Citrus Sinensis ID: 034910

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------8
Protein Sequence
MAYSTSSSSSIASDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEMLNIS
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHccEEEEEHHHHHHHHHHHHHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHcccHHHHHHHHHHHHHHHHHHHccccccHHEEEccccEEEEccHHHHHHHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
maystssssSIASDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEMLNIS
Flexible Loop (DISEMBL)
maystsssssiaSDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTtnqkataseqkhldvtkrklemlnis
Low Complexity Region (SEG)
MAYstsssssiasDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEMLNIS
Disordered region (IsUnstruct)
*******************I******EVAIAEL*******AVYQKNGNIFFR***************************
Disordered Region (DISOPRED)
*******************IKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQ****************LEML***
Disordered Region (DISEMBL)
*************DLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEMLNIS
Disordered Region (DISPRO)
************SDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKL******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAYSTSSSSSIASDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEMLNIS
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

No hits with e-value below 0.001 by BLAST

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	79
224126083	70	predicted protein [Populus trichocarpa]	0.848	0.957	0.710	5e-18
255566028	81	conserved hypothetical protein [Ricinus	0.810	0.790	0.703	3e-17
296088757	125	unnamed protein product [Vitis vinifera]	0.835	0.528	0.636	2e-16
359489177	85	PREDICTED: uncharacterized protein LOC10	0.835	0.776	0.636	3e-16
388491556	68	unknown [Medicago truncatula]	0.797	0.926	0.641	1e-13
388501666	77	unknown [Medicago truncatula]	0.772	0.792	0.646	1e-13
357448385	68	hypothetical protein MTR_2g029000 [Medic	0.797	0.926	0.641	2e-13
356555845	76	PREDICTED: uncharacterized protein LOC10	0.772	0.802	0.639	2e-13
222636970	78	hypothetical protein OsJ_24109 [Oryza sa	0.810	0.820	0.546	9e-13
414884476	81	TPA: hypothetical protein ZEAMMB73_57726	0.784	0.765	0.564	8e-12

>gi|224126083|ref|XP_002319751.1| predicted protein [Populus trichocarpa] gi|118484516|gb|ABK94133.1| unknown [Populus trichocarpa] gi|222858127|gb|EEE95674.1| predicted protein [Populus trichocarpa]

 Score = 95.1 bits (235), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 49/69 (71%), Positives = 59/69 (85%), Gaps = 2/69 (2%)

Query: 6  SSSSSIASDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKH 65
          SSSS+  ++L   L+K+V+SHEVAIAEL++LSSSR VYQKNGN+FFRTT+QKATASEQK 
Sbjct: 3  SSSSATGTNL--DLMKKVRSHEVAIAELSNLSSSRTVYQKNGNLFFRTTSQKATASEQKQ 60

Query: 66 LDVTKRKLE 74
          LD  K KLE
Sbjct: 61 LDSAKAKLE 69

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255566028|ref|XP_002524002.1| conserved hypothetical protein [Ricinus communis] gi|223536729|gb|EEF38370.1| conserved hypothetical protein [Ricinus communis]

 Score = 92.4 bits (228), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 45/64 (70%), Positives = 52/64 (81%)

Query: 14 DLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKL 73
          D K  L+++V+SHEVA+AELN+LSSSR VYQKNGN+FFRTT QKATASEQK LD  K  L
Sbjct: 16 DPKLDLVRKVRSHEVALAELNNLSSSRGVYQKNGNLFFRTTIQKATASEQKQLDSAKANL 75

Query: 74 EMLN 77
            LN
Sbjct: 76 GKLN 79

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296088757|emb|CBI38207.3| unnamed protein product [Vitis vinifera]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 52/66 (78%)

Query: 12  ASDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKR 71
           ASD K H + +++SHE AI EL++L +SR VYQKNGN+FFRTT QKATASEQK L+  K 
Sbjct: 58  ASDPKLHFLMQIRSHETAIGELSNLPTSRNVYQKNGNLFFRTTIQKATASEQKQLNSAKA 117

Query: 72  KLEMLN 77
           KL+ LN
Sbjct: 118 KLQKLN 123

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489177|ref|XP_003633893.1| PREDICTED: uncharacterized protein LOC100854074 [Vitis vinifera]

 Score = 89.0 bits (219), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 42/66 (63%), Positives = 52/66 (78%)

Query: 12 ASDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKR 71
          ASD K H + +++SHE AI EL++L +SR VYQKNGN+FFRTT QKATASEQK L+  K 
Sbjct: 18 ASDPKLHFLMQIRSHETAIGELSNLPTSRNVYQKNGNLFFRTTIQKATASEQKQLNSAKA 77

Query: 72 KLEMLN 77
          KL+ LN
Sbjct: 78 KLQKLN 83

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388491556|gb|AFK33844.1| unknown [Medicago truncatula]

 Score = 80.9 bits (198), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 43/67 (64%), Positives = 49/67 (73%), Gaps = 4/67 (5%)

Query: 13 SDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRK 72
          SDLK     E++SHEV+IAELN+L SSR VYQKNGN+FFRTT Q A   EQK LD  K K
Sbjct: 5  SDLK----NEMRSHEVSIAELNALPSSRTVYQKNGNLFFRTTAQTAANMEQKQLDSAKAK 60

Query: 73 LEMLNIS 79
          L+ LN S
Sbjct: 61 LKNLNSS 67

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388501666|gb|AFK38899.1| unknown [Medicago truncatula]

 Score = 80.5 bits (197), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 42/65 (64%), Positives = 48/65 (73%), Gaps = 4/65 (6%)

Query: 13 SDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRK 72
          SDLK     E++SHEV+IAELN+L SSR VYQKNGN+FFRTT Q A   EQK LD  K K
Sbjct: 14 SDLK----NEMRSHEVSIAELNALPSSRTVYQKNGNLFFRTTVQTAANMEQKQLDSAKAK 69

Query: 73 LEMLN 77
          L+ LN
Sbjct: 70 LKNLN 74

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357448385|ref|XP_003594468.1| hypothetical protein MTR_2g029000 [Medicago truncatula] gi|355483516|gb|AES64719.1| hypothetical protein MTR_2g029000 [Medicago truncatula]

 Score = 80.1 bits (196), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 43/67 (64%), Positives = 49/67 (73%), Gaps = 4/67 (5%)

Query: 13 SDLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRK 72
          SDLK     E++SHEV+IAELN+L SSR VYQKNGN+FFRTT Q A   EQK LD  K K
Sbjct: 5  SDLK----NEMRSHEVSIAELNALPSSRTVYQKNGNLFFRTTVQTAANMEQKQLDSAKAK 60

Query: 73 LEMLNIS 79
          L+ LN S
Sbjct: 61 LKNLNSS 67

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356555845|ref|XP_003546240.1| PREDICTED: uncharacterized protein LOC100799098 [Glycine max]

 Score = 80.1 bits (196), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 39/61 (63%), Positives = 49/61 (80%)

Query: 17 AHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEML 76
          A L K+++ HEVAIAELN+  SSRAVYQ++GNIFFRTT Q ATA+EQK L+  + KL+ L
Sbjct: 16 ADLTKQLRLHEVAIAELNNQPSSRAVYQRDGNIFFRTTIQTATATEQKQLESAQAKLKSL 75

Query: 77 N 77
          N
Sbjct: 76 N 76

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222636970|gb|EEE67102.1| hypothetical protein OsJ_24109 [Oryza sativa Japonica Group]

 Score = 77.4 bits (189), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 35/64 (54%), Positives = 47/64 (73%)

Query: 14 DLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKL 73
          D K  L+KE+++HEVAI ELN+L  SRAVYQK  N+FFR + + A  SEQK LD+ K +L
Sbjct: 13 DKKVQLMKEIRAHEVAIGELNNLPPSRAVYQKTCNLFFRKSVKSAVTSEQKQLDMAKSRL 72

Query: 74 EMLN 77
          + L+
Sbjct: 73 QKLD 76

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414884476|tpg|DAA60490.1| TPA: hypothetical protein ZEAMMB73_577262 [Zea mays]

 Score = 74.3 bits (181), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 35/62 (56%), Positives = 46/62 (74%)

Query: 16 KAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEM 75
          K  L+KE+++HEVAIAEL++L+ SRAVYQK GNIFFR + +    +EQK LD  K +L  
Sbjct: 18 KVELLKEIRAHEVAIAELDNLNPSRAVYQKAGNIFFRKSVKSVITTEQKQLDQAKARLSK 77

Query: 76 LN 77
          LN
Sbjct: 78 LN 79

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	79
TAIR|locus:505006175	74	AT1G49245 [Arabidopsis thalian	0.797	0.851	0.507	8.2e-12

TAIR|locus:505006175 AT1G49245 [Arabidopsis thaliana (taxid:3702)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 32/63 (50%), Positives = 45/63 (71%)

Query:    14 DLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKL 73
             D +  L KE+K  EV++ EL+SLSSSR++YQKNGN+FF T+ +KA  S QK LD  K ++
Sbjct:     8 DREFELEKEIKRQEVSLDELSSLSSSRSIYQKNGNLFFLTSAEKAKISAQKQLDYAKSEI 67

Query:    74 EML 76
               +
Sbjct:    68 NKI 70


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.312   0.123   0.316    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       79        69   0.00091  102 3  10 23  0.44    28
                                                     29  0.39    29


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  469 (50 KB)
  Total size of DFA:  93 KB (2070 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  12.50u 0.19s 12.69t   Elapsed:  00:00:00
  Total cpu time:  12.50u 0.19s 12.69t   Elapsed:  00:00:00
  Start:  Fri May 10 03:30:45 2013   End:  Fri May 10 03:30:45 2013

GO:0005634 "nucleus" evidence=ISM

GO:0006457 "protein folding" evidence=IEA

GO:0016272 "prefoldin complex" evidence=IEA

GO:0051082 "unfolded protein binding" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00130711 SubName- Full=Putative uncharacterized protein; (70 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	79
PF01920	106	Prefoldin_2: Prefoldin subunit; InterPro: IPR00277	98.69
TIGR02338	110	gimC_beta prefoldin, beta subunit, archaeal. Chape	98.03
cd00632	105	Prefoldin_beta Prefoldin beta; Prefoldin is a hexa	97.9
PRK09343	121	prefoldin subunit beta; Provisional	97.56
COG1382	119	GimC Prefoldin, chaperonin cofactor [Posttranslati	96.6
cd00890	129	Prefoldin Prefoldin is a hexameric molecular chape	94.39

>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=98.69  E-value=3.5e-08  Score=60.99  Aligned_cols=64  Identities=19%  Similarity=0.447  Sum_probs=57.7

Q ss_pred             hhHHHHHHHHhhhhhhHHHhhCCCchhhhHhhhCceeeeechhhhhhhhhhhhhHHHHHhhhcc
Q 034910           14 DLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEMLN   77 (79)
Q Consensus        14 ~kk~~L~kevr~heVai~ELnnLp~sRaVYQK~GNlFFrts~q~a~~seQKqLd~aka~l~kl~   77 (79)
                      .....|..+++.+++++.||+.||+.|.||..=|++||..+..++...-.++.+..+.++.+|.
T Consensus        19 ~q~~~l~~~~~~~~~~~~eL~~l~~~~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~   82 (106)
T PF01920_consen   19 QQIQQLERQLRELELTLEELEKLDDDRKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLE   82 (106)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSSTT-EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566788999999999999999999999999999999999999999999999999888888764

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.

>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal

Probab=98.03  E-value=1.3e-05  Score=52.43  Aligned_cols=63  Identities=22%  Similarity=0.390  Sum_probs=56.4

Q ss_pred             hHHHHHHHHhhhhhhHHHhhCCCchhhhHhhhCceeeeechhhhhhhhhhhhhHHHHHhhhcc
Q 034910           15 LKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEMLN   77 (79)
Q Consensus        15 kk~~L~kevr~heVai~ELnnLp~sRaVYQK~GNlFFrts~q~a~~seQKqLd~aka~l~kl~   77 (79)
                      ....|..+++.|+..+.||+.||+.+.||.-=|++|...++.++...-.+.++....+++.|.
T Consensus        25 q~~~le~~~~E~~~v~~eL~~l~~d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~le   87 (110)
T TIGR02338        25 QKQQVEAQLKEAEKALEELERLPDDTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQ   87 (110)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCcchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455678889999999999999999999999999999999999999988888888888777664

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.

>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=97.90  E-value=2.3e-05  Score=50.60  Aligned_cols=63  Identities=17%  Similarity=0.390  Sum_probs=55.3

Q ss_pred             hHHHHHHHHhhhhhhHHHhhCCCchhhhHhhhCceeeeechhhhhhhhhhhhhHHHHHhhhcc
Q 034910           15 LKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEMLN   77 (79)
Q Consensus        15 kk~~L~kevr~heVai~ELnnLp~sRaVYQK~GNlFFrts~q~a~~seQKqLd~aka~l~kl~   77 (79)
                      ....|.-+++.|+-++.||..||+.+.||..=|++|+..+..+|...--++++....++..|.
T Consensus        21 ~~~~l~~~~~E~~~v~~EL~~l~~d~~vy~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~   83 (105)
T cd00632          21 QRQKVEAQLNENKKALEELEKLADDAEVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLE   83 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCcchHHHHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456677788999999999999999999999999999999999999888887777777776654

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

>PRK09343 prefoldin subunit beta; Provisional

Probab=97.56  E-value=0.00014  Score=48.91  Aligned_cols=63  Identities=17%  Similarity=0.325  Sum_probs=56.4

Q ss_pred             hhHHHHHHHHhhhhhhHHHhhCCCchhhhHhhhCceeeeechhhhhhhhhhhhhHHHHHhhhc
Q 034910           14 DLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEML   76 (79)
Q Consensus        14 ~kk~~L~kevr~heVai~ELnnLp~sRaVYQK~GNlFFrts~q~a~~seQKqLd~aka~l~kl   76 (79)
                      ..+-.|.-+++..+.++.||+.||+.-.||.--|++|.+++..+|...--+.++....+++.|
T Consensus        28 ~q~~~le~q~~e~~~~~~EL~~L~~d~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ie~~ik~l   90 (121)
T PRK09343         28 QQKSQIDLELREINKALEELEKLPDDTPIYKIVGNLLVKVDKTKVEKELKERKELLELRSRTL   90 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHhhHHHhhccHHHHHHHHHHHHHHHHHHHHHH
Confidence            345567778889999999999999999999999999999999999999888888888888766

>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]

Probab=96.60  E-value=0.0042  Score=43.48  Aligned_cols=63  Identities=24%  Similarity=0.388  Sum_probs=52.0

Q ss_pred             hhHHHHHHHHhhhhhhHHHhhCCCchhhhHhhhCceeeeechhhhhhhhhhhhhHHHHHhhhc
Q 034910           14 DLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEML   76 (79)
Q Consensus        14 ~kk~~L~kevr~heVai~ELnnLp~sRaVYQK~GNlFFrts~q~a~~seQKqLd~aka~l~kl   76 (79)
                      -.|-.|.-+++.-+-++.||+-|+..=.||.+-||+||.++..+++..-.+.++.-.-|++-|
T Consensus        27 ~qk~~le~qL~E~~~al~Ele~l~eD~~vYk~VG~llvk~~k~~~~~eL~er~E~Le~ri~tL   89 (119)
T COG1382          27 LQKQQLEAQLKEIEKALEELEKLDEDAPVYKKVGNLLVKVSKEEAVDELEERKETLELRIKTL   89 (119)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCcccHHHHHhhhHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            345667778888999999999999999999999999999999999887666666655555444

>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=94.39  E-value=0.065  Score=33.98  Aligned_cols=61  Identities=20%  Similarity=0.300  Sum_probs=50.9

Q ss_pred             HHHHHHHhhhhhhHHHhhCCC-----------------------chhhhHhhhC-ceeeeechhhhhhhhhhhhhHHHHH
Q 034910           17 AHLIKEVKSHEVAIAELNSLS-----------------------SSRAVYQKNG-NIFFRTTNQKATASEQKHLDVTKRK   72 (79)
Q Consensus        17 ~~L~kevr~heVai~ELnnLp-----------------------~sRaVYQK~G-NlFFrts~q~a~~seQKqLd~aka~   72 (79)
                      ..|...+..++-++.+|++|+                       +...||-.=| |+|...+...|...-.+.++..+.+
T Consensus        23 ~~l~~~~~e~~~~~~~l~~l~~~~~~~~~l~~~g~~~~~~~~i~~~~~v~v~iG~~~~ve~~~~eA~~~l~~r~~~l~~~  102 (129)
T cd00890          23 QKLEAQLTEYEKAKETLETLKKAEEEKELLVPLGAGLFVKAEVKDDDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQ  102 (129)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhccCCCCeEEEecCCceEEEEEECCCCEEEEEecCCEEEEecHHHHHHHHHHHHHHHHHH
Confidence            345556667888899999988                       7888999999 9999999999999888888888877


Q ss_pred             hhhcc
Q 034910           73 LEMLN   77 (79)
Q Consensus        73 l~kl~   77 (79)
                      +.+|+
T Consensus       103 ~~~l~  107 (129)
T cd00890         103 IEKLE  107 (129)
T ss_pred             HHHHH
Confidence            77664

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.

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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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	79
1fxk_A	107	Prefoldin; archaeal protein, chaperone; 2.30A {Met	97.99
2zqm_A	117	Prefoldin beta subunit 1; chaperone; HET: CIT; 1.9	97.98

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

Probab=97.99  E-value=7.1e-06  Score=50.66  Aligned_cols=64  Identities=20%  Similarity=0.348  Sum_probs=55.6

Q ss_pred             hhHHHHHHHHhhhhhhHHHhhCCCchhhhHhhhCceeeeechhhhhhhhhhhhhHHHHHhhhcc
Q 034910           14 DLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEMLN   77 (79)
Q Consensus        14 ~kk~~L~kevr~heVai~ELnnLp~sRaVYQK~GNlFFrts~q~a~~seQKqLd~aka~l~kl~   77 (79)
                      ...-.+..+++.|+.++.||..||+.+.||..=|.+|+..+...|...-.+..+....++..|.
T Consensus        22 ~q~~~l~~~~~e~~~~~~EL~~l~~d~~vy~~iG~vfv~~~~~e~~~~L~~~~e~i~~~i~~le   85 (107)
T 1fxk_A           22 VQKQTVEMQINETQKALEELSRAADDAEVYKSSGNILIRVAKDELTEELQEKLETLQLREKTIE   85 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSCTTCCEEEEETTEEEEECHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCCchHHHHHhHHHHhccHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455677899999999999999999999999999999999999999888888777777776653

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

Probab=97.98  E-value=1e-05  Score=50.53  Aligned_cols=62  Identities=26%  Similarity=0.418  Sum_probs=53.9

Q ss_pred             hHHHHHHHHhhhhhhHHHhhCCCchhhhHhhhCceeeeechhhhhhhhhhhhhHHHHHhhhc
Q 034910           15 LKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEML   76 (79)
Q Consensus        15 kk~~L~kevr~heVai~ELnnLp~sRaVYQK~GNlFFrts~q~a~~seQKqLd~aka~l~kl   76 (79)
                      ..-.|..+++.|+.++.||..||+.+.||..=|.+|+..++..|...-.+..+....+++.|
T Consensus        28 q~~~l~~~~~e~~~~~~eL~~l~~d~~vy~~iG~vfv~~~~~ea~~~L~~~~e~ie~~i~~l   89 (117)
T 2zqm_A           28 QKQKVQLELTEAKKALDEIESLPDDAVVYKTVGTLIVKTTKDKAVAELKEKIETLEVRLNAL   89 (117)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSCTTCCEEEEETTEEEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCCcHhHHHhhHHHhhccHHHHHHHHHHHHHHHHHHHHHH
Confidence            44567788999999999999999999999999999999999999988777777777766655

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Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	79
d1fxka_	107	Prefoldin beta subunit {Archaeon Methanobacterium	97.9

>d1fxka_ a.2.5.1 (A:) Prefoldin beta subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

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

Probab=97.90  E-value=5.5e-06  Score=51.30  Aligned_cols=64  Identities=20%  Similarity=0.348  Sum_probs=58.7

Q ss_pred             hhHHHHHHHHhhhhhhHHHhhCCCchhhhHhhhCceeeeechhhhhhhhhhhhhHHHHHhhhcc
Q 034910           14 DLKAHLIKEVKSHEVAIAELNSLSSSRAVYQKNGNIFFRTTNQKATASEQKHLDVTKRKLEMLN   77 (79)
Q Consensus        14 ~kk~~L~kevr~heVai~ELnnLp~sRaVYQK~GNlFFrts~q~a~~seQKqLd~aka~l~kl~   77 (79)
                      ..+-+|..+++.|+-.+.||..+|+.|.||.--|++|...+...+...-.+.++....+++.|.
T Consensus        22 ~q~~~le~q~~E~~~vl~eL~~l~~d~~vyk~vG~vLv~~~~~e~~~~l~~~~e~l~~~i~~l~   85 (107)
T d1fxka_          22 VQKQTVEMQINETQKALEELSRAADDAEVYKSSGNILIRVAKDELTEELQEKLETLQLREKTIE   85 (107)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSCTTCCEEEEETTEEEEECHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHhcchhhcCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567888999999999999999999999999999999999999999999999998888887764