 (147)
T PRK13400         12 RGGRGRYTPKRKICSFCAEKVSRIDYKDSAKLARYISD-RGKIEP   55 (147)
T ss_pred             cCCCCccCCCCCCCCccCCCCCccCCcCHHHHHHhcCc-CccCcC
Confidence            344567778889999999764 6999999999999999 799974

>CHL00077 rps18 ribosomal protein S18

Probab=98.71  E-value=7.1e-09  Score=78.90  Aligned_cols=35  Identities=29%  Similarity=0.407  Sum_probs=30.3

Q ss_pred             ccCCceeeecCCCCCCCCCCHHHHHhhccCCccceee
Q psy6417         156 QKEKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       156 ~k~~k~C~lC~~~i~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      .++++.|++|.. ..||||||+||+||||+ +|+|+.
T Consensus        14 ~~rrk~~~~~~~-~~iDYKnv~lL~~Fis~-~GkIlp   48 (86)
T CHL00077         14 SFRRRLPPIQSG-DRIDYKNMSLLSRFISE-QGKILS   48 (86)
T ss_pred             hcccCCCCCCCC-CcCCccCHHHHHHhcCC-CCeEcC
Confidence            345678999997 46999999999999999 799985

>KOG3162|consensus

Probab=98.70  E-value=7.8e-09  Score=85.98  Aligned_cols=46  Identities=39%  Similarity=0.558  Sum_probs=40.1

Q ss_pred             CCccccCCCcccCCceeeecCCCCC--CCCCCHHHHHhhccCCccceee
Q psy6417         146 KPAEDLKNPFQKEKVVCILCKMKIK--PDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       146 ~p~~~~~~Py~k~~k~C~lC~~~i~--iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      +++...+||+++..++|++|..+|+  .+||||.||+|||+|++| ||.
T Consensus        53 e~~~~~~n~~~~~~~~c~~c~~~Vd~~~~yknv~iLsqFv~~~G~-il~  100 (159)
T KOG3162|consen   53 ELPIASNNPEKKSEPQCILCTKGVDIKLSYKNVLLLSQFVSEDGG-ILP  100 (159)
T ss_pred             hhhhhcCCCcccCcccCcccccCCCcccccCccchhhhhcccccc-eec
Confidence            3478999999999899999999875  469999999999999866 874

>PF01084 Ribosomal_S18: Ribosomal protein S18; InterPro: IPR001648 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.50  E-value=6e-08  Score=67.64  Aligned_cols=27  Identities=48%  Similarity=0.785  Sum_probs=23.9

Q ss_pred             cCCCCCCCCCCHHHHHhhccCCccceee
Q psy6417         165 CKMKIKPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       165 C~~~i~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      |..+..||||||+||+||||| +|+|+.
T Consensus         1 ~~~~~~idykn~~lL~~Fi~~-~GkIl~   27 (54)
T PF01084_consen    1 CNNNEYIDYKNVELLSQFISP-TGKILP   27 (54)
T ss_dssp             -SSSSSSSSSSHHHHGCGBTT-SSSBST
T ss_pred             CCCCCcCCcCCHHHHHHHcCc-ccceeh
Confidence            666778999999999999999 899985

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S18 is known to be involved in binding the aminoacyl-tRNA complex in Escherichia coli [], and appears to be situated at the tRNA A-site. Experimental evidence has revealed that S18 is well exposed on the surface of the E. coli ribosome, and is a secondary rRNA binding protein []. S18 belongs to a family of ribosomal proteins [] that includes: eubacterial S18; metazoan mitochondrial S18, algal and plant chloroplast S18; and cyanelle S18.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2UXD_R 3I8G_U 3UZ7_U 1N33_R 2XSY_R 3V24_R 3OGY_R 2XUY_R 2XFZ_R 3UXT_R ....

>KOG4021|consensus

Probab=98.22  E-value=3.7e-07  Score=79.43  Aligned_cols=32  Identities=34%  Similarity=0.595  Sum_probs=28.6

Q ss_pred             ceeeecCC-CCCCCCCCHHHHHhhccCCcccee
Q psy6417         160 VVCILCKM-KIKPDYKNIKLLSQFVSAFTGRVC  191 (194)
Q Consensus       160 k~C~lC~~-~i~iDYKNV~LLsqFiS~~tG~I~  191 (194)
                      ..||+|++ ++.+||+|++||.||+++|||.|.
T Consensus       109 npCPICRDeyL~~DyRN~~LlEQF~~~htg~~i  141 (239)
T KOG4021|consen  109 NPCPICRDEYLYFDYRNPGLLEQFLADHTGQPI  141 (239)
T ss_pred             CCCCccccceEEEeccCHHHHHHHhccCCCCch
Confidence            57899995 689999999999999999999664

>PRK14011 prefoldin subunit alpha; Provisional

Probab=97.56  E-value=0.00035  Score=57.06  Aligned_cols=64  Identities=20%  Similarity=0.262  Sum_probs=60.4

Q ss_pred             ccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccee
Q psy6417          18 EAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTT   81 (194)
Q Consensus        18 d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTt   81 (194)
                      .++|.+|.|.++|+|.+=+|+++-+|-+++||+++|+++++..+++.+.+.+.|+=+.+++...
T Consensus        58 ~s~yV~g~i~d~dkVlVdIGtGy~VEk~~~eA~~~~~~ri~~l~~~~~~l~~~i~~~~~~~~~l  121 (144)
T PRK14011         58 PGAFLKAKIVDPDKAILGVGSDIYLEKDVSEVIEDFKKSVEELDKTKKEGNKKIEELNKEITKL  121 (144)
T ss_pred             CCcEEeEEecCCCeEEEEccCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999999999999999999999999999999888754

>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]

Probab=97.05  E-value=0.0025  Score=52.49  Aligned_cols=62  Identities=19%  Similarity=0.283  Sum_probs=58.0

Q ss_pred             cceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccce
Q psy6417          19 AAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTT   80 (194)
Q Consensus        19 ~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITT   80 (194)
                      ++|.+|.|...|+|-.=+|+++-+|=+++||++.|+++++...++++.+++-|+=|-.+++.
T Consensus        65 g~fv~~kv~~~~kviV~iGsg~~ae~~~~eAie~l~k~~~~l~~~~~~l~~~l~~l~~~~~~  126 (145)
T COG1730          65 GLFVKAKVKDMDKVIVSIGSGYYAEKSADEAIEFLKKRIEELEKAIEKLQQALAELAQRIEQ  126 (145)
T ss_pred             CceEEEEeccCceEEEEcCCceeeeecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999888777664

>PRK01203 prefoldin subunit alpha; Provisional

Probab=96.53  E-value=0.013  Score=47.68  Aligned_cols=62  Identities=15%  Similarity=0.250  Sum_probs=57.4

Q ss_pred             ccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccc
Q psy6417          18 EAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFT   79 (194)
Q Consensus        18 d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQIT   79 (194)
                      .++|.+|.|.++++|-+=+|+++-+|=++++|+++|+++++..+..+....+.++=|-+|+-
T Consensus        57 ~slYV~gki~d~~kVlVdIGTGy~VEK~~e~kie~L~~~ie~Le~~i~~K~~~l~~i~~~~~  118 (130)
T PRK01203         57 SGIFADGNIKKDKDLIVPIGSGVYIAEERERTIERLKENLEDLKDSIQKLNDQRKTLVDQYN  118 (130)
T ss_pred             CCceEeEEecCCCeEEEEcCCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999998888888877753

>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea

Probab=94.10  E-value=0.036  Score=41.99  Aligned_cols=55  Identities=13%  Similarity=0.278  Sum_probs=47.3

Q ss_pred             cCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccee
Q psy6417          26 IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTT   81 (194)
Q Consensus        26 I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTt   81 (194)
                      ++|..+||.-+|. |+++.+.+||...|+++++..+..++.++..++.+.+++.-.
T Consensus        42 l~~d~~vy~~VG~-vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~el   96 (105)
T cd00632          42 LADDAEVYKLVGN-VLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKEL   96 (105)
T ss_pred             CCCcchHHHHhhh-HHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455667666664 999999999999999999999999999999999999987643

Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st

>KOG3047|consensus

Probab=92.60  E-value=0.5  Score=39.55  Aligned_cols=61  Identities=16%  Similarity=0.289  Sum_probs=50.6

Q ss_pred             cceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccc
Q psy6417          19 AAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFT   79 (194)
Q Consensus        19 ~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQIT   79 (194)
                      ++|-...||.|..|++-||-++.||..+.||+++...+.+..+.-.+.+..|--=|+--|+
T Consensus        76 nfFmdi~VpDTk~i~VaL~~~fflElkLadAiKf~DRK~dlLkel~ekLqKdsmkiKa~ih  136 (157)
T KOG3047|consen   76 NFFMDIEVPDTKHIVVALCDDFFLELKLADAIKFCDRKMDLLKELMEKLQKDSMKIKADIH  136 (157)
T ss_pred             eeeEeeecCCcceEEEEeecceeeeehHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHHHHH
Confidence            5788889999999999999999999999999999888887777766666666555555544

>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal

Probab=92.31  E-value=0.037  Score=42.37  Aligned_cols=60  Identities=13%  Similarity=0.268  Sum_probs=50.4

Q ss_pred             cCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeEEeee
Q psy6417          26 IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMA   86 (194)
Q Consensus        26 I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtEVN~A   86 (194)
                      +|+..+||-=+|. |+++-+.+||..-|+++++..+..++.+++.+++|+.++.-++=++.
T Consensus        46 l~~d~~vyk~VG~-vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~~l~  105 (110)
T TIGR02338        46 LPDDTPVYKSVGN-LLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLKELQEKIQ  105 (110)
T ss_pred             CCCcchhHHHhch-hhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455566666665 99999999999999999999999999999999999999876554443

Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.

>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea

Probab=92.28  E-value=0.8  Score=33.36  Aligned_cols=56  Identities=18%  Similarity=0.359  Sum_probs=46.5

Q ss_pred             cCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeE
Q psy6417          26 IPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTE   82 (194)
Q Consensus        26 I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtE   82 (194)
                      +|+..+||.=+| ++.++.+.+|+.+-|++.++.++..++.++.-+.++.+++.-.+
T Consensus        41 l~~~~~~y~~vG-~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~   96 (106)
T PF01920_consen   41 LDDDRKVYKSVG-KMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKELK   96 (106)
T ss_dssp             SSTT-EEEEEET-TEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcchhHHHHh-HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345556665554 58999999999999999999999999999999999999886544

Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	194
3i1m_R	75	30S ribosomal protein S18; ribosome structure, pro	4e-04

>3i1m_R 30S ribosomal protein S18; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_R* 1vs5_R 3i1o_R 3i1q_R 3i1s_R 3i1z_R 3i21_R 3izv_V* 3izw_V* 3kc4_R 3or9_R 3ora_R 3sfs_R* 3uoq_R* 2qal_R* 1p6g_R 1p87_R 2aw7_R 2avy_R 2i2u_R ... Length = 75

 Score = 36.4 bits (85), Expect = 4e-04
 Identities = 6/31 (19%), Positives = 15/31 (48%), Gaps = 1/31 (3%)

Query: 155 FQKEKVVCILCKMKIKP-DYKNIKLLSQFVS 184
           + + +  C      ++  DYK+I  L  +++
Sbjct: 4   YFRRRKFCRFTAEGVQEIDYKDIATLKNYIT 34

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	194
1fxk_C	133	Protein (prefoldin); archaeal protein, chaperone;	99.68
2zdi_C	151	Prefoldin subunit alpha; chaperone, cytoplasm; 3.0	99.68
3i1m_R	75	30S ribosomal protein S18; ribosome structure, pro	99.28
2vqe_R	88	30S ribosomal protein S18; tRNA-binding, rRNA-bind	99.15
3bbn_R	103	Ribosomal protein S18; small ribosomal subunit, sp	98.87
3r8n_R	55	30S ribosomal protein S18; protein biosynthesis, R	98.26
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	95.51
1fxk_A	107	Prefoldin; archaeal protein, chaperone; 2.30A {Met	95.09

>1fxk_C Protein (prefoldin); archaeal protein, chaperone; 2.30A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: a.2.5.1

Probab=99.68  E-value=4.8e-17  Score=124.94  Aligned_cols=67  Identities=16%  Similarity=0.243  Sum_probs=64.0

Q ss_pred             ccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeEEe
Q psy6417          18 EAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVN   84 (194)
Q Consensus        18 d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtEVN   84 (194)
                      +++|.+|.|+++++|++|||+|+|+||+++||+++|+++++.++.+++.++++++|+++||++++--
T Consensus        58 ~~~yv~a~i~~~~~V~v~lG~g~~vE~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~i~~~~~~  124 (133)
T 1fxk_C           58 AGSFIKAELKDTSEVIMSVGAGVAIKKNFEDAMESIKSQKNELESTLQKMGENLRAITDIMMKLSPQ  124 (133)
T ss_dssp             TTEEEEEECCSTTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCEEEEEcCCCEEEEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999999999999999999999999999987643

>2zdi_C Prefoldin subunit alpha; chaperone, cytoplasm; 3.00A {Pyrococcus horikoshii}

Probab=99.68  E-value=2.1e-17  Score=130.28  Aligned_cols=72  Identities=11%  Similarity=0.177  Sum_probs=69.4

Q ss_pred             ccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeEEeeeeee
Q psy6417          18 EAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVY   89 (194)
Q Consensus        18 d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtEVN~ARvY   89 (194)
                      +++|.+|.|+++++|++|||||+|+||+++||+++|+++++.++.+++.++++++++++||+++++++..++
T Consensus        68 ~~~yv~g~i~~~~~V~v~lG~g~~vE~~~~eA~~~l~~ri~~l~~~l~~l~~~l~~l~~~i~~~~~~l~~l~  139 (151)
T 2zdi_C           68 AGSFLKGVIVDKNNAIVSVGSGYAVERSIDEAISFLEKRLKEYDEAIKKTQGALAELEKRIGEVARKAQEVQ  139 (151)
T ss_dssp             SSCEEEEECSCTTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHH
T ss_pred             CCeEEEEEECCCCEEEEEeCCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999999999999999999999999999999999987765

>3i1m_R 30S ribosomal protein S18; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_R* 1vs5_R 3i1o_R 3i1q_R 3i1s_R 3i1z_R 3i21_R 3izv_V* 3izw_V* 3kc4_R 3or9_R 3ora_R 3sfs_R* 3uoq_R* 4gaq_R* 4gas_R* 2qal_R* 1p6g_R 1p87_R 2aw7_R ...

Probab=99.28  E-value=8.5e-13  Score=96.51  Aligned_cols=39  Identities=18%  Similarity=0.516  Sum_probs=20.5

Q ss_pred             CCcccCCceeeecCCCC-CCCCCCHHHHHhhccCCccceee
Q psy6417         153 NPFQKEKVVCILCKMKI-KPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       153 ~Py~k~~k~C~lC~~~i-~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      .||++++|.|+||..++ .||||||+||+||||+ +|+|+.
T Consensus         2 ~~~~~r~k~C~fc~~~~~~iDYknv~lL~~Fis~-~GkIlp   41 (75)
T 3i1m_R            2 ARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITE-SGKIVP   41 (75)
T ss_dssp             ------------------CCSTTCHHHHGGGBCT-TCCBCC
T ss_pred             CccCCCCCCCCcccCCCCcCCcCCHHHHHHHcCc-CCCCcC
Confidence            47889999999999987 5999999999999999 899974

>2vqe_R 30S ribosomal protein S18; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.4.8.1 PDB: 1fka_R 1fjg_R 1gix_U* 1hnw_R* 1hnx_R* 1hnz_R* 1hr0_R 1ibk_R* 1ibl_R* 1ibm_R 1j5e_R 1jgo_U* 1jgp_U* 1jgq_U* 1ml5_U* 1n32_R* 1n33_R* 1n34_R 1n36_R 1xmo_R* ...

Probab=99.15  E-value=1.1e-11  Score=92.94  Aligned_cols=43  Identities=21%  Similarity=0.341  Sum_probs=32.2

Q ss_pred             ccccCCCcccCCceeeecCCCC-CCCCCCHHHHHhhccCCccceee
Q psy6417         148 AEDLKNPFQKEKVVCILCKMKI-KPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       148 ~~~~~~Py~k~~k~C~lC~~~i-~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      ...|.+++ ++++.|+||..++ .||||||+||+||||+ +|+|+.
T Consensus         9 ~~~~~~~~-~r~k~C~~c~~~~~~iDYKnv~lL~~Fise-~GkIlp   52 (88)
T 2vqe_R            9 KKEAQRRP-SRKAKVKATLGEFDLRDYRNVEVLKRFLSE-TGKILP   52 (88)
T ss_dssp             -------C-CCSCCTTTSCCCEETTCTTCHHHHGGGBCS-SSCBCC
T ss_pred             cccccccC-CCCCCCCccCCCCCcCCcCCHHHHHHHccc-CCCCCc
Confidence            44555665 5669999999886 5999999999999999 899974

>3bbn_R Ribosomal protein S18; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1

Probab=98.87  E-value=5.2e-10  Score=86.34  Aligned_cols=33  Identities=24%  Similarity=0.445  Sum_probs=21.6

Q ss_pred             CCceeeecCCCCCCCCCCHHHHHhhccCCccceee
Q psy6417         158 EKVVCILCKMKIKPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       158 ~~k~C~lC~~~i~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      +++.||+|.. ..||||||+||+||||+ +|+|+.
T Consensus        16 rr~~cpi~~~-~~IDYKnv~lL~~FIse-~GKIlp   48 (103)
T 3bbn_R           16 RRRLPPIQSG-DRIDYRNMSLISRFISE-QGKILS   48 (103)
T ss_dssp             ---------C-CSSCCSCHHHHTTTSCS-SSSCCC
T ss_pred             cCCCCCcCCC-CcCCcCCHHHHHHHhcc-CCCCcC
Confidence            4579999984 56999999999999999 899974

>2zqm_A Prefoldin beta subunit 1; chaperone; HET: CIT; 1.90A {Thermococcus SP} PDB: 2zdi_A

Probab=95.51  E-value=0.048  Score=39.87  Aligned_cols=57  Identities=18%  Similarity=0.261  Sum_probs=50.5

Q ss_pred             CCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeEEe
Q psy6417          27 PPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVN   84 (194)
Q Consensus        27 ~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtEVN   84 (194)
                      ++..+||.=+| .|.++-+.+||...|+++++..+..++.++..++.+++++.-.+.+
T Consensus        50 ~~d~~vy~~iG-~vfv~~~~~ea~~~L~~~~e~ie~~i~~le~~~~~l~~~l~~lk~~  106 (117)
T 2zqm_A           50 PDDAVVYKTVG-TLIVKTTKDKAVAELKEKIETLEVRLNALERQEKKLNEKLKELTAQ  106 (117)
T ss_dssp             CTTCCEEEEET-TEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcHhHHHhh-HHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45557888888 8999999999999999999999999999999999999998755443

>1fxk_A Prefoldin; archaeal protein, chaperone; 2.30A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: a.2.5.1 PDB: 1fxk_B

Probab=95.09  E-value=0.081  Score=38.16  Aligned_cols=56  Identities=16%  Similarity=0.209  Sum_probs=49.1

Q ss_pred             CCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeEE
Q psy6417          27 PPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV   83 (194)
Q Consensus        27 ~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtEV   83 (194)
                      |+..+||-=+| .|.++-+.+||..-|+++++..+..++.++..++.+++++.-.+.
T Consensus        45 ~~d~~vy~~iG-~vfv~~~~~e~~~~L~~~~e~i~~~i~~le~~~~~~~~~l~~lk~  100 (107)
T 1fxk_A           45 ADDAEVYKSSG-NILIRVAKDELTEELQEKLETLQLREKTIERQEERVMKKLQEMQV  100 (107)
T ss_dssp             CTTCCEEEEET-TEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCchHHHHHh-HHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55557887777 899999999999999999999999999999999999998765443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	194
d1fxkc_	133	a.2.5.1 (C:) Prefoldin alpha subunit {Archaeon Met	2e-10

>d1fxkc_ a.2.5.1 (C:) Prefoldin alpha subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 133

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Prefoldin
family: Prefoldin
domain: Prefoldin alpha subunit
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score = 54.2 bits (130), Expect = 2e-10
 Identities = 11/66 (16%), Positives = 25/66 (37%)

Query: 23  NSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTE 82
            + +  T +V + +GA V ++ N  DA   ++      +  L  +  +L  + D      
Sbjct: 63  KAELKDTSEVIMSVGAGVAIKKNFEDAMESIKSQKNELESTLQKMGENLRAITDIMMKLS 122

Query: 83  VNMARV 88
                +
Sbjct: 123 PQAEEL 128

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	194
d1fxkc_	133	Prefoldin alpha subunit {Archaeon Methanobacterium	99.07
d2uubr1	70	Ribosomal protein S18 {Thermus thermophilus [TaxId	98.34
d2qalr1	55	Ribosomal protein S18 {Escherichia coli [TaxId: 56	98.2

>d1fxkc_ a.2.5.1 (C:) Prefoldin alpha subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Prefoldin
family: Prefoldin
domain: Prefoldin alpha subunit
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=99.07  E-value=5.2e-11  Score=89.05  Aligned_cols=70  Identities=16%  Similarity=0.232  Sum_probs=65.0

Q ss_pred             ccceeeeecCCCCeEEEEeccceeeeechHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhccceeEEeeee
Q psy6417          18 EAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMAR   87 (194)
Q Consensus        18 d~lyakA~I~p~d~V~LWLGANVMLEY~ldEA~~LL~~nL~~A~~~l~~~eeDLdFLRdQITTtEVN~AR   87 (194)
                      .++|.+|.|+++++|++|||+|+++|++++||.++|.++++..++.++.+.+++..++++|+.++..+.+
T Consensus        58 ~~~~v~~~i~~~~~vlV~lG~g~~vE~~~~eA~~~l~~ri~~l~~~~~~l~~~~~~~~~~i~~l~~~~~~  127 (133)
T d1fxkc_          58 AGSFIKAELKDTSEVIMSVGAGVAIKKNFEDAMESIKSQKNELESTLQKMGENLRAITDIMMKLSPQAEE  127 (133)
T ss_dssp             TTEEEEEECCSTTEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CceEEEEEecCCCceEEEecCCeeeeecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4699999999999999999999999999999999999999999999999999999999999877655443

>d2uubr1 a.4.8.1 (R:19-88) Ribosomal protein S18 {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Ribosomal protein S18
family: Ribosomal protein S18
domain: Ribosomal protein S18
species: Thermus thermophilus [TaxId: 274]

Probab=98.34  E-value=9.4e-08  Score=67.32  Aligned_cols=31  Identities=26%  Similarity=0.438  Sum_probs=24.2

Q ss_pred             eeeecCCCC-CCCCCCHHHHHhhccCCccceee
Q psy6417         161 VCILCKMKI-KPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       161 ~C~lC~~~i-~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      +|..+..++ .|||||++||+||||+ +|+|+.
T Consensus         3 k~k~~~~~~~~iDYKn~~lL~~Fis~-~GkIlp   34 (70)
T d2uubr1           3 KVKATLGEFDLRDYRNVEVLKRFLSE-TGKILP   34 (70)
T ss_dssp             CTTTSSCSCCTTCTTCHHHHGGGBCS-SSCBCC
T ss_pred             CccccccccCccCccCHHHHHHhcCC-CCeEec
Confidence            344444444 4899999999999999 799974

>d2qalr1 a.4.8.1 (R:19-73) Ribosomal protein S18 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Ribosomal protein S18
family: Ribosomal protein S18
domain: Ribosomal protein S18
species: Escherichia coli [TaxId: 562]

Probab=98.20  E-value=2.4e-07  Score=62.38  Aligned_cols=22  Identities=27%  Similarity=0.676  Sum_probs=20.1

Q ss_pred             CCCCCCHHHHHhhccCCccceee
Q psy6417         170 KPDYKNIKLLSQFVSAFTGRVCI  192 (194)
Q Consensus       170 ~iDYKNV~LLsqFiS~~tG~I~~  192 (194)
                      +||||||++|+||||+ +|+|+.
T Consensus         1 ~iDYKn~~lL~~Fis~-~GkI~~   22 (55)
T d2qalr1           1 EIDYKDIATLKNYITE-SGKIVP   22 (55)
T ss_dssp             CCCSSCHHHHGGGBCT-TSSBCC
T ss_pred             CCCcccHHHHHHHcCC-CCeEeC
Confidence            5899999999999999 599975