Citrus Sinensis ID: 029889

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180------
Protein Sequence
MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIGIQ
Secondary Structure (PSIPRED)
cccccccccHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHccccccEEEEEccHHHHHHHHccccHHHHHHHHHccccEEEEcHHHHHHHHHHHHHHHHHHHHcccccEEEEccccccccHHHHHHHHHHcccEEEEEcccHHHHHHHHcccccEEEEEccccEEEEc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHcccccHHHHHHHHHcHHHHccccccccccccccccHHHHHHccccccccEEEEEcHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHcHHHHHHHHHHccccEEEcccccccccccHHHHHHHccccEEEEEEccHHHHHHHHccccccEEEEEEccEEEEc
Coil and Loop (DISEMBL)
mgkakkapkFAAMKKIITKRAIKNYkedvlnpnkkdltkekmprnvpnvssalffthntalgppyrvlvDTNFINFSIQNKLDLEKGMMdclyakctpciTDCVMAELEKLGQKYRVALRIakdprferlpcthkgtyaddclveRVTQHKCFIVATCDRDLKRRIRKvrstdlylgtafhdigiq
Flexible Loop (DISEMBL)
mgkakkapkfaamKKIITkraiknykedvlnpnkkdltkekmprnVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRiakdprferlpcthkgtyADDCLVERVTQhkcfivatcdrdlkrrirkvrstdlylgtafhdigiq
Low Complexity Region (SEG)
MGkakkapkfaamkkIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIGIQ
Disordered region (IsUnstruct)
**************KIITKRAIKNY***********************VSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIG**
Disordered Region (DISOPRED)
****KKAPKFAAMKKI**********************************SALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIGIQ
Disordered Region (DISEMBL)
MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIGIQ
Disordered Region (DISPRO)
********KFAAMKKIITKRAIKNYKED*LN*********KMPRN*PNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIGIQ
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIGIQ
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	186	2.2.26 [Sep-21-2011]
Q5RFQ0	198	rRNA-processing protein F	yes	no	0.908	0.853	0.701	8e-62
Q9Y324	198	rRNA-processing protein F	yes	no	0.908	0.853	0.701	8e-62
Q32PD0	198	rRNA-processing protein F	yes	no	0.908	0.853	0.701	8e-62
Q9CTH6	198	rRNA-processing protein F	yes	no	0.983	0.924	0.650	5e-61
Q05498	189	rRNA-processing protein F	yes	no	0.908	0.894	0.615	1e-56
O13610	192	rRNA-processing protein f	yes	no	0.994	0.963	0.564	6e-55
Q55GM5	194	rRNA-processing protein F	yes	no	0.876	0.840	0.530	1e-47
Q9BRU9	249	rRNA-processing protein U	no	no	0.612	0.457	0.296	1e-07
Q08DU1	248	rRNA-processing protein U	no	no	0.612	0.459	0.296	2e-07
O74862	260	rRNA-processing protein u	no	no	0.612	0.438	0.293	4e-07

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

 Score =  236 bits (601), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 120/171 (70%), Positives = 137/171 (80%), Gaps = 2/171 (1%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKM--PRNVPNVSSALFFTHN 58
           MGK KK  K+A MK++++ R  +  ++D L P KK+         R VP   S LFF +N
Sbjct: 1   MGKQKKTRKYATMKRMLSLRDQRLKEKDRLKPKKKEKKDPSALKEREVPQHPSCLFFQYN 60

Query: 59  TALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVA 118
           T LGPPY +LVDTNFINFSI+ KLDL + MMDCLYAKC PCITDCVMAE+EKLGQKYRVA
Sbjct: 61  TQLGPPYHILVDTNFINFSIKAKLDLVQSMMDCLYAKCIPCITDCVMAEIEKLGQKYRVA 120

Query: 119 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           LRIAKDPRFERLPCTHKGTYADDCLV+RVTQHKC+IVAT DRDLKRRIRK+
Sbjct: 121 LRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATVDRDLKRRIRKI 171

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 =  236 bits (601), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 120/171 (70%), Positives = 137/171 (80%), Gaps = 2/171 (1%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKM--PRNVPNVSSALFFTHN 58
           MGK KK  K+A MK++++ R  +  ++D L P KK+         R VP   S LFF +N
Sbjct: 1   MGKQKKTRKYATMKRMLSLRDQRLKEKDRLKPKKKEKKDPSALKEREVPQHPSCLFFQYN 60

Query: 59  TALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVA 118
           T LGPPY +LVDTNFINFSI+ KLDL + MMDCLYAKC PCITDCVMAE+EKLGQKYRVA
Sbjct: 61  TQLGPPYHILVDTNFINFSIKAKLDLVQSMMDCLYAKCIPCITDCVMAEIEKLGQKYRVA 120

Query: 119 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           LRIAKDPRFERLPCTHKGTYADDCLV+RVTQHKC+IVAT DRDLKRRIRK+
Sbjct: 121 LRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATVDRDLKRRIRKI 171

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 =  236 bits (601), Expect = 8e-62,   Method: Compositional matrix adjust.
 Identities = 120/171 (70%), Positives = 137/171 (80%), Gaps = 2/171 (1%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKM--PRNVPNVSSALFFTHN 58
           MGK KK  K+A MK++++ R  +  ++D L P KK+         R VP   S LFF +N
Sbjct: 1   MGKQKKTRKYATMKRMLSLRDQRLKEKDRLKPKKKEKKDPSALKEREVPQHPSCLFFQYN 60

Query: 59  TALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVA 118
           T LGPPY +LVDTNFINFSI+ KLDL + MMDCLYAKC PCITDCVMAE+EKLGQKYRVA
Sbjct: 61  TQLGPPYHILVDTNFINFSIKAKLDLVQSMMDCLYAKCIPCITDCVMAEIEKLGQKYRVA 120

Query: 119 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           LRIAKDPRFERLPCTHKGTYADDCLV+RVTQHKC+IVAT DRDLKRRIRK+
Sbjct: 121 LRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATVDRDLKRRIRKI 171

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 =  233 bits (594), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 121/186 (65%), Positives = 143/186 (76%), Gaps = 3/186 (1%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKM--PRNVPNVSSALFFTHN 58
           MGK KK  K+A MK++++ R  +  ++D L P KK+         R VP   S LFF +N
Sbjct: 1   MGKQKKTRKYATMKRMLSLRDERLKEKDRLKPKKKEKKDPSALKEREVPQHPSCLFFQYN 60

Query: 59  TALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVA 118
           T LGPPY +LVDTNFINFSI+ KLDL + MMDCLYAKC PCITDCVMAE+EKLGQK+RVA
Sbjct: 61  TQLGPPYHILVDTNFINFSIKAKLDLVQSMMDCLYAKCIPCITDCVMAEIEKLGQKFRVA 120

Query: 119 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTD-LYLG 177
           LRIAKDPRF+RLPCTHKGTYADDCLV+RVTQHKC+IVAT DRDLKRRIRK+     +YL 
Sbjct: 121 LRIAKDPRFDRLPCTHKGTYADDCLVQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYLS 180

Query: 178 TAFHDI 183
              ++I
Sbjct: 181 NHRYNI 186

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

Mus musculus (taxid: 10090)

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

 Score =  218 bits (556), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 109/177 (61%), Positives = 135/177 (76%), Gaps = 8/177 (4%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDL-TKE--KMPRNVPNVSSALFFTH 57
           MGKAKK  KF      + KR +   K+  L  N++++ TKE  ++ RN+P VSSALFF +
Sbjct: 1   MGKAKKTRKFG-----LVKRTLNTKKDQRLKKNQENIKTKEDPELTRNIPQVSSALFFQY 55

Query: 58  NTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRV 117
           N A+ PPY+VL+DTNFINFSIQ K+D+ +GMMDCL AKC P ITDCVMAELEKLG KYR+
Sbjct: 56  NQAIKPPYQVLIDTNFINFSIQKKVDIVRGMMDCLLAKCNPLITDCVMAELEKLGPKYRI 115

Query: 118 ALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDL 174
           AL++A+DPR +RL C+HKGTYADDCLV RV QHKC+IVAT D  LK+RIRK+    L
Sbjct: 116 ALKLARDPRIKRLSCSHKGTYADDCLVHRVLQHKCYIVATNDAGLKQRIRKIPGIPL 172

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

 Score =  213 bits (542), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 105/186 (56%), Positives = 138/186 (74%), Gaps = 1/186 (0%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTA 60
           MGKAK   KFA +K++I  +  +  K+D     +K     ++ R +P ++S LFF  N +
Sbjct: 1   MGKAKTTRKFAQVKRVINLKDQRLQKKDQKKEKEKTTKNGELVREIPQMASNLFFQFNES 60

Query: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120
           LGPPY V++DTNFINF +Q K+DL +G+M CLYAK  PCI+DCVMAELEKLG +YR+ALR
Sbjct: 61  LGPPYHVIIDTNFINFCLQQKIDLFEGLMTCLYAKTIPCISDCVMAELEKLGIRYRIALR 120

Query: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAF 180
           IAKD RFERLPCTHKGTYADDC+V+RV QHKC++VAT D++LK+RIRK+    + L  A 
Sbjct: 121 IAKDERFERLPCTHKGTYADDCIVQRVMQHKCYLVATNDKNLKQRIRKIPGIPI-LSVAN 179

Query: 181 HDIGIQ 186
           H I ++
Sbjct: 180 HKIRVE 185

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

 Score =  189 bits (480), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 87/164 (53%), Positives = 123/164 (75%), Gaps = 1/164 (0%)

Query: 7   APKFAAMKKI-ITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPY 65
           APK   ++K+  T     N ++ +    ++D  ++K+     + +S +FF++N AL PPY
Sbjct: 8   APKKVPLQKLNKTNPNFSNRQKQIQRSKQEDEHRKKLEEIPEDNTSHMFFSYNEALVPPY 67

Query: 66  RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDP 125
            V++DTNFINFSI +KLD+   +MDCLYAKC P I+DCV AE+E+LG K++VAL+I+KDP
Sbjct: 68  HVIIDTNFINFSISHKLDIIHSLMDCLYAKCIPYISDCVAAEIERLGSKFKVALKISKDP 127

Query: 126 RFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           RF+RL C+HKGTYADDC++ R+T H+ FIVATCD DL+RRIRK+
Sbjct: 128 RFQRLTCSHKGTYADDCIINRITMHRMFIVATCDADLRRRIRKI 171

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

Dictyostelium discoideum (taxid: 44689)

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

 Score = 56.2 bits (134), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 58/118 (49%), Gaps = 4/118 (3%)

Query: 54  FFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ 113
           FF +N  +  PY++L+D  F   +++ ++ L + +   L  +   C T CV+ ELE LG+
Sbjct: 15  FFRNNFGVREPYQILLDGTFCQAALRGRIQLREQLPRYLMGETQLCTTRCVLKELETLGK 74

Query: 114 KYRVALRIAKDPRFERLPCTHKGTYADDCL---VERVTQHKCFIVATCDRDLKRRIRK 168
               A  IA+  +    P         +CL   VE    H  F VAT D++L  +++K
Sbjct: 75  DLYGAKLIAQKCQVRNCPHFKNAVSGSECLLSMVEEGNPHHYF-VATQDQNLSVKVKK 131

Involved in rRNA-processing and ribosome biogenesis.

Homo sapiens (taxid: 9606)

>sp|Q08DU1|UTP23_BOVIN rRNA-processing protein UTP23 homolog OS=Bos taurus GN=UTP23 PE=2 SV=1

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 59/118 (50%), Gaps = 4/118 (3%)

Query: 54  FFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ 113
           FF +N  +  PY++L+D  F   +++ ++ L + +   L A+   C T CV+ ELE LG+
Sbjct: 15  FFRNNFGVREPYQILLDGTFCQAALRGRIQLREQLPRYLMAETQLCTTRCVLKELETLGK 74

Query: 114 KYRVALRIAKDPRFERLPCTHKGTYADDCL---VERVTQHKCFIVATCDRDLKRRIRK 168
               A  IA+  +    P         +CL   VE    H  F+ AT D++L  +++K
Sbjct: 75  DLYGAKLIAQKCQVRNCPHFKNAVSGSECLLSMVEDGNPHHYFL-ATQDQNLSMKVKK 131

Involved in rRNA-processing and ribosome biogenesis.

Bos taurus (taxid: 9913)

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

 Score = 54.7 bits (130), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 37/126 (29%), Positives = 62/126 (49%), Gaps = 12/126 (9%)

Query: 53  LFFTHNTALG--PPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEK 110
           L  T+    G   PY+VLVD +F+    Q K+D++  +   +     P IT C + +L  
Sbjct: 12  LMHTYQLLFGFREPYQVLVDADFLKDLSQQKIDIQAALARTVQGAIKPMITQCCIRQLYS 71

Query: 111 LGQKYRVALRIAKDPRFERLPCTH--KGTYADDCLVERV-----TQHKCFIVATCDRDLK 163
              + +  +RIAK   FER  C H  +     +C+   V      +H+ ++VAT D +L+
Sbjct: 72  KSDELKQEIRIAKS--FERRRCGHIDEALSPSECIQSVVNINGRNKHR-YVVATQDPELR 128

Query: 164 RRIRKV 169
           + +R V
Sbjct: 129 QALRSV 134

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	186
449437727	198	PREDICTED: rRNA-processing protein FCF1	0.908	0.853	0.899	2e-86
356543662	198	PREDICTED: rRNA-processing protein FCF1	0.908	0.853	0.887	2e-84
255638538	198	unknown [Glycine max]	0.908	0.853	0.887	3e-84
294461424	198	unknown [Picea sitchensis]	0.908	0.853	0.875	1e-83
388522413	198	unknown [Lotus japonicus]	0.908	0.853	0.869	4e-83
356504145	216	PREDICTED: LOW QUALITY PROTEIN: rRNA-pro	0.908	0.782	0.869	6e-83
224130438	198	predicted protein [Populus trichocarpa]	0.908	0.853	0.857	1e-82
115466536	199	Os06g0158600 [Oryza sativa Japonica Grou	0.908	0.849	0.876	4e-82
224067950	198	predicted protein [Populus trichocarpa]	0.908	0.853	0.852	4e-82
226529278	199	uncharacterized protein LOC100272977 [Ze	0.908	0.849	0.876	2e-81

>gi|449437727|ref|XP_004136642.1| PREDICTED: rRNA-processing protein FCF1 homolog [Cucumis sativus] gi|449511643|ref|XP_004164015.1| PREDICTED: rRNA-processing protein FCF1 homolog [Cucumis sativus]

 Score =  323 bits (828), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 152/169 (89%), Positives = 162/169 (95%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTA 60
           MG+AKK PKFA MKK++T +AIKNYKE+VLNP +KDLTKE +PRNVPNV SALFF +NTA
Sbjct: 1   MGRAKKGPKFAVMKKMVTSKAIKNYKEEVLNPKRKDLTKENLPRNVPNVPSALFFKYNTA 60

Query: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120
           LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELE+LGQKYRVALR
Sbjct: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELERLGQKYRVALR 120

Query: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           IAKDPRFERLPCTHKGTYADDCLVERVTQHKC+IVATCDRDLKRRIRKV
Sbjct: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCYIVATCDRDLKRRIRKV 169

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543662|ref|XP_003540279.1| PREDICTED: rRNA-processing protein FCF1 homolog [Glycine max] gi|356550034|ref|XP_003543395.1| PREDICTED: rRNA-processing protein FCF1 homolog [Glycine max]

 Score =  316 bits (810), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 150/169 (88%), Positives = 160/169 (94%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTA 60
           MGKAKK PKFA MKKI+T +AIK+YKE+VLNP KK+L KEK+PRNVP  SSALFF +NTA
Sbjct: 1   MGKAKKGPKFAVMKKIVTSKAIKSYKEEVLNPEKKNLMKEKLPRNVPTHSSALFFQYNTA 60

Query: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120
           LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR
Sbjct: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120

Query: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           IAKDPRFER+ CTHKGTYADDCLVERVTQHKC+IVATCDRDLKRRIRK+
Sbjct: 121 IAKDPRFERILCTHKGTYADDCLVERVTQHKCYIVATCDRDLKRRIRKI 169

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255638538|gb|ACU19577.1| unknown [Glycine max]

 Score =  316 bits (809), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 150/169 (88%), Positives = 160/169 (94%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTA 60
           MGKAKK PKFA MKKI+T +AIK+YKE+VLNP KK+L KEK+PRNVP  SSALFF +NTA
Sbjct: 1   MGKAKKGPKFAVMKKIVTSKAIKSYKEEVLNPEKKNLMKEKLPRNVPTHSSALFFQYNTA 60

Query: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120
           LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR
Sbjct: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120

Query: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           IAKDPRFER+ CTHKGTYADDCLVERVTQHKC+IVATCDRDLKRRIRK+
Sbjct: 121 IAKDPRFERILCTHKGTYADDCLVERVTQHKCYIVATCDRDLKRRIRKI 169

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294461424|gb|ADE76273.1| unknown [Picea sitchensis]

 Score =  314 bits (804), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 148/169 (87%), Positives = 159/169 (94%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTA 60
           MGK+KK PKFA MK II+ +AIK YKE+VLNPNKK+  K+K+PRNVPNVSSALFF +NTA
Sbjct: 1   MGKSKKTPKFAKMKSIISSKAIKKYKEEVLNPNKKNAEKQKLPRNVPNVSSALFFKYNTA 60

Query: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120
           LGPPY VLVDTNFINFSIQNKLDLEK MMDCLYAKCTPCITDCVMAELEKLGQKYRVALR
Sbjct: 61  LGPPYLVLVDTNFINFSIQNKLDLEKAMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120

Query: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           IAKDPRFERLPCTH+GTYADDCLVERVTQHKC+IVATCDRDLKRRIRK+
Sbjct: 121 IAKDPRFERLPCTHEGTYADDCLVERVTQHKCYIVATCDRDLKRRIRKI 169

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388522413|gb|AFK49268.1| unknown [Lotus japonicus]

 Score =  312 bits (799), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 147/169 (86%), Positives = 159/169 (94%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTA 60
           MGKAKK PKFA  KK++T +AIKNYKE+VLNP KK+L KEK+PRN+P+ SSALFF +NTA
Sbjct: 1   MGKAKKGPKFAVRKKLVTSKAIKNYKEEVLNPEKKNLLKEKLPRNIPSYSSALFFQYNTA 60

Query: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120
           LGPPYRVLVDTNFINFSIQNKLDLEKGMM CLYAKCTPCITDCVMAELEKLGQKYRVALR
Sbjct: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMGCLYAKCTPCITDCVMAELEKLGQKYRVALR 120

Query: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           IAKDPRFER+ CTHKGTYADDCLVERVTQHKC+IVATCDRDLKRRIRK+
Sbjct: 121 IAKDPRFERILCTHKGTYADDCLVERVTQHKCYIVATCDRDLKRRIRKI 169

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504145|ref|XP_003520859.1| PREDICTED: LOW QUALITY PROTEIN: rRNA-processing protein FCF1 homolog [Glycine max]

 Score =  311 bits (798), Expect = 6e-83,   Method: Compositional matrix adjust.
 Identities = 147/169 (86%), Positives = 158/169 (93%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTA 60
           MGKAKK PKFA MKK +T +AIKNYKE VLNP KK+L KEK+PRN+P+ SSALFF +NTA
Sbjct: 1   MGKAKKGPKFAVMKKAVTSKAIKNYKEKVLNPEKKNLLKEKLPRNIPSHSSALFFQYNTA 60

Query: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120
           LGPPYR+LVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR
Sbjct: 61  LGPPYRILVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120

Query: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           IAKDPRFER+ CTHKG YADDCLVERVTQHKC+IVATCDRDLKRRIRK+
Sbjct: 121 IAKDPRFERILCTHKGMYADDCLVERVTQHKCYIVATCDRDLKRRIRKI 169

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130438|ref|XP_002320837.1| predicted protein [Populus trichocarpa] gi|222861610|gb|EEE99152.1| predicted protein [Populus trichocarpa]

 Score =  311 bits (796), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 145/169 (85%), Positives = 160/169 (94%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTA 60
           MG+AKK PKFA MKK+IT +AIK +KE+VLNP KKDL+ EK+PRNVP VSSAL+F++NTA
Sbjct: 1   MGRAKKGPKFAKMKKMITSKAIKQHKEEVLNPKKKDLSLEKLPRNVPQVSSALYFSYNTA 60

Query: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120
           LGPPYRVLVDTNFINFSIQNKLDLEK M+DCLYAKCTPCITDCVMAELEKLGQKYRVALR
Sbjct: 61  LGPPYRVLVDTNFINFSIQNKLDLEKAMLDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120

Query: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           IAKDPRFERLPC HKGTYADDC+VERVT+HKC+IVATCDRDLKRRIRK+
Sbjct: 121 IAKDPRFERLPCIHKGTYADDCIVERVTKHKCYIVATCDRDLKRRIRKI 169

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115466536|ref|NP_001056867.1| Os06g0158600 [Oryza sativa Japonica Group] gi|55296600|dbj|BAD69198.1| unknown protein [Oryza sativa Japonica Group] gi|113594907|dbj|BAF18781.1| Os06g0158600 [Oryza sativa Japonica Group] gi|215715283|dbj|BAG95034.1| unnamed protein product [Oryza sativa Japonica Group] gi|215765556|dbj|BAG87253.1| unnamed protein product [Oryza sativa Japonica Group] gi|218197628|gb|EEC80055.1| hypothetical protein OsI_21758 [Oryza sativa Indica Group] gi|222634998|gb|EEE65130.1| hypothetical protein OsJ_20200 [Oryza sativa Japonica Group]

 Score =  309 bits (791), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 149/170 (87%), Positives = 160/170 (94%), Gaps = 1/170 (0%)

Query: 1   MGKAK-KAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNT 59
           MG+AK K PKFAA+KKIITK+ I+ YKEDVLNP KKD  KEK+ RNVP VSSALFF++NT
Sbjct: 1   MGRAKSKGPKFAAVKKIITKKTIQKYKEDVLNPKKKDNEKEKLGRNVPQVSSALFFSYNT 60

Query: 60  ALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVAL 119
           ALGPPYRV+VDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVAL
Sbjct: 61  ALGPPYRVIVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVAL 120

Query: 120 RIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           RIAKDPRF+RL CTHKGTYADDC+VERVTQHKC+IVATCDRDLKRRIRKV
Sbjct: 121 RIAKDPRFQRLACTHKGTYADDCIVERVTQHKCYIVATCDRDLKRRIRKV 170

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224067950|ref|XP_002302614.1| predicted protein [Populus trichocarpa] gi|222844340|gb|EEE81887.1| predicted protein [Populus trichocarpa]

 Score =  309 bits (791), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 144/169 (85%), Positives = 158/169 (93%)

Query: 1   MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTA 60
           MG+AKK PKFA MK +IT RAIK +KE+VLNP K+DL  EK+PRNVP VSSALFF++NTA
Sbjct: 1   MGRAKKGPKFAKMKTMITSRAIKQHKEEVLNPKKRDLYLEKLPRNVPQVSSALFFSYNTA 60

Query: 61  LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120
           LGPPYRVLVDTNFINFSIQNKLDLEK M+DCLYAKCTPCITDCVMAELEKLGQKYRVALR
Sbjct: 61  LGPPYRVLVDTNFINFSIQNKLDLEKAMLDCLYAKCTPCITDCVMAELEKLGQKYRVALR 120

Query: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           IAKDPRFERLPC HKGTYADDC+VERVT+HKC++VATCDRDLKRRIRK+
Sbjct: 121 IAKDPRFERLPCVHKGTYADDCIVERVTKHKCYVVATCDRDLKRRIRKI 169

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226529278|ref|NP_001140900.1| uncharacterized protein LOC100272977 [Zea mays] gi|194701666|gb|ACF84917.1| unknown [Zea mays] gi|195620862|gb|ACG32261.1| nucleolar protein involved in pre-mRNA processing [Zea mays]

 Score =  306 bits (785), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 149/170 (87%), Positives = 159/170 (93%), Gaps = 1/170 (0%)

Query: 1   MGKAK-KAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNT 59
           MGKAK K PKFAA+KKIITK+ I  YKEDVLN  KKD+ KEK+ RNVP VSSALFF++NT
Sbjct: 1   MGKAKSKGPKFAAVKKIITKKTINKYKEDVLNHKKKDVDKEKLGRNVPQVSSALFFSYNT 60

Query: 60  ALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVAL 119
           ALGPPYRV+VDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVAL
Sbjct: 61  ALGPPYRVIVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVAL 120

Query: 120 RIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           RIAKDPRF+RL CTHKGTYADDC+VERVTQHKC+IVATCDRDLKRRIRKV
Sbjct: 121 RIAKDPRFQRLACTHKGTYADDCIVERVTQHKCYIVATCDRDLKRRIRKV 170

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

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	186
TAIR|locus:2062902	196	AT2G46230 "AT2G46230" [Arabido	0.817	0.775	0.824	2.1e-68
UNIPROTKB|Q32PD0	198	FCF1 "rRNA-processing protein	0.849	0.797	0.695	1.2e-56
UNIPROTKB|Q9Y324	198	FCF1 "rRNA-processing protein	0.849	0.797	0.695	1.2e-56
MGI|MGI:1920986	198	Fcf1 "FCF1 small subunit (SSU)	0.849	0.797	0.689	4.2e-56
ZFIN|ZDB-GENE-050417-67	198	fcf1 "FCF1 small subunit (SSU)	0.801	0.752	0.688	4.9e-53
SGD|S000002747	189	FCF1 "Putative PINc domain nuc	0.822	0.809	0.641	5.6e-52
TAIR|locus:2197885	178	AT1G26530 "AT1G26530" [Arabido	0.387	0.404	0.743	2.9e-50
POMBASE|SPBC32H8.04c	192	SPBC32H8.04c "rRNA processing	0.881	0.854	0.590	3.6e-50
FB|FBgn0010520	200	Bka "Bekka" [Drosophila melano	0.731	0.68	0.700	9.5e-50
CGD|CAL0003244	201	orf19.3220 [Candida albicans (	0.693	0.641	0.705	1.1e-48

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

 Score = 694 (249.4 bits), Expect = 2.1e-68, P = 2.1e-68
 Identities = 127/154 (82%), Positives = 143/154 (92%)

Query:    16 IITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFIN 75
             +I+ +A+K+YKE+VLNPNKKDLT+  +PRNVP+V + LFF++N+ L PPYRVLVDTNFIN
Sbjct:    16 MISHKALKHYKEEVLNPNKKDLTE--LPRNVPSVPAGLFFSYNSTLVPPYRVLVDTNFIN 73

Query:    76 FSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHK 135
             FSIQNK+DLEKGM DCLYA CTPCITDCVMAELEKLGQKYRVALRIAKDP FERLPC HK
Sbjct:    74 FSIQNKIDLEKGMRDCLYANCTPCITDCVMAELEKLGQKYRVALRIAKDPHFERLPCIHK 133

Query:   136 GTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
             GTYADDCLV+RVTQHKCFIVATCDRDLKRRIRK+
Sbjct:   134 GTYADDCLVDRVTQHKCFIVATCDRDLKRRIRKI 167

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0051604 "protein maturation" evidence=RCA

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

 Score = 583 (210.3 bits), Expect = 1.2e-56, P = 1.2e-56
 Identities = 112/161 (69%), Positives = 127/161 (78%)

Query:    26 KEDVLNPNKKDLTKEKM--PRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLD 83
             ++D L P KK+         R VP   S LFF +NT LGPPY +LVDTNFINFSI+ KLD
Sbjct:    26 EKDRLKPKKKEKKDPSALKEREVPQHPSCLFFQYNTQLGPPYHILVDTNFINFSIKAKLD 85

Query:    84 LEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCL 143
             L + MMDCLYAKC PCITDCVMAE+EKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCL
Sbjct:    86 LVQSMMDCLYAKCIPCITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCL 145

Query:   144 VERVTQHKCFIVATCDRDLKRRIRKVRSTDL-YLGTAFHDI 183
             V+RVTQHKC+IVAT DRDLKRRIRK+    + Y+    ++I
Sbjct:   146 VQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYISNHRYNI 186

GO:0005730 "nucleolus" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

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

 Score = 583 (210.3 bits), Expect = 1.2e-56, P = 1.2e-56
 Identities = 112/161 (69%), Positives = 127/161 (78%)

Query:    26 KEDVLNPNKKDLTKEKM--PRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLD 83
             ++D L P KK+         R VP   S LFF +NT LGPPY +LVDTNFINFSI+ KLD
Sbjct:    26 EKDRLKPKKKEKKDPSALKEREVPQHPSCLFFQYNTQLGPPYHILVDTNFINFSIKAKLD 85

Query:    84 LEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCL 143
             L + MMDCLYAKC PCITDCVMAE+EKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCL
Sbjct:    86 LVQSMMDCLYAKCIPCITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCL 145

Query:   144 VERVTQHKCFIVATCDRDLKRRIRKVRSTDL-YLGTAFHDI 183
             V+RVTQHKC+IVAT DRDLKRRIRK+    + Y+    ++I
Sbjct:   146 VQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYISNHRYNI 186

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 = 578 (208.5 bits), Expect = 4.2e-56, P = 4.2e-56
 Identities = 111/161 (68%), Positives = 127/161 (78%)

Query:    26 KEDVLNPNKKDLTKEKM--PRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLD 83
             ++D L P KK+         R VP   S LFF +NT LGPPY +LVDTNFINFSI+ KLD
Sbjct:    26 EKDRLKPKKKEKKDPSALKEREVPQHPSCLFFQYNTQLGPPYHILVDTNFINFSIKAKLD 85

Query:    84 LEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCL 143
             L + MMDCLYAKC PCITDCVMAE+EKLGQK+RVALRIAKDPRF+RLPCTHKGTYADDCL
Sbjct:    86 LVQSMMDCLYAKCIPCITDCVMAEIEKLGQKFRVALRIAKDPRFDRLPCTHKGTYADDCL 145

Query:   144 VERVTQHKCFIVATCDRDLKRRIRKVRSTDL-YLGTAFHDI 183
             V+RVTQHKC+IVAT DRDLKRRIRK+    + YL    ++I
Sbjct:   146 VQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYLSNHRYNI 186

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 = 549 (198.3 bits), Expect = 4.9e-53, P = 4.9e-53
 Identities = 104/151 (68%), Positives = 122/151 (80%)

Query:    34 KKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLY 93
             K+D +  K  + +    S LFF +NT LGPPY +LVDTNFINFSI+ KLD+ + MMDCLY
Sbjct:    37 KEDPSAIK-EQEIAKYPSCLFFQYNTQLGPPYYILVDTNFINFSIKAKLDVVQSMMDCLY 95

Query:    94 AKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCF 153
             AKC PCITDCVMAELEKLG KYRVALRIAKDPRF+RLPC+HKGTYADDCLV+RVTQHKC+
Sbjct:    96 AKCVPCITDCVMAELEKLGMKYRVALRIAKDPRFDRLPCSHKGTYADDCLVQRVTQHKCY 155

Query:   154 IVATCDRDLKRRIRKVRSTDL-YLGTAFHDI 183
             IVAT DRDLKRRIRK+    + Y+    ++I
Sbjct:   156 IVATVDRDLKRRIRKIPGVPIMYISNHRYNI 186

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

SGD|S000002747 FCF1 "Putative PINc domain nuclease" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 539 (194.8 bits), Expect = 5.6e-52, P = 5.6e-52
 Identities = 100/156 (64%), Positives = 126/156 (80%)

Query:    17 ITKRAIKNYKEDVLNPNKKDL-TKE--KMPRNVPNVSSALFFTHNTALGPPYRVLVDTNF 73
             + KR +   K+  L  N++++ TKE  ++ RN+P VSSALFF +N A+ PPY+VL+DTNF
Sbjct:    12 LVKRTLNTKKDQRLKKNQENIKTKEDPELTRNIPQVSSALFFQYNQAIKPPYQVLIDTNF 71

Query:    74 INFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCT 133
             INFSIQ K+D+ +GMMDCL AKC P ITDCVMAELEKLG KYR+AL++A+DPR +RL C+
Sbjct:    72 INFSIQKKVDIVRGMMDCLLAKCNPLITDCVMAELEKLGPKYRIALKLARDPRIKRLSCS 131

Query:   134 HKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
             HKGTYADDCLV RV QHKC+IVAT D  LK+RIRK+
Sbjct:   132 HKGTYADDCLVHRVLQHKCYIVATNDAGLKQRIRKI 167

GO:0032040 "small-subunit processome" evidence=IDA;IPI

GO:0006364 "rRNA processing" 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=IMP

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA;IDA

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

TAIR|locus:2197885 AT1G26530 "AT1G26530" [Arabidopsis thaliana (taxid:3702)]

 Score = 292 (107.8 bits), Expect = 2.9e-50, Sum P(2) = 2.9e-50
 Identities = 55/74 (74%), Positives = 68/74 (91%)

Query:    16 IITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFIN 75
             +I+ +A+K+YKE+VLNPNKKDLT+  +PRNVP+V S LFF+HN++L PPYRVLVDTNFIN
Sbjct:    16 MISHKALKHYKEEVLNPNKKDLTE--LPRNVPSVPSGLFFSHNSSLVPPYRVLVDTNFIN 73

Query:    76 FSIQNKLDLEKGMM 89
             FSIQNK+DLEKGMM
Sbjct:    74 FSIQNKIDLEKGMM 87

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0009855 "determination of bilateral symmetry" evidence=RCA

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=RCA

GO:0010014 "meristem initiation" evidence=RCA

GO:0010075 "regulation of meristem growth" evidence=RCA

POMBASE|SPBC32H8.04c SPBC32H8.04c "rRNA processing protein Fcf1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 522 (188.8 bits), Expect = 3.6e-50, P = 3.6e-50
 Identities = 104/176 (59%), Positives = 130/176 (73%)

Query:    19 KRAIKNYKEDVLNPNKKDLTKEK--------MPRNVPNVSSALFFTHNTALGPPYRVLVD 70
             KR I N K+  L   KKD  KEK        + R +P ++S LFF  N +LGPPY V++D
Sbjct:    14 KRVI-NLKDQRLQ--KKDQKKEKEKTTKNGELVREIPQMASNLFFQFNESLGPPYHVIID 70

Query:    71 TNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERL 130
             TNFINF +Q K+DL +G+M CLYAK  PCI+DCVMAELEKLG +YR+ALRIAKD RFERL
Sbjct:    71 TNFINFCLQQKIDLFEGLMTCLYAKTIPCISDCVMAELEKLGIRYRIALRIAKDERFERL 130

Query:   131 PCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIGIQ 186
             PCTHKGTYADDC+V+RV QHKC++VAT D++LK+RIRK+    + L  A H I ++
Sbjct:   131 PCTHKGTYADDCIVQRVMQHKCYLVATNDKNLKQRIRKIPGIPI-LSVANHKIRVE 185

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=ISO;IDA

GO:0006364 "rRNA processing" evidence=ISO

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

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

 Score = 518 (187.4 bits), Expect = 9.5e-50, P = 9.5e-50
 Identities = 96/137 (70%), Positives = 112/137 (81%)

Query:    50 SSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELE 109
             SSALFF +NT LGPPY +++DTNFINFSI+NKLD+ +GMMDCLYAKC P I+DCV AELE
Sbjct:    55 SSALFFQYNTQLGPPYHIVLDTNFINFSIKNKLDIVQGMMDCLYAKCIPYISDCVRAELE 114

Query:   110 KLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
             KLG KY++ALRI  DPRFERLPC HKGTYADDCLVERV QHKC+IVAT D+DLK RIRK+
Sbjct:   115 KLGNKYKLALRIISDPRFERLPCLHKGTYADDCLVERVRQHKCYIVATNDKDLKNRIRKI 174

Query:   170 RSTDLYLGTAFHDIGIQ 186
                 + +  A H   I+
Sbjct:   175 PGVPI-MYVAAHKYAIE 190

GO:0005634 "nucleus" evidence=NAS

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

GO:0048812 "neuron projection morphogenesis" evidence=IMP

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

 Score = 508 (183.9 bits), Expect = 1.1e-48, P = 1.1e-48
 Identities = 91/129 (70%), Positives = 111/129 (86%)

Query:    41 KMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCI 100
             ++ R+VP VSSALFF +N ++ PPY+VL+DTNFINFSIQ K+D+ +G+MDCL AKC P I
Sbjct:    51 ELTRSVPQVSSALFFKYNESIKPPYQVLIDTNFINFSIQKKIDIIRGLMDCLMAKCIPII 110

Query:   101 TDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDR 160
             TDCV+AELEKLG KYR+AL++AKDPR +RL C+H GTYADDCLV RV QHKC+IVAT D 
Sbjct:   111 TDCVIAELEKLGSKYRIALKLAKDPRIQRLKCSHVGTYADDCLVNRVIQHKCYIVATNDA 170

Query:   161 DLKRRIRKV 169
             DLKRRIRK+
Sbjct:   171 DLKRRIRKI 179

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

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q55GM5	FCF1_DICDI	No assigned EC number	0.5304	0.8763	0.8402	yes	no
Q9Y324	FCF1_HUMAN	No assigned EC number	0.7017	0.9086	0.8535	yes	no
Q9CTH6	FCF1_MOUSE	No assigned EC number	0.6505	0.9838	0.9242	yes	no
Q32PD0	FCF1_BOVIN	No assigned EC number	0.7017	0.9086	0.8535	yes	no
Q05498	FCF1_YEAST	No assigned EC number	0.6158	0.9086	0.8941	yes	no
O13610	FCF1_SCHPO	No assigned EC number	0.5645	0.9946	0.9635	yes	no
Q5RFQ0	FCF1_PONAB	No assigned EC number	0.7017	0.9086	0.8535	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	186
cd09864	143	cd09864, PIN_Fcf1, PIN domain of rRNA-processing p	8e-90
COG1412	136	COG1412, COG1412, Uncharacterized proteins of PilT	8e-43
pfam04900	101	pfam04900, Fcf1, Fcf1	3e-42
cd08553	120	cd08553, PIN_Fcf1-like, PIN domain of rRNA-process	9e-41
cd09854	125	cd09854, PIN_VapC-Smg6_family, PIN domains of VapC	3e-29
cd09866	147	cd09866, PIN_Fcf1-Utp23-H, PIN domain of rRNA-proc	2e-22
cd09852	120	cd09852, PIN_SF, PIN (PilT N terminus) domain: Sup	8e-16
cd09879	117	cd09879, PIN_AF0591, PIN domain of Archaeoglobus f	4e-12
cd09865	148	cd09865, PIN_Utp23, PIN domain of rRNA-processing	5e-11
smart00670	111	smart00670, PINc, Large family of predicted nucleo	3e-10

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

 Score =  258 bits (662), Expect = 8e-90
 Identities = 105/117 (89%), Positives = 112/117 (95%)

Query: 53  LFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLG 112
           LFF +NTALGPPY VLVDTNFINFSI+NKLDL +GMMDCLYAKC PCITDCVMAELEKLG
Sbjct: 9   LFFQYNTALGPPYHVLVDTNFINFSIKNKLDLVEGMMDCLYAKCIPCITDCVMAELEKLG 68

Query: 113 QKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           QKYRVAL+IAKDPRFERLPC HKGTYADDCLVERVTQH+C+IVATCDRDLKRRIRK+
Sbjct: 69  QKYRVALKIAKDPRFERLPCDHKGTYADDCLVERVTQHRCYIVATCDRDLKRRIRKI 125

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|224330 COG1412, COG1412, Uncharacterized proteins of PilT N-term

 Score =  139 bits (352), Expect = 8e-43
 Identities = 55/116 (47%), Positives = 73/116 (62%), Gaps = 1/116 (0%)

Query: 55  FTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK 114
           F  N     PY+VLVDTNF+ +  Q K+D+ + +   L AK  P I  CV+ ELEKL +K
Sbjct: 1   FQDNFGFRKPYQVLVDTNFLLYPYQFKVDIFEELERLLGAKYKPAIPSCVIRELEKLKRK 60

Query: 115 YRVALRIA-KDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
           +R   RIA      ERL C HKG YAD+CL+E   +H  +IVAT D++LKRR+R+ 
Sbjct: 61  HRGKARIAIALKYAERLECIHKGRYADECLLEAALKHGRYIVATNDKELKRRLREN 116

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

>gnl|CDD|218319 pfam04900, Fcf1, Fcf1

 Score =  136 bits (345), Expect = 3e-42
 Identities = 56/84 (66%), Positives = 68/84 (80%), Gaps = 2/84 (2%)

Query: 89  MDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGT--YADDCLVER 146
           M CL AK  P ITDCV+AELEKLG K+R AL+IAKD RFERL C HKGT  YADDC+++R
Sbjct: 1   MKCLQAKVKPYITDCVIAELEKLGPKFRGALKIAKDKRFERLKCNHKGTEVYADDCILDR 60

Query: 147 VTQHKCFIVATCDRDLKRRIRKVR 170
           V +H C+IVAT DR+L+RR+RK+ 
Sbjct: 61  VGKHNCYIVATQDRELRRRLRKIP 84

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 =  133 bits (337), Expect = 9e-41
 Identities = 52/106 (49%), Positives = 72/106 (67%), Gaps = 5/106 (4%)

Query: 67  VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPR 126
           VLVD NFI   + +K+DL++ +  CLY KC PCIT CV+AELE LG+K + A +IAK   
Sbjct: 1   VLVDGNFIKACLDHKIDLKEQLPKCLYGKCWPCITPCVLAELESLGKKLKDAFKIAKTL- 59

Query: 127 FERLPCTHKGT-YADDCLVERVTQH--KCFIVATCDRDLKRRIRKV 169
            ERL C HK    AD+CL++ V +H    + VAT D+DL+ ++RK+
Sbjct: 60  -ERLNCNHKEGASADECLLDIVKKHNNHRYFVATQDQDLRVKLRKI 104

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|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 =  104 bits (260), Expect = 3e-29
 Identities = 49/118 (41%), Positives = 65/118 (55%), Gaps = 16/118 (13%)

Query: 68  LVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRF 127
           ++DTN I F+I +KLD+   ++DCL A C   I+D V AE+   G K++VALRI KD R 
Sbjct: 1   ILDTNVILFAISHKLDIIHDLLDCLNAFCDVYISDIVAAEIRNKGSKFKVALRIRKDCRD 60

Query: 128 -ERLPCTHKGT---------------YADDCLVERVTQHKCFIVATCDRDLKRRIRKV 169
            +R  C HK                  ADDC + +   H+ FIVATCD DL+   RK 
Sbjct: 61  HKRFICFHKEFSEHTFVERLPNETINDADDCAINKTCMHRMFIVATCDADLREAARKE 118

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 = 87.6 bits (218), Expect = 2e-22
 Identities = 41/120 (34%), Positives = 67/120 (55%), Gaps = 6/120 (5%)

Query: 54  FFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ 113
           F+ +N     PY+VLVD  F + +++NK+++++ +   L  +     T CV+AELEKLG 
Sbjct: 14  FYRNNFGFREPYQVLVDGTFCHAALKNKVNIKEQLPKYLGGEVKLFTTRCVIAELEKLGP 73

Query: 114 KYRVALRIAKDPRFERLPCTHKG--TYADDCLVE--RVTQHKCFIVATCDRDLKRRIRKV 169
               AL IAK  RF+   C H+     A +CL         + + VAT D++L+ ++RK+
Sbjct: 74  DLYGALLIAK--RFQVAKCGHEKSPVSASECLKSMIGDNNPEHYFVATQDKELREKLRKI 131

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

 Score = 69.9 bits (171), Expect = 8e-16
 Identities = 27/113 (23%), Positives = 48/113 (42%), Gaps = 13/113 (11%)

Query: 68  LVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKL-------GQKYRVALR 120
           ++DT+ + F +  ++ L K +   L    T  I   V+AEL KL        +K RVA  
Sbjct: 1   VIDTSALLFRLLTEIRLRKSLKRLLEGDITVIIVFDVVAELLKLEAQKGLRRKKGRVAEL 60

Query: 121 IAKDPRF---ERLPCTHKGT--YADDCLVERVTQH-KCFIVATCDRDLKRRIR 167
           + +D        +P  H     Y  D  +  + +      + T D DL+++ +
Sbjct: 61  LLRDLELLDLMGIPVVHAPGDLYEADAQIAALAKKGHVVALITNDSDLRQKAK 113

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

 Score = 59.9 bits (146), Expect = 4e-12
 Identities = 32/110 (29%), Positives = 55/110 (50%), Gaps = 15/110 (13%)

Query: 67  VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKY--------RVA 118
           VL+DTN + + +Q  +D+ + +    Y +    +   V+ ELEKL +K         RVA
Sbjct: 1   VLLDTNALMYPVQFGVDIFEELERLGYPEFV--VPSAVLEELEKLSRKGKGKDKRAARVA 58

Query: 119 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRK 168
           L++A+      +  +  G  ADD ++E   +     V T DR+LK+R+  
Sbjct: 59  LQLAERC---EVVESEGG-PADDAILELAKELGA-AVVTNDRELKKRLLD 103

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

 Score = 57.8 bits (140), Expect = 5e-11
 Identities = 40/114 (35%), Positives = 59/114 (51%), Gaps = 11/114 (9%)

Query: 64  PYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAK 123
           PY+VLVD +F+    + K+DL   +   L  K  P IT C +  L  LG+  + A+ +AK
Sbjct: 22  PYQVLVDADFLLDVTKFKMDLISQLERTLQGKVKPMITQCCIRALYALGKTVQRAIDLAK 81

Query: 124 DPRFERLPCTHKGTYA---DDCLVERV-----TQHKCFIVATCDRDLKRRIRKV 169
              FER  C H+   A   D+CL   V      +H+ +IVAT D  L+  +R +
Sbjct: 82  --TFERRRCNHRDADALSPDECLKSVVDPKGKNKHR-YIVATQDPPLRTDLRSI 132

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 = 54.7 bits (132), Expect = 3e-10
 Identities = 26/116 (22%), Positives = 46/116 (39%), Gaps = 21/116 (18%)

Query: 65  YRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELE-----------KLGQ 113
            +V++DTN +   +     LEK +      K    I   V+ ELE           +L  
Sbjct: 1   MKVVLDTNVLIDGLIRDA-LEKLLEK----KGEVYIPQTVLEELEYLALRSLKKLEELAL 55

Query: 114 KYRVALRIAKDPRFERLPCTHKGTYA----DDCLVERVTQH-KCFIVATCDRDLKR 164
           + ++ L++ K+ R E               +D L+    +     ++ T DRDL+R
Sbjct: 56  EGKIILKVLKEERIEEEILERLSLKLELLPNDALILATAKELGNVVLVTNDRDLRR 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	186
KOG3165	195	consensus Predicted nucleic-acid-binding protein,	100.0
COG1412	136	Uncharacterized proteins of PilT N-term./Vapc supe	100.0
KOG3164	236	consensus Uncharacterized proteins of PilT N-term.	100.0
PF04900	101	Fcf1: Fcf1; InterPro: IPR006984 This family is com	99.96
smart00670	111	PINc Large family of predicted nucleotide-binding	98.44
PF13638	133	PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_	98.25
PRK13764	602	ATPase; Provisional	97.78
TIGR00305	114	probable toxin-antitoxin system toxin component, P	97.22
PF01850	121	PIN: PIN domain; InterPro: IPR002716 The PilT prot	96.91
TIGR00028	142	Mtu_PIN_fam Mycobacterium tuberculosis PIN domain	96.68
PF13470	119	PIN_3: PIN domain	95.31
PRK00124	151	hypothetical protein; Validated	94.35
COG1848	140	Predicted nucleic acid-binding protein, contains P	93.82
COG1569	142	Predicted nucleic acid-binding protein, contains P	93.28
COG2402	135	Predicted nucleic acid-binding protein, contains P	92.94
PRK13725	132	plasmid maintenance protein; Provisional	91.78
PRK12496	164	hypothetical protein; Provisional	90.36
PF05991	166	NYN_YacP: YacP-like NYN domain; InterPro: IPR01029	89.88
PF02639	130	DUF188: Uncharacterized BCR, YaiI/YqxD family COG1	89.07
COG1487	133	VapC Predicted nucleic acid-binding protein, conta	85.97
COG4956	356	Integral membrane protein (PIN domain superfamily)	84.57
COG2405	157	Predicted nucleic acid-binding protein, contains P	83.61
COG1656	165	Uncharacterized conserved protein [Function unknow	81.65

>KOG3165 consensus Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]

Probab=100.00  E-value=3.3e-76  Score=475.82  Aligned_cols=182  Identities=68%  Similarity=1.089  Sum_probs=172.7

Q ss_pred             CCccccchhhHHhhhccCccccccccccccCCCCcCCCCCCCCcccCCCchhhHHHHhhCCCCCeEEEeehHHHHHHHHc
Q 029889            1 MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQN   80 (186)
Q Consensus         1 mg~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fy~~n~gf~~PY~VLvDtNFl~~~~~~   80 (186)
                      |||+|||||||.||+||+.+ .|++++++.+.++++.+.++.++++||+||++||+||+.++|||+||||||||++|+++
T Consensus         1 mgk~kktrk~~~vk~~i~~k-~~~~~~dr~k~k~K~d~~~~~~~e~Pq~~s~lffqyn~~L~PPy~vivDTNFINfsi~~   79 (195)
T KOG3165|consen    1 MGKAKKTRKFAVVKRMIKTK-QRLKKKDRVKNKEKKDENELLTREVPQVPSALFFQYNTTLGPPYHVIVDTNFINFSIQN   79 (195)
T ss_pred             CCcccchHHHHHHHHHHHHH-HHHHHHHhhhcccCCCchhhhcccCcCcchhHHHhcccccCCCeEEEEecchhhHHHHh
Confidence            99999999999999999987 88888887665555555566799999999999999999999999999999999999999


Q ss_pred             CCChHHhHHHhhcccceeeecHHHHHHHHHhchhhHHHHHhccCCCceeeecCCCCCChHHHHHHHhhcCceEEEEecCH
Q 029889           81 KLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDR  160 (186)
Q Consensus        81 kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k~r~Al~lak~~~~e~~kC~H~g~~addCI~~~v~~~~~yiVATnD~  160 (186)
                      |+|++++||+||+++|+||||+|||+|||+||++|+.||++|+||+|+|++|.|+|+||||||+++|.+|+||||||||+
T Consensus        80 KiDi~~gmmdcl~Ak~~pcitDCVmaELEkLg~kyrvALri~kDpr~eRL~C~HKGTYADDClv~RV~qHkCYIVAT~D~  159 (195)
T KOG3165|consen   80 KIDLFEGMMDCLYAKCIPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATNDR  159 (195)
T ss_pred             HHHHHHHHHHHHHhccccchhHHHHHHHHHhcchhhhhhhhhcCCcccccccccCCcchhhHHHHHHhhcceEEEEeccH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCCccEEEEeecccc
Q 029889          161 DLKRRIRKVRSTDLYLGTAFHDI  183 (186)
Q Consensus       161 ~LrrrlRkipGVPiiyi~~~~~~  183 (186)
                      +|++|+|+||||||||+.++...
T Consensus       160 dLK~RIrkIPGVPim~v~~hk~~  182 (195)
T KOG3165|consen  160 DLKQRIRKIPGVPIMYVANHKYS  182 (195)
T ss_pred             HHHHHHhcCCCCceEEEecceee
Confidence            99999999999999999988654

>COG1412 Uncharacterized proteins of PilT N-term

Probab=100.00  E-value=1.6e-40  Score=262.52  Aligned_cols=128  Identities=43%  Similarity=0.629  Sum_probs=119.2

Q ss_pred             HHHhhCCCCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchhhHHHHH--hccCCCceeeec
Q 029889           55 FTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR--IAKDPRFERLPC  132 (186)
Q Consensus        55 y~~n~gf~~PY~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k~r~Al~--lak~~~~e~~kC  132 (186)
                      |++|+||++||+||||||||+++.++++|+++.++++++++++|+||+||++||++|++.++.+++  +|.. .+++++|
T Consensus         1 ~~~~~~~~~~~~VlvDTNfl~~~~q~~vdi~~~l~r~l~~~~~~~Ip~~Vi~EL~~l~~~~~~~~r~~ia~~-~~er~~~   79 (136)
T COG1412           1 FQDNFGFRKPYQVLVDTNFLLYPYQFKVDIFEELERLLGAKYKPAIPSCVIRELEKLKRKHRGKARIAIALK-YAERLEC   79 (136)
T ss_pred             CccccccCCceEEEecchHHHHHHHccCCHHHHHHHHhcccccccchHHHHHHHHHHHHhcCchHHHHHHHH-HhhccCc
Confidence            678999999999999999999999999999999999999999999999999999999998777776  4443 6889999


Q ss_pred             CCCCCChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEEEeeccccC
Q 029889          133 THKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIG  184 (186)
Q Consensus       133 ~H~g~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~~~~~~~  184 (186)
                      .|.+.++||||.++|.+++||+|||||++|++|||+. |||+||+++++...
T Consensus        80 ~~~~~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~-GIPvi~lr~r~~~~  130 (136)
T COG1412          80 IHKGRYADECLLEAALKHGRYIVATNDKELKRRLREN-GIPVITLRQRKLLI  130 (136)
T ss_pred             cccCCChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHc-CCCEEEEeCCeEEE
Confidence            9998899999999999999999999999999999999 99999999887654

/Vapc superfamily [General function prediction only]

>KOG3164 consensus Uncharacterized proteins of PilT N-term

Probab=100.00  E-value=3.1e-40  Score=277.15  Aligned_cols=127  Identities=34%  Similarity=0.529  Sum_probs=121.0

Q ss_pred             hhHHHHhhCCCCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchhhHHHHHhccCCCceeee
Q 029889           52 ALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLP  131 (186)
Q Consensus        52 ~~fy~~n~gf~~PY~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k~r~Al~lak~~~~e~~k  131 (186)
                      ..||++|||||+|||||||++|+.++++.+|++.++|.++|.|.++++||+|||.|||.+|+.+.+|+.+|+  .|++++
T Consensus        13 l~ff~~~fgfRePYQVLvD~tF~~a~~~~~i~l~~~i~r~l~~~vKL~tTqCvikele~~g~~l~ga~~iAK--~fe~~~   90 (236)
T KOG3164|consen   13 LKFFSVNFGFREPYQVLVDGTFCQAALQQKIGLDEQIKRYLQGEVKLMTTQCVIKELEELGKDLYGAKGIAK--QFEIRN   90 (236)
T ss_pred             eeeeeeccCccCceEEEehhHHHHHHHHhhhChHHHHHHHhcCCCeeeehHHHHHHHHHhCcchhhhHHHHH--HHhHhc
Confidence            469999999999999999999999999999999999999999999999999999999999999999999999  799999


Q ss_pred             cCCCCC-ChHHHHHHHhhcC--ceEEEEecCHHHHHHHhhcCCccEEEEeec
Q 029889          132 CTHKGT-YADDCLVERVTQH--KCFIVATCDRDLKRRIRKVRSTDLYLGTAF  180 (186)
Q Consensus       132 C~H~g~-~addCI~~~v~~~--~~yiVATnD~~LrrrlRkipGVPiiyi~~~  180 (186)
                      |+|++. ++++||.++++..  +||+|||||.+|++.||.+||||+||+.+.
T Consensus        91 C~H~~~~s~seCl~svv~~~Nk~~YvvATQD~el~~kLr~~pgvPli~~~r~  142 (236)
T KOG3164|consen   91 CNHKDARSPSECLRSVVRISNKHHYVVATQDQELRRKLRKEPGVPLIYLKRN  142 (236)
T ss_pred             CCCCCCCCHHHHHHHHHhccCCceEEEecCCHHHHHHHhcCCCCceEEEecc
Confidence            999664 8999999999763  679999999999999999999999999875

/Vapc superfamily [General function prediction only]

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

Probab=99.96  E-value=3.1e-29  Score=187.44  Aligned_cols=92  Identities=41%  Similarity=0.675  Sum_probs=85.1

Q ss_pred             HHhhcccceeeecHHHHHHHHHhchhhHHHHHhccCCCceeeecCCCCC--ChHHHHHHHhhcCceEEEEecCHHHHHHH
Q 029889           89 MDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGT--YADDCLVERVTQHKCFIVATCDRDLKRRI  166 (186)
Q Consensus        89 ~~~L~~k~~~~iT~CVi~ELekLg~k~r~Al~lak~~~~e~~kC~H~g~--~addCI~~~v~~~~~yiVATnD~~Lrrrl  166 (186)
                      +++|+|+++|+||+||++||++||+.++++..+|+...+++++|+|.+.  +|||||++++.+++.|||||||++||++|
T Consensus         1 ~~~L~~~~~~~vt~cVl~EL~~L~~~~~~~~~~a~~~~~~~~~c~h~~~~~~addci~~~~~~~~~~~VaT~D~~Lr~~l   80 (101)
T PF04900_consen    1 KKLLGGKVKPYVTQCVLEELESLGKKFKGALRIAKRKALERRKCNHKETPGSADDCILDLAGKNNKYIVATQDKELRRRL   80 (101)
T ss_pred             CccccCccEEEecHHHHHHHHHhcccccchhhhhhchhhHhhcCCCCCCCcCHHHHHHHHhccCCeEEEEecCHHHHHHH
Confidence            3689999999999999999999999999999999944499999999865  99999999999887799999999999999


Q ss_pred             hhcCCccEEEEeec
Q 029889          167 RKVRSTDLYLGTAF  180 (186)
Q Consensus       167 RkipGVPiiyi~~~  180 (186)
                      |++|||||||++++
T Consensus        81 r~~~GvPvi~l~~~   94 (101)
T PF04900_consen   81 RKIPGVPVIYLRRN   94 (101)
T ss_pred             hcCCCCCEEEEECC
Confidence            99999999999944

>smart00670 PINc Large family of predicted nucleotide-binding domains

Probab=98.44  E-value=6.9e-07  Score=65.44  Aligned_cols=93  Identities=24%  Similarity=0.261  Sum_probs=59.5

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhch--hhHHHHHhcc----------CCC-ceeeecC
Q 029889           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ--KYRVALRIAK----------DPR-FERLPCT  133 (186)
Q Consensus        67 VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~--k~r~Al~lak----------~~~-~e~~kC~  133 (186)
                      +++|||+++..+..  ++.+   .+..++..++||.+|+.||.....  .++.--.++.          +.. +....+.
T Consensus         1 ~vlDTnvli~~~~~--~~~~---~~~~~~~~~~i~~~v~~El~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~   75 (111)
T smart00670        1 VVLDTNVLIDGLIG--KALE---KLLEKKGEVYIPPTVLEELEYLAKLRSLKKLEELALEGKIKLKVLKEERKLEEEILE   75 (111)
T ss_pred             CEeeHHHHHHHHHH--HHHH---HHHcCCCcEEECHHHHHHHHHHHHHHHHhhHHHHHHhcccccceeecCCCeEEEecc
Confidence            58999999998766  3333   334447889999999999999762  1111111111          000 1112233


Q ss_pred             CCCC-----ChHHHHHHHhhcCceEEEEecCHHHHH
Q 029889          134 HKGT-----YADDCLVERVTQHKCFIVATCDRDLKR  164 (186)
Q Consensus       134 H~g~-----~addCI~~~v~~~~~yiVATnD~~Lrr  164 (186)
                      +.+.     ..|.+|+..+...++.+++|+|.+|++
T Consensus        76 ~~~~~~~~~~~D~~il~~a~~~~~~~lvT~D~~l~~  111 (111)
T smart00670       76 RLSLKLELLPNDALILATAKELGNVVLVTNDRDLRR  111 (111)
T ss_pred             cCChhhcCCCChHHHHHHHHHCCCCEEEeCCcccCC
Confidence            3222     368899999988756899999998863

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.

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

Probab=98.25  E-value=8.7e-06  Score=62.11  Aligned_cols=101  Identities=17%  Similarity=0.171  Sum_probs=60.9

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchh-----------hHHHHHhccCC---Cceeeec
Q 029889           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK-----------YRVALRIAKDP---RFERLPC  132 (186)
Q Consensus        67 VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k-----------~r~Al~lak~~---~~e~~kC  132 (186)
                      +++|||+|+...       +.+.++  +...++||.+|+.||..+...           .+.|.++....   ....+..
T Consensus         1 ~V~DTnvll~~~-------~~l~~~--~~~~ivIP~~Vl~ELd~lk~~~~~~~~~~~~~ar~~~~~l~~~~~~~~~~i~~   71 (133)
T PF13638_consen    1 YVLDTNVLLHHP-------DLLEKL--EQNKIVIPLTVLEELDRLKKSSRDRDRELRKRAREAIRWLEKLLKRGSRSIRV   71 (133)
T ss_dssp             EEE-HHHHHHHH-------HHHHHH--SSSEEEEEHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHCT-TTEEE
T ss_pred             CEeehhHHhCCh-------HHHhcc--ccCEEEechHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHhcCCCeEec
Confidence            589999999772       334433  788999999999999888432           23344333210   0001111


Q ss_pred             CCC-----------CCChHHHHHHHhhc------CceEEEEecCHHHHHHHhhcCCccEEEE
Q 029889          133 THK-----------GTYADDCLVERVTQ------HKCFIVATCDRDLKRRIRKVRSTDLYLG  177 (186)
Q Consensus       133 ~H~-----------g~~addCI~~~v~~------~~~yiVATnD~~LrrrlRkipGVPiiyi  177 (186)
                      ...           ....|+.|++.+..      ....++.|+|..|+.+++.. |+|...+
T Consensus        72 q~~~~~~~~~~~~~~~~~D~~Il~~a~~~~~~~~~~~vvLvT~D~~l~~~A~~~-gi~~~~~  132 (133)
T PF13638_consen   72 QTSDEEIDEDLNLDAQRNDDRILNCALYLQEENPGRKVVLVTNDKNLRLKARAE-GIPAVSY  132 (133)
T ss_dssp             CTTTS-EES--S----HHHHHHHHHHHHHHHHCGCEEEEEEE--HHHHHHHHHT-T--EE--
T ss_pred             chhhhhcchhhhccccccHHHHHHHHHHHHHhcCCCeEEEEeCCHHHHHHHhhc-ccccccC
Confidence            110           12678999988743      23579999999999999998 9998864

>PRK13764 ATPase; Provisional

Probab=97.78  E-value=9.5e-05  Score=71.14  Aligned_cols=109  Identities=19%  Similarity=0.131  Sum_probs=71.5

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchh----hHHHHHhccC---------CCceeeec
Q 029889           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK----YRVALRIAKD---------PRFERLPC  132 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k----~r~Al~lak~---------~~~e~~kC  132 (186)
                      .+++|||.|+.--     +.+.+..-+.-...++||.-|++||+.+...    =+.|++.++.         ..++.. .
T Consensus         2 ~yVlDTSVIIDGr-----i~~~i~~g~~~~~~IiIP~~Vl~ELe~~A~~~r~~G~~gLeeL~~L~~l~~~g~i~ie~~-~   75 (602)
T PRK13764          2 KIVPDTSVVIDGR-----VSELIEKGEYIGGTIIIPEAVVAELEAQANQGREIGFSGLEELKKLRELAEEGLIELEFV-G   75 (602)
T ss_pred             eEEccceEEEech-----HHHHHHcCCccCCEEEeehHHHHHHHHHhhccchhhHHHHHHHHHHHHhhccCceEEEEe-c
Confidence            4677777775540     1122221111245699999999999999542    1234433331         011111 1


Q ss_pred             CCC---------CCChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEEEeeccc
Q 029889          133 THK---------GTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHD  182 (186)
Q Consensus       133 ~H~---------g~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~~~~~  182 (186)
                      .+.         +...|+-|++++.+++ .++.|+|..|+..++.. |||++|+++.+.
T Consensus        76 ~~p~~~~~~~~~~gevD~~I~~~A~~~~-~~lvT~D~~l~~~A~~~-GI~V~~l~~~~~  132 (602)
T PRK13764         76 ERPTLEQIKLAKGGEIDALIREVAKELG-ATLVTSDRVQAEVARAK-GIDVIYLKPERE  132 (602)
T ss_pred             cccchhhcccccCCCHHHHHHHHHHHcC-CEEEeCCHHHHHHHHHc-CCEEEEeCCCCC
Confidence            111         1368999999999887 59999999999999999 999999998764

>TIGR00305 probable toxin-antitoxin system toxin component, PIN family

Probab=97.22  E-value=0.005  Score=46.15  Aligned_cols=96  Identities=18%  Similarity=0.103  Sum_probs=60.4

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHH-HhhcccceeeecHHHHHHH-HHhc-hhh---------HHHHHhccCCCceeeecC
Q 029889           66 RVLVDTNFINFSIQNKLDLEKGMM-DCLYAKCTPCITDCVMAEL-EKLG-QKY---------RVALRIAKDPRFERLPCT  133 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~~l~-~~L~~k~~~~iT~CVi~EL-ekLg-~k~---------r~Al~lak~~~~e~~kC~  133 (186)
                      +|++|||.++.++-.+-. ...+. -+..+.+.++++..++.|+ +.+. +++         +..+..... .++...-.
T Consensus         1 rvvlDTNVli~all~~~~-~~~l~~~~~~~~~~~~~s~~~l~E~~~~l~~~~~~~~~~~~~~~~~l~~l~~-~~~~~~~~   78 (114)
T TIGR00305         1 KVVIDTNVWISALIWKGL-PGKLIKLIIDNKIVNCTSVEILQEVEFVLLYPKLQKYFALETILEILLLLGE-KSTIINPN   78 (114)
T ss_pred             CEEEEhHHHHHHHhCCCC-HHHHHHHHHhCCEEEEECHHHHHHHHHHHhhHhhhhhcCHHHHHHHHHHHHH-hcEEecCC
Confidence            489999999998876654 33343 3466889999999999999 4443 111         112221111 22222211


Q ss_pred             C----CCCChHHHHHHHhhcCceEEEEecCHHHH
Q 029889          134 H----KGTYADDCLVERVTQHKCFIVATCDRDLK  163 (186)
Q Consensus       134 H----~g~~addCI~~~v~~~~~yiVATnD~~Lr  163 (186)
                      .    ..-+.|+.+++.+...++=++.|.|++|-
T Consensus        79 ~~~~~~~D~~D~~~l~~A~~~~ad~iVT~Dkdll  112 (114)
T TIGR00305        79 PEFDDCRDKKDNKFLNTAYASKANALITGDTDLL  112 (114)
T ss_pred             CCCCCCCCchhHHHHHHHHhcCCCEEEECCHHHh
Confidence            1    02256888888888776657779999874

This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.

>PF01850 PIN: PIN domain; InterPro: IPR002716 The PilT protein, N-terminal domain (PIN) is a compact domain of about 100 amino acids

Probab=96.91  E-value=0.0066  Score=44.18  Aligned_cols=99  Identities=22%  Similarity=0.283  Sum_probs=62.2

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchh-----h---HHHHHhccCCCceeeecCCC---
Q 029889           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK-----Y---RVALRIAKDPRFERLPCTHK---  135 (186)
Q Consensus        67 VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k-----~---r~Al~lak~~~~e~~kC~H~---  135 (186)
                      |+||||++...+ ..=...+...+++.....++++.-++.|+...-.+     .   ....... .+.++..+.+..   
T Consensus         1 i~lDTsili~~~-~~~~~~~~~~~~~~~~~~~~is~~~~~E~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~~~~~~~~   78 (121)
T PF01850_consen    1 ILLDTSILIALL-RDEENHEKARELLERAIEIVISSLVLAELLYVLRRRSKQQKAIALLELLIL-LSNFNILPITSEVFE   78 (121)
T ss_dssp             EEE-HHHHHHHH-SHSCHHHHHHHHHHTHSEEEEEHHHHHHHHHHHHHSHCHHHHHHHHHHHHH-HCTSEEEEBCHHHHH
T ss_pred             EEEcChhhcccc-CCChhHHHHHHHHhcCCCEEEcHHHHHHHHHHhhhccccchhhhHHHHHHH-HhhhccccchhHHHH
Confidence            799999999998 43444455666666558899999999999776433     1   1111112 235666665421   


Q ss_pred             ---------CCChHHHHH-HHhhcCceEEEEecCHHHHHHHh
Q 029889          136 ---------GTYADDCLV-ERVTQHKCFIVATCDRDLKRRIR  167 (186)
Q Consensus       136 ---------g~~addCI~-~~v~~~~~yiVATnD~~LrrrlR  167 (186)
                               +.+..||+. ..+..+++-.|.|+|+++++-.+
T Consensus        79 ~~~~~~~~~~~~~~Da~~~a~A~~~~~~~v~T~D~~f~~~a~  120 (121)
T PF01850_consen   79 RAAELMRKYGLDFADALIAATAKENGAPLVVTFDKDFRKVAK  120 (121)
T ss_dssp             HHHHHHHHHHSSHHHHHHHHHHHHHT-EEE-ESSHHHHHHHC
T ss_pred             HHHHHHHhccCChhHHHHHHHHHHcCCEEEEECCcCHHhccC
Confidence                     135556655 55666787788899999887544

The domain has two nearly invariant aspartates and forms a coiled-coil with other monomer units to polymerise a pilus fibre []. The function of the PIN domain is unknown but a role in signalling appears likely given the presence of this domain in some bacterial plasmid stability proteins and Dis3 from yeast that is implicated in mitotic control [].; PDB: 3TND_G 2H1O_B 2BSQ_B 2H1C_A 2FE1_A 3ZVK_C 1V8P_F 1V8O_C 3H87_A 1O4W_A ....

>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family

Probab=96.68  E-value=0.0049  Score=46.55  Aligned_cols=104  Identities=16%  Similarity=0.150  Sum_probs=56.5

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhc---ccceeeecHHHHHHHHHh-ch-----------hhHHHHH-hccCCCceee
Q 029889           67 VLVDTNFINFSIQNKLDLEKGMMDCLY---AKCTPCITDCVMAELEKL-GQ-----------KYRVALR-IAKDPRFERL  130 (186)
Q Consensus        67 VLvDtNFl~~~~~~kldl~~~l~~~L~---~k~~~~iT~CVi~ELekL-g~-----------k~r~Al~-lak~~~~e~~  130 (186)
                      +++|||++++.+...=...+...+.+.   +...++++.-++.|+... .+           .....++ +...+.+...
T Consensus         2 i~lDTnvli~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vl~E~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   81 (142)
T TIGR00028         2 LLLDVNVLLAAVNRDHPHHDAARAWLDRFAAGGDWATCPLTLAGFVRLLTNPRVLPAPLSPAEAIAVVAAFLATPRHRLL   81 (142)
T ss_pred             ccchhhHHHHhcCCCCcchHHHHHHHHHHhcCCCceechhhhhhheeeeccCCcCCCCCCHHHHHHHHHHHHhCCCeeec
Confidence            689999999887644322222333332   445577888999998553 11           1112221 1111112111


Q ss_pred             ec--------------CCC-CC-ChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEE
Q 029889          131 PC--------------THK-GT-YADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLY  175 (186)
Q Consensus       131 kC--------------~H~-g~-~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPii  175 (186)
                      .-              ... +. .+|..|+..+..+++ .+.|.|+++    ...+|++++
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~D~~i~a~A~~~~~-~lvT~D~~f----~~~~~~~i~  137 (142)
T TIGR00028        82 WPGPRHLAVLRGLADPVIAGGRLVTDAHLAALAREHGA-ELVTFDRGF----ARFAGIRWR  137 (142)
T ss_pred             CCCcchHHHHHHHHHHhccCCCCchHHHHHHHHHHcCC-EEEecCCCc----cccCCCeee
Confidence            11              001 12 455556677778875 555999865    456788775

Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.

>PF13470 PIN_3: PIN domain

Probab=95.31  E-value=0.19  Score=37.17  Aligned_cols=46  Identities=22%  Similarity=0.351  Sum_probs=35.6

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHh-hcccceeeecHHHHHHHHHh
Q 029889           66 RVLVDTNFINFSIQNKLDLEKGMMDC-LYAKCTPCITDCVMAELEKL  111 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~~l~~~-L~~k~~~~iT~CVi~ELekL  111 (186)
                      +|++|||.++.++-..=.....+.+. ..|.+.++++.-++.|++..
T Consensus         1 RVvlDTNVli~~ll~~~~~~~~l~~~~~~~~~~~~~s~~~l~E~~~v   47 (119)
T PF13470_consen    1 RVVLDTNVLISALLSREPAARKLLDLAEDGRIELYISPEILDELERV   47 (119)
T ss_pred             CEEEEechhHHHHhCCCchHHHHHHHHHcCCCeEEecHHHHHHHHHH
Confidence            58999999999877554334444444 46889999999999999855

>PRK00124 hypothetical protein; Validated

Probab=94.35  E-value=0.071  Score=43.21  Aligned_cols=74  Identities=14%  Similarity=0.118  Sum_probs=50.9

Q ss_pred             HHHHHHHhchhhHHHHHhcc-------CCC---ceeeecCCCCCChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCcc
Q 029889          104 VMAELEKLGQKYRVALRIAK-------DPR---FERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTD  173 (186)
Q Consensus       104 Vi~ELekLg~k~r~Al~lak-------~~~---~e~~kC~H~g~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVP  173 (186)
                      |.+|+.+++.++..-+-+.-       .|.   .+.+-.+.....||+-|++.+.+..  +|.|||-.|-.++-.. |+-
T Consensus        12 Vk~~i~r~a~r~~i~v~~Vas~n~~~~~~~~~~v~~v~V~~g~D~AD~~Iv~~~~~gD--iVIT~Di~LAa~~l~K-ga~   88 (151)
T PRK00124         12 VKDIIIRVAERHGIPVTLVASFNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKGD--IVITQDYGLAALALEK-GAI   88 (151)
T ss_pred             HHHHHHHHHHHHCCeEEEEEeCCcccCCCCCCceEEEEeCCCCChHHHHHHHhCCCCC--EEEeCCHHHHHHHHHC-CCE
Confidence            88888888876543322211       111   2222233222379999999998886  9999999999999999 999


Q ss_pred             EEEEeec
Q 029889          174 LYLGTAF  180 (186)
Q Consensus       174 iiyi~~~  180 (186)
                      +|.-++.
T Consensus        89 vl~prG~   95 (151)
T PRK00124         89 VLNPRGY   95 (151)
T ss_pred             EECCCCc
Confidence            8865543

>COG1848 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]

Probab=93.82  E-value=0.33  Score=37.20  Aligned_cols=100  Identities=20%  Similarity=0.283  Sum_probs=58.8

Q ss_pred             EEEeehHHHHHHHHcCC----ChHHhHHHhhcccceeeecHHHHHHHHHhchh------hHHHHHhc----cCCCc----
Q 029889           66 RVLVDTNFINFSIQNKL----DLEKGMMDCLYAKCTPCITDCVMAELEKLGQK------YRVALRIA----KDPRF----  127 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kl----dl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k------~r~Al~la----k~~~~----  127 (186)
                      .+++|||++.+.+-..-    .-.+.+.....+....+++.-|+.|+-.+-.+      ...+....    -.+.+    
T Consensus         1 ~i~~Dtnvlv~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~v~~e~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (140)
T COG1848           1 MIVIDTNVLVYALFRDHPHHDRARELLERLEAGDIRVYTPELVLAELLRVLTRRRRPLSLAEAIEVVAALLALPRFELLL   80 (140)
T ss_pred             CeeeehHHHHHHHHccChhHHHHHHHHHHHhcCCCceeecHHHHHHHHHHHhhcccCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            37899999999976653    23455666666677899999999998666322      11111111    00011    


Q ss_pred             eeee--cC----------CCCCChHHHHH-HHhhcCceEEEEecCHHHHHH
Q 029889          128 ERLP--CT----------HKGTYADDCLV-ERVTQHKCFIVATCDRDLKRR  165 (186)
Q Consensus       128 e~~k--C~----------H~g~~addCI~-~~v~~~~~yiVATnD~~Lrrr  165 (186)
                      +..+  ..          +.+..+.|++. ..+..++.--++|.|+++++-
T Consensus        81 ~~~~~~~~~~~~a~~~~~~~~l~~~DAl~lA~a~~~gi~~i~T~D~df~~~  131 (140)
T COG1848          81 DILEVTAEAYRLAAALALKYGLLPNDALLLATAKRYGIKAIATFDEDFARV  131 (140)
T ss_pred             hcccchHHHHHHHHHHHHHcCCCCcHHHHHHHHHHcCcceeeecchhhhhc
Confidence            1111  10          11223566666 455556567999999988763

>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]

Probab=93.28  E-value=0.75  Score=37.01  Aligned_cols=95  Identities=25%  Similarity=0.276  Sum_probs=63.4

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhc-ccceeeecHHHHHHHH-Hhc-hhhHH------------HH-----HhccCC
Q 029889           66 RVLVDTNFINFSIQNKLDLEKGMMDCLY-AKCTPCITDCVMAELE-KLG-QKYRV------------AL-----RIAKDP  125 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~~l~~~L~-~k~~~~iT~CVi~ELe-kLg-~k~r~------------Al-----~lak~~  125 (186)
                      +|++|||.++.++=.+=.+...+.+++. .+...+++.-.+.||+ .++ ++++.            ++     .++-.|
T Consensus         2 kVViDTNV~isaLi~p~Gl~~~l~~ll~~~~i~n~tS~eil~El~~v~~~pKl~k~l~~e~~~~~v~~l~~~~~~i~I~p   81 (142)
T COG1569           2 KVVIDTNVWISALISPGGLPGELISLLIKEKIENYTSEEILDELEEVLSYPKLKKYLPLEVLGELVLVLFESVSLIAINP   81 (142)
T ss_pred             eEEEEhhHHHHHHhCCCCCcHHHHHHHhhCceEEEecHHHHHHHHHHHhhHHHHhhcchHHHHHHHHHHHHhheeEeecc
Confidence            7999999999998777666666666665 4678899999999994 333 22111            11     111223


Q ss_pred             CceeeecCCCCCChHHHHHHHhhcCceEEEEecCHHHH
Q 029889          126 RFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLK  163 (186)
Q Consensus       126 ~~e~~kC~H~g~~addCI~~~v~~~~~yiVATnD~~Lr  163 (186)
                      .++...|.-   .-|.-++++|-..+..++.|-|++|-
T Consensus        82 ~~~f~~~RD---p~Dn~~L~~A~~~kA~~lvTgD~dLL  116 (142)
T COG1569          82 LEKFNICRD---PKDNKLLALAYESKADYLVTGDQDLL  116 (142)
T ss_pred             cccccccCC---chHHHHHHHHHhccCCEEEEcchhhh
Confidence            333233532   45778899998877778889999874

>COG2402 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]

Probab=92.94  E-value=0.66  Score=36.87  Aligned_cols=96  Identities=17%  Similarity=0.137  Sum_probs=55.6

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccc-----eeeecHHHHHHHHHhchh-hHHHH----HhccCCCceeeecC---
Q 029889           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKC-----TPCITDCVMAELEKLGQK-YRVAL----RIAKDPRFERLPCT---  133 (186)
Q Consensus        67 VLvDtNFl~~~~~~kldl~~~l~~~L~~k~-----~~~iT~CVi~ELekLg~k-~r~Al----~lak~~~~e~~kC~---  133 (186)
                      |||||||+.+....+-.--+.-..++.+..     .+++++|++.|..-|.++ +..|.    ..+....+.+..|.   
T Consensus         2 v~vDT~~~~a~~~~~d~~H~~a~~~~~~~~~~~~~~~~~~~~v~~e~~~l~k~r~~~aa~~l~~~i~~~~~~~~~~~t~~   81 (135)
T COG2402           2 VLVDTSVLLALFDKRDKNHEAAVQLFVSLADNKFRRLVVSDHVLDETLTLLKKRVVDAAAFLLEALEEGALEIFESVTEE   81 (135)
T ss_pred             EEEechHHHHHHhchhhhHHHHHHHHhhcccCccceEEEeeeeHHHHHHHHHHhhhhHHHHHHHHhccCceEEEecccHH
Confidence            899999998876555433333333444333     689999999999988653 22222    22222345555553   


Q ss_pred             -------------CCCCChHHHHH-HHhhcCceEEEEecCHHH
Q 029889          134 -------------HKGTYADDCLV-ERVTQHKCFIVATCDRDL  162 (186)
Q Consensus       134 -------------H~g~~addCI~-~~v~~~~~yiVATnD~~L  162 (186)
                                   |.+-+=+||+. -++.+.++-=+-|.|.+.
T Consensus        82 ~~~~a~~~~k~~d~~~~df~Da~~~ala~k~g~~~ilSfD~dF  124 (135)
T COG2402          82 LEEAAEAVFKRQDDLGLDFVDATSVALAEKLGILKILSFDSDF  124 (135)
T ss_pred             HHHHHHHHHHhhcccCCCHHHHHHHHHHHHcCCCcEEEecccc
Confidence                         23334445554 445556655566777653

>PRK13725 plasmid maintenance protein; Provisional

Probab=91.78  E-value=1.4  Score=34.04  Aligned_cols=99  Identities=22%  Similarity=0.360  Sum_probs=54.6

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhch------hhHHHHH-hccCCCceeeecC------
Q 029889           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ------KYRVALR-IAKDPRFERLPCT------  133 (186)
Q Consensus        67 VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~------k~r~Al~-lak~~~~e~~kC~------  133 (186)
                      .|+|||.+...++.+-+......+ . ..-.++|+.-++.||..=-.      +....++ +..  +|+.++-+      
T Consensus         4 yLLDTni~i~~~~~~~~~v~~~~~-~-~~~~~~iS~It~~EL~~G~~~~~~~~~~~~~~~~~l~--~~~ilp~d~~~a~~   79 (132)
T PRK13725          4 FMLDTNICIFTIKNKPEHVRERFN-L-NTGRMCISSVTLMELIYGAEKSQMPERNLAVIEGFVS--RLEVLDYDTAAATH   79 (132)
T ss_pred             hhhhHHHHHHHHhCCcHHHHHHHh-C-CCcceeehHHHHHHHHHHHHhCCCHHHHHHHHHHHHh--cCccCCCCHHHHHH
Confidence            599999999998866432222222 1 23458899888999964211      1111111 122  34444332      


Q ss_pred             ---------CCC--CChHHHHH-HHhhcCceEEEEecC-HHHHHHHhhcCCccE
Q 029889          134 ---------HKG--TYADDCLV-ERVTQHKCFIVATCD-RDLKRRIRKVRSTDL  174 (186)
Q Consensus       134 ---------H~g--~~addCI~-~~v~~~~~yiVATnD-~~LrrrlRkipGVPi  174 (186)
                               ..|  ....|+++ ..+..|+ +.|.|+| +++    ..+||+-+
T Consensus        80 ~a~i~~~l~~~g~~i~~~D~lIAA~Al~~~-~~LvT~N~kdF----~~i~gl~~  128 (132)
T PRK13725         80 TGQIRAELARQGRPVGPFDQMIAGHARSRG-LIVVTNNTREF----ERVPGIRI  128 (132)
T ss_pred             HHHHHHHHHHcCCCCChhHHHHHHHHHHCC-CEEEECCHHHH----hcCCCCcc
Confidence                     112  23345554 5667777 6888986 454    35677654

>PRK12496 hypothetical protein; Provisional

Probab=90.36  E-value=1.7  Score=35.29  Aligned_cols=98  Identities=13%  Similarity=0.050  Sum_probs=62.7

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchhhHHHHHhccC-CCceeeecCC----------
Q 029889           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKD-PRFERLPCTH----------  134 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k~r~Al~lak~-~~~e~~kC~H----------  134 (186)
                      .+++||+.++....           .+.+  .++||.-|++|+..-.  .+..+..+.. ..++...=+.          
T Consensus         3 ~~VlDtS~~I~~~~-----------~~~~--~i~tp~~V~~Ev~d~~--~~~~~~~l~~~~~i~v~~p~~~~i~~v~~~a   67 (164)
T PRK12496          3 IKVLDASAFIHGYN-----------PEDG--EHYTTPSVVEEVKDKE--SRLILESAISAGKLKILEPSPESIEKVEEAA   67 (164)
T ss_pred             EEEEEChHHHccch-----------hhCC--CEEecHHHHHHHhCHH--HHHHHHHhcccCCeEEECCCHHHHHHHHHHH
Confidence            58999999986522           1233  4799999999998732  2222222221 0122211110          


Q ss_pred             --CC-----CChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEEEeec
Q 029889          135 --KG-----TYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAF  180 (186)
Q Consensus       135 --~g-----~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~~~  180 (186)
                        .|     ..+|.-++.++...+ ..+.|.|..+++-++.. |++++-+.++
T Consensus        68 ~~tgd~~~Ls~~D~~~iaLA~el~-~~lvtDD~~~~~vA~~l-gi~v~~~~~~  118 (164)
T PRK12496         68 IKTGDLMRLSNTDIEVLALALELN-GTLYTDDYGIQNVAKKL-NIKFENIKTK  118 (164)
T ss_pred             HhcCCccccchhhHHHHHHHHHhC-CcEECcHHHHHHHHHHc-CCeEeccccc
Confidence              01     146667777777766 48999999999999999 9999988744

>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=89.88  E-value=0.86  Score=36.89  Aligned_cols=41  Identities=27%  Similarity=0.357  Sum_probs=33.8

Q ss_pred             CCCChHHHHHHHhhc----CceEEEEecCHHHHHHHhhcCCccEEE
Q 029889          135 KGTYADDCLVERVTQ----HKCFIVATCDRDLKRRIRKVRSTDLYL  176 (186)
Q Consensus       135 ~g~~addCI~~~v~~----~~~yiVATnD~~LrrrlRkipGVPiiy  176 (186)
                      .|.+||+.|.+++..    +...+|+|.|..+++.++.. |.-.|.
T Consensus        75 ~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~~-GA~~is  119 (166)
T PF05991_consen   75 EGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARGR-GAKRIS  119 (166)
T ss_pred             CCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhhC-CCEEEc
Confidence            356999999999965    24589999999999999988 776654

The function of this family is unknown.

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

Probab=89.07  E-value=0.97  Score=35.58  Aligned_cols=52  Identities=19%  Similarity=0.089  Sum_probs=42.3

Q ss_pred             CCceeeecCCCCCChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEEEee
Q 029889          125 PRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTA  179 (186)
Q Consensus       125 ~~~e~~kC~H~g~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~~  179 (186)
                      +..+..-|+.....||+-|++.+.+..  +|.|||-.|-.++-.. |+.+|.-++
T Consensus        27 ~~~~~i~Vd~g~DaaD~~I~~~~~~gD--iVITqDigLA~~~l~K-ga~vl~~rG   78 (130)
T PF02639_consen   27 PYVEMIVVDSGFDAADFYIVNHAKPGD--IVITQDIGLASLLLAK-GAYVLNPRG   78 (130)
T ss_pred             CCeEEEEECCCCChHHHHHHHcCCCCC--EEEECCHHHHHHHHHC-CCEEECCCC
Confidence            345666676644479999999998887  8999999999999998 999886443

>COG1487 VapC Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]

Probab=85.97  E-value=4.7  Score=30.66  Aligned_cols=43  Identities=19%  Similarity=0.060  Sum_probs=28.9

Q ss_pred             eEEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHH
Q 029889           65 YRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEK  110 (186)
Q Consensus        65 Y~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELek  110 (186)
                      ...++|||.+.......-.-  .+...+.. ...+++.-++.||..
T Consensus         2 ~~~llDTnv~i~l~~~~~~~--~~~~~~~~-~~~~~s~it~~El~~   44 (133)
T COG1487           2 MMYLLDTSVIIALLRGEPKE--LLELRLAE-FEIYLSSITVAELLL   44 (133)
T ss_pred             CceeeeHHHHHHHHhcCChH--HHHHHHhc-CCeeecHHHHHHHHH
Confidence            35799999999987765542  22222222 567888888888854

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

Probab=84.57  E-value=3.4  Score=37.53  Aligned_cols=80  Identities=19%  Similarity=0.115  Sum_probs=54.9

Q ss_pred             eeeecHHHHHHHHHhchh--------hHHHHHhcc------CCCceeeecCCCC-CChHHHHHHHhhcCceEEEEecCHH
Q 029889           97 TPCITDCVMAELEKLGQK--------YRVALRIAK------DPRFERLPCTHKG-TYADDCLVERVTQHKCFIVATCDRD  161 (186)
Q Consensus        97 ~~~iT~CVi~ELekLg~k--------~r~Al~lak------~~~~e~~kC~H~g-~~addCI~~~v~~~~~yiVATnD~~  161 (186)
                      .++||+-|++||..++..        =|..|++.-      .++.+.+.-+-.+ ...|.-++.+++..+ -.|.|||-.
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            589999999999998531        133444332      1134443333222 267899999998876 599999999


Q ss_pred             HHHHHhhcCCccEEEEe
Q 029889          162 LKRRIRKVRSTDLYLGT  178 (186)
Q Consensus       162 LrrrlRkipGVPiiyi~  178 (186)
                      |-+=..=. |||++.++
T Consensus       266 LnKVae~q-gV~vLNIN  281 (356)
T COG4956         266 LNKVAELQ-GVQVLNIN  281 (356)
T ss_pred             HHHHHhhc-CCceecHH
Confidence            97766655 99999765

>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]

Probab=83.61  E-value=6.7  Score=31.91  Aligned_cols=99  Identities=17%  Similarity=0.055  Sum_probs=61.3

Q ss_pred             EEeehHHHHHH-HHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchhhHHHHHhccCCCceeeecC-C---------C
Q 029889           67 VLVDTNFINFS-IQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCT-H---------K  135 (186)
Q Consensus        67 VLvDtNFl~~~-~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k~r~Al~lak~~~~e~~kC~-H---------~  135 (186)
                      |+.||+-|... .=-++++..++-    .  +++||.-|-.|++-....-   ...+.-..++.+.-. |         -
T Consensus         2 vvsdts~i~nla~ig~i~ll~~~y----e--~viip~~v~~E~~~~~~s~---~~~~~l~~iei~~~~n~~lv~~lre~L   72 (157)
T COG2405           2 VVSDTSPIINLANIGEIDLLHALY----E--KVIIPEQVAEEFEFGVNSG---VLPALLGWIEILRLKNRDLVNLLREKL   72 (157)
T ss_pred             eeecchhHHHHHhcchhhHHHHHh----h--cccCCchHHHHHHHhhccc---ccccccCceEEeccCcHHHHHHHHHhc
Confidence            67888877544 333666665443    3  3689999999999886421   111110012222211 0         1


Q ss_pred             CCChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEE
Q 029889          136 GTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYL  176 (186)
Q Consensus       136 g~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiy  176 (186)
                      +....+||. ++.+.++-.+.+.|++=|+-+.+. |+||+-
T Consensus        73 d~GEa~aIA-LA~e~~ad~Ll~Ddr~aR~~A~~l-gL~V~G  111 (157)
T COG2405          73 DKGEAEAIA-LALELKADLLLMDDRDARNVAKSL-GLKVTG  111 (157)
T ss_pred             ccchHHHHH-HHHHcCCCeeeeccHHHHHHHHHc-CCeeee
Confidence            223456665 555666669999999999999998 999984

>COG1656 Uncharacterized conserved protein [Function unknown]

Probab=81.65  E-value=2.8  Score=34.57  Aligned_cols=43  Identities=23%  Similarity=0.200  Sum_probs=36.7

Q ss_pred             CChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEEEeeccc
Q 029889          137 TYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHD  182 (186)
Q Consensus       137 ~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~~~~~  182 (186)
                      ...|+-|+.++.++++ |+-|-|++|-+|. +. |++.||+...+.
T Consensus        34 ~~~d~~i~~i~~~e~r-IllTRDr~L~~r~-k~-g~~~i~i~~~s~   76 (165)
T COG1656          34 NESDDEIILIAKKEGR-ILLTRDRELYKRA-KL-GIKAILIRSDSI   76 (165)
T ss_pred             cCCcHHHHHHHhcCCe-EEEeccHHHHHHh-hc-cCceEEEeCCCH
Confidence            4678889989888875 9999999999999 77 999999987653

---

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	186
1o4w_A	147	PIN (PILT N-terminus) domain; structural genomics,	2e-38

>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 =  127 bits (322), Expect = 2e-38
 Identities = 28/106 (26%), Positives = 49/106 (46%), Gaps = 6/106 (5%)

Query: 66  RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKD- 124
             +VDTN + +   NK D+   + +  +++    IT  V  ELEKL    R   ++A   
Sbjct: 25  CAVVDTNVLMYVYLNKADVVGQLREFGFSR--FLITASVKRELEKLEMSLRGKEKVAARF 82

Query: 125 --PRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRK 168
                E        +  D  L+E   ++ C I+ T D++LKR+ ++
Sbjct: 83  ALKLLEHFEVVETESEGDPSLIEAAEKYGC-ILITNDKELKRKAKQ 127

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	186
1o4w_A	147	PIN (PILT N-terminus) domain; structural genomics,	99.89
3ix7_A	134	Uncharacterized protein TTHA0540; unknown function	98.97
2dok_A	186	Telomerase-binding protein EST1A; telomerase-assoc	98.86
3i8o_A	142	KH domain-containing protein MJ1533; APC89320.5, m	98.73
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	97.25
3tnd_A	132	TRNA(FMet)-specific endonuclease VAPC; PIN domain,	96.36
3zvk_A	134	VAPC2, toxin of toxin-antitoxin system; antitoxin-	96.25
3h87_A	156	Putative uncharacterized protein; toxin antitoxin	95.9
1v96_A	149	Hypothetical protein PH0500; rossmann fold, tRNA s	95.57
2fe1_A	156	Conserved hypothetical protein PAE0151; PIN domain	94.67
1w8i_A	156	Putative VAPC ribonuclease AF_1683; structural gen	94.37
2hwy_A	164	Protein SMG5; RNA degradation, decay, NMD, EST1A,	93.32
2h1c_A	139	Trafficking protein B; DNA binding, PIN domain, RH	92.79
3dbo_B	150	Uncharacterized protein; toxin antitoxin complex,	90.41

>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=99.89  E-value=3.3e-23  Score=161.59  Aligned_cols=122  Identities=25%  Similarity=0.289  Sum_probs=99.2

Q ss_pred             HHHhhCCCCCeE-EEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhch--------hhHHHHHhccCC
Q 029889           55 FTHNTALGPPYR-VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ--------KYRVALRIAKDP  125 (186)
Q Consensus        55 y~~n~gf~~PY~-VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~--------k~r~Al~lak~~  125 (186)
                      ...|||||+||+ +|+|||+++.++..+.++.+.+.+++.  ..++||.||+.||+.+..        ..+.++.++.  
T Consensus        13 ~~~~~~~~~pmk~vvLDTNvli~~~~~~~~~~~~l~~~l~--~~~~I~~~vl~EL~~~~~~~~~~~~~~~~~~~~ll~--   88 (147)
T 1o4w_A           13 MEADRGRNNKVRCAVVDTNVLMYVYLNKADVVGQLREFGF--SRFLITASVKRELEKLEMSLRGKEKVAARFALKLLE--   88 (147)
T ss_dssp             ---------CCEEEEECHHHHHHHHHHTCCHHHHHHHTTE--EEEEEEHHHHHHHHHHHHHCCHHHHHHHHHHHHHHT--
T ss_pred             hhhhhccCCCCCEEEEEhhHHHHHHHcCchHHHHHHHhcc--CCEEEcHHHHHHHHHHHhccCcchHHHHHHHHHHHh--
Confidence            467999999999 999999999999999999999999875  789999999999999863        3455677777  


Q ss_pred             CceeeecCCCCCChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEEEeeccccCC
Q 029889          126 RFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIGI  185 (186)
Q Consensus       126 ~~e~~kC~H~g~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~~~~~~~~  185 (186)
                      .++.++|+ .+ + |+||++.+..++ ++|+|+|++|+++++.. |||++|+++.....+
T Consensus        89 ~~~vv~~~-~~-~-D~~Ila~A~~~~-~~LvT~D~~l~~~a~~~-Gv~vi~~~~~~~~~~  143 (147)
T 1o4w_A           89 HFEVVETE-SE-G-DPSLIEAAEKYG-CILITNDKELKRKAKQR-GIPVGYLKEDKRVFV  143 (147)
T ss_dssp             TSEEECCS-SC-S-HHHHHHHHHHHT-CEEECCCHHHHHHHHHT-TCCEECCCCCCCCCC
T ss_pred             cCcEeeCC-CC-c-hHHHHHHHHHhC-CEEEECCHHHHHHHHHC-CCeEEEecCCcEEEE
Confidence            46788887 45 7 999999998887 79999999999999999 999999999877654

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

Probab=98.97  E-value=3.1e-09  Score=82.97  Aligned_cols=101  Identities=19%  Similarity=0.166  Sum_probs=73.3

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhccc---ceeeecHHHHHHHHHhch--------hhHHHHHhccC----CCceeee
Q 029889           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAK---CTPCITDCVMAELEKLGQ--------KYRVALRIAKD----PRFERLP  131 (186)
Q Consensus        67 VLvDtNFl~~~~~~kldl~~~l~~~L~~k---~~~~iT~CVi~ELekLg~--------k~r~Al~lak~----~~~e~~k  131 (186)
                      .++|||+|+..         .+.+++...   -.++||.+|++||+.+..        +-+.+|++.+.    ..++...
T Consensus         8 ~vlDTSviIdG---------ri~~~~~~gf~eg~liIP~~Vl~ELq~lA~s~d~~~r~rGr~gL~iL~~L~~~~~vei~~   78 (134)
T 3ix7_A            8 KVLDTSVLVDG---------RVAEVAAVGFLEGPLWVPHFVLKELQHFADSQDPLRRAKGRRGLETLERLREAAPLEVLE   78 (134)
T ss_dssp             EEECHHHHHHC---------HHHHHHTTTCCCSCEEEEHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHSCEEEEC
T ss_pred             eEcccceEEec---------HHHHHHHhccccCceecHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHhcCCEEEeC
Confidence            47799999854         222222211   269999999999999962        24556666552    1134432


Q ss_pred             cCCC-CCChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEEEee
Q 029889          132 CTHK-GTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTA  179 (186)
Q Consensus       132 C~H~-g~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~~  179 (186)
                       +.. +..+|+.|++++.+.++ +|.|+|..|++.++.. |||++|++.
T Consensus        79 -~~~~~~~vD~~ll~lA~~~~~-~lvTnD~~L~kvA~~~-GI~Vl~l~~  124 (134)
T 3ix7_A           79 -TTPKGESVDEKLLFLARDLEA-ALVTNDHALLQMARIY-GVKALSIQA  124 (134)
T ss_dssp             -CCCSCSSHHHHHHHHHHHTTC-EEEESCHHHHHHHHHT-TCCEEEHHH
T ss_pred             -CCCCcccHHHHHHHHHHHhCC-EEEeCCHHHHHHHHHC-CCeEEehHH
Confidence             222 24799999999999885 9999999999999999 999999864

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

Probab=98.86  E-value=9.4e-09  Score=82.93  Aligned_cols=108  Identities=18%  Similarity=0.150  Sum_probs=73.7

Q ss_pred             CeEEEeehHHHHHHHHcCCChHHhHHHhhc-ccceeeecHHHHHHHHHhch-----------------hhHHHHHhccC-
Q 029889           64 PYRVLVDTNFINFSIQNKLDLEKGMMDCLY-AKCTPCITDCVMAELEKLGQ-----------------KYRVALRIAKD-  124 (186)
Q Consensus        64 PY~VLvDtNFl~~~~~~kldl~~~l~~~L~-~k~~~~iT~CVi~ELekLg~-----------------k~r~Al~lak~-  124 (186)
                      |..+++|||+|+..       .+.|.++.. +...++||..|+.||+.+..                 ..|.|+++..+ 
T Consensus        12 ~~~~VlDTNvLl~~-------~~~l~~~~~~~~~~viIP~~VleELd~lk~~~~~~~~~~~~~~~~~~~AR~a~~~L~~~   84 (186)
T 2dok_A           12 PLFLVPDTNGFIDH-------LASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGGYARVVQEKARKSIEFLEQR   84 (186)
T ss_dssp             EEEEEECHHHHHHH-------HHHHHHHHHHTSSEEEEEHHHHHHHHHHHC-------CCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEhHHHHcC-------HHHHHHHHcCCCeEEEECHHHHHHHHHhccCCCccccccchhHHHHHHHHHHHHHHHHH
Confidence            45689999999776       344555443 45889999999999999832                 34555554432 


Q ss_pred             -----CCcee----------eecCCC-----CCChHHHHHHHhhcC--------------------ceEEEEecCHHHHH
Q 029889          125 -----PRFER----------LPCTHK-----GTYADDCLVERVTQH--------------------KCFIVATCDRDLKR  164 (186)
Q Consensus       125 -----~~~e~----------~kC~H~-----g~~addCI~~~v~~~--------------------~~yiVATnD~~Lrr  164 (186)
                           +.+..          +...+.     ...+|+.|++.+...                    ...++.|+|..||.
T Consensus        85 ~~~~~~~i~~~~~~g~~l~~v~~~~~~~~~~~~~~D~~IL~~a~~l~~~~~~~~~~~~~~~~~~~~~~vvLvTnD~nLr~  164 (186)
T 2dok_A           85 FESRDSCLRALTSRGNELESIAFRSEDITGQLGNNDDLILSCCLHYCKDKAKDFMPASKEEPIRLLREVVLLTDDRNLRV  164 (186)
T ss_dssp             HHTTCTTEEEECTTSCEESCCTTCCCCC----CCHHHHHHHHHHTTCCCCGGGGCCC---CCCEEEEEEEEECCCHHHHH
T ss_pred             HhhCCCeEEEEeccCcccccccccccccccCCCCccHHHHHHHHHHHHhcccccccccccccccCCCcEEEEeCcHHHHH
Confidence                 11110          001111     237899999998631                    14789999999999


Q ss_pred             HHhhcCCccEEEEee
Q 029889          165 RIRKVRSTDLYLGTA  179 (186)
Q Consensus       165 rlRkipGVPiiyi~~  179 (186)
                      +++.. |||++.++.
T Consensus       165 KA~~~-Gi~~~~~~~  178 (186)
T 2dok_A          165 KALTR-NVPVRDIPA  178 (186)
T ss_dssp             HHHHT-TCCEECHHH
T ss_pred             HHHHC-CCeeCcHHH
Confidence            99999 999987653

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

Probab=98.73  E-value=4.6e-08  Score=77.06  Aligned_cols=110  Identities=16%  Similarity=0.092  Sum_probs=77.2

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchh----hHHHHHhccC---------CCceeeec
Q 029889           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK----YRVALRIAKD---------PRFERLPC  132 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k----~r~Al~lak~---------~~~e~~kC  132 (186)
                      .+++|||.|+.-.     +.+.+..-+.....++||..|++||+.+...    -+.+|++++.         ..++...-
T Consensus         5 ~~vlDTSviIdGr-----I~~~~~~g~leg~~iiIP~~Vl~EL~~~a~~~r~~GrrGLe~L~~L~~~~~~~~i~vei~~~   79 (142)
T 3i8o_A            5 KVCVDTCVVIDGR-----ITELIERGKLKDATIIIPEAVVSELEYQANMGREIGYKGIEELRKLIEKASEHNIKVEYYGE   79 (142)
T ss_dssp             EEEECHHHHHTTH-----HHHHHHTTTTTTCEEEEEHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHTTCCEEEESC
T ss_pred             EEEeecceEEEcH-----HHHHHHcCCccCCeEEehHHHHHHHHHHHHccchhhHHHHHHHHHHHHHhhccCceEEEecc
Confidence            6899999998541     3333333333335799999999999999542    3455555441         01121100


Q ss_pred             C-------C-CCCChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEEEeeccc
Q 029889          133 T-------H-KGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHD  182 (186)
Q Consensus       133 ~-------H-~g~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~~~~~  182 (186)
                      .       + .+..+|+-|+++|.+.++ .|.|+|..|++.++.. |||++|+++..+
T Consensus        80 r~~~~~i~~~~~~~vD~~l~~lA~~~~a-~lvTnD~~l~kvA~~~-GI~V~~l~~~~~  135 (142)
T 3i8o_A           80 RPTREEIFLAKSGEIDAMIRKVAKETNS-ILLTSDWIQYNLAKAQ-GIEAYFLEAAEE  135 (142)
T ss_dssp             CCCHHHHHSCCSSSHHHHHHHHHHHTTC-EEEESCHHHHHHHHHT-TCCEEECCCCCC
T ss_pred             cCchhhhccccCCcHHHHHHHHHHHhCC-EEEcCCHHHHHHHHHc-CCEEEEeccccc
Confidence            0       1 124789999999999884 8889999999999999 999999998765

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

Probab=97.25  E-value=0.00013  Score=57.28  Aligned_cols=93  Identities=12%  Similarity=0.083  Sum_probs=63.1

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchhhHHHHHhcc-CCCceeee-c-----------
Q 029889           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAK-DPRFERLP-C-----------  132 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k~r~Al~lak-~~~~e~~k-C-----------  132 (186)
                      .+|+|||.|+...    ++            .++||..|+.||....  .+..+..+. ...++... .           
T Consensus        12 ~~VlDTs~lI~~~----~~------------~l~~p~~V~~El~~~~--~r~~l~~l~~~~~l~v~~~~~~~i~~v~~~~   73 (165)
T 2lcq_A           12 TLVLDSSVFIQGI----DI------------EGYTTPSVVEEIKDRE--SKIFLESLISAGKVKIAEPSKESIDRIIQVA   73 (165)
T ss_dssp             SCEECHHHHHHTC----CC------------CEEECHHHHTTCCSSH--HHHHHHHHHHTTSEEECCCCHHHHHHHHHHH
T ss_pred             EEEEcChHHHcCC----CC------------CEEEChhhHHhhcCHH--HHHHHHHhhccCCEEEecCCHHHHHHHHHHH
Confidence            4799999999853    11            7899999999996432  222332221 10122210 0           


Q ss_pred             ---CC-CC-CChHHHHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEEEe
Q 029889          133 ---TH-KG-TYADDCLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGT  178 (186)
Q Consensus       133 ---~H-~g-~~addCI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~  178 (186)
                         +. .+ ..+|..++.++.+.+. .|.|+|..|++.++.. ||+++.+.
T Consensus        74 ~~~gd~~~Ls~~D~~lIaLA~~l~~-~lvT~D~~l~~vA~~~-Gv~v~~~~  122 (165)
T 2lcq_A           74 KETGEVNELSKADIEVLALAYELKG-EIFSDDYNVQNIASLL-GLRFRTLK  122 (165)
T ss_dssp             HHHSCSSCSCHHHHHHHHHHHHHTC-CEECCCHHHHHHHHHT-TCCEECCS
T ss_pred             HHcCCcccCCHHHHHHHHhHHHhCC-eEEcCcHHHHHHHHHC-CCeEEchh
Confidence               00 01 2488999999988774 8889999999999999 99999776

>3tnd_A TRNA(FMet)-specific endonuclease VAPC; PIN domain, spovt/ABRB-like domain, ribonuclease, DNA-bindin translation; 2.70A {Shigella flexneri}

Probab=96.36  E-value=0.023  Score=41.48  Aligned_cols=100  Identities=20%  Similarity=0.267  Sum_probs=61.6

Q ss_pred             EEEeehHHHHHHHHcCCC-hHHhHHHhhcccceeeecHHHHHHHHHhchh------hHHHH-HhccCCCceeeecC----
Q 029889           66 RVLVDTNFINFSIQNKLD-LEKGMMDCLYAKCTPCITDCVMAELEKLGQK------YRVAL-RIAKDPRFERLPCT----  133 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kld-l~~~l~~~L~~k~~~~iT~CVi~ELekLg~k------~r~Al-~lak~~~~e~~kC~----  133 (186)
                      .+|+|||.++..+...-+ +.+.+....   -.++|+.-++.|+...-.+      ....+ .+..  .++.++-+    
T Consensus         3 ~~llDTnvli~~~~~~~~~~~~~l~~~~---~~~~iS~i~~~El~~~~~~~~~~~~~~~~l~~~l~--~~~il~~~~~~~   77 (132)
T 3tnd_A            3 KFMLDTNICIFTIKNKPASVRERFNLNQ---GKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVS--RIDVLDYDAAAA   77 (132)
T ss_dssp             CEEECHHHHHHHHHHCCHHHHHHHHHHT---TSEEEEHHHHHHHHHHHHTSSCHHHHHHHHHHHHH--TSEEECBCHHHH
T ss_pred             eeeeeHHHHHHHHcCCcHHHHHHHHhcC---CCEEeeHHHHHHHHHHHHhcCcHHHHHHHHHHHHH--cCcccCCCHHHH
Confidence            489999999999876643 444444432   3689999999999754211      11112 1222  34444432    


Q ss_pred             -----------CCC--CChHHHH-HHHhhcCceEEEEecC-HHHHHHHhhcCCccEE
Q 029889          134 -----------HKG--TYADDCL-VERVTQHKCFIVATCD-RDLKRRIRKVRSTDLY  175 (186)
Q Consensus       134 -----------H~g--~~addCI-~~~v~~~~~yiVATnD-~~LrrrlRkipGVPii  175 (186)
                                 |.|  ....||+ ...+..+++ .+.|.| +++    ..+||+.+.
T Consensus        78 ~~a~~l~~~~~~~g~~~~~~D~lIaA~A~~~~~-~lvT~d~~dF----~~~~gl~v~  129 (132)
T 3tnd_A           78 THTGQIRAELARQGRPVGPFDQMIAGHARSRGL-IIVTNNTREF----ERVGGLRTE  129 (132)
T ss_dssp             HHHHHHHHHHHHHTCCCCHHHHHHHHHHHHTTC-EEEESCCHHH----HTSTTCCEE
T ss_pred             HHHHHHHHHHHHCCCCCCchHHHHHHHHHHcCC-EEEECCHHHh----CCCCCCeec
Confidence                       112  2444454 466677886 788999 876    457899875

>3zvk_A VAPC2, toxin of toxin-antitoxin system; antitoxin-toxin-DNA complex, protein-DNA complex; HET: DNA MES; 2.50A {Rickettsia felis}

Probab=96.25  E-value=0.018  Score=42.19  Aligned_cols=102  Identities=20%  Similarity=0.204  Sum_probs=61.8

Q ss_pred             EEEeehHHHHHHHHcCCC-hHHhHHHhhcccceeeecHHHHHHHHHhchh------hHHHH-HhccCCCceeeecCC---
Q 029889           66 RVLVDTNFINFSIQNKLD-LEKGMMDCLYAKCTPCITDCVMAELEKLGQK------YRVAL-RIAKDPRFERLPCTH---  134 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kld-l~~~l~~~L~~k~~~~iT~CVi~ELekLg~k------~r~Al-~lak~~~~e~~kC~H---  134 (186)
                      .+|+|||.++..+...-. +.+.+..+.. .-.++|+.-++.|+...-.+      ....+ .+..  .++.++.+.   
T Consensus         2 ~~llDTnvli~~~~~~~~~~~~~l~~~~~-~~~~~is~i~~~El~~~~~~~~~~~~~~~~l~~~l~--~~~il~~~~~~~   78 (134)
T 3zvk_A            2 IYMLGTNICVYAINKHPDSYYNNLELLAK-NNTIAISSIVLAELQYGVSKSKKKEQNQSKLDIFLS--RLEIIDFSAKCT   78 (134)
T ss_dssp             EEEECHHHHHHHHHHCCHHHHHHHHHHHT-TSEEEEEHHHHHHHHHHHHHSSCHHHHHHHHHHHHT--TSEEECBCHHHH
T ss_pred             eEEeeHHHHHHHHcCCcHHHHHHHHhcCc-CCcEEeeheeHHHHHHHHHhcCCHHHHHHHHHHHHh--cCceecCCHHHH
Confidence            589999999999876643 3344444332 14789999999999754211      11222 1222  355554421   


Q ss_pred             ------------CC--CC-hHHHHHHHhhcCceEEEEecC-HHHHHHHhhcCCccEE
Q 029889          135 ------------KG--TY-ADDCLVERVTQHKCFIVATCD-RDLKRRIRKVRSTDLY  175 (186)
Q Consensus       135 ------------~g--~~-addCI~~~v~~~~~yiVATnD-~~LrrrlRkipGVPii  175 (186)
                                  .|  .. .|--|...+..+++ .+.|.| +++.    .+||+.++
T Consensus        79 ~~a~~l~~~~~~~g~~~~~~D~lIaA~A~~~~~-~lvT~d~~df~----~~~gl~~~  130 (134)
T 3zvk_A           79 FYYGELRTELEQKGLIIGNNDLLIASHAIAENA-TLVTNNIKEFK----RIPNLILE  130 (134)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTC-EEEESSTTTSC----SCTTCEEE
T ss_pred             HHHHHHHHHHHHcCCCCCccHHHHHHHHHHCCC-EEEECCHHHhc----CCCCCeee
Confidence                        12  23 44444466677886 788999 7664    57888875

>3h87_A Putative uncharacterized protein; toxin antitoxin complex, vapbc complex, RHH motif, structura genomics; 1.49A {Mycobacterium tuberculosis}

Probab=95.90  E-value=0.047  Score=42.56  Aligned_cols=115  Identities=15%  Similarity=0.027  Sum_probs=69.0

Q ss_pred             CCCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhch---hhHHHHHh--ccCCCceeeecC--
Q 029889           61 LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ---KYRVALRI--AKDPRFERLPCT--  133 (186)
Q Consensus        61 f~~PY~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~---k~r~Al~l--ak~~~~e~~kC~--  133 (186)
                      ...+..+|||||.++..+...  ....+.+.+.. -.++|+.-++.||..-..   .......+  ..  .++.++.+  
T Consensus        15 ~~~~~~~LLDTnvli~~l~~~--~~~~l~~~~~~-~~l~iS~it~~El~~G~~~~~~~~~l~~~~~L~--~~~vlp~d~~   89 (156)
T 3h87_A           15 MVTDQRWLIDKSALVRLTDSP--DMEIWSNRIER-GLVHITGVTRLEVGFSAECGEIARREFREPPLS--AMPVEYLTPR   89 (156)
T ss_dssp             --CCCCEEECHHHHTTGGGCT--THHHHHHHHHT-TCEEEEHHHHHHHHHHSSSHHHHHHHHHSTTGG--GSCEECCCHH
T ss_pred             hhcCCCEEEEHHHHHHHHcCH--HHHHHHHhccC-CCEEEccccHHHHhhhhhCchHHHHHHHhhccc--CCCeecCCHH
Confidence            345668999999999987543  34556665543 247899999999975311   12222222  22  34444432  


Q ss_pred             -----------------CCCCChHHHHH-HHhhcCceEEEEecCHHHHHHHhhcCCccEEEEeeccc
Q 029889          134 -----------------HKGTYADDCLV-ERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHD  182 (186)
Q Consensus       134 -----------------H~g~~addCI~-~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~~~~~  182 (186)
                                       |.+....||++ ..+..++ ..+.|+|+++.+--. +.|.|+-.+.....
T Consensus        90 ~a~~a~~i~~~l~~~G~~~~i~~~D~lIAAtA~~~g-l~LvT~d~dF~~i~~-~~~l~~~~~~~~~~  154 (156)
T 3h87_A           90 IEDRALEVQTLLADRGHHRGPSIPDLLIAATAELSG-LTVLHVDKDFDAIAA-LTGQKTERLTHRPP  154 (156)
T ss_dssp             HHHHHHHHHHHHHHTTCTTSSCHHHHHHHHHHHHHT-CEEEESCTHHHHHHH-HHCCCEEECCCC--
T ss_pred             HHHHHHHHHHHHHhcCCCCCCChhHHHHHHHHHHCC-CEEEEeChhhhhhhh-cCCCceEEecCCCC
Confidence                             11224556655 4556677 577799999876544 44888887765543

>1v96_A Hypothetical protein PH0500; rossmann fold, tRNA synthetase, nucleotide binding protein, structural genomics; 1.75A {Pyrococcus horikoshii} SCOP: c.120.1.1 PDB: 1ye5_A 1y82_A

Probab=95.57  E-value=0.038  Score=41.16  Aligned_cols=104  Identities=13%  Similarity=0.087  Sum_probs=60.2

Q ss_pred             eEEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchh----hHHHH-HhccCCCceeeecC------
Q 029889           65 YRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK----YRVAL-RIAKDPRFERLPCT------  133 (186)
Q Consensus        65 Y~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k----~r~Al-~lak~~~~e~~kC~------  133 (186)
                      -.+++|||.++..+.   +-...+.+.+.+...++++.-++.|+...-..    -...+ .+..  .++.++.+      
T Consensus         5 ~~~llDTnvli~~l~---~~~~~~~~~~~~~~~~~is~i~~~El~~~~~~~~~~~~~~~~~~l~--~~~il~~~~~~~~~   79 (149)
T 1v96_A            5 PDITFDSLALIKMHS---QNMKRILEVTLAKFTVNLSIVTVYRYLTARAYLKKNIEAEFEILKD--IYNIVPLLDDIAIK   79 (149)
T ss_dssp             SEEEECHHHHHHHTS---GGGHHHHHHHHHHCEEEEEHHHHHHHHHHC--CCSCHHHHHHHHHH--HSEEECCCHHHHHH
T ss_pred             CEEEeehHHHHHHHc---cchHHHHHHHhcCCCEEeeHhhHHHHHHHHHhcCcchHHHHHHHHh--cCCeeCCCHHHHHH
Confidence            469999999999875   22234444444445689999999999854211    01111 1111  23333332      


Q ss_pred             -------C--CC--CChHHHHH-HHhhcCceEEEEecCH-HHHHHHhhcCCccEEE
Q 029889          134 -------H--KG--TYADDCLV-ERVTQHKCFIVATCDR-DLKRRIRKVRSTDLYL  176 (186)
Q Consensus       134 -------H--~g--~~addCI~-~~v~~~~~yiVATnD~-~LrrrlRkipGVPiiy  176 (186)
                             +  .|  .+..||++ ..+..+++ .+.|.|. ++.+ +... |++++.
T Consensus        80 a~~l~~~~~~~g~~~~~~D~lIaA~A~~~~~-~lvT~D~kdf~~-i~~~-~i~~i~  132 (149)
T 1v96_A           80 AAQIEANLIKKEITLDMEDIITATTAIYTNS-LLVTDDPKRYEP-IRRF-GLDTMP  132 (149)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHHHTC-EEEESCHHHHGG-GGGG-TCCEEE
T ss_pred             HHHHHHHHHHCCCCCCHhHHHHHHHHHHcCC-EEEECCHHHHhh-hhhC-CeeecC
Confidence                   0  12  34456655 66677786 6889995 6643 5555 777774

>2fe1_A Conserved hypothetical protein PAE0151; PIN domain, structural genomics, unknown function; 2.20A {Pyrobaculum aerophilum} SCOP: c.120.1.1

Probab=94.67  E-value=0.058  Score=41.07  Aligned_cols=104  Identities=16%  Similarity=0.105  Sum_probs=62.7

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHh-------ch----hhHHHHHh----ccCCCceee
Q 029889           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKL-------GQ----KYRVALRI----AKDPRFERL  130 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekL-------g~----k~r~Al~l----ak~~~~e~~  130 (186)
                      .+++|||.++..+... +..+.+.+.+.+...++++.-++.|+...       |+    ....++..    .....+...
T Consensus        27 ~ivlDTsvli~~l~~~-~~~~~a~~~l~~~~~~~is~~~~~Ev~~vl~r~~~~~~l~~~~~~~~l~~~~~~l~~l~i~~~  105 (156)
T 2fe1_A           27 ELVVDASAIAALYVPE-ERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHSY  105 (156)
T ss_dssp             EEEECHHHHHTTSSSC-CCCHHHHHHHHHCSEEEEEHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHTTSEEECG
T ss_pred             eEEEEHHHHHHHHhCC-CCcHHHHHHHhhccCeehHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHhcccccc
Confidence            5899999999987543 22355566665545789999999999642       11    12222222    221111111


Q ss_pred             e----------cCCCCCChHHHH-HHHhhcCceEEEEecCHHHHHHHhhcCCcc
Q 029889          131 P----------CTHKGTYADDCL-VERVTQHKCFIVATCDRDLKRRIRKVRSTD  173 (186)
Q Consensus       131 k----------C~H~g~~addCI-~~~v~~~~~yiVATnD~~LrrrlRkipGVP  173 (186)
                      .          -.| +.+..||+ +..+..+++ -++|.|++|.+..+.. |+|
T Consensus       106 ~~~~~~A~~l~~~~-~l~~~Dal~lA~A~~~~~-~LvT~D~~l~~~a~~~-Gi~  156 (156)
T 2fe1_A          106 AEVLKDAFALALKH-GVTVYDAAYVALAEKIGG-KLLTLDRQLAEKFPAL-VTP  156 (156)
T ss_dssp             GGTHHHHHHHHHHH-TCCHHHHHHHHHHHHHTC-EEECSCHHHHHHCTTT-BC-
T ss_pred             hHHHHHHHHHHHHh-CcCHHHHHHHHHHHHcCC-CEEeCCHHHHHHHHHc-CCC
Confidence            1          011 32444554 567777776 4999999999998886 875

>1w8i_A Putative VAPC ribonuclease AF_1683; structural genomics, unknown function, hypothetical protein, PSI, protein structure initiative, MCSG; 2.10A {Archaeoglobus fulgidus} SCOP: c.120.1.1

Probab=94.37  E-value=0.12  Score=38.98  Aligned_cols=98  Identities=12%  Similarity=-0.057  Sum_probs=58.5

Q ss_pred             EEEeehHHHHHHHHcCCChHH----hHH-HhhcccceeeecHHHHHHHHHhch----hhHHHHHhc-cCCCceeeecC--
Q 029889           66 RVLVDTNFINFSIQNKLDLEK----GMM-DCLYAKCTPCITDCVMAELEKLGQ----KYRVALRIA-KDPRFERLPCT--  133 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~----~l~-~~L~~k~~~~iT~CVi~ELekLg~----k~r~Al~la-k~~~~e~~kC~--  133 (186)
                      .++||||+++..+...=...+    .+. .+..+...++|+.-|+.|+...-.    .....++.. ..+.++.++.+  
T Consensus         2 mi~lDTnvli~~l~~~~~~~~~a~~~l~~~~~~~~~~~~is~~vl~E~~~~l~~~~~~~~~~l~~l~~~~~~~v~~~~~~   81 (156)
T 1w8i_A            2 AALIDTGIFFGFYSLKDVHHMDSVAIVVHAVEGKWGRLFVTNHILDETLTLLKYKKLPADKFLEGFVESGVLNIIYTDDE   81 (156)
T ss_dssp             EEEECHHHHHHHHCTTSTTHHHHHHHHHHHHTTTTSEEEEEHHHHHHHHHHHHHTTCCHHHHHHHHTTTSSSEEECCCHH
T ss_pred             eEEEEhHHHHHHHcCCcHhHHHHHHHHHHHHhcCCCcEEecHHHHHHHHHHHHhhHHHHHHHHHHHhhCCCeEEEeCCHH
Confidence            489999999999865433222    233 344446789999999999976522    222222222 11234443321  


Q ss_pred             ------------CC--CCChHHHH-HHHhhcCceEEEEecCHHHHH
Q 029889          134 ------------HK--GTYADDCL-VERVTQHKCFIVATCDRDLKR  164 (186)
Q Consensus       134 ------------H~--g~~addCI-~~~v~~~~~yiVATnD~~Lrr  164 (186)
                                  +.  +.+..||+ ...+..+++ .++|.|+++.+
T Consensus        82 ~~~~A~~l~~~~~~~~~l~~~Dali~A~A~~~g~-~l~T~D~dF~~  126 (156)
T 1w8i_A           82 VERKALEVFKARVYEKGFSYTDAISEVVAEELKL-KLISYDSRFSL  126 (156)
T ss_dssp             HHHHHHHHHHHTTTSTTCCHHHHHHHHHHHHHTC-EEECSCTTCSS
T ss_pred             HHHHHHHHHHHHhccCCCCHhHHHHHHHHHHcCC-EEEEeCcccCc
Confidence                        11  23444555 566777887 99999988765

>2hwy_A Protein SMG5; RNA degradation, decay, NMD, EST1A, P bodies, RNA binding protein; 2.75A {Homo sapiens}

Probab=93.32  E-value=0.12  Score=41.18  Aligned_cols=51  Identities=18%  Similarity=0.206  Sum_probs=36.3

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhch---hhHHHHHhc
Q 029889           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ---KYRVALRIA  122 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~---k~r~Al~la  122 (186)
                      ..++|||+|+..    +++...|.+  .++..++||.-|+.||..|.+   .+|.|+++.
T Consensus         4 ylVlDTN~Li~~----l~~i~~l~~--~~~~~IvIP~~Vi~ELD~LK~~~~~AR~Air~L   57 (164)
T 2hwy_A            4 YLVPDTQALCHH----LPVIRQLAT--SGRFIVIIPRTVIDGLDLLKKEHPGARDGIRYL   57 (164)
T ss_dssp             EEEECHHHHHHC----HHHHHHHHH--HSSSEEEECHHHHHHHHHHC-CCHHHHHHHHHH
T ss_pred             eEEechHHHHhC----HHHHHHHHh--CCCcEEEEcHHHHHHHHHhccCCHHHHHHHHHH
Confidence            357899999875    233344432  257899999999999999954   367777665

>2h1c_A Trafficking protein B; DNA binding, PIN domain, RHH domain, gene regulation; 1.80A {Neisseria gonorrhoeae} SCOP: c.120.1.1 PDB: 2bsq_A* 2h1o_A*

Probab=92.79  E-value=0.5  Score=33.86  Aligned_cols=99  Identities=22%  Similarity=0.240  Sum_probs=57.3

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhc--ccceeeecHHHHHHHHHh-chh--------hHHHHHh--ccCCCc--eeee
Q 029889           67 VLVDTNFINFSIQNKLDLEKGMMDCLY--AKCTPCITDCVMAELEKL-GQK--------YRVALRI--AKDPRF--ERLP  131 (186)
Q Consensus        67 VLvDtNFl~~~~~~kldl~~~l~~~L~--~k~~~~iT~CVi~ELekL-g~k--------~r~Al~l--ak~~~~--e~~k  131 (186)
                      +++|||.++..+...-+  ....+.|.  +...++|+.-++.|+... .+.        ....++-  ..  .+  +.++
T Consensus         2 ~llDTnvli~~~~~~~~--~~~~~~l~~~~~~~~~is~~~~~El~~~~~~~~~~~~~~~~~~~l~~~l~~--~~~~~il~   77 (139)
T 2h1c_A            2 ILLDTNVISEPLRPQPN--ERVVAWLDSLILEDVYLSAITVAELRLGVALLLNGKKKNVLHERLEQSILP--LFAGRILP   77 (139)
T ss_dssp             EEECHHHHTGGGSSSCC--HHHHHHHHHSCGGGEEEEHHHHHHHHHHHHTCSCHHHHHHHHHHHHHTTGG--GGTTCEEC
T ss_pred             EeeehHHHHHHHcCCCC--HHHHHHHHhCCcccEEeeHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHH--hccCCcCC
Confidence            68999999998765431  22333332  234689999999999754 221        1112221  12  23  4444


Q ss_pred             cCC---------------CC--CChHHHH-HHHhhcCceEEEEecC-HHHHHHHhhcCCccEE
Q 029889          132 CTH---------------KG--TYADDCL-VERVTQHKCFIVATCD-RDLKRRIRKVRSTDLY  175 (186)
Q Consensus       132 C~H---------------~g--~~addCI-~~~v~~~~~yiVATnD-~~LrrrlRkipGVPii  175 (186)
                      .+.               .|  ....||+ ...+..+++ .+.|.| +++.+    + |++++
T Consensus        78 ~~~~~~~~a~~l~~~~~~~g~~~~~~D~liaA~A~~~~~-~lvT~d~~df~~----~-~l~~~  134 (139)
T 2h1c_A           78 FDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSL-TVATRDTGSFFA----A-DVAVF  134 (139)
T ss_dssp             CCHHHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHHHHTC-EEECSCCHHHHH----T-TCCEE
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCCccHHHHHHHHHHcCC-eEEECCHHHHhh----C-CCeee
Confidence            331               12  2444554 456667786 789999 77754    4 77765

>3dbo_B Uncharacterized protein; toxin antitoxin complex, vapbc, structural genomics, PSI-2, protein structure initiative; 1.76A {Mycobacterium tuberculosis}

Probab=90.41  E-value=0.43  Score=36.54  Aligned_cols=104  Identities=18%  Similarity=0.147  Sum_probs=55.6

Q ss_pred             CCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHh----chh--hHHHHH---hccCCCceeeec
Q 029889           62 GPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKL----GQK--YRVALR---IAKDPRFERLPC  132 (186)
Q Consensus        62 ~~PY~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekL----g~k--~r~Al~---lak~~~~e~~kC  132 (186)
                      .+|-++|+|||.++..++..-.. .    .+ ..-.++|+.-++.||..-    +..  ....++   +..  .|+.++-
T Consensus        18 ~~~~~~LlDTnvlI~~l~g~~~~-~----~~-~~~~l~iS~It~~El~~G~~~~~~~~~~~~~l~~~~~l~--~~~ilp~   89 (150)
T 3dbo_B           18 TTPAAGVLDTSVFIATESGRQLD-E----AL-IPDRVATTVVTLAELRVGVLAAATTDIRAQRLATLESVA--DMETLPV   89 (150)
T ss_dssp             --CCEEEECSGGGBC-----CCC-G----GG-SCSEEEEEHHHHHHHHHHHHHCSSHHHHHHHHHHHHTTT--TBCEECC
T ss_pred             cccCEEEEeHHHHHHHHcCCcch-h----hc-CCCcEEEchhHHHHHHHHHHhCcchHHHHHHHHHHHHhh--CCeEecc
Confidence            56778999999999887655322 2    22 345789999999998643    111  112232   222  4665554


Q ss_pred             CC---------------CC--CChHHHH-HHHhhcCceEEEEecCHHHHHHHhhcCCccEE
Q 029889          133 TH---------------KG--TYADDCL-VERVTQHKCFIVATCDRDLKRRIRKVRSTDLY  175 (186)
Q Consensus       133 ~H---------------~g--~~addCI-~~~v~~~~~yiVATnD~~LrrrlRkipGVPii  175 (186)
                      +.               .|  ...-||+ ...+..++. .+.|+|+++.+ +-.+-|.+++
T Consensus        90 d~~~a~~a~~l~~~l~~~G~~~~~~D~lIaA~A~~~~~-~LvT~d~dF~~-i~~l~~l~~~  148 (150)
T 3dbo_B           90 DDDAARMWARLRIHLAESGRRVRINDLWIAAVAASRAL-PVITQDDDFAA-LDGAASVEII  148 (150)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCCCBHHHHHHHHHHHHTTC-CEEESSSSGGG-GTTSTTCCEE
T ss_pred             CHHHHHHHHHHHHHHHHcCCCCCCchHHHHHHHHHCCC-EEEECChhhhh-CCCccCceee
Confidence            31               12  2334554 456667774 78899976533 3333344543

---

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	186
d1o4wa_	125	c.120.1.1 (A:) Hypothetical protein AF0591 {Archae	1e-30

>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 =  106 bits (265), Expect = 1e-30
 Identities = 28/106 (26%), Positives = 49/106 (46%), Gaps = 6/106 (5%)

Query: 66  RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKD- 124
             +VDTN + +   NK D+   + +  +++    IT  V  ELEKL    R   ++A   
Sbjct: 4   CAVVDTNVLMYVYLNKADVVGQLREFGFSRF--LITASVKRELEKLEMSLRGKEKVAARF 61

Query: 125 --PRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRK 168
                E        +  D  L+E   ++ C I+ T D++LKR+ ++
Sbjct: 62  ALKLLEHFEVVETESEGDPSLIEAAEKYGC-ILITNDKELKRKAKQ 106

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	186
d1o4wa_	125	Hypothetical protein AF0591 {Archaeon Archaeoglobu	99.95
d1v96a1	148	Hypothetical protein PH0500 {Pyrococcus horikoshii	96.79
d2fe1a1	130	Conserved hypothetical protein PAE0151 {Pyrobaculu	96.74
d1w8ia_	155	Hypothetical protein AF1683 {Archaeoglobus fulgidu	95.18
d2h1ca1	138	Trafficking protein B {Neisseria gonorrhoeae [TaxI	93.31

>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=99.95  E-value=6.2e-29  Score=189.26  Aligned_cols=117  Identities=24%  Similarity=0.262  Sum_probs=94.7

Q ss_pred             eEEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchhhHHHHHhccC---CCceeeecCCCCCChHH
Q 029889           65 YRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKD---PRFERLPCTHKGTYADD  141 (186)
Q Consensus        65 Y~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k~r~Al~lak~---~~~e~~kC~H~g~~add  141 (186)
                      ..||||||||++++++++|+.++++++  +..+++||.||+.||++|+++.+++...++.   ..++..++.+.+.++||
T Consensus         3 ~~~llDtn~l~~~~~~~id~~~~l~~~--~~~~~~ip~~Vi~EL~~L~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~Dd   80 (125)
T d1o4wa_           3 RCAVVDTNVLMYVYLNKADVVGQLREF--GFSRFLITASVKRELEKLEMSLRGKEKVAARFALKLLEHFEVVETESEGDP   80 (125)
T ss_dssp             EEEEECHHHHHHHHHHTCCHHHHHHHT--TEEEEEEEHHHHHHHHHHHHHCCHHHHHHHHHHHHHHTTSEEECCSSCSHH
T ss_pred             ceEEEecHHHHHHHHcCCcHHHHHHhh--cCceEEecHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhCCCCCCCCcHHH
Confidence            368999999999999999999999985  5678999999999999998765444333321   01222333445678999


Q ss_pred             HHHHHhhcCceEEEEecCHHHHHHHhhcCCccEEEEeeccccCC
Q 029889          142 CLVERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGTAFHDIGI  185 (186)
Q Consensus       142 CI~~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~~~~~~~~  185 (186)
                      ||++.+.+++ |+|||||++|+++++. |||||||++++++.-+
T Consensus        81 ~il~~a~~~~-~iv~T~D~~Lr~~~~~-~GVpvi~l~~~~~l~~  122 (125)
T d1o4wa_          81 SLIEAAEKYG-CILITNDKELKRKAKQ-RGIPVGYLKEDKRVFV  122 (125)
T ss_dssp             HHHHHHHHHT-CEEECCCHHHHHHHHH-TTCCEECCCCCCCCCC
T ss_pred             HHHHHHhhCC-eEEEecCHHHHHHHHH-cCCcEEEEeCCceEEE
Confidence            9999999887 8999999999999997 7999999999987644

>d1v96a1 c.120.1.1 (A:2-149) Hypothetical protein PH0500 {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: PIN domain
domain: Hypothetical protein PH0500
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=96.79  E-value=0.0013  Score=49.27  Aligned_cols=108  Identities=15%  Similarity=0.114  Sum_probs=70.5

Q ss_pred             eEEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHh----chhhHHHHHhccCCCceeeecC-------
Q 029889           65 YRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKL----GQKYRVALRIAKDPRFERLPCT-------  133 (186)
Q Consensus        65 Y~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekL----g~k~r~Al~lak~~~~e~~kC~-------  133 (186)
                      =++|+|||.++...+.+   .+.+.+.+.++..++++..++.|+..=    ++.....++...+ .++.++.+       
T Consensus         4 ~~~l~DT~~li~~~~~~---~k~~~e~~~~~~~~~iS~itv~E~l~g~~~~~~~~~~~~~~l~~-~~~vlp~~~~~a~~a   79 (148)
T d1v96a1           4 PDITFDSLALIKMHSQN---MKRILEVTLAKFTVNLSIVTVYRYLTARAYLKKNIEAEFEILKD-IYNIVPLLDDIAIKA   79 (148)
T ss_dssp             SEEEECHHHHHHHTSGG---GHHHHHHHHHHCEEEEEHHHHHHHHHHC--CCSCHHHHHHHHHH-HSEEECCCHHHHHHH
T ss_pred             cceEechHHHHHHHccC---hHhHHHHHhccCCEEeeHHHHHHHHHHHHHhCCcHHHHHHHHHH-HhhHhhCChHHHHHH
Confidence            38999999999865433   245556666778899999999998531    2223333332222 33444332       


Q ss_pred             --------CCC--CChHHHHH-HHhhcCceEEEEecCHHHHHHHhhcCCccEEEEe
Q 029889          134 --------HKG--TYADDCLV-ERVTQHKCFIVATCDRDLKRRIRKVRSTDLYLGT  178 (186)
Q Consensus       134 --------H~g--~~addCI~-~~v~~~~~yiVATnD~~LrrrlRkipGVPiiyi~  178 (186)
                              +.|  ....||++ ..+..++ +.++|+|..--+++.+. |+.++.+.
T Consensus        80 ~~i~a~l~~~g~~i~~~D~lIAAtAi~~~-~~LVT~n~kdF~~i~~~-Gl~vi~~~  133 (148)
T d1v96a1          80 AQIEANLIKKEITLDMEDIITATTAIYTN-SLLVTDDPKRYEPIRRF-GLDTMPLD  133 (148)
T ss_dssp             HHHHHHHHHTTCCCCHHHHHHHHHHHHHT-CEEEESCHHHHGGGGGG-TCCEEEHH
T ss_pred             HHHHHHHHhccCCCChhHHHHHHHHHHcC-CEEEeCCHHHhhHHHHC-CceEecHH
Confidence                    223  24556655 5566677 69999999888888877 99988653

>d2fe1a1 c.120.1.1 (A:1-130) Conserved hypothetical protein PAE0151 {Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: PIN domain
domain: Conserved hypothetical protein PAE0151
species: Pyrobaculum aerophilum [TaxId: 13773]

Probab=96.74  E-value=0.0014  Score=45.82  Aligned_cols=99  Identities=15%  Similarity=0.060  Sum_probs=60.3

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceeeecHHHHHHHHHhchh-----------hHHHHHhccC-CCceeeec-
Q 029889           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK-----------YRVALRIAKD-PRFERLPC-  132 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kldl~~~l~~~L~~k~~~~iT~CVi~ELekLg~k-----------~r~Al~lak~-~~~e~~kC-  132 (186)
                      +|++|||+++..+... +..+.+.+.+.....++++..++.|+.....+           ...++..... +......+ 
T Consensus         2 ~ivlDTnvli~~~~~~-~~~~~~~~~~~~~~~~~i~~~~~~E~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (130)
T d2fe1a1           2 ELVVDASAIAALYVPE-ERSEQAERAVSQAQELHTLDLAAYEVANDLWKHARRGLLREDEASNMLEELWEFFKALKVHSY   80 (130)
T ss_dssp             EEEECHHHHHTTSSSC-CCCHHHHHHHHHCSEEEEEHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHTTSEEECG
T ss_pred             EEEEehHHHHHHHhCC-ccHHHHHHHHhhcCCEEecHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHhhcccceeecCc
Confidence            6899999999876544 34566677777677899999999999543211           1111111110 00001111 


Q ss_pred             ------------CCCCC-ChHHHHHHHhhcCceEEEEecCHHHHHHHh
Q 029889          133 ------------THKGT-YADDCLVERVTQHKCFIVATCDRDLKRRIR  167 (186)
Q Consensus       133 ------------~H~g~-~addCI~~~v~~~~~yiVATnD~~LrrrlR  167 (186)
                                  .| +. ..|--++..+..+++ -++|.|+.|.+++.
T Consensus        81 ~~~~~~a~~l~~~~-~l~~~Da~i~A~A~~~~~-~l~T~D~~l~~~~~  126 (130)
T d2fe1a1          81 AEVLKDAFALALKH-GVTVYDAAYVALAEKIGG-KLLTLDRQLAEKFP  126 (130)
T ss_dssp             GGTHHHHHHHHHHH-TCCHHHHHHHHHHHHHTC-EEECSCHHHHHHCT
T ss_pred             HHHHHHHHHHHHHc-CCCccHHHHHHHHHHcCC-EEEECCHHHHHhcC
Confidence                        12 33 455556677777886 69999998887643

>d1w8ia_ c.120.1.1 (A:) Hypothetical protein AF1683 {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 AF1683
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.18  E-value=0.064  Score=39.40  Aligned_cols=96  Identities=14%  Similarity=0.032  Sum_probs=57.2

Q ss_pred             EEEeehHHHHHHHHcCCC----hHHhHHHhhcc-cceeeecHHHHHHHHHh-chh----hHHHHHhccCCCceeeecCC-
Q 029889           66 RVLVDTNFINFSIQNKLD----LEKGMMDCLYA-KCTPCITDCVMAELEKL-GQK----YRVALRIAKDPRFERLPCTH-  134 (186)
Q Consensus        66 ~VLvDtNFl~~~~~~kld----l~~~l~~~L~~-k~~~~iT~CVi~ELekL-g~k----~r~Al~lak~~~~e~~kC~H-  134 (186)
                      .+|||||++.+.+..+=.    ..+.+..++.+ ...+++|+.|+.|+-.+ ++.    ......+...+.++..+++. 
T Consensus         2 ~~lvDT~~liA~~~~~D~~H~~a~~~~~~~~~~~~~~lvtt~~VL~E~~~ll~~~~~~a~~~l~~ll~~~~v~Vi~~~~e   81 (155)
T d1w8ia_           2 AALIDTGIFFGFYSLKDVHHMDSVAIVVHAVEGKWGRLFVTNHILDETLTLLKYKKLPADKFLEGFVESGVLNIIYTDDE   81 (155)
T ss_dssp             EEEECHHHHHHHHCTTSTTHHHHHHHHHHHHTTTTSEEEEEHHHHHHHHHHHHHTTCCHHHHHHHHTTTSSSEEECCCHH
T ss_pred             eEEEEhHHHHHHHcCCchhHHHHHHHHHHHHhccCCceeecchhHHHHHHHHHhhhHHHHHHHHHHHhCCCeEEEecchH
Confidence            689999999998754421    23334455554 45689999999997555 322    12222344445677666642 


Q ss_pred             ---------------CCCChHHHHH-HHhhcCceEEEEecCHHH
Q 029889          135 ---------------KGTYADDCLV-ERVTQHKCFIVATCDRDL  162 (186)
Q Consensus       135 ---------------~g~~addCI~-~~v~~~~~yiVATnD~~L  162 (186)
                                     ++.+-.||++ .++.+.+. =|+|-|+++
T Consensus        82 ~~~rA~eL~~~~~~d~~lsftDa~~~alA~~l~i-~i~TfD~~F  124 (155)
T d1w8ia_          82 VERKALEVFKARVYEKGFSYTDAISEVVAEELKL-KLISYDSRF  124 (155)
T ss_dssp             HHHHHHHHHHHTTTSTTCCHHHHHHHHHHHHHTC-EEECSCTTC
T ss_pred             HHHHHHHHHHhhccccCCCHHHHHHHHHHHHcCC-CEEEecCCc
Confidence                           1223345554 55566665 567988764

>d2h1ca1 c.120.1.1 (A:1-138) Trafficking protein B {Neisseria gonorrhoeae [TaxId: 485]}

class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: PIN domain
domain: Trafficking protein B
species: Neisseria gonorrhoeae [TaxId: 485]

Probab=93.31  E-value=0.07  Score=37.30  Aligned_cols=42  Identities=21%  Similarity=0.263  Sum_probs=28.7

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhh--cccceeeecHHHHHHHHH
Q 029889           67 VLVDTNFINFSIQNKLDLEKGMMDCL--YAKCTPCITDCVMAELEK  110 (186)
Q Consensus        67 VLvDtNFl~~~~~~kldl~~~l~~~L--~~k~~~~iT~CVi~ELek  110 (186)
                      +|||||.+...++.+-+-  .....|  .+.-.++|+.-++.||..
T Consensus         2 iLlDTnvli~~~r~~~~~--~v~~~l~~~~~~~~~iS~it~~El~~   45 (138)
T d2h1ca1           2 ILLDTNVISEPLRPQPNE--RVVAWLDSLILEDVYLSAITVAELRL   45 (138)
T ss_dssp             EEECHHHHTGGGSSSCCH--HHHHHHHHSCGGGEEEEHHHHHHHHH
T ss_pred             EEEecHHHHHHHccCCCH--HHHHHHHhcCccceeecHHHHHHHHH
Confidence            689999999987765442  222222  233457899999999963