Psyllid ID: psy3003

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100------
Protein Sequence
MEQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHHHHHHccHHHHHHHHHccccEEEEccccccccHHHHHHHHHHccccEEEEcccHHHHHHHHccccccEEEEEccEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEcccccHHHHHHHHHHcHHHHHHHHEcccccEEEEEcccccccccHHHHHHHccccEEEEEEccHHHHHHHHccccccEEEEEccEEEEEcccHHccccc
Coil and Loop (DISEMBL)
meqlqmgipyitdCVLGEIEKLGQKYKVALRIIkdprferipcmhkgtyaddcivnrvtqhkcYIVATCDKDLKRrirkvpgvpimyiSQHRYtiermpdaygapk
Flexible Loop (DISEMBL)
MEQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKdprferipcmhkgtyADDCIVNRVTQHKCYIVatcdkdlkrrirkvpgvpimyisqhrytiermpdaygapk
Low Complexity Region (SEG)
MEQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK
Disordered region (IsUnstruct)
*****MGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIE**********
Disordered Region (DISOPRED)
**QLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTI***********
Disordered Region (DISEMBL)
MEQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK
Disordered Region (DISPRO)
MEQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAY****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK
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	106	2.2.26 [Sep-21-2011]
Q5RFQ0	198	rRNA-processing protein F	yes	N/A	0.933	0.5	0.838	4e-45
Q9Y324	198	rRNA-processing protein F	yes	N/A	0.933	0.5	0.838	4e-45
Q32PD0	198	rRNA-processing protein F	yes	N/A	0.933	0.5	0.838	4e-45
Q9CTH6	198	rRNA-processing protein F	yes	N/A	0.933	0.5	0.808	4e-44
Q55GM5	194	rRNA-processing protein F	yes	N/A	0.877	0.479	0.698	2e-36
O13610	192	rRNA-processing protein f	yes	N/A	0.886	0.489	0.648	2e-33
Q05498	189	rRNA-processing protein F	yes	N/A	0.886	0.497	0.617	1e-32
Q9BRU9	249	rRNA-processing protein U	no	N/A	0.811	0.345	0.306	6e-06
Q9CX11	249	rRNA-processing protein U	no	N/A	0.811	0.345	0.284	1e-05
O74862	260	rRNA-processing protein u	no	N/A	0.801	0.326	0.326	2e-05

>sp|Q5RFQ0|FCF1_PONAB rRNA-processing protein FCF1 homolog OS=Pongo abelii GN=FCF1 PE=2 SV=1

 Score =  179 bits (454), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 83/99 (83%), Positives = 90/99 (90%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IP ITDCV+ EIEKLGQKY+VALRI KDPRFER+PC HKGTYADDC+V RVTQHKCYIVA
Sbjct: 99  IPCITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVA 158

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T D+DLKRRIRK+PGVPIMYIS HRY IERMPD YGAP+
Sbjct: 159 TVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDYGAPR 197

Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly.
Pongo abelii (taxid: 9601)

>sp|Q9Y324|FCF1_HUMAN rRNA-processing protein FCF1 homolog OS=Homo sapiens GN=FCF1 PE=2 SV=1

 Score =  179 bits (454), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 83/99 (83%), Positives = 90/99 (90%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IP ITDCV+ EIEKLGQKY+VALRI KDPRFER+PC HKGTYADDC+V RVTQHKCYIVA
Sbjct: 99  IPCITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVA 158

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T D+DLKRRIRK+PGVPIMYIS HRY IERMPD YGAP+
Sbjct: 159 TVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDYGAPR 197

Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly.

Homo sapiens (taxid: 9606)

>sp|Q32PD0|FCF1_BOVIN rRNA-processing protein FCF1 homolog OS=Bos taurus GN=FCF1 PE=2 SV=1

 Score =  179 bits (454), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 83/99 (83%), Positives = 90/99 (90%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IP ITDCV+ EIEKLGQKY+VALRI KDPRFER+PC HKGTYADDC+V RVTQHKCYIVA
Sbjct: 99  IPCITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVA 158

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T D+DLKRRIRK+PGVPIMYIS HRY IERMPD YGAP+
Sbjct: 159 TVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDYGAPR 197

Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly.

Bos taurus (taxid: 9913)

>sp|Q9CTH6|FCF1_MOUSE rRNA-processing protein FCF1 homolog OS=Mus musculus GN=Fcf1 PE=2 SV=2

 Score =  176 bits (446), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 80/99 (80%), Positives = 90/99 (90%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IP ITDCV+ EIEKLGQK++VALRI KDPRF+R+PC HKGTYADDC+V RVTQHKCYIVA
Sbjct: 99  IPCITDCVMAEIEKLGQKFRVALRIAKDPRFDRLPCTHKGTYADDCLVQRVTQHKCYIVA 158

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T D+DLKRRIRK+PGVPIMY+S HRY IERMPD YGAP+
Sbjct: 159 TVDRDLKRRIRKIPGVPIMYLSNHRYNIERMPDDYGAPR 197

Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly.

Mus musculus (taxid: 10090)

>sp|Q55GM5|FCF1_DICDI rRNA-processing protein FCF1 homolog OS=Dictyostelium discoideum GN=fcf1 PE=3 SV=1

 Score =  150 bits (380), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 65/93 (69%), Positives = 81/93 (87%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IPYI+DCV  EIE+LG K+KVAL+I KDPRF+R+ C HKGTYADDCI+NR+T H+ +IVA
Sbjct: 99  IPYISDCVAAEIERLGSKFKVALKISKDPRFQRLTCSHKGTYADDCIINRITMHRMFIVA 158

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPD 100
           TCD DL+RRIRK+PGVPI+Y+   +YT+ERMPD
Sbjct: 159 TCDADLRRRIRKIPGVPIVYLKGKKYTVERMPD 191

Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly.

Dictyostelium discoideum (taxid: 44689)

>sp|O13610|FCF1_SCHPO rRNA-processing protein fcf1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=fcf1 PE=3 SV=1

 Score =  140 bits (354), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 61/94 (64%), Positives = 79/94 (84%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IP I+DCV+ E+EKLG +Y++ALRI KD RFER+PC HKGTYADDCIV RV QHKCY+VA
Sbjct: 97  IPCISDCVMAELEKLGIRYRIALRIAKDERFERLPCTHKGTYADDCIVQRVMQHKCYLVA 156

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDA 101
           T DK+LK+RIRK+PG+PI+ ++ H+  +ER+ D 
Sbjct: 157 TNDKNLKQRIRKIPGIPILSVANHKIRVERLVDV 190

Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Required for the early cleavage steps of 35S rRNA at the A(0), A(1), and A(2) sites.

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

>sp|Q05498|FCF1_YEAST rRNA-processing protein FCF1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=FCF1 PE=1 SV=1

 Score =  138 bits (347), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 58/94 (61%), Positives = 77/94 (81%)

Query: 9   PYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVAT 68
           P ITDCV+ E+EKLG KY++AL++ +DPR +R+ C HKGTYADDC+V+RV QHKCYIVAT
Sbjct: 96  PLITDCVMAELEKLGPKYRIALKLARDPRIKRLSCSHKGTYADDCLVHRVLQHKCYIVAT 155

Query: 69  CDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAY 102
            D  LK+RIRK+PG+P+M +  H Y IE++PD +
Sbjct: 156 NDAGLKQRIRKIPGIPLMSVGGHAYVIEKLPDVF 189

Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Required for the early cleavage steps of 35S rRNA at the A(0), A(1), and A(2) sites.

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

>sp|Q9BRU9|UTP23_HUMAN rRNA-processing protein UTP23 homolog OS=Homo sapiens GN=UTP23 PE=1 SV=2

 Score = 49.3 bits (116), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/88 (30%), Positives = 47/88 (53%), Gaps = 2/88 (2%)

Query: 12  TDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHK--CYIVATC 69
           T CVL E+E LG+    A  I +  +    P         +C+++ V +     Y VAT 
Sbjct: 62  TRCVLKELETLGKDLYGAKLIAQKCQVRNCPHFKNAVSGSECLLSMVEEGNPHHYFVATQ 121

Query: 70  DKDLKRRIRKVPGVPIMYISQHRYTIER 97
           D++L  +++K PGVP+M+I Q+   +++
Sbjct: 122 DQNLSVKVKKKPGVPLMFIIQNTMVLDK 149

Involved in rRNA-processing and ribosome biogenesis.

Homo sapiens (taxid: 9606)

>sp|Q9CX11|UTP23_MOUSE rRNA-processing protein UTP23 homolog OS=Mus musculus GN=Utp23 PE=2 SV=1

 Score = 48.5 bits (114), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 48/88 (54%), Gaps = 2/88 (2%)

Query: 12  TDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHK--CYIVATC 69
           T CVL E+E LG++   A  I +  +    P         +C+++ V +     Y VAT 
Sbjct: 62  TRCVLKELETLGKELYGAKLIAQKCQVRNCPHFKSPVSGSECLLSMVDEGNPHHYFVATQ 121

Query: 70  DKDLKRRIRKVPGVPIMYISQHRYTIER 97
           D++L  ++++ PG+P+M+I Q+   +++
Sbjct: 122 DQNLSVKVKRTPGIPLMFIIQNTIVLDK 149

Involved in rRNA-processing and ribosome biogenesis.

Mus musculus (taxid: 10090)

>sp|O74862|UTP23_SCHPO rRNA-processing protein utp23 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=utp23 PE=3 SV=1

 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 31/95 (32%), Positives = 51/95 (53%), Gaps = 10/95 (10%)

Query: 9   PYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMH--KGTYADDCI-----VNRVTQH 61
           P IT C + ++     + K  +RI K   FER  C H  +     +CI     +N   +H
Sbjct: 59  PMITQCCIRQLYSKSDELKQEIRIAKS--FERRRCGHIDEALSPSECIQSVVNINGRNKH 116

Query: 62  KCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIE 96
           + Y+VAT D +L++ +R VPGVP++Y+ +    +E
Sbjct: 117 R-YVVATQDPELRQALRSVPGVPLIYMKRSVVILE 150

Involved in rRNA-processing and ribosome biogenesis.

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

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	106
383865094	216	PREDICTED: rRNA-processing protein FCF1	0.933	0.458	0.898	1e-48
270005079	299	hypothetical protein TcasGA2_TC007087 [T	0.933	0.331	0.919	2e-48
350418961	203	PREDICTED: rRNA-processing protein FCF1	0.933	0.487	0.909	2e-48
91081659	211	PREDICTED: similar to Bekka CG4539-PA [T	0.933	0.469	0.919	3e-48
332375558	203	unknown [Dendroctonus ponderosae]	0.933	0.487	0.919	5e-48
307194558	186	rRNA-processing protein FCF1-like protei	0.933	0.532	0.878	5e-48
322789015	217	hypothetical protein SINV_03889 [Solenop	0.924	0.451	0.887	1e-47
48140222	213	PREDICTED: rRNA-processing protein FCF1	0.933	0.464	0.868	2e-47
380028706	213	PREDICTED: rRNA-processing protein FCF1	0.933	0.464	0.868	2e-47
405969918	399	rRNA-processing protein FCF1-like protei	0.933	0.248	0.828	3e-47

>gi|383865094|ref|XP_003708010.1| PREDICTED: rRNA-processing protein FCF1 homolog [Megachile rotundata]

 Score =  196 bits (499), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 89/99 (89%), Positives = 97/99 (97%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IPYITDCVLGE+EKLGQKYK+AL+IIKDPRFER+ C+HKGTYADDCIVNRVTQHKCYIVA
Sbjct: 117 IPYITDCVLGELEKLGQKYKIALKIIKDPRFERLNCIHKGTYADDCIVNRVTQHKCYIVA 176

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T DKDLKRRIRK+PGVPIMY++QHRYTIERMPDAYGAPK
Sbjct: 177 TNDKDLKRRIRKIPGVPIMYVAQHRYTIERMPDAYGAPK 215

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270005079|gb|EFA01527.1| hypothetical protein TcasGA2_TC007087 [Tribolium castaneum]

 Score =  196 bits (498), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 91/99 (91%), Positives = 96/99 (96%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IPYITDCVLGE+EKLGQKYKVALRIIKDPRFERI CMHKGTYADDC+V RVTQHKCYIVA
Sbjct: 200 IPYITDCVLGELEKLGQKYKVALRIIKDPRFERIKCMHKGTYADDCLVQRVTQHKCYIVA 259

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T DKDLKRRIRK+PGVPIMY++QHRYTIERMPDAYGAPK
Sbjct: 260 TNDKDLKRRIRKIPGVPIMYVAQHRYTIERMPDAYGAPK 298

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350418961|ref|XP_003492025.1| PREDICTED: rRNA-processing protein FCF1 homolog [Bombus impatiens]

 Score =  196 bits (497), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 90/99 (90%), Positives = 97/99 (97%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IPYITDCVLGE+EKLGQKYK+ALRI+KDPRFER+ CMHKGTYADDCIVNRVTQHKCYIVA
Sbjct: 104 IPYITDCVLGEMEKLGQKYKIALRIMKDPRFERLNCMHKGTYADDCIVNRVTQHKCYIVA 163

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T DKDLKRRIRK+PGVPIMY++QHRYTIERMPDAYGAPK
Sbjct: 164 TNDKDLKRRIRKIPGVPIMYVAQHRYTIERMPDAYGAPK 202

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91081659|ref|XP_969257.1| PREDICTED: similar to Bekka CG4539-PA [Tribolium castaneum]

 Score =  195 bits (495), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 91/99 (91%), Positives = 96/99 (96%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IPYITDCVLGE+EKLGQKYKVALRIIKDPRFERI CMHKGTYADDC+V RVTQHKCYIVA
Sbjct: 112 IPYITDCVLGELEKLGQKYKVALRIIKDPRFERIKCMHKGTYADDCLVQRVTQHKCYIVA 171

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T DKDLKRRIRK+PGVPIMY++QHRYTIERMPDAYGAPK
Sbjct: 172 TNDKDLKRRIRKIPGVPIMYVAQHRYTIERMPDAYGAPK 210

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332375558|gb|AEE62920.1| unknown [Dendroctonus ponderosae]

 Score =  194 bits (493), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 91/99 (91%), Positives = 96/99 (96%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IPYITDCVLGE+EKLGQKYKVALRIIKDPRFERI CMHKGTYADDC+V RVTQHKCYIVA
Sbjct: 104 IPYITDCVLGELEKLGQKYKVALRIIKDPRFERIHCMHKGTYADDCLVQRVTQHKCYIVA 163

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T D+DLKRRIRK+PGVPIMY+SQHRYTIERMPDAYGAPK
Sbjct: 164 TNDRDLKRRIRKIPGVPIMYVSQHRYTIERMPDAYGAPK 202

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307194558|gb|EFN76850.1| rRNA-processing protein FCF1-like protein [Harpegnathos saltator]

 Score =  194 bits (493), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 87/99 (87%), Positives = 98/99 (98%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           +PYITDCV+GE+EKLGQKYK+AL+IIKDPRFER+PC+HKGTYADDC+VNRVTQHKCYIVA
Sbjct: 87  VPYITDCVMGELEKLGQKYKLALKIIKDPRFERLPCIHKGTYADDCLVNRVTQHKCYIVA 146

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T DKDLKRRIRK+PGVPIMY+SQHRYTIERMPDAYGAP+
Sbjct: 147 TNDKDLKRRIRKIPGVPIMYVSQHRYTIERMPDAYGAPR 185

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322789015|gb|EFZ14473.1| hypothetical protein SINV_03889 [Solenopsis invicta]

 Score =  193 bits (491), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 87/98 (88%), Positives = 96/98 (97%)

Query: 9   PYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVAT 68
           PYITDCV+GE+EKLGQKYK+AL+IIKDPRFER+ CMHKGTYADDC+VNRVTQHKCYIVAT
Sbjct: 119 PYITDCVMGELEKLGQKYKLALKIIKDPRFERLKCMHKGTYADDCLVNRVTQHKCYIVAT 178

Query: 69  CDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
            D+DLKRRIRK+PGVPIMYISQHR+TIERMPDAYGAPK
Sbjct: 179 NDRDLKRRIRKIPGVPIMYISQHRFTIERMPDAYGAPK 216

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|48140222|ref|XP_397091.1| PREDICTED: rRNA-processing protein FCF1 homolog [Apis mellifera]

 Score =  192 bits (488), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 86/99 (86%), Positives = 97/99 (97%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IPYITDCV+GE+EKLGQKY++ALRI+KDPRFER+ CMHKGTYADDCI+NRVTQHKCYIVA
Sbjct: 114 IPYITDCVIGEMEKLGQKYRIALRIMKDPRFERLNCMHKGTYADDCIINRVTQHKCYIVA 173

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T DKDLK+RIRK+PGVPIMY+SQHRYTIERMPDAYGAP+
Sbjct: 174 TNDKDLKKRIRKIPGVPIMYVSQHRYTIERMPDAYGAPR 212

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380028706|ref|XP_003698031.1| PREDICTED: rRNA-processing protein FCF1 homolog [Apis florea]

 Score =  192 bits (488), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 86/99 (86%), Positives = 97/99 (97%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IPYITDCV+GE+EKLGQKY++ALRI+KDPRFER+ CMHKGTYADDCI+NRVTQHKCYIVA
Sbjct: 114 IPYITDCVIGEMEKLGQKYRIALRIMKDPRFERLNCMHKGTYADDCIINRVTQHKCYIVA 173

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           T DKDLK+RIRK+PGVPIMY+SQHRYTIERMPDAYGAP+
Sbjct: 174 TNDKDLKKRIRKIPGVPIMYVSQHRYTIERMPDAYGAPR 212

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405969918|gb|EKC34861.1| rRNA-processing protein FCF1-like protein [Crassostrea gigas]

 Score =  192 bits (487), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 82/99 (82%), Positives = 95/99 (95%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IPYITDCV+GE+EKLG KY+VALRI +DPRF+R+PC+HKGTYADDCIV R+TQHKCYIVA
Sbjct: 300 IPYITDCVMGELEKLGSKYRVALRIARDPRFKRLPCLHKGTYADDCIVQRITQHKCYIVA 359

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
           TCDKDL+RRIRK+PGVPIMY+ QHRY+IERMPDA+GAPK
Sbjct: 360 TCDKDLRRRIRKIPGVPIMYLQQHRYSIERMPDAFGAPK 398

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

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	106
UNIPROTKB|Q32PD0	198	FCF1 "rRNA-processing protein	0.933	0.5	0.838	6.4e-44
UNIPROTKB|Q9Y324	198	FCF1 "rRNA-processing protein	0.933	0.5	0.838	6.4e-44
MGI|MGI:1920986	198	Fcf1 "FCF1 small subunit (SSU)	0.933	0.5	0.808	5.7e-43
ZFIN|ZDB-GENE-050417-67	198	fcf1 "FCF1 small subunit (SSU)	0.933	0.5	0.797	9.3e-43
FB|FBgn0010520	200	Bka "Bekka" [Drosophila melano	0.905	0.48	0.781	1.6e-40
TAIR|locus:2062902	196	AT2G46230 "AT2G46230" [Arabido	0.924	0.5	0.73	1.1e-39
WB|WBGene00009266	196	F30A10.9 [Caenorhabditis elega	0.915	0.494	0.734	6.1e-39
DICTYBASE|DDB_G0267606	194	fcf1 "FCF1 family protein" [Di	0.877	0.479	0.698	1.2e-35
CGD|CAL0003244	201	orf19.3220 [Candida albicans (	0.896	0.472	0.673	1.3e-34
UNIPROTKB|Q59MK3	201	CaO19.10731 "Potential essenti	0.896	0.472	0.673	1.3e-34

UNIPROTKB|Q32PD0 FCF1 "rRNA-processing protein FCF1 homolog" [Bos taurus (taxid:9913)]

 Score = 463 (168.0 bits), Expect = 6.4e-44, P = 6.4e-44
 Identities = 83/99 (83%), Positives = 90/99 (90%)

Query:     8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
             IP ITDCV+ EIEKLGQKY+VALRI KDPRFER+PC HKGTYADDC+V RVTQHKCYIVA
Sbjct:    99 IPCITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVA 158

Query:    68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
             T D+DLKRRIRK+PGVPIMYIS HRY IERMPD YGAP+
Sbjct:   159 TVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDYGAPR 197

GO:0005730 "nucleolus" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

UNIPROTKB|Q9Y324 FCF1 "rRNA-processing protein FCF1 homolog" [Homo sapiens (taxid:9606)]

 Score = 463 (168.0 bits), Expect = 6.4e-44, P = 6.4e-44
 Identities = 83/99 (83%), Positives = 90/99 (90%)

Query:     8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
             IP ITDCV+ EIEKLGQKY+VALRI KDPRFER+PC HKGTYADDC+V RVTQHKCYIVA
Sbjct:    99 IPCITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVA 158

Query:    68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
             T D+DLKRRIRK+PGVPIMYIS HRY IERMPD YGAP+
Sbjct:   159 TVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDYGAPR 197

GO:0006364 "rRNA processing" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

MGI|MGI:1920986 Fcf1 "FCF1 small subunit (SSU) processome component homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 454 (164.9 bits), Expect = 5.7e-43, P = 5.7e-43
 Identities = 80/99 (80%), Positives = 90/99 (90%)

Query:     8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
             IP ITDCV+ EIEKLGQK++VALRI KDPRF+R+PC HKGTYADDC+V RVTQHKCYIVA
Sbjct:    99 IPCITDCVMAEIEKLGQKFRVALRIAKDPRFDRLPCTHKGTYADDCLVQRVTQHKCYIVA 158

Query:    68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
             T D+DLKRRIRK+PGVPIMY+S HRY IERMPD YGAP+
Sbjct:   159 TVDRDLKRRIRKIPGVPIMYLSNHRYNIERMPDDYGAPR 197

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0042254 "ribosome biogenesis" evidence=IEA

ZFIN|ZDB-GENE-050417-67 fcf1 "FCF1 small subunit (SSU) processome component homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 452 (164.2 bits), Expect = 9.3e-43, P = 9.3e-43
 Identities = 79/99 (79%), Positives = 89/99 (89%)

Query:     8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
             +P ITDCV+ E+EKLG KY+VALRI KDPRF+R+PC HKGTYADDC+V RVTQHKCYIVA
Sbjct:    99 VPCITDCVMAELEKLGMKYRVALRIAKDPRFDRLPCSHKGTYADDCLVQRVTQHKCYIVA 158

Query:    68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
             T D+DLKRRIRK+PGVPIMYIS HRY IERMPD YGAP+
Sbjct:   159 TVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDYGAPR 197

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

FB|FBgn0010520 Bka "Bekka" [Drosophila melanogaster (taxid:7227)]

 Score = 431 (156.8 bits), Expect = 1.6e-40, P = 1.6e-40
 Identities = 75/96 (78%), Positives = 86/96 (89%)

Query:     8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
             IPYI+DCV  E+EKLG KYK+ALRII DPRFER+PC+HKGTYADDC+V RV QHKCYIVA
Sbjct:   102 IPYISDCVRAELEKLGNKYKLALRIISDPRFERLPCLHKGTYADDCLVERVRQHKCYIVA 161

Query:    68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYG 103
             T DKDLK RIRK+PGVPIMY++ H+Y IERMP+AYG
Sbjct:   162 TNDKDLKNRIRKIPGVPIMYVAAHKYAIERMPEAYG 197

GO:0005634 "nucleus" evidence=NAS

GO:0048096 "chromatin-mediated maintenance of transcription" evidence=NAS

GO:0048812 "neuron projection morphogenesis" evidence=IMP

TAIR|locus:2062902 AT2G46230 "AT2G46230" [Arabidopsis thaliana (taxid:3702)]

 Score = 423 (154.0 bits), Expect = 1.1e-39, P = 1.1e-39
 Identities = 73/100 (73%), Positives = 91/100 (91%)

Query:     9 PYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVAT 68
             P ITDCV+ E+EKLGQKY+VALRI KDP FER+PC+HKGTYADDC+V+RVTQHKC+IVAT
Sbjct:    96 PCITDCVMAELEKLGQKYRVALRIAKDPHFERLPCIHKGTYADDCLVDRVTQHKCFIVAT 155

Query:    69 CDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAY--GAPK 106
             CD+DLKRRIRK+PGVPIMY++  +Y+IE++P+A   GAP+
Sbjct:   156 CDRDLKRRIRKIPGVPIMYVTNRKYSIEKLPEATLGGAPR 195

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0051604 "protein maturation" evidence=RCA

WB|WBGene00009266 F30A10.9 [Caenorhabditis elegans (taxid:6239)]

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 72/98 (73%), Positives = 88/98 (89%)

Query:     8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
             I Y TDCVL E+EK+ +++K+AL+++KDPR +R+ C HKGTYADDC+V RVTQHKCYIVA
Sbjct:    98 IVYATDCVLAELEKV-RRFKIALKVLKDPRVQRLKCEHKGTYADDCLVQRVTQHKCYIVA 156

Query:    68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAYGAP 105
             TCD+DLKRRIRK+PGVPIMYI  HR++IERMPDAYGAP
Sbjct:   157 TCDRDLKRRIRKIPGVPIMYIVNHRFSIERMPDAYGAP 194

GO:0000003 "reproduction" evidence=IMP

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

DICTYBASE|DDB_G0267606 fcf1 "FCF1 family protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 385 (140.6 bits), Expect = 1.2e-35, P = 1.2e-35
 Identities = 65/93 (69%), Positives = 81/93 (87%)

Query:     8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
             IPYI+DCV  EIE+LG K+KVAL+I KDPRF+R+ C HKGTYADDCI+NR+T H+ +IVA
Sbjct:    99 IPYISDCVAAEIERLGSKFKVALKISKDPRFQRLTCSHKGTYADDCIINRITMHRMFIVA 158

Query:    68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPD 100
             TCD DL+RRIRK+PGVPI+Y+   +YT+ERMPD
Sbjct:   159 TCDADLRRRIRKIPGVPIVYLKGKKYTVERMPD 191

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

CGD|CAL0003244 orf19.3220 [Candida albicans (taxid:5476)]

 Score = 375 (137.1 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 64/95 (67%), Positives = 78/95 (82%)

Query:     8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
             IP ITDCV+ E+EKLG KY++AL++ KDPR +R+ C H GTYADDC+VNRV QHKCYIVA
Sbjct:   107 IPIITDCVIAELEKLGSKYRIALKLAKDPRIQRLKCSHVGTYADDCLVNRVIQHKCYIVA 166

Query:    68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAY 102
             T D DLKRRIRK+PG+PIM +  H Y IER+PD +
Sbjct:   167 TNDADLKRRIRKIPGIPIMSVGGHSYVIERLPDVF 201

GO:0003674 "molecular_function" evidence=ND

GO:0032040 "small-subunit processome" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0000472 "endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IEA

GO:0000447 "endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IEA

GO:0000480 "endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IEA

UNIPROTKB|Q59MK3 CaO19.10731 "Potential essential protein" [Candida albicans SC5314 (taxid:237561)]

 Score = 375 (137.1 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 64/95 (67%), Positives = 78/95 (82%)

Query:     8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
             IP ITDCV+ E+EKLG KY++AL++ KDPR +R+ C H GTYADDC+VNRV QHKCYIVA
Sbjct:   107 IPIITDCVIAELEKLGSKYRIALKLAKDPRIQRLKCSHVGTYADDCLVNRVIQHKCYIVA 166

Query:    68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERMPDAY 102
             T D DLKRRIRK+PG+PIM +  H Y IER+PD +
Sbjct:   167 TNDADLKRRIRKIPGIPIMSVGGHSYVIERLPDVF 201

GO:0003674 "molecular_function" evidence=ND

---

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)
Q55GM5	FCF1_DICDI	No assigned EC number	0.6989	0.8773	0.4793	yes	N/A
Q9Y324	FCF1_HUMAN	No assigned EC number	0.8383	0.9339	0.5	yes	N/A
Q9CTH6	FCF1_MOUSE	No assigned EC number	0.8080	0.9339	0.5	yes	N/A
Q32PD0	FCF1_BOVIN	No assigned EC number	0.8383	0.9339	0.5	yes	N/A
Q05498	FCF1_YEAST	No assigned EC number	0.6170	0.8867	0.4973	yes	N/A
O13610	FCF1_SCHPO	No assigned EC number	0.6489	0.8867	0.4895	yes	N/A
Q5RFQ0	FCF1_PONAB	No assigned EC number	0.8383	0.9339	0.5	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	106
cd09864	143	cd09864, PIN_Fcf1, PIN domain of rRNA-processing p	8e-66
pfam04900	101	pfam04900, Fcf1, Fcf1	5e-46
cd08553	120	cd08553, PIN_Fcf1-like, PIN domain of rRNA-process	4e-31
COG1412	136	COG1412, COG1412, Uncharacterized proteins of PilT	6e-31
cd09854	125	cd09854, PIN_VapC-Smg6_family, PIN domains of VapC	3e-23
cd09866	147	cd09866, PIN_Fcf1-Utp23-H, PIN domain of rRNA-proc	2e-17
cd09879	117	cd09879, PIN_AF0591, PIN domain of Archaeoglobus f	6e-12
cd09852	120	cd09852, PIN_SF, PIN (PilT N terminus) domain: Sup	3e-08
cd09865	148	cd09865, PIN_Utp23, PIN domain of rRNA-processing	2e-06
smart00670	111	smart00670, PINc, Large family of predicted nucleo	8e-06

>gnl|CDD|189034 cd09864, PIN_Fcf1, PIN domain of rRNA-processing protein, Fcf1 (Utp24, YDR339C), and other eukaryotic homologs

 Score =  194 bits (495), Expect = 8e-66
 Identities = 72/91 (79%), Positives = 84/91 (92%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           IP ITDCV+ E+EKLGQKY+VAL+I KDPRFER+PC HKGTYADDC+V RVTQH+CYIVA
Sbjct: 53  IPCITDCVMAELEKLGQKYRVALKIAKDPRFERLPCDHKGTYADDCLVERVTQHRCYIVA 112

Query: 68  TCDKDLKRRIRKVPGVPIMYISQHRYTIERM 98
           TCD+DLKRRIRK+PGVPIMYI  H+Y+IER+
Sbjct: 113 TCDRDLKRRIRKIPGVPIMYIRNHKYSIERL 143

Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) is an essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Component of the small subunit (SSU) processome, Fcf1 is an essential nucleolar protein that is required for processing of the 18S pre-rRNA at sites A0-A2. The Fcf1 protein was reported to interact with Pmc1p (vacuolar Ca2+ ATPase) and Cor1p (core subunit of the ubiquinol-cytochrome c reductase complex). The PIN (PilT N terminus) domain of this protein is a homolog of flap endonuclease-1 (FEN1)-like PIN domains, but apparently lack the H3TH domain or extensive arch/clamp region seen in the latter. PIN domains typically contain three or four conserved acidic residues (putative metal-binding, active site residues). The Fcf1 PIN domain subfamily has four of these putative active site residues and the Fcf1-Utp23 homolog PIN domain subfamily has three of them. Point mutation studies of the conserved acidic residues in the putative active site of Saccharomyces cerevisiae Fcf1 determined they were essential for pre-rRNA processing at sites A1 and A2, whereas the presence of the Fcf1 protein itself is also required for cleavage at site A0. Length = 143

>gnl|CDD|218319 pfam04900, Fcf1, Fcf1

 Score =  143 bits (362), Expect = 5e-46
 Identities = 56/93 (60%), Positives = 75/93 (80%), Gaps = 2/93 (2%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGT--YADDCIVNRVTQHKCYI 65
            PYITDCV+ E+EKLG K++ AL+I KD RFER+ C HKGT  YADDCI++RV +H CYI
Sbjct: 9   KPYITDCVIAELEKLGPKFRGALKIAKDKRFERLKCNHKGTEVYADDCILDRVGKHNCYI 68

Query: 66  VATCDKDLKRRIRKVPGVPIMYISQHRYTIERM 98
           VAT D++L+RR+RK+PGVPI+YI+++   +E  
Sbjct: 69  VATQDRELRRRLRKIPGVPIIYINRNVMVLEPP 101

Fcf1 is a nucleolar protein involved in pre-rRNA processing. Depletion of yeast Fcf1 and Fcf2 leads to a decrease in synthesis of the 18S rRNA and results in a deficit in 40S ribosomal subunits. Length = 101

>gnl|CDD|189021 cd08553, PIN_Fcf1-like, PIN domain of rRNA-processing proteins, Fcf1 (Utp24, YDR339C), Utp23 (YOR004W), and other eukaryotic homologs

 Score =  105 bits (265), Expect = 4e-31
 Identities = 42/92 (45%), Positives = 61/92 (66%), Gaps = 5/92 (5%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGT-YADDCIVNRVTQH--KCY 64
            P IT CVL E+E LG+K K A +I K    ER+ C HK    AD+C+++ V +H    Y
Sbjct: 31  WPCITPCVLAELESLGKKLKDAFKIAKTL--ERLNCNHKEGASADECLLDIVKKHNNHRY 88

Query: 65  IVATCDKDLKRRIRKVPGVPIMYISQHRYTIE 96
            VAT D+DL+ ++RK+PGVP++YI Q++  +E
Sbjct: 89  FVATQDQDLRVKLRKIPGVPLVYILQNKMILE 120

Fcf1 (FAF1-copurifying factor 1, also known as Utp24) and Utp23 (U three-associated protein 23) are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly. Components of the small subunit (SSU) processome, Fcf1 and Utp23 are essential nucleolar proteins that are required for processing of the 18S pre-rRNA at sites A0-A2. The Fcf1 protein was reported to interact with Pmc1p (vacuolar Ca2+ ATPase) and Cor1p (core subunit of the ubiquinol-cytochrome c reductase complex). The PIN (PilT N terminus) domains of these proteins are homologs of flap endonuclease-1 (FEN1)-like PIN domains, but apparently lack the H3TH domain or extensive arch/clamp region seen in the latter. PIN domains typically contain three or four conserved acidic residues (putative metal-binding, active site residues). The Fcf1 PIN domain subfamily has four of these putative active site residues. Point mutation studies showed that the conserved acidic residues in the putative active site of Saccharomyces cerevisiae Fcf1 are essential for pre-rRNA processing at sites A1 and A2, whereas the presence of the Fcf1 protein itself is also required for cleavage at site A0. S. cerevisiae Utp23 lacks several of these key residues and mutation of the conserved acidic residues seen in Utp23 did not interfere with rRNA maturation and cell viability. The subfamily of Fcf1- and Utp23-like homologs found in eukaryotes (except fungi) posses three of the four conserved residues seen in S. cerevisiae Fcf1. Length = 120

>gnl|CDD|224330 COG1412, COG1412, Uncharacterized proteins of PilT N-term

 Score =  105 bits (265), Expect = 6e-31
 Identities = 42/94 (44%), Positives = 61/94 (64%), Gaps = 3/94 (3%)

Query: 9   PYITDCVLGEIEKLGQKYKVALRI-IKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
           P I  CV+ E+EKL +K++   RI I     ER+ C+HKG YAD+C++    +H  YIVA
Sbjct: 44  PAIPSCVIRELEKLKRKHRGKARIAIALKYAERLECIHKGRYADECLLEAALKHGRYIVA 103

Query: 68  TCDKDLKRRIRKVPGVPIMYISQ-HRYTIERMPD 100
           T DK+LKRR+R+  G+P++ + Q     IER+ D
Sbjct: 104 TNDKELKRRLREN-GIPVITLRQRKLLIIERLSD 136

/Vapc superfamily [General function prediction only]. Length = 136

>gnl|CDD|189024 cd09854, PIN_VapC-Smg6_family, PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, rRNA-processing protein Fcf1, Archaeoglobus fulgidus AF0591 protein, and homologs

 Score = 86.2 bits (213), Expect = 3e-23
 Identities = 41/96 (42%), Positives = 49/96 (51%), Gaps = 16/96 (16%)

Query: 8   IPYITDCVLGEIEKLGQKYKVALRIIKDPRF-ERIPCMHKGT---------------YAD 51
             YI+D V  EI   G K+KVALRI KD R  +R  C HK                  AD
Sbjct: 30  DVYISDIVAAEIRNKGSKFKVALRIRKDCRDHKRFICFHKEFSEHTFVERLPNETINDAD 89

Query: 52  DCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMY 87
           DC +N+   H+ +IVATCD DL+   RK PGV I  
Sbjct: 90  DCAINKTCMHRMFIVATCDADLREAARKEPGVIIKS 125

PIN (PilT N terminus) domains of such ribonucleases as the toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and, rRNA-processing protein Fcf1, are included in this family. Also included are the PIN domains of the Pyrobaculum aerophilum Pea0151 and Archaeoglobus fulgidus AF0591 proteins and other similar archaeal homologs. These PIN domains are structural homologs of flap endonuclease-1 (FEN1)-like PIN domains, but lack the extensive arch/clamp region and the H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region, seen in FEN1-like PIN domains. PIN domains typically contain three or four highly conserved acidic residues (putative metal-binding, active site residues) which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Length = 125

>gnl|CDD|189036 cd09866, PIN_Fcf1-Utp23-H, PIN domain of rRNA-processing protein Fcf1- and Utp23-like homologs found in eukaryotes except fungi

 Score = 72.2 bits (178), Expect = 2e-17
 Identities = 32/84 (38%), Positives = 49/84 (58%), Gaps = 6/84 (7%)

Query: 9   PYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKG--TYADDCIVN--RVTQHKCY 64
            + T CV+ E+EKLG     AL I K  RF+   C H+     A +C+ +       + Y
Sbjct: 58  LFTTRCVIAELEKLGPDLYGALLIAK--RFQVAKCGHEKSPVSASECLKSMIGDNNPEHY 115

Query: 65  IVATCDKDLKRRIRKVPGVPIMYI 88
            VAT DK+L+ ++RK+PGVP++Y+
Sbjct: 116 FVATQDKELREKLRKIPGVPLLYL 139

PIN domain homologs of Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23, essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly, are included in this subfamily. Fcf1 is a component of the small subunit (SSU) processome and an essential nucleolar protein required for processing of the 18S pre-rRNA at sites A0-A2. These PIN (PilT N terminus) domains are homologs of flap endonuclease-1 (FEN1)-like PIN domains, but apparently lack the H3TH domain or extensive arch/clamp region seen in the latter. PIN domains typically contain three or four conserved acidic residues (putative metal-binding, active site residues). The Fcf1-Utp23 homolog PIN domain subfamily has three of these conserved acidic residues rather than the four seen in the Fcf1 PIN domain subfamily. Length = 147

>gnl|CDD|189049 cd09879, PIN_AF0591, PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal homologs

 Score = 57.2 bits (139), Expect = 6e-12
 Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 14/93 (15%)

Query: 9   PYITDCVLGEIEKLGQKY--------KVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQ 60
             +   VL E+EKL +K         +VAL++ +               ADD I+    +
Sbjct: 30  FVVPSAVLEELEKLSRKGKGKDKRAARVALQLAERCEVVESEGG----PADDAILELAKE 85

Query: 61  HKCYIVATCDKDLKRRIRKVPGVPIMYISQHRY 93
                V T D++LK+R+    G+P++Y+ Q + 
Sbjct: 86  LGA-AVVTNDRELKKRLLDA-GIPVIYLRQKKK 116

PIN (PilT N terminus) domain of Archaeoglobus fulgidus AF0591 protein and other similar uncharacterized archaeal homologs are included in this family. These PIN domains are structural homologs of flap endonuclease-1 (FEN1)-like PIN domains, but lack the extensive arch/clamp region and the H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region, seen in FEN1-like PIN domains. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues) which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Length = 117

>gnl|CDD|189022 cd09852, PIN_SF, PIN (PilT N terminus) domain: Superfamily

 Score = 47.5 bits (113), Expect = 3e-08
 Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 15/93 (16%)

Query: 8   IPYITDCVLGEIEKL----------GQKYKVALRIIKDPRFERIPCMHKGT--YADDCIV 55
              I   V+ E+ KL          G+  ++ LR ++      IP +H     Y  D  +
Sbjct: 30  TVIIVFDVVAELLKLEAQKGLRRKKGRVAELLLRDLELLDLMGIPVVHAPGDLYEADAQI 89

Query: 56  NRVTQH-KCYIVATCDKDLKRRIRKVPGVPIMY 87
             + +      + T D DL+++ +  PGV +  
Sbjct: 90  AALAKKGHVVALITNDSDLRQKAK--PGVKVFS 120

PIN_SF The PIN (PilT N terminus) domain belongs to a large nuclease superfamily with representatives from eukaryota, eubacteria, and archaea. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues) is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Seen here, are two major divisions in the PIN domain superfamily. The first major division, the structure-specific 5' nuclease family, is represented by FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4 RNase H nuclease PIN domains. These 5' nucleases are involved in DNA replication, repair, and recombination. They are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated DNA, in an endonucleolytic, structure-specific manner. Unique to FEN1-like nucleases, the PIN domain has a helical arch/clamp region (I domain) of variable length (approximately 16 to 800 residues) and, inserted within the C-terminal region of the PIN domain, a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA binding. With the exception of Mkt1, these nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or Co2+). The second major division of the PIN domain superfamily, the VapC-Smg6 family, includes such eukaryotic ribonucleases as, Smg6, an essential factor in nonsense-mediated mRNA decay; Rrp44, the catalytic subunit of the exosome; and Nob1, a ribosome assembly factor critical in pre-rRNA processing. A large percentage of members in this family are bacterial ribonuclease toxins of TA operons such as Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB, as well as, archaeal homologs, Pyrobaculum aerophilum Pea0151 and P. aerophilum Pae2754. Also included are the eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23-like proteins. Components of the small subunit processome, Fcf1/Utp24 and Utp23 are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly. Length = 120

>gnl|CDD|189035 cd09865, PIN_Utp23, PIN domain of rRNA-processing protein, Utp23 (YOR004W), and other fungal homologs

 Score = 43.5 bits (103), Expect = 2e-06
 Identities = 31/90 (34%), Positives = 51/90 (56%), Gaps = 11/90 (12%)

Query: 9   PYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYA---DDCIVNRV-----TQ 60
           P IT C +  +  LG+  + A+ + K   FER  C H+   A   D+C+ + V      +
Sbjct: 56  PMITQCCIRALYALGKTVQRAIDLAK--TFERRRCNHRDADALSPDECLKSVVDPKGKNK 113

Query: 61  HKCYIVATCDKDLKRRIRKVPGVPIMYISQ 90
           H+ YIVAT D  L+  +R +PGVP+++I++
Sbjct: 114 HR-YIVATQDPPLRTDLRSIPGVPLIHINR 142

Saccharomyces cerevisiae Utp23 (U three-associated protein 23), component of the small subunit (SSU) processome, is an essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. The PIN (PilT N terminus) domain of this protein is a homolog of flap endonuclease-1 (FEN1)-like PIN domains, but apparently lack the H3TH domain or extensive arch/clamp region seen in the latter. PIN domains typically contain three or four conserved acidic residues (putative metal-binding, active site residues. S. cerevisiae Utp23 lacks several of these key residues and mutation of the conserved acidic residues seen in Utp23 did not interfere with rRNA maturation and cell viability. Length = 148

>gnl|CDD|214771 smart00670, PINc, Large family of predicted nucleotide-binding domains

 Score = 40.9 bits (96), Expect = 8e-06
 Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 16/85 (18%)

Query: 7   GIPYITDCVLGEIE-----------KLGQKYKVALRIIKDPRFERIPCMHKGTYA----D 51
           G  YI   VL E+E           +L  + K+ L+++K+ R E               +
Sbjct: 27  GEVYIPQTVLEELEYLALRSLKKLEELALEGKIILKVLKEERIEEEILERLSLKLELLPN 86

Query: 52  DCIVNRVTQH-KCYIVATCDKDLKR 75
           D ++    +     ++ T D+DL+R
Sbjct: 87  DALILATAKELGNVVLVTNDRDLRR 111

From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi. Length = 111

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	106
KOG3165|consensus	195		100.0
PF04900	101	Fcf1: Fcf1; InterPro: IPR006984 This family is com	100.0
KOG3164|consensus	236		99.98
COG1412	136	Uncharacterized proteins of PilT N-term./Vapc supe	99.95
PRK13764	602	ATPase; Provisional	97.93
PF13638	133	PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_	97.13
smart00670	111	PINc Large family of predicted nucleotide-binding	96.77
PRK00124	151	hypothetical protein; Validated	95.34
COG4956	356	Integral membrane protein (PIN domain superfamily)	93.34
PF02639	130	DUF188: Uncharacterized BCR, YaiI/YqxD family COG1	93.29
PF05991	166	NYN_YacP: YacP-like NYN domain; InterPro: IPR01029	92.85
PRK12496	164	hypothetical protein; Provisional	89.1
smart00500	44	SFM Splicing Factor Motif, present in Prp18 and Pr	87.33
COG1656	165	Uncharacterized conserved protein [Function unknow	83.8
PF13344	101	Hydrolase_6: Haloacid dehalogenase-like hydrolase;	82.76

>KOG3165|consensus

Probab=100.00  E-value=8.7e-37  Score=217.49  Aligned_cols=103  Identities=72%  Similarity=1.246  Sum_probs=99.5

Q ss_pred             ccccceeeecHHHHHHHHhhCcchHHHHhhccCCceEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCC
Q psy3003           3 QLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPG   82 (106)
Q Consensus         3 l~g~~~~~vt~cVl~EL~~Lg~~~~~al~~ak~~~~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~G   82 (106)
                      |++++.|++|.||+.|||+||..|+.||.+|+||+|++++|.|+|++|||||++.+..|++|||||||++|++|+|+|||
T Consensus        91 l~Ak~~pcitDCVmaELEkLg~kyrvALri~kDpr~eRL~C~HKGTYADDClv~RV~qHkCYIVAT~D~dLK~RIrkIPG  170 (195)
T KOG3165|consen   91 LYAKCIPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATNDRDLKQRIRKIPG  170 (195)
T ss_pred             HHhccccchhHHHHHHHHHhcchhhhhhhhhcCCcccccccccCCcchhhHHHHHHhhcceEEEEeccHHHHHHHhcCCC
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccEEEEecceEEEeeCCCCCCCC
Q psy3003          83 VPIMYISQHRYTIERMPDAYGAP  105 (106)
Q Consensus        83 VPviy~~~~~l~lE~~s~as~~~  105 (106)
                      ||+||+.+.++.+|.+++|+-.+
T Consensus       171 VPim~v~~hk~~IEr~pda~~g~  193 (195)
T KOG3165|consen  171 VPIMYVANHKYSIERLPDATLGG  193 (195)
T ss_pred             CceEEEecceeeeeeCCcccccC
Confidence            99999999999999999996554

>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins

Probab=100.00  E-value=2.7e-35  Score=194.94  Aligned_cols=95  Identities=49%  Similarity=0.817  Sum_probs=89.6

Q ss_pred             cccccceeeecHHHHHHHHhhCcchHHHHhhccCCc--eEEEecCCCCC--CHHHHHHHhhhcCCeEEEEecCHHHHHHH
Q psy3003           2 EQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPR--FERIPCMHKGT--YADDCIVNRVTQHKCYIVATCDKDLKRRI   77 (106)
Q Consensus         2 ~l~g~~~~~vt~cVl~EL~~Lg~~~~~al~~ak~~~--~~~~~c~h~~~--~ad~ci~~~~~~~~~~iVaTqD~~Lr~~L   77 (106)
                      .|+|+++++||+||++||++||++++++..+|+  +  +++++|+|.+.  ++||||++++++++.|+|||||++||++|
T Consensus         3 ~L~~~~~~~vt~cVl~EL~~L~~~~~~~~~~a~--~~~~~~~~c~h~~~~~~addci~~~~~~~~~~~VaT~D~~Lr~~l   80 (101)
T PF04900_consen    3 LLGGKVKPYVTQCVLEELESLGKKFKGALRIAK--RKALERRKCNHKETPGSADDCILDLAGKNNKYIVATQDKELRRRL   80 (101)
T ss_pred             cccCccEEEecHHHHHHHHHhcccccchhhhhh--chhhHhhcCCCCCCCcCHHHHHHHHhccCCeEEEEecCHHHHHHH
Confidence            478999999999999999999999999999999  7  99999999964  89999999998875699999999999999


Q ss_pred             hcCCCccEEEEecceEEEeeC
Q psy3003          78 RKVPGVPIMYISQHRYTIERM   98 (106)
Q Consensus        78 r~i~GVPviy~~~~~l~lE~~   98 (106)
                      |++||||+||+++++++||+|
T Consensus        81 r~~~GvPvi~l~~~~~~le~p  101 (101)
T PF04900_consen   81 RKIPGVPVIYLRRNVLILEPP  101 (101)
T ss_pred             hcCCCCCEEEEECCEEEecCC
Confidence            988999999999999999997

>KOG3164|consensus

Probab=99.98  E-value=5.4e-33  Score=205.44  Aligned_cols=99  Identities=32%  Similarity=0.560  Sum_probs=93.3

Q ss_pred             ccccceeeecHHHHHHHHhhCcchHHHHhhccCCceEEEecCCCCC-CHHHHHHHhhhc--CCeEEEEecCHHHHHHHhc
Q psy3003           3 QLQMGIPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGT-YADDCIVNRVTQ--HKCYIVATCDKDLKRRIRK   79 (106)
Q Consensus         3 l~g~~~~~vt~cVl~EL~~Lg~~~~~al~~ak~~~~~~~~c~h~~~-~ad~ci~~~~~~--~~~~iVaTqD~~Lr~~Lr~   79 (106)
                      |.|.+++|||+|||.||+.+|+++.+|+.+|+  +|++++|+|+.. +|++||.++++.  ..||+|||||.+||+.||.
T Consensus        53 l~~~vKL~tTqCvikele~~g~~l~ga~~iAK--~fe~~~C~H~~~~s~seCl~svv~~~Nk~~YvvATQD~el~~kLr~  130 (236)
T KOG3164|consen   53 LQGEVKLMTTQCVIKELEELGKDLYGAKGIAK--QFEIRNCNHKDARSPSECLRSVVRISNKHHYVVATQDQELRRKLRK  130 (236)
T ss_pred             hcCCCeeeehHHHHHHHHHhCcchhhhHHHHH--HHhHhcCCCCCCCCHHHHHHHHHhccCCceEEEecCCHHHHHHHhc
Confidence            67899999999999999999999999999999  999999999654 999999999985  2389999999999999999


Q ss_pred             CCCccEEEEecceEEEeeCCCCCC
Q psy3003          80 VPGVPIMYISQHRYTIERMPDAYG  103 (106)
Q Consensus        80 i~GVPviy~~~~~l~lE~~s~as~  103 (106)
                      +||||+||++++.++||+||.||.
T Consensus       131 ~pgvPli~~~r~t~vld~~S~at~  154 (236)
T KOG3164|consen  131 EPGVPLIYLKRNTLVLDAPSQATA  154 (236)
T ss_pred             CCCCceEEEecceEEecCcchhhH
Confidence            999999999999999999999983

>COG1412 Uncharacterized proteins of PilT N-term

Probab=99.95  E-value=8.1e-28  Score=167.56  Aligned_cols=95  Identities=43%  Similarity=0.725  Sum_probs=82.0

Q ss_pred             cccceeeecHHHHHHHHhhCcchHHHHh--hccCCceEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCC
Q psy3003           4 LQMGIPYITDCVLGEIEKLGQKYKVALR--IIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVP   81 (106)
Q Consensus         4 ~g~~~~~vt~cVl~EL~~Lg~~~~~al~--~ak~~~~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~   81 (106)
                      +.+++++||+||++||++|++.++++..  ++.. .+++++|.|.+.++||||.+.+.++++|+|||||++||+|||+. 
T Consensus        39 ~~~~~~~Ip~~Vi~EL~~l~~~~~~~~r~~ia~~-~~er~~~~~~~~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~-  116 (136)
T COG1412          39 GAKYKPAIPSCVIRELEKLKRKHRGKARIAIALK-YAERLECIHKGRYADECLLEAALKHGRYIVATNDKELKRRLREN-  116 (136)
T ss_pred             cccccccchHHHHHHHHHHHHhcCchHHHHHHHH-HhhccCccccCCChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHc-
Confidence            3348999999999999999987666555  4541 36788999998899999999999988899999999999999997 


Q ss_pred             CccEEEEec-ceEEEeeCCC
Q psy3003          82 GVPIMYISQ-HRYTIERMPD  100 (106)
Q Consensus        82 GVPviy~~~-~~l~lE~~s~  100 (106)
                      |||+||+++ +.+++|++++
T Consensus       117 GIPvi~lr~r~~~~ie~~~~  136 (136)
T COG1412         117 GIPVITLRQRKLLIIERLSD  136 (136)
T ss_pred             CCCEEEEeCCeEEEeeCCCC
Confidence            999999995 5599998763

/Vapc superfamily [General function prediction only]

>PRK13764 ATPase; Provisional

Probab=97.93  E-value=2e-05  Score=66.44  Aligned_cols=91  Identities=20%  Similarity=0.211  Sum_probs=65.0

Q ss_pred             cceeeecHHHHHHHHhhCcc----hHHHHhhccCC-------ceEEEecCCCC----------CCHHHHHHHhhhcCCeE
Q psy3003           6 MGIPYITDCVLGEIEKLGQK----YKVALRIIKDP-------RFERIPCMHKG----------TYADDCIVNRVTQHKCY   64 (106)
Q Consensus         6 ~~~~~vt~cVl~EL~~Lg~~----~~~al~~ak~~-------~~~~~~c~h~~----------~~ad~ci~~~~~~~~~~   64 (106)
                      .-.++||.-|++||+.++..    -..|++.++..       .+++.-.++..          ...|+-|.+++.+.+ +
T Consensus        26 ~~~IiIP~~Vl~ELe~~A~~~r~~G~~gLeeL~~L~~l~~~g~i~ie~~~~~p~~~~~~~~~~gevD~~I~~~A~~~~-~  104 (602)
T PRK13764         26 GGTIIIPEAVVAELEAQANQGREIGFSGLEELKKLRELAEEGLIELEFVGERPTLEQIKLAKGGEIDALIREVAKELG-A  104 (602)
T ss_pred             CCEEEeehHHHHHHHHHhhccchhhHHHHHHHHHHHHhhccCceEEEEeccccchhhcccccCCCHHHHHHHHHHHcC-C
Confidence            35799999999999999754    23345555410       12121112111          368999999999875 9


Q ss_pred             EEEecCHHHHHHHhcCCCccEEEEecce--EEEeeC
Q psy3003          65 IVATCDKDLKRRIRKVPGVPIMYISQHR--YTIERM   98 (106)
Q Consensus        65 iVaTqD~~Lr~~Lr~i~GVPviy~~~~~--l~lE~~   98 (106)
                      ++.|||..|++.++.. |||++|+++..  +.+|..
T Consensus       105 ~lvT~D~~l~~~A~~~-GI~V~~l~~~~~~L~ie~~  139 (602)
T PRK13764        105 TLVTSDRVQAEVARAK-GIDVIYLKPEREPLEIEKF  139 (602)
T ss_pred             EEEeCCHHHHHHHHHc-CCEEEEeCCCCCccchHHH
Confidence            9999999999999995 99999999643  666664

>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J

Probab=97.13  E-value=0.0013  Score=44.17  Aligned_cols=84  Identities=23%  Similarity=0.298  Sum_probs=48.5

Q ss_pred             ccceeeecHHHHHHHHhhCcc-----------hHHHHhhccCC---ceEEEecC--CC---------CCCHHHHHHHhhh
Q psy3003           5 QMGIPYITDCVLGEIEKLGQK-----------YKVALRIIKDP---RFERIPCM--HK---------GTYADDCIVNRVT   59 (106)
Q Consensus         5 g~~~~~vt~cVl~EL~~Lg~~-----------~~~al~~ak~~---~~~~~~c~--h~---------~~~ad~ci~~~~~   59 (106)
                      ++..++||.+|++||+++...           ++.+..+....   ....+...  +.         ....|+.|++.+.
T Consensus        19 ~~~~ivIP~~Vl~ELd~lk~~~~~~~~~~~~~ar~~~~~l~~~~~~~~~~i~~q~~~~~~~~~~~~~~~~~D~~Il~~a~   98 (133)
T PF13638_consen   19 EQNKIVIPLTVLEELDRLKKSSRDRDRELRKRAREAIRWLEKLLKRGSRSIRVQTSDEEIDEDLNLDAQRNDDRILNCAL   98 (133)
T ss_dssp             SSSEEEEEHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHCT-TTEEECTTTS-EES--S----HHHHHHHHHHH
T ss_pred             ccCEEEechHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHhcCCCeEecchhhhhcchhhhccccccHHHHHHHHH
Confidence            467899999999999887542           33344443200   00011111  10         1257888888774


Q ss_pred             c------CCeEEEEecCHHHHHHHhcCCCccEEEEe
Q psy3003          60 Q------HKCYIVATCDKDLKRRIRKVPGVPIMYIS   89 (106)
Q Consensus        60 ~------~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~   89 (106)
                      .      ....++.|+|..||.+.+.. |+|...++
T Consensus        99 ~~~~~~~~~~vvLvT~D~~l~~~A~~~-gi~~~~~~  133 (133)
T PF13638_consen   99 YLQEENPGRKVVLVTNDKNLRLKARAE-GIPAVSYE  133 (133)
T ss_dssp             HHHHHCGCEEEEEEE--HHHHHHHHHT-T--EE---
T ss_pred             HHHHhcCCCeEEEEeCCHHHHHHHhhc-ccccccCC
Confidence            2      23589999999999999995 99988653

>smart00670 PINc Large family of predicted nucleotide-binding domains

Probab=96.77  E-value=0.0022  Score=41.24  Aligned_cols=70  Identities=26%  Similarity=0.323  Sum_probs=42.3

Q ss_pred             cceeeecHHHHHHHHhhCc--c---hHHHHh-------hccCCc-eEEEecCCCCC-----CHHHHHHHhhhcCCeEEEE
Q psy3003           6 MGIPYITDCVLGEIEKLGQ--K---YKVALR-------IIKDPR-FERIPCMHKGT-----YADDCIVNRVTQHKCYIVA   67 (106)
Q Consensus         6 ~~~~~vt~cVl~EL~~Lg~--~---~~~al~-------~ak~~~-~~~~~c~h~~~-----~ad~ci~~~~~~~~~~iVa   67 (106)
                      ...+++|.+|+.||+....  .   +..-..       ...+.. +....+.+.+.     ..|.+|.+.+...+..+++
T Consensus        24 ~~~~~i~~~v~~El~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~~il~~a~~~~~~~lv  103 (111)
T smart00670       24 KGEVYIPPTVLEELEYLAKLRSLKKLEELALEGKIKLKVLKEERKLEEEILERLSLKLELLPNDALILATAKELGNVVLV  103 (111)
T ss_pred             CCcEEECHHHHHHHHHHHHHHHHhhHHHHHHhcccccceeecCCCeEEEecccCChhhcCCCChHHHHHHHHHCCCCEEE
Confidence            4678999999999999762  1   111111       010000 22222322221     3688999999876458999


Q ss_pred             ecCHHHHH
Q psy3003          68 TCDKDLKR   75 (106)
Q Consensus        68 TqD~~Lr~   75 (106)
                      |+|.+|++
T Consensus       104 T~D~~l~~  111 (111)
T smart00670      104 TNDRDLRR  111 (111)
T ss_pred             eCCcccCC
Confidence            99998863

From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.

>PRK00124 hypothetical protein; Validated

Probab=95.34  E-value=0.025  Score=40.21  Aligned_cols=79  Identities=20%  Similarity=0.194  Sum_probs=53.5

Q ss_pred             HH-HHHHHHhhCcchHHHHhh-c------cCCc---eEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCC
Q psy3003          13 DC-VLGEIEKLGQKYKVALRI-I------KDPR---FERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVP   81 (106)
Q Consensus        13 ~c-Vl~EL~~Lg~~~~~al~~-a------k~~~---~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~   81 (106)
                      .| |.+|+.+++.+++.-+-+ |      ..+.   .+.+-.+.....||+-|++.+.+.  -+|.|||-.|-.++-.. 
T Consensus         9 ACPVk~~i~r~a~r~~i~v~~Vas~n~~~~~~~~~~v~~v~V~~g~D~AD~~Iv~~~~~g--DiVIT~Di~LAa~~l~K-   85 (151)
T PRK00124          9 ACPVKDIIIRVAERHGIPVTLVASFNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKG--DIVITQDYGLAALALEK-   85 (151)
T ss_pred             CCcHHHHHHHHHHHHCCeEEEEEeCCcccCCCCCCceEEEEeCCCCChHHHHHHHhCCCC--CEEEeCCHHHHHHHHHC-
Confidence            35 899999998764332111 1      1111   122333222237999999999876  68899999999999995 


Q ss_pred             CccEEEEecceEE
Q psy3003          82 GVPIMYISQHRYT   94 (106)
Q Consensus        82 GVPviy~~~~~l~   94 (106)
                      |.-+|.-++..+.
T Consensus        86 ga~vl~prG~~yt   98 (151)
T PRK00124         86 GAIVLNPRGYIYT   98 (151)
T ss_pred             CCEEECCCCcCCC
Confidence            9999988876654

>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]

Probab=93.34  E-value=0.15  Score=40.44  Aligned_cols=80  Identities=20%  Similarity=0.239  Sum_probs=56.5

Q ss_pred             eeeecHHHHHHHHhhCcc--------hHHHHhhccC-----C-ceEEEecCCCC-CCHHHHHHHhhhcCCeEEEEecCHH
Q psy3003           8 IPYITDCVLGEIEKLGQK--------YKVALRIIKD-----P-RFERIPCMHKG-TYADDCIVNRVTQHKCYIVATCDKD   72 (106)
Q Consensus         8 ~~~vt~cVl~EL~~Lg~~--------~~~al~~ak~-----~-~~~~~~c~h~~-~~ad~ci~~~~~~~~~~iVaTqD~~   72 (106)
                      .++||+-|+.||..++..        =+.+|++...     + +.+++.-+-.+ ...|.=++.+++..+ ..|.|||-.
T Consensus       187 ~iiiP~FVL~ELQ~iADssD~lKR~RGRRGLdILn~iqk~~~~~v~I~~~Df~di~eVD~KLvklAk~~~-g~lvTND~N  265 (356)
T COG4956         187 TIIIPQFVLLELQHIADSSDDLKRNRGRRGLDILNEIQKEDPIQVEIYEGDFEDIPEVDSKLVKLAKVTG-GKLVTNDFN  265 (356)
T ss_pred             eEeeeHHHHHHHHHHhhccchhhhhcccchhHHHHHHHhhCCCcEEEccCCccchhhHHHHHHHHHHHhC-CEEEeccCc
Confidence            579999999999999743        2456666641     0 23333332111 267889999998874 789999999


Q ss_pred             HHHHHhcCCCccEEEEe
Q psy3003          73 LKRRIRKVPGVPIMYIS   89 (106)
Q Consensus        73 Lr~~Lr~i~GVPviy~~   89 (106)
                      |-+-..- -|||++.++
T Consensus       266 LnKVae~-qgV~vLNIN  281 (356)
T COG4956         266 LNKVAEL-QGVQVLNIN  281 (356)
T ss_pred             HHHHHhh-cCCceecHH
Confidence            9776654 599999877

>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function

Probab=93.29  E-value=0.11  Score=35.89  Aligned_cols=58  Identities=28%  Similarity=0.157  Sum_probs=45.2

Q ss_pred             ceEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEEEecceEEEee
Q psy3003          37 RFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIER   97 (106)
Q Consensus        37 ~~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~~l~lE~   97 (106)
                      ..+.+-++.....||.-|++.+.+.  -+|.|||-.|-.++-.. |+.+|.-++..+.-|+
T Consensus        28 ~~~~i~Vd~g~DaaD~~I~~~~~~g--DiVITqDigLA~~~l~K-ga~vl~~rG~~yt~~n   85 (130)
T PF02639_consen   28 YVEMIVVDSGFDAADFYIVNHAKPG--DIVITQDIGLASLLLAK-GAYVLNPRGKEYTKEN   85 (130)
T ss_pred             CeEEEEECCCCChHHHHHHHcCCCC--CEEEECCHHHHHHHHHC-CCEEECCCCCCCCHHH
Confidence            3455666543348999999999876  57889999999999995 9999988877665443

>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana

Probab=92.85  E-value=0.33  Score=34.54  Aligned_cols=39  Identities=31%  Similarity=0.429  Sum_probs=31.8

Q ss_pred             CCCHHHHHHHhhhc----CCeEEEEecCHHHHHHHhcCCCccEE
Q psy3003          47 GTYADDCIVNRVTQ----HKCYIVATCDKDLKRRIRKVPGVPIM   86 (106)
Q Consensus        47 ~~~ad~ci~~~~~~----~~~~iVaTqD~~Lr~~Lr~i~GVPvi   86 (106)
                      +.+||+.|.+++..    +....|+|.|..++...+.. |.-.+
T Consensus        76 ~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~~-GA~~i  118 (166)
T PF05991_consen   76 GETADDYIERLVRELKNRPRQVTVVTSDREIQRAARGR-GAKRI  118 (166)
T ss_pred             CCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhhC-CCEEE
Confidence            35899999999964    34699999999999999985 65544

The function of this family is unknown.

>PRK12496 hypothetical protein; Provisional

Probab=89.10  E-value=1.4  Score=31.45  Aligned_cols=80  Identities=14%  Similarity=0.167  Sum_probs=50.5

Q ss_pred             eeeecHHHHHHHHhhCcchHHHHhhccCC-ceEEEecCCC------------C-----CCHHHHHHHhhhcCCeEEEEec
Q psy3003           8 IPYITDCVLGEIEKLGQKYKVALRIIKDP-RFERIPCMHK------------G-----TYADDCIVNRVTQHKCYIVATC   69 (106)
Q Consensus         8 ~~~vt~cVl~EL~~Lg~~~~~al~~ak~~-~~~~~~c~h~------------~-----~~ad~ci~~~~~~~~~~iVaTq   69 (106)
                      +++||+-|++|+..-..  +..++.+... .+.+..=...            |     ..+|.-++.++...+ ..+.|.
T Consensus        21 ~i~tp~~V~~Ev~d~~~--~~~~~~l~~~~~i~v~~p~~~~i~~v~~~a~~tgd~~~Ls~~D~~~iaLA~el~-~~lvtD   97 (164)
T PRK12496         21 EHYTTPSVVEEVKDKES--RLILESAISAGKLKILEPSPESIEKVEEAAIKTGDLMRLSNTDIEVLALALELN-GTLYTD   97 (164)
T ss_pred             CEEecHHHHHHHhCHHH--HHHHHHhcccCCeEEECCCHHHHHHHHHHHHhcCCccccchhhHHHHHHHHHhC-CcEECc
Confidence            57999999999987322  2222333200 1333321110            0     134555666666554 689999


Q ss_pred             CHHHHHHHhcCCCccEEEEecc
Q psy3003          70 DKDLKRRIRKVPGVPIMYISQH   91 (106)
Q Consensus        70 D~~Lr~~Lr~i~GVPviy~~~~   91 (106)
                      |..+|+-++.. |++++-+++.
T Consensus        98 D~~~~~vA~~l-gi~v~~~~~~  118 (164)
T PRK12496         98 DYGIQNVAKKL-NIKFENIKTK  118 (164)
T ss_pred             HHHHHHHHHHc-CCeEeccccc
Confidence            99999999996 9999998843

>smart00500 SFM Splicing Factor Motif, present in Prp18 and Pr04

Probab=87.33  E-value=0.44  Score=27.17  Aligned_cols=21  Identities=33%  Similarity=0.632  Sum_probs=19.2

Q ss_pred             ecCHHHHHHHhcCCCccEEEEe
Q psy3003          68 TCDKDLKRRIRKVPGVPIMYIS   89 (106)
Q Consensus        68 TqD~~Lr~~Lr~i~GVPviy~~   89 (106)
                      |.|.+.+++||+. |=||.++-
T Consensus         1 ~~d~eV~~~LR~l-gePi~lFG   21 (44)
T smart00500        1 LPDSEVIRRLREL-GEPITLFG   21 (44)
T ss_pred             CCHHHHHHHHHHc-CCCeeecC
Confidence            6899999999997 99999886

>COG1656 Uncharacterized conserved protein [Function unknown]

Probab=83.80  E-value=2.6  Score=30.48  Aligned_cols=50  Identities=22%  Similarity=0.368  Sum_probs=39.5

Q ss_pred             ceEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHhcCCCccEEEEecce
Q psy3003          37 RFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHR   92 (106)
Q Consensus        37 ~~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~~~~   92 (106)
                      ++..+-++   ...|+=|..++.+++ -|+-|-|.+|-+|. +. |++.||++.+.
T Consensus        26 Gydt~~~~---~~~d~~i~~i~~~e~-rIllTRDr~L~~r~-k~-g~~~i~i~~~s   75 (165)
T COG1656          26 GYDTVYSS---NESDDEIILIAKKEG-RILLTRDRELYKRA-KL-GIKAILIRSDS   75 (165)
T ss_pred             CCceeeec---cCCcHHHHHHHhcCC-eEEEeccHHHHHHh-hc-cCceEEEeCCC
Confidence            45555453   256888888888875 88999999999999 64 99999999764

>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A

Probab=82.76  E-value=3.4  Score=26.74  Aligned_cols=36  Identities=17%  Similarity=0.351  Sum_probs=29.2

Q ss_pred             CHHHHHHHhhhcCCeEEEEecC-----HHHHHHHhcCCCccE
Q psy3003          49 YADDCIVNRVTQHKCYIVATCD-----KDLKRRIRKVPGVPI   85 (106)
Q Consensus        49 ~ad~ci~~~~~~~~~~iVaTqD-----~~Lr~~Lr~i~GVPv   85 (106)
                      .|.++|..+-..+.++++.||.     .++.++|++. |+++
T Consensus        18 ga~e~l~~L~~~g~~~~~lTNns~~s~~~~~~~L~~~-Gi~~   58 (101)
T PF13344_consen   18 GAVEALDALRERGKPVVFLTNNSSRSREEYAKKLKKL-GIPV   58 (101)
T ss_dssp             THHHHHHHHHHTTSEEEEEES-SSS-HHHHHHHHHHT-TTT-
T ss_pred             CHHHHHHHHHHcCCCEEEEeCCCCCCHHHHHHHHHhc-CcCC
Confidence            6889999888876689999999     4899999985 9984

...

---

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	106
1o4w_A	147	PIN (PILT N-terminus) domain; structural genomics,	7e-34

>1o4w_A PIN (PILT N-terminus) domain; structural genomics, joint CEN structural genomics, JCSG, protein structure initiative, PS translation; 1.90A {Archaeoglobus fulgidus} SCOP: c.120.1.1 Length = 147

 Score =  113 bits (284), Expect = 7e-34
 Identities = 21/103 (20%), Positives = 44/103 (42%), Gaps = 5/103 (4%)

Query: 1   MEQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKD---PRFERIPCMHKGTYADDCIVNR 57
           + +       IT  V  E+EKL    +   ++         E    +   +  D  ++  
Sbjct: 47  LREFGFSRFLITASVKRELEKLEMSLRGKEKVAARFALKLLEHFEVVETESEGDPSLIEA 106

Query: 58  VTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIERMPD 100
             ++ C I+ T DK+LKR+ ++  G+P+ Y+ + +     + D
Sbjct: 107 AEKYGC-ILITNDKELKRKAKQ-RGIPVGYLKEDKRVFVELLD 147

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	106
1o4w_A	147	PIN (PILT N-terminus) domain; structural genomics,	99.39
3ix7_A	134	Uncharacterized protein TTHA0540; unknown function	98.94
3i8o_A	142	KH domain-containing protein MJ1533; APC89320.5, m	98.55
2dok_A	186	Telomerase-binding protein EST1A; telomerase-assoc	98.09
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	93.58

>1o4w_A PIN (PILT N-terminus) domain; structural genomics, joint CEN structural genomics, JCSG, protein structure initiative, PS translation; 1.90A {Archaeoglobus fulgidus} SCOP: c.120.1.1

Probab=99.39  E-value=5.5e-13  Score=91.52  Aligned_cols=79  Identities=28%  Similarity=0.463  Sum_probs=68.9

Q ss_pred             ceeeecHHHHHHHHhhCc--------chHHHHhhccCCceEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHHHh
Q psy3003           7 GIPYITDCVLGEIEKLGQ--------KYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIR   78 (106)
Q Consensus         7 ~~~~vt~cVl~EL~~Lg~--------~~~~al~~ak~~~~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~Lr   78 (106)
                      .+++||.||+.||+.+..        ..+.++.+++  .++++.|+ .+ + |+||.+.+..++ ++++|+|++|+++++
T Consensus        53 ~~~~I~~~vl~EL~~~~~~~~~~~~~~~~~~~~ll~--~~~vv~~~-~~-~-D~~Ila~A~~~~-~~LvT~D~~l~~~a~  126 (147)
T 1o4w_A           53 SRFLITASVKRELEKLEMSLRGKEKVAARFALKLLE--HFEVVETE-SE-G-DPSLIEAAEKYG-CILITNDKELKRKAK  126 (147)
T ss_dssp             EEEEEEHHHHHHHHHHHHHCCHHHHHHHHHHHHHHT--TSEEECCS-SC-S-HHHHHHHHHHHT-CEEECCCHHHHHHHH
T ss_pred             CCEEEcHHHHHHHHHHHhccCcchHHHHHHHHHHHh--cCcEeeCC-CC-c-hHHHHHHHHHhC-CEEEECCHHHHHHHH
Confidence            689999999999998863        3456778888  78888887 44 6 999999998876 999999999999999


Q ss_pred             cCCCccEEEEecce
Q psy3003          79 KVPGVPIMYISQHR   92 (106)
Q Consensus        79 ~i~GVPviy~~~~~   92 (106)
                      .. |||++|+++++
T Consensus       127 ~~-Gv~vi~~~~~~  139 (147)
T 1o4w_A          127 QR-GIPVGYLKEDK  139 (147)
T ss_dssp             HT-TCCEECCCCCC
T ss_pred             HC-CCeEEEecCCc
Confidence            97 99999999876

>3ix7_A Uncharacterized protein TTHA0540; unknown function, thermus thermophilus HB8, structural genom 2, protein structure initiative; HET: MSE; 2.15A {Thermus thermophilus}

Probab=98.94  E-value=1.7e-09  Score=74.38  Aligned_cols=80  Identities=19%  Similarity=0.246  Sum_probs=63.0

Q ss_pred             eeeecHHHHHHHHhhCc--------chHHHHhhccCC----ceEEEecCCC-CCCHHHHHHHhhhcCCeEEEEecCHHHH
Q psy3003           8 IPYITDCVLGEIEKLGQ--------KYKVALRIIKDP----RFERIPCMHK-GTYADDCIVNRVTQHKCYIVATCDKDLK   74 (106)
Q Consensus         8 ~~~vt~cVl~EL~~Lg~--------~~~~al~~ak~~----~~~~~~c~h~-~~~ad~ci~~~~~~~~~~iVaTqD~~Lr   74 (106)
                      +++||++|++||+.++.        ..+.++++.+..    .+++.. .-. +..+|+-|++++.+.+ .+|.|||..|+
T Consensus        32 ~liIP~~Vl~ELq~lA~s~d~~~r~rGr~gL~iL~~L~~~~~vei~~-~~~~~~~vD~~ll~lA~~~~-~~lvTnD~~L~  109 (134)
T 3ix7_A           32 PLWVPHFVLKELQHFADSQDPLRRAKGRRGLETLERLREAAPLEVLE-TTPKGESVDEKLLFLARDLE-AALVTNDHALL  109 (134)
T ss_dssp             CEEEEHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHSCEEEEC-CCCSCSSHHHHHHHHHHHTT-CEEEESCHHHH
T ss_pred             ceecHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHhcCCEEEeC-CCCCcccHHHHHHHHHHHhC-CEEEeCCHHHH
Confidence            69999999999999973        246677777611    145554 211 2479999999999886 89999999999


Q ss_pred             HHHhcCCCccEEEEec
Q psy3003          75 RRIRKVPGVPIMYISQ   90 (106)
Q Consensus        75 ~~Lr~i~GVPviy~~~   90 (106)
                      +.++.. |||++|++.
T Consensus       110 kvA~~~-GI~Vl~l~~  124 (134)
T 3ix7_A          110 QMARIY-GVKALSIQA  124 (134)
T ss_dssp             HHHHHT-TCCEEEHHH
T ss_pred             HHHHHC-CCeEEehHH
Confidence            999995 999999873

>3i8o_A KH domain-containing protein MJ1533; APC89320.5, methanocaldococcus jannaschii DSM 2661, structural genomics, PSI-2; 2.64A {Methanocaldococcus jannaschii}

Probab=98.55  E-value=1.9e-07  Score=64.65  Aligned_cols=82  Identities=15%  Similarity=0.126  Sum_probs=62.1

Q ss_pred             ceeeecHHHHHHHHhhCcc----hHHHHhhccCCce-----------EEEecC-------C-CCCCHHHHHHHhhhcCCe
Q psy3003           7 GIPYITDCVLGEIEKLGQK----YKVALRIIKDPRF-----------ERIPCM-------H-KGTYADDCIVNRVTQHKC   63 (106)
Q Consensus         7 ~~~~vt~cVl~EL~~Lg~~----~~~al~~ak~~~~-----------~~~~c~-------h-~~~~ad~ci~~~~~~~~~   63 (106)
                      .+++||+.|++||+.++..    -+.||++++  ++           ++..-.       + .+..+|+-|++++.+.+ 
T Consensus        30 ~~iiIP~~Vl~EL~~~a~~~r~~GrrGLe~L~--~L~~~~~~~~i~vei~~~r~~~~~i~~~~~~~vD~~l~~lA~~~~-  106 (142)
T 3i8o_A           30 ATIIIPEAVVSELEYQANMGREIGYKGIEELR--KLIEKASEHNIKVEYYGERPTREEIFLAKSGEIDAMIRKVAKETN-  106 (142)
T ss_dssp             CEEEEEHHHHHHHHHHHTTTCHHHHHHHHHHH--HHHHHHHHTTCCEEEESCCCCHHHHHSCCSSSHHHHHHHHHHHTT-
T ss_pred             CeEEehHHHHHHHHHHHHccchhhHHHHHHHH--HHHHHhhccCceEEEecccCchhhhccccCCcHHHHHHHHHHHhC-
Confidence            3699999999999999753    345666665  33           222110       0 11368999999999885 


Q ss_pred             EEEEecCHHHHHHHhcCCCccEEEEecce
Q psy3003          64 YIVATCDKDLKRRIRKVPGVPIMYISQHR   92 (106)
Q Consensus        64 ~iVaTqD~~Lr~~Lr~i~GVPviy~~~~~   92 (106)
                      ..+.|||..|++.++.. |||++|+++..
T Consensus       107 a~lvTnD~~l~kvA~~~-GI~V~~l~~~~  134 (142)
T 3i8o_A          107 SILLTSDWIQYNLAKAQ-GIEAYFLEAAE  134 (142)
T ss_dssp             CEEEESCHHHHHHHHHT-TCCEEECCCCC
T ss_pred             CEEEcCCHHHHHHHHHc-CCEEEEecccc
Confidence            88999999999999995 99999998643

>2dok_A Telomerase-binding protein EST1A; telomerase-associated protein, unknown function; 1.80A {Homo sapiens} PDB: 2hww_A 2hwx_A

Probab=98.09  E-value=2.2e-06  Score=60.68  Aligned_cols=83  Identities=18%  Similarity=0.243  Sum_probs=56.5

Q ss_pred             cceeeecHHHHHHHHhhCc-----------------chHHHHhhccC------CceEE----------EecCCC-----C
Q psy3003           6 MGIPYITDCVLGEIEKLGQ-----------------KYKVALRIIKD------PRFER----------IPCMHK-----G   47 (106)
Q Consensus         6 ~~~~~vt~cVl~EL~~Lg~-----------------~~~~al~~ak~------~~~~~----------~~c~h~-----~   47 (106)
                      ...++||..|++||+.+.+                 .++.|+.+..+      +.+..          +...+.     .
T Consensus        37 ~~~viIP~~VleELd~lk~~~~~~~~~~~~~~~~~~~AR~a~~~L~~~~~~~~~~i~~~~~~g~~l~~v~~~~~~~~~~~  116 (186)
T 2dok_A           37 KYILVVPLIVINELDGLAKGQETDHRAGGYARVVQEKARKSIEFLEQRFESRDSCLRALTSRGNELESIAFRSEDITGQL  116 (186)
T ss_dssp             SSEEEEEHHHHHHHHHHHC-------CCHHHHHHHHHHHHHHHHHHHHHHTTCTTEEEECTTSCEESCCTTCCCCC----
T ss_pred             CeEEEECHHHHHHHHHhccCCCccccccchhHHHHHHHHHHHHHHHHHHhhCCCeEEEEeccCcccccccccccccccCC
Confidence            4789999999999999853                 34555554441      01110          001111     1


Q ss_pred             CCHHHHHHHhhhc--------------------CCeEEEEecCHHHHHHHhcCCCccEEEEe
Q psy3003          48 TYADDCIVNRVTQ--------------------HKCYIVATCDKDLKRRIRKVPGVPIMYIS   89 (106)
Q Consensus        48 ~~ad~ci~~~~~~--------------------~~~~iVaTqD~~Lr~~Lr~i~GVPviy~~   89 (106)
                      ...|+.|++.+..                    ....++.|+|..||.+.+.. |||+..++
T Consensus       117 ~~~D~~IL~~a~~l~~~~~~~~~~~~~~~~~~~~~~vvLvTnD~nLr~KA~~~-Gi~~~~~~  177 (186)
T 2dok_A          117 GNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRVKALTR-NVPVRDIP  177 (186)
T ss_dssp             CCHHHHHHHHHHTTCCCCGGGGCCC---CCCEEEEEEEEECCCHHHHHHHHHT-TCCEECHH
T ss_pred             CCccHHHHHHHHHHHHhcccccccccccccccCCCcEEEEeCcHHHHHHHHHC-CCeeCcHH
Confidence            3689999998863                    11478999999999999995 99998654

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}

Probab=93.58  E-value=0.031  Score=38.30  Aligned_cols=78  Identities=15%  Similarity=0.094  Sum_probs=51.8

Q ss_pred             eeeecHHHHHHHHhhCcchHHHHhhcc-CCceEEEe---------------cCCC-C-CCHHHHHHHhhhcCCeEEEEec
Q psy3003           8 IPYITDCVLGEIEKLGQKYKVALRIIK-DPRFERIP---------------CMHK-G-TYADDCIVNRVTQHKCYIVATC   69 (106)
Q Consensus         8 ~~~vt~cVl~EL~~Lg~~~~~al~~ak-~~~~~~~~---------------c~h~-~-~~ad~ci~~~~~~~~~~iVaTq   69 (106)
                      +++||..|++||....  .+..+.... ...+++..               -+.. . ..+|..++.++.+.+ ..|.|+
T Consensus        27 ~l~~p~~V~~El~~~~--~r~~l~~l~~~~~l~v~~~~~~~i~~v~~~~~~~gd~~~Ls~~D~~lIaLA~~l~-~~lvT~  103 (165)
T 2lcq_A           27 EGYTTPSVVEEIKDRE--SKIFLESLISAGKVKIAEPSKESIDRIIQVAKETGEVNELSKADIEVLALAYELK-GEIFSD  103 (165)
T ss_dssp             CEEECHHHHTTCCSSH--HHHHHHHHHHTTSEEECCCCHHHHHHHHHHHHHHSCSSCSCHHHHHHHHHHHHHT-CCEECC
T ss_pred             CEEEChhhHHhhcCHH--HHHHHHHhhccCCEEEecCCHHHHHHHHHHHHHcCCcccCCHHHHHHHHhHHHhC-CeEEcC
Confidence            6899999999996422  222333221 00132221               1110 1 247888999998765 688999


Q ss_pred             CHHHHHHHhcCCCccEEEEe
Q psy3003          70 DKDLKRRIRKVPGVPIMYIS   89 (106)
Q Consensus        70 D~~Lr~~Lr~i~GVPviy~~   89 (106)
                      |..||+.++.. ||+++.++
T Consensus       104 D~~l~~vA~~~-Gv~v~~~~  122 (165)
T 2lcq_A          104 DYNVQNIASLL-GLRFRTLK  122 (165)
T ss_dssp             CHHHHHHHHHT-TCCEECCS
T ss_pred             cHHHHHHHHHC-CCeEEchh
Confidence            99999999996 99999876

---

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	106
d1o4wa_	125	c.120.1.1 (A:) Hypothetical protein AF0591 {Archae	1e-23

>d1o4wa_ c.120.1.1 (A:) Hypothetical protein AF0591 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 125

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: PIN domain
domain: Hypothetical protein AF0591
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 85.3 bits (211), Expect = 1e-23
 Identities = 20/102 (19%), Positives = 44/102 (43%), Gaps = 6/102 (5%)

Query: 1   MEQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKD---PRFERIPCMHKGTYADDCIVNR 57
           + +       IT  V  E+EKL    +   ++         E    +   +  D  ++  
Sbjct: 26  LREFGFSRFLITASVKRELEKLEMSLRGKEKVAARFALKLLEHFEVVETESEGDPSLIEA 85

Query: 58  VTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRY-TIERM 98
             ++   I+ T DK+LKR+ ++  G+P+ Y+ + +   +E +
Sbjct: 86  AEKYG-CILITNDKELKRKAKQ-RGIPVGYLKEDKRVFVELL 125

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	106
d1o4wa_	125	Hypothetical protein AF0591 {Archaeon Archaeoglobu	99.87

>d1o4wa_ c.120.1.1 (A:) Hypothetical protein AF0591 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: PIN domain
domain: Hypothetical protein AF0591
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.87  E-value=7.4e-24  Score=142.24  Aligned_cols=85  Identities=27%  Similarity=0.471  Sum_probs=68.9

Q ss_pred             ccceeeecHHHHHHHHhhCcchHH--------HHhhccCCceEEEecCCCCCCHHHHHHHhhhcCCeEEEEecCHHHHHH
Q psy3003           5 QMGIPYITDCVLGEIEKLGQKYKV--------ALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRR   76 (106)
Q Consensus         5 g~~~~~vt~cVl~EL~~Lg~~~~~--------al~~ak~~~~~~~~c~h~~~~ad~ci~~~~~~~~~~iVaTqD~~Lr~~   76 (106)
                      |.++++||+||++||++|+++.++        +++.++  +++..   +.+.++||||+++++++ +|+|||||++||++
T Consensus        30 ~~~~~~ip~~Vi~EL~~L~~~~~~~~~~~~~~~l~~~~--~~~~~---~~~~~~Dd~il~~a~~~-~~iv~T~D~~Lr~~  103 (125)
T d1o4wa_          30 GFSRFLITASVKRELEKLEMSLRGKEKVAARFALKLLE--HFEVV---ETESEGDPSLIEAAEKY-GCILITNDKELKRK  103 (125)
T ss_dssp             TEEEEEEEHHHHHHHHHHHHHCCHHHHHHHHHHHHHHT--TSEEE---CCSSCSHHHHHHHHHHH-TCEEECCCHHHHHH
T ss_pred             cCceEEecHHHHHHHHHHHhcccHHHHHHHHHHHHHHH--hCCCC---CCCCcHHHHHHHHHhhC-CeEEEecCHHHHHH
Confidence            678999999999999999876433        444444  44433   33458999999999887 49999999999999


Q ss_pred             HhcCCCccEEEEecce-EEEe
Q psy3003          77 IRKVPGVPIMYISQHR-YTIE   96 (106)
Q Consensus        77 Lr~i~GVPviy~~~~~-l~lE   96 (106)
                      ++. +|||+||+++++ +.||
T Consensus       104 ~~~-~GVpvi~l~~~~~l~~~  123 (125)
T d1o4wa_         104 AKQ-RGIPVGYLKEDKRVFVE  123 (125)
T ss_dssp             HHH-TTCCEECCCCCCCCCCC
T ss_pred             HHH-cCCcEEEEeCCceEEEE
Confidence            998 899999999866 6666