Citrus Sinensis ID: 036886

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-----
Protein Sequence
MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFAR
Secondary Structure (PSIPRED)
cEEEEEEccHHcccHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHcHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIirkqkdpskahqTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFAR
Flexible Loop (DISEMBL)
myivlkkvdlqvhssrKYFGLFNFIYSLSCYIIRKQkdpskahqtkLDVIVKALKWLEMDMDVDEVECVVALLLhknlvkgyfar
Low Complexity Region (SEG)
MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLemdmdvdevecvvALLLHKNLVKGYFAR
Disordered region (IsUnstruct)
*YIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQK****AHQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYF**
Disordered Region (DISOPRED)
MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQK***KAHQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFA*
Disordered Region (DISEMBL)
MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQ********TKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFAR
Disordered Region (DISPRO)
MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFAR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFAR
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	85	2.2.26 [Sep-21-2011]
Q5FWP8	399	PCI domain-containing pro	N/A	no	0.517	0.110	0.444	0.0001
Q5JVF3	399	PCI domain-containing pro	yes	no	0.517	0.110	0.444	0.0005

>sp|Q5FWP8|PCID2_XENLA PCI domain-containing protein 2 OS=Xenopus laevis GN=pcid2 PE=2 SV=1

 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 33/45 (73%), Gaps = 1/45 (2%)

Query: 41  KAHQTKLDVIVKALKWLEM-DMDVDEVECVVALLLHKNLVKGYFA 84
           K HQ  LD  + ALK++E+ D+D+DEV+C++A L++   +KGY +
Sbjct: 334 KTHQLSLDAFLVALKFMEVGDVDIDEVQCIIANLIYMGHIKGYIS 378

Xenopus laevis (taxid: 8355)

>sp|Q5JVF3|PCID2_HUMAN PCI domain-containing protein 2 OS=Homo sapiens GN=PCID2 PE=1 SV=2

 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/45 (44%), Positives = 33/45 (73%), Gaps = 1/45 (2%)

Query: 41  KAHQTKLDVIVKALKWLEM-DMDVDEVECVVALLLHKNLVKGYFA 84
           K HQ  LD  + ALK++++ D+D+DEV+C++A L++   VKGY +
Sbjct: 334 KTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHVKGYIS 378

Required for B-cell survival through the regulation of the expression of cell-cycle checkpoint MAD2L1 protein during B cell differentiation.

Homo sapiens (taxid: 9606)

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	85
255546087	412	PCI domain-containing protein, putative	0.870	0.179	0.642	6e-20
224088756	413	predicted protein [Populus trichocarpa]	0.870	0.179	0.630	9e-20
356547787	410	PREDICTED: PCI domain-containing protein	0.870	0.180	0.595	1e-19
225444936	413	PREDICTED: PCI domain-containing protein	0.870	0.179	0.595	1e-19
356561961	413	PREDICTED: PCI domain-containing protein	0.870	0.179	0.619	7e-19
148906436	414	unknown [Picea sitchensis]	0.870	0.178	0.595	9e-19
212720664	409	uncharacterized protein LOC100193209 [Ze	0.870	0.180	0.595	1e-18
414885291	295	TPA: hypothetical protein ZEAMMB73_56506	0.870	0.250	0.595	2e-18
414885289	193	TPA: hypothetical protein ZEAMMB73_56506	0.870	0.383	0.595	2e-18
414885290	256	TPA: hypothetical protein ZEAMMB73_56506	0.870	0.289	0.559	2e-18

>gi|255546087|ref|XP_002514103.1| PCI domain-containing protein, putative [Ricinus communis] gi|223546559|gb|EEF48057.1| PCI domain-containing protein, putative [Ricinus communis]

 Score =  101 bits (251), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 54/84 (64%), Positives = 66/84 (78%), Gaps = 10/84 (11%)

Query: 1   MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD 60
           +Y+VL+K++LQV     Y  L   IY     II+K KDPSKAHQ KL+VI+KALKWLEMD
Sbjct: 315 VYLVLEKLELQV-----YQRLLKKIY-----IIQKNKDPSKAHQMKLEVIIKALKWLEMD 364

Query: 61  MDVDEVECVVALLLHKNLVKGYFA 84
           MD+DEVEC+VA+L+ KNLVKGYFA
Sbjct: 365 MDLDEVECIVAMLIFKNLVKGYFA 388

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224088756|ref|XP_002308527.1| predicted protein [Populus trichocarpa] gi|222854503|gb|EEE92050.1| predicted protein [Populus trichocarpa]

 Score =  100 bits (250), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 53/84 (63%), Positives = 68/84 (80%), Gaps = 10/84 (11%)

Query: 1   MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD 60
           +++VL+K++LQV     Y  L   IY     II+KQ+DPSKAHQ KL+VIVKALKWLE+D
Sbjct: 316 VFLVLEKLELQV-----YQRLLKKIY-----IIQKQRDPSKAHQIKLEVIVKALKWLEID 365

Query: 61  MDVDEVECVVALLLHKNLVKGYFA 84
           MD+DEVEC+VA+L++KNLVKGYFA
Sbjct: 366 MDLDEVECIVAILIYKNLVKGYFA 389

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356547787|ref|XP_003542290.1| PREDICTED: PCI domain-containing protein 2-like [Glycine max]

 Score =  100 bits (250), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 50/84 (59%), Positives = 65/84 (77%), Gaps = 10/84 (11%)

Query: 1   MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD 60
           +Y+VL+K++LQV+                 YII+KQKDP +AHQ KL+VIVKALKWLE+D
Sbjct: 313 VYLVLEKLELQVYQR----------LVKKIYIIQKQKDPGRAHQVKLEVIVKALKWLEID 362

Query: 61  MDVDEVECVVALLLHKNLVKGYFA 84
           MDVDEVEC+VA+L++KNL+KGYFA
Sbjct: 363 MDVDEVECIVAILIYKNLMKGYFA 386

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225444936|ref|XP_002282302.1| PREDICTED: PCI domain-containing protein 2 [Vitis vinifera] gi|297738675|emb|CBI27920.3| unnamed protein product [Vitis vinifera]

 Score =  100 bits (248), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 50/84 (59%), Positives = 65/84 (77%), Gaps = 10/84 (11%)

Query: 1   MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD 60
           +Y+VL+K++LQV+                 Y I+KQKDPSKAHQ KL+VIVKALKWLEMD
Sbjct: 316 VYLVLEKLELQVYQR----------LVKKIYFIQKQKDPSKAHQLKLEVIVKALKWLEMD 365

Query: 61  MDVDEVECVVALLLHKNLVKGYFA 84
           MDVDEVEC++++L++KNL+KGYFA
Sbjct: 366 MDVDEVECIMSILIYKNLMKGYFA 389

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356561961|ref|XP_003549244.1| PREDICTED: PCI domain-containing protein 2-like [Glycine max]

 Score = 97.8 bits (242), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 52/84 (61%), Positives = 67/84 (79%), Gaps = 10/84 (11%)

Query: 1   MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD 60
           +Y+VL+K++LQV     Y  L   IY     II+KQ+DPS+AHQ KL+VIVKALKWL +D
Sbjct: 316 VYLVLEKLELQV-----YQRLVKKIY-----IIQKQRDPSRAHQVKLEVIVKALKWLVID 365

Query: 61  MDVDEVECVVALLLHKNLVKGYFA 84
           MDVDEVEC+VA+L++KNL+KGYFA
Sbjct: 366 MDVDEVECIVAILIYKNLMKGYFA 389

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|148906436|gb|ABR16371.1| unknown [Picea sitchensis]

 Score = 97.4 bits (241), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 50/84 (59%), Positives = 67/84 (79%), Gaps = 10/84 (11%)

Query: 1   MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD 60
           +Y+VL+K++LQV     Y  L   IY     II+KQKD S+AHQ K+D+IVKALKWLE+D
Sbjct: 317 VYLVLEKLELQV-----YQRLIKKIY-----IIQKQKDASRAHQVKMDIIVKALKWLEID 366

Query: 61  MDVDEVECVVALLLHKNLVKGYFA 84
           MDV+EVEC++A+L+HKNL+KGYF+
Sbjct: 367 MDVEEVECIMAILIHKNLMKGYFS 390

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|212720664|ref|NP_001131834.1| uncharacterized protein LOC100193209 [Zea mays] gi|194692672|gb|ACF80420.1| unknown [Zea mays] gi|414885294|tpg|DAA61308.1| TPA: hypothetical protein ZEAMMB73_565062 [Zea mays]

 Score = 97.1 bits (240), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 50/84 (59%), Positives = 67/84 (79%), Gaps = 10/84 (11%)

Query: 1   MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD 60
           +Y+VL+K++LQV     Y  L   I+     II++QK+P+KAHQ KLDV+VKALKWLE+D
Sbjct: 314 VYLVLEKLELQV-----YQRLVKKIH-----IIQRQKEPAKAHQIKLDVVVKALKWLEID 363

Query: 61  MDVDEVECVVALLLHKNLVKGYFA 84
           MDVDEVEC++A L++KNL+KGYFA
Sbjct: 364 MDVDEVECIMACLIYKNLIKGYFA 387

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414885291|tpg|DAA61305.1| TPA: hypothetical protein ZEAMMB73_565062 [Zea mays]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/84 (59%), Positives = 67/84 (79%), Gaps = 10/84 (11%)

Query: 1   MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD 60
           +Y+VL+K++LQV     Y  L   I+     II++QK+P+KAHQ KLDV+VKALKWLE+D
Sbjct: 200 VYLVLEKLELQV-----YQRLVKKIH-----IIQRQKEPAKAHQIKLDVVVKALKWLEID 249

Query: 61  MDVDEVECVVALLLHKNLVKGYFA 84
           MDVDEVEC++A L++KNL+KGYFA
Sbjct: 250 MDVDEVECIMACLIYKNLIKGYFA 273

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414885289|tpg|DAA61303.1| TPA: hypothetical protein ZEAMMB73_565062 [Zea mays]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/84 (59%), Positives = 67/84 (79%), Gaps = 10/84 (11%)

Query: 1   MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD 60
           +Y+VL+K++LQV     Y  L   I+     II++QK+P+KAHQ KLDV+VKALKWLE+D
Sbjct: 98  VYLVLEKLELQV-----YQRLVKKIH-----IIQRQKEPAKAHQIKLDVVVKALKWLEID 147

Query: 61  MDVDEVECVVALLLHKNLVKGYFA 84
           MDVDEVEC++A L++KNL+KGYFA
Sbjct: 148 MDVDEVECIMACLIYKNLIKGYFA 171

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414885290|tpg|DAA61304.1| TPA: hypothetical protein ZEAMMB73_565062 [Zea mays]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 47/84 (55%), Positives = 65/84 (77%), Gaps = 10/84 (11%)

Query: 1   MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD 60
           +Y+VL+K++LQV+                 +II++QK+P+KAHQ KLDV+VKALKWLE+D
Sbjct: 161 VYLVLEKLELQVYQR----------LVKKIHIIQRQKEPAKAHQIKLDVVVKALKWLEID 210

Query: 61  MDVDEVECVVALLLHKNLVKGYFA 84
           MDVDEVEC++A L++KNL+KGYFA
Sbjct: 211 MDVDEVECIMACLIYKNLIKGYFA 234

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	85
TAIR|locus:2050414	413	EER5 "ENHANCED ETHYLENE RESPON	0.870	0.179	0.416	2e-08

TAIR|locus:2050414 EER5 "ENHANCED ETHYLENE RESPONSE 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 136 (52.9 bits), Expect = 2.0e-08, P = 2.0e-08
 Identities = 35/84 (41%), Positives = 48/84 (57%)

Query:     1 MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLXXX 60
             +Y+VL+K++LQV     Y  L   IY     I +K  DP++AHQ KL+ I KAL+WL   
Sbjct:   316 VYLVLEKLELQV-----YQRLMKKIY-----INQKLSDPARAHQLKLEGIAKALRWLDMD 365

Query:    61 XXXXXXXXXXALLLHKNLVKGYFA 84
                        +L++KNLVKGY A
Sbjct:   366 MDLDEVECIMTILIYKNLVKGYLA 389


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        0.329   0.141   0.424    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       85        72   0.00091  102 3  11 22  0.39    28
                                                     29  0.43    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:  506 (54 KB)
  Total size of DFA:  95 KB (2069 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:  7.41u 0.16s 7.57t   Elapsed:  00:00:00
  Total cpu time:  7.41u 0.16s 7.57t   Elapsed:  00:00:00
  Start:  Fri May 10 10:19:49 2013   End:  Fri May 10 10:19:49 2013

GO:0005739 "mitochondrion" evidence=ISM

GO:0009723 "response to ethylene stimulus" evidence=IMP

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA;IPI

GO:0048364 "root development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0016973 "poly(A)+ mRNA export from nucleus" evidence=IMP

GO:0000303 "response to superoxide" evidence=RCA

GO:0007165 "signal transduction" evidence=RCA

GO:0008219 "cell death" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

GO:0009733 "response to auxin stimulus" evidence=RCA

GO:0009737 "response to abscisic acid stimulus" evidence=RCA

GO:0009743 "response to carbohydrate stimulus" evidence=RCA

GO:0009751 "response to salicylic acid stimulus" evidence=RCA

GO:0009755 "hormone-mediated signaling pathway" evidence=RCA

GO:0009863 "salicylic acid mediated signaling pathway" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_fgenesh4_pm.C_LG_VI0641 hypothetical protein (413 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

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	85
KOG2688	394	consensus Transcription-associated recombination p	99.8
COG5600	413	Transcription-associated recombination protein [DN	99.52
PF01399	105	PCI: PCI domain; InterPro: IPR000717 A homology do	97.92
smart00753	88	PAM PCI/PINT associated module.	92.41
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	92.41
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	84.45

>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]

Probab=99.80  E-value=4.5e-21  Score=154.06  Aligned_cols=70  Identities=34%  Similarity=0.576  Sum_probs=66.3

Q ss_pred             CeEEeeehhheeeccccccccccccccceEEEEccccCCCCCceeeHHHHHHHHhhcC-CCCCchhHHHHHHHHhhcCcc
Q 036886            1 MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLE-MDMDVDEVECVVALLLHKNLV   79 (85)
Q Consensus         1 ~YL~lEklr~iv~r~~~~~nLfkk~~~~~v~~i~~~~~p~k~~~ipl~~f~~Al~~~~-~~~d~DEvECilANLI~kg~i   79 (85)
                      +|+++|+++.+|||     |||||     ||.+++     |++++|++.|+.|++..+ .|.|+||+||++||||+.|+|
T Consensus       305 i~l~l~~l~lv~yr-----nL~kk-----v~~~~~-----~~~~lpls~~~~al~~~~~~~~~~deveciLa~lI~~G~i  369 (394)
T KOG2688|consen  305 IYLTLEKLPLVVYR-----NLFKK-----VIQLWG-----KTSQLPLSRFLTALQFSGVTDVDLDEVECILANLIDLGRI  369 (394)
T ss_pred             cHHHhhhhhHHHHH-----HHHHH-----HHHHhC-----CCCCCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhhhccc
Confidence            58999999999999     99999     999994     899999999999999999 569999999999999999999


Q ss_pred             cccccC
Q 036886           80 KGYFAR   85 (85)
Q Consensus        80 KGYisr   85 (85)
                      |||||+
T Consensus       370 kgYish  375 (394)
T KOG2688|consen  370 KGYISH  375 (394)
T ss_pred             cchhch
Confidence            999985

>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]

Probab=99.52  E-value=1.5e-15  Score=122.84  Aligned_cols=69  Identities=25%  Similarity=0.510  Sum_probs=62.8

Q ss_pred             eEE-eeehhheeeccccccccccccccceEEEEccccCCCCCceeeHHHHHHHHhhcCCC--CCchhHHHHHHHHhhcCc
Q 036886            2 YIV-LKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD--MDVDEVECVVALLLHKNL   78 (85)
Q Consensus         2 YL~-lEklr~iv~r~~~~~nLfkk~~~~~v~~i~~~~~p~k~~~ipl~~f~~Al~~~~~~--~d~DEvECilANLI~kg~   78 (85)
                      |++ .++.+.+|+|     |||||     +|.+.     .+.+++|++.++.|++.++.|  .+.|||||++|+||.+|+
T Consensus       323 ~ltl~~~~~~V~~R-----NL~rk-----~w~~~-----~~qsrlp~sil~~~~qls~~dn~~~~~~VEciL~tlI~~G~  387 (413)
T COG5600         323 YLTLLAHYPLVCFR-----NLFRK-----IWRLH-----GKQSRLPLSILLIVLQLSAIDNFHSFKEVECILVTLIGLGL  387 (413)
T ss_pred             HHHHHhhccHHHHH-----HHHHH-----HHhhc-----cccccCcHHHHHHHHHccCCCcccChHHHHHHHHHHHhhhh
Confidence            444 5678999999     99999     99888     488999999999999999977  899999999999999999


Q ss_pred             ccccccC
Q 036886           79 VKGYFAR   85 (85)
Q Consensus        79 iKGYisr   85 (85)
                      +|||||+
T Consensus       388 lrgYis~  394 (413)
T COG5600         388 LRGYISH  394 (413)
T ss_pred             hhheecc
Confidence            9999986

>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins

Probab=97.92  E-value=1.3e-05  Score=50.10  Aligned_cols=39  Identities=26%  Similarity=0.359  Sum_probs=34.7

Q ss_pred             CCceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccccccc
Q 036886           41 KAHQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFA   84 (85)
Q Consensus        41 k~~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iKGYis   84 (85)
                      .-..++++.+.+++.+     +.+|||+++++||..|.|+|+|.
T Consensus        57 ~y~~i~~~~ia~~l~~-----~~~~vE~~l~~~I~~~~i~~~ID   95 (105)
T PF01399_consen   57 PYSSISISEIAKALQL-----SEEEVESILIDLISNGLIKAKID   95 (105)
T ss_dssp             C-SEEEHHHHHHHHTC-----CHHHHHHHHHHHHHTTSSEEEEE
T ss_pred             HhcccchHHHHHHhcc-----chHHHHHHHHHHHHCCCEEEEEE
Confidence            3578999999999986     56999999999999999999986

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.

>smart00753 PAM PCI/PINT associated module

Probab=92.41  E-value=0.24  Score=30.57  Aligned_cols=37  Identities=22%  Similarity=0.236  Sum_probs=31.8

Q ss_pred             ceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccccccc
Q 036886           43 HQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFA   84 (85)
Q Consensus        43 ~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iKGYis   84 (85)
                      ..|+++.+..++.+     +.||+|=.+.++|..|.++|-|.
T Consensus        23 ~~i~~~~i~~~~~l-----~~~~vE~~i~~~i~~~~l~~~ID   59 (88)
T smart00753       23 SSISLSDLAKLLGL-----SVPEVEKLVSKAIRDGEISAKID   59 (88)
T ss_pred             ceeeHHHHHHHhCc-----CHHHHHHHHHHHHHCCCeEEEEc
Confidence            56899999988864     67799999999999999998764

>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

Probab=92.41  E-value=0.24  Score=30.57  Aligned_cols=37  Identities=22%  Similarity=0.236  Sum_probs=31.8

Q ss_pred             ceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccccccc
Q 036886           43 HQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFA   84 (85)
Q Consensus        43 ~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iKGYis   84 (85)
                      ..|+++.+..++.+     +.||+|=.+.++|..|.++|-|.
T Consensus        23 ~~i~~~~i~~~~~l-----~~~~vE~~i~~~i~~~~l~~~ID   59 (88)
T smart00088       23 SSISLSDLAKLLGL-----SVPEVEKLVSKAIRDGEISAKID   59 (88)
T ss_pred             ceeeHHHHHHHhCc-----CHHHHHHHHHHHHHCCCeEEEEc
Confidence            56899999988864     67799999999999999998764

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=84.45  E-value=1.5  Score=26.71  Aligned_cols=34  Identities=15%  Similarity=0.373  Sum_probs=25.8

Q ss_pred             CceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccc
Q 036886           42 AHQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVK   80 (85)
Q Consensus        42 ~~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iK   80 (85)
                      .+.++++.+..-|.     ++.+.||-++.-|+.+|+|+
T Consensus        12 ~~~~S~~eLa~~~~-----~s~~~ve~mL~~l~~kG~I~   45 (69)
T PF09012_consen   12 RGRVSLAELAREFG-----ISPEAVEAMLEQLIRKGYIR   45 (69)
T ss_dssp             S-SEEHHHHHHHTT-------HHHHHHHHHHHHCCTSCE
T ss_pred             cCCcCHHHHHHHHC-----cCHHHHHHHHHHHHHCCcEE
Confidence            45567777766665     58999999999999999996

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_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	85
3t5x_A	203	PCI domain-containing protein 2; PCI, mRNA nuclear	5e-07
3t5v_B	455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	2e-05

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens} Length = 203

 Score = 44.1 bits (104), Expect = 5e-07
 Identities = 21/55 (38%), Positives = 36/55 (65%), Gaps = 1/55 (1%)

Query: 32  IIRKQKDPSKAHQTKLDVIVKALKWLEM-DMDVDEVECVVALLLHKNLVKGYFAR 85
           + +K     K HQ  LD  + ALK++++ D+D+DEV+C++A L++   VKGY + 
Sbjct: 129 LFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHVKGYISH 183

>3t5v_B Nuclear mRNA export protein THP1; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae} Length = 455

 Score = 39.7 bits (92), Expect = 2e-05
 Identities = 8/70 (11%), Positives = 20/70 (28%), Gaps = 16/70 (22%)

Query: 32  IIRKQKDPSKAHQTKLDVIVKALK----------------WLEMDMDVDEVECVVALLLH 75
           +I+        ++    +I + L+                          VE V+  L++
Sbjct: 350 VIKSWTTEWGQNKLPYSLIERVLQLSIGPTFEDPGAQEITIYNGIHSPKNVENVLVTLIN 409

Query: 76  KNLVKGYFAR 85
             L++     
Sbjct: 410 LGLLRANCFP 419

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	85
3t5x_A	203	PCI domain-containing protein 2; PCI, mRNA nuclear	99.81
3t5v_B	455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	99.75
4b4t_S	523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	98.75
4b4t_O	393	26S proteasome regulatory subunit RPN9; hydrolase,	97.18
1ufm_A	84	COP9 complex subunit 4; helix-turn-helix, structur	92.63
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	91.94
3chm_A	169	COP9 signalosome complex subunit 7; heat/ARM repea	90.67
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	90.19
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	86.31
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	85.26

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens}

Probab=99.81  E-value=5.3e-22  Score=142.95  Aligned_cols=69  Identities=35%  Similarity=0.725  Sum_probs=63.4

Q ss_pred             CeEEeeehhheeeccccccccccccccceEEEEccccCCCCCceeeHHHHHHHHhhcCCC-CCchhHHHHHHHHhhcCcc
Q 036886            1 MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMD-MDVDEVECVVALLLHKNLV   79 (85)
Q Consensus         1 ~YL~lEklr~iv~r~~~~~nLfkk~~~~~v~~i~~~~~p~k~~~ipl~~f~~Al~~~~~~-~d~DEvECilANLI~kg~i   79 (85)
                      +|+++||+|.+|+|     ||+||     +|++.      +.|+||++.|++|+++++.+ +|.|||||++||||++|+|
T Consensus       114 ~~lll~rlr~~v~r-----~l~rk-----v~~~~------~~~rI~l~~i~~~l~~~~~~~~~~~evE~ila~lI~~G~I  177 (203)
T 3t5x_A          114 IFLILEKLKIITYR-----NLFKK-----VYLLL------KTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHV  177 (203)
T ss_dssp             CHHHHHTHHHHHHH-----HHHHH-----HHHHH------CCSEEEHHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSS
T ss_pred             hHHHHHHHHHHHHH-----HHHHH-----HHHhc------CCCcccHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHcCce
Confidence            57889999999999     99999     77766      57999999999999999864 8999999999999999999


Q ss_pred             cccccC
Q 036886           80 KGYFAR   85 (85)
Q Consensus        80 KGYisr   85 (85)
                      ||||++
T Consensus       178 kg~I~~  183 (203)
T 3t5x_A          178 KGYISH  183 (203)
T ss_dssp             CEEEET
T ss_pred             EEEEcc
Confidence            999985

>3t5v_B Nuclear mRNA export protein THP1; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae}

Probab=99.75  E-value=3.4e-20  Score=148.11  Aligned_cols=69  Identities=14%  Similarity=0.166  Sum_probs=61.2

Q ss_pred             eEEeeehhheeeccccccccccccccceE---EEEccccCCCCCceeeHHHHHHHHhhcCC----------------CCC
Q 036886            2 YIVLKKVDLQVHSSRKYFGLFNFIYSLSC---YIIRKQKDPSKAHQTKLDVIVKALKWLEM----------------DMD   62 (85)
Q Consensus         2 YL~lEklr~iv~r~~~~~nLfkk~~~~~v---~~i~~~~~p~k~~~ipl~~f~~Al~~~~~----------------~~d   62 (85)
                      |+++||+|.+|||     ||+||     |   |.+.     .++|+||++.|++|+++++.                ++|
T Consensus       332 y~LlerLr~~v~R-----nLirk-----v~~~~~~~-----~~~srI~l~~i~~aL~~~~~~~~~~~~~~~~~~~~~~~~  396 (455)
T 3t5v_B          332 IVLLEKLPMVTYR-----NLIKT-----VIKSWTTE-----WGQNKLPYSLIERVLQLSIGPTFEDPGAQEITIYNGIHS  396 (455)
T ss_dssp             HHHHHHHHHHHHH-----HHHHH-----HHHHHTTT-----TCCCEEEHHHHHHHHHHHHCCCTTSTTCCCCCTTTSSCC
T ss_pred             HHHHHHHHHHHHH-----HHHHH-----HHHHHHhc-----CCCCeeeHHHHHHHHhhccCccccccccccccccccCCC
Confidence            7889999999999     99999     6   5433     46799999999999999743                279


Q ss_pred             chhHHHHHHHHhhcCcccccccC
Q 036886           63 VDEVECVVALLLHKNLVKGYFAR   85 (85)
Q Consensus        63 ~DEvECilANLI~kg~iKGYisr   85 (85)
                      .||||||+||||++|+||||||+
T Consensus       397 ~devEcIlA~LI~~G~IkGyIsh  419 (455)
T 3t5v_B          397 PKNVENVLVTLINLGLLRANCFP  419 (455)
T ss_dssp             SSCHHHHHHHHHHHTSCCEEEET
T ss_pred             HHHHHHHHHHHHHcCCeEEEEec
Confidence            99999999999999999999985

>4b4t_S RPN3, 26S proteasome regulatory subunit RPN3; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.75  E-value=5.5e-10  Score=91.40  Aligned_cols=63  Identities=13%  Similarity=0.132  Sum_probs=54.2

Q ss_pred             CeEEeeehhheeeccccccccccccccceEEEEccccCCCCCceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccc
Q 036886            1 MYIVLKKVDLQVHSSRKYFGLFNFIYSLSCYIIRKQKDPSKAHQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVK   80 (85)
Q Consensus         1 ~YL~lEklr~iv~r~~~~~nLfkk~~~~~v~~i~~~~~p~k~~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iK   80 (85)
                      +|++++|++..|+|     +.+|+     +....        .+||++.+...+++.+    .+|+||++||||..|.|+
T Consensus       376 ty~LI~rLr~~vir-----~~irk-----is~~Y--------srIsL~dIa~kL~L~s----~eeaE~iVAkmI~dG~I~  433 (523)
T 4b4t_S          376 TYQLCVRLRSNVIK-----TGIRI-----ISLTY--------KKISLRDICLKLNLDS----EQTVEYMVSRAIRDGVIE  433 (523)
T ss_dssp             CTHHHHHHHHHHHH-----HHHHH-----SCCCS--------SEECHHHHHHHHHHHH----SSCHHHHHHHHHHHTSSC
T ss_pred             hhHHHHHHHHHHHH-----HHHHH-----HHHHH--------hcccHHHHHHHhCCCC----HHHHHHHHHHHHHcCCce
Confidence            47789999999999     99999     44332        6799999999999843    478999999999999999


Q ss_pred             ccccC
Q 036886           81 GYFAR   85 (85)
Q Consensus        81 GYisr   85 (85)
                      |||++
T Consensus       434 A~Idh  438 (523)
T 4b4t_S          434 AKINH  438 (523)
T ss_dssp             CEECT
T ss_pred             EEEec
Confidence            99974

>4b4t_O 26S proteasome regulatory subunit RPN9; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.18  E-value=0.00011  Score=56.34  Aligned_cols=38  Identities=26%  Similarity=0.312  Sum_probs=34.7

Q ss_pred             CceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccccccc
Q 036886           42 AHQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFA   84 (85)
Q Consensus        42 ~~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iKGYis   84 (85)
                      ...||++.+..+++     ++.||||++++++|+.|+|+|.|.
T Consensus       305 ~~~i~f~~ia~~l~-----i~~~evE~lli~aI~~glI~GkID  342 (393)
T 4b4t_O          305 IRMLSFEDISKATH-----LPKDNVEHLVMRAISLGLLKGSID  342 (393)
T ss_dssp             CCCEEHHHHHHHHT-----CCHHHHHHHHHHHHHHSCSSSCEE
T ss_pred             CCcCcHHHHHHHhC-----cCHHHHHHHHHHHHHcCCEEEEEc
Confidence            45799999999998     478999999999999999999986

>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: a.4.5.47

Probab=92.63  E-value=0.14  Score=32.27  Aligned_cols=37  Identities=8%  Similarity=0.301  Sum_probs=30.2

Q ss_pred             ceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccccccc
Q 036886           43 HQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFA   84 (85)
Q Consensus        43 ~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iKGYis   84 (85)
                      +.|.++.+...|.     ++.+|+|-++++||..|.+.|-|.
T Consensus        29 ~~Isl~~La~ll~-----ls~~~vE~~ls~mI~~~~l~akID   65 (84)
T 1ufm_A           29 NNITFEELGALLE-----IPAAKAEKIASQMITEGRMNGFID   65 (84)
T ss_dssp             SEEEHHHHHHHTT-----SCHHHHHHHHHHHHHTTSSCEEEE
T ss_pred             CeeeHHHHHHHHC-----cCHHHHHHHHHHHHhCCcEEEEEe
Confidence            4466777776666     579999999999999999988764

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.94  E-value=0.16  Score=35.66  Aligned_cols=37  Identities=16%  Similarity=0.320  Sum_probs=32.1

Q ss_pred             ceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccccccc
Q 036886           43 HQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFA   84 (85)
Q Consensus        43 ~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iKGYis   84 (85)
                      ++|+++.+..++.     ++.+|+|..+++||..|.+.|-|.
T Consensus       355 ~~i~l~~la~~l~-----~~~~~~E~~l~~lI~~~~i~a~id  391 (434)
T 4b4t_Q          355 ECVEISHISKIIG-----LDTQQVEGKLSQMILDKIFYGVLD  391 (434)
T ss_dssp             SCEEHHHHHHHHT-----CCHHHHHHHHHHHHHHTSSCCEEE
T ss_pred             HhcCHHHHHHHhC-----cCHHHHHHHHHHHHhCCCcceecc
Confidence            5688888888887     478999999999999999998775

>3chm_A COP9 signalosome complex subunit 7; heat/ARM repeats, winged helix motif, developmental protein, phosphoprotein; 1.50A {Arabidopsis thaliana}

Probab=90.67  E-value=0.23  Score=34.82  Aligned_cols=39  Identities=18%  Similarity=0.238  Sum_probs=33.8

Q ss_pred             CceeeHHHHHHHHhhcCCCCCchhHHHHHH-HHhhcCccccccc
Q 036886           42 AHQTKLDVIVKALKWLEMDMDVDEVECVVA-LLLHKNLVKGYFA   84 (85)
Q Consensus        42 ~~~ipl~~f~~Al~~~~~~~d~DEvECilA-NLI~kg~iKGYis   84 (85)
                      ...+|.+.+..+++..    +.+|||-++- ..|+.|+|+|.|.
T Consensus       107 ~~~lsy~~I~~~l~i~----~~~evE~lvI~~ai~~gLI~gkiD  146 (169)
T 3chm_A          107 NKVLPYDTLMVELDVS----NVRELEDFLINECMYAGIVRGKLD  146 (169)
T ss_dssp             CSEEEHHHHHHHHTCC----SHHHHHHHHHHTHHHHTSEEEEEE
T ss_pred             CCCcCHHHHHHHhCCC----CHHHHHHHHHHHHHHhCCeEEEEc
Confidence            4679999999999862    2899999999 9999999999875

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.19  E-value=0.26  Score=38.08  Aligned_cols=26  Identities=15%  Similarity=0.330  Sum_probs=23.6

Q ss_pred             CCCchhHHHHHHHHhhcCcccccccC
Q 036886           60 DMDVDEVECVVALLLHKNLVKGYFAR   85 (85)
Q Consensus        60 ~~d~DEvECilANLI~kg~iKGYisr   85 (85)
                      +++.+|+|-.+++||..|.|.|-|.|
T Consensus       370 ~l~~~evE~~ls~mI~~g~i~akIDq  395 (445)
T 4b4t_P          370 DLTESQTETYISDLVNQGIIYAKVNR  395 (445)
T ss_dssp             TSCHHHHHHHHHHHHHHTSSCCEEET
T ss_pred             CcCHHHHHHHHHHHHHCCCEEEEEcC
Confidence            37899999999999999999998864

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=86.31  E-value=0.74  Score=35.88  Aligned_cols=37  Identities=8%  Similarity=0.284  Sum_probs=32.6

Q ss_pred             ceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccccccc
Q 036886           43 HQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFA   84 (85)
Q Consensus        43 ~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iKGYis   84 (85)
                      .+|+++.+..++.     ++.+|+|-.++.||..|.|.|-|.
T Consensus       315 srIsl~~iA~~l~-----ls~~evE~~L~~lI~dg~I~a~ID  351 (394)
T 3txn_A          315 SRVQVAHVAESIQ-----LPMPQVEKKLSQMILDKKFSGILD  351 (394)
T ss_dssp             SEEEHHHHHHHHT-----CCHHHHHHHHHHHHHTTSSCEEEE
T ss_pred             ceeeHHHHHHHHC-----cCHHHHHHHHHHHHHCCCeeEEEc
Confidence            5688888888887     478999999999999999999875

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.26  E-value=0.85  Score=34.78  Aligned_cols=37  Identities=8%  Similarity=0.129  Sum_probs=30.6

Q ss_pred             ceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccccccc
Q 036886           43 HQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFA   84 (85)
Q Consensus        43 ~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iKGYis   84 (85)
                      +.|.++.+..+|.     ++.+++|-.+++||..|.|.|-|.
T Consensus       346 s~I~l~~mA~~l~-----~s~~~~E~~L~~lI~~g~l~akID  382 (429)
T 4b4t_R          346 KTLSLKSMASAFG-----VSVAFLDNDLGKFIPNKQLNCVID  382 (429)
T ss_dssp             SEEEHHHHHHHHT-----SCHHHHHHHHHHHHHHTSSCEEEE
T ss_pred             ceeeHHHHHHHhC-----cCHHHHHHHHHHHHHcCCeEEEEc
Confidence            4466777777765     689999999999999999998774

---

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	85
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	93.08

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: COP9 signalosome complex subunit 4, GSN4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.08  E-value=0.051  Score=32.74  Aligned_cols=37  Identities=8%  Similarity=0.301  Sum_probs=31.4

Q ss_pred             ceeeHHHHHHHHhhcCCCCCchhHHHHHHHHhhcCccccccc
Q 036886           43 HQTKLDVIVKALKWLEMDMDVDEVECVVALLLHKNLVKGYFA   84 (85)
Q Consensus        43 ~~ipl~~f~~Al~~~~~~~d~DEvECilANLI~kg~iKGYis   84 (85)
                      ..|.++.+...|.     ++.+|+|=++++||..|.+.|-|.
T Consensus        29 ~~Isl~~la~~l~-----l~~~evE~~l~~mI~~~~i~akID   65 (84)
T d1ufma_          29 NNITFEELGALLE-----IPAAKAEKIASQMITEGRMNGFID   65 (84)
T ss_dssp             SEEEHHHHHHHTT-----SCHHHHHHHHHHHHHTTSSCEEEE
T ss_pred             ceeeHHHHHHHHC-----CCHHHHHHHHHHHHhcCeEEEEEe
Confidence            4577888888776     588999999999999999998774