Citrus Sinensis ID: 029148

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------20
Protein Sequence
MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEATVGGAPRI
Secondary Structure (PSIPRED)
cccccccccHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHccccccEEEEEcHHHHHHHHHccHHHHHHHHHHHcccEEEEEcHHHHHHHHHHHHHHHHHHHHccccccEEEcccccccccHHHHHHHHHcccEEEEEEccHHHHHHHHccccccEEEEEccEEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHccccHHHHHHHHHHcHHHcccccccccccccccccHHHHHHccccccccEEEEEcHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHcHHHHHHHHHHccccEEEEccccccccccHHHHHHHHcccEEEEEEccHHHHHHHHccccccEEEEEccEEEEEcccHcHccccccc
Coil and Loop (DISEMBL)
mgkakkapkFAAMKKIITKRAIKNYkedvlnpnkkdltkekmprnvpnvssalffthntalgppyrvlvDTNFINFSIQNKLDLEKGMMdclyakctpciTDCVMAELEKLGQKYRVALRIakdprferlpcthkgtyaddclveRVTQHKCFIVATCDRDLKRrirkvpgvpimyiTRHKysierlpeatvggapri
Flexible Loop (DISEMBL)
mgkakkapkfaamKKIITkraiknykedvlnpnkkdltkekmprnVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRiakdprferlpcthkgtyADDCLVERVTQHKcfivatcdrdlkrrirkvpgvpimyitrhkysierlpeatvggapri
Low Complexity Region (SEG)
MGkakkapkfaamkkIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEATVGGAPRI
Disordered region (IsUnstruct)
**************KIITKRAIKNY***********************VSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIER************
Disordered Region (DISOPRED)
****KKAPKFAAMKKI***********************************ALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLP**********
Disordered Region (DISEMBL)
MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEATVGGAPRI
Disordered Region (DISPRO)
*******PKFAAMKKIITKRAIKNYKEDVLN*********KMPR***NVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEATV******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEATVGGAPRI
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	198	2.2.26 [Sep-21-2011]
Q5RFQ0	198	rRNA-processing protein F	yes	no	0.989	0.989	0.69	5e-73
Q9Y324	198	rRNA-processing protein F	yes	no	0.989	0.989	0.69	5e-73
Q32PD0	198	rRNA-processing protein F	yes	no	0.989	0.989	0.69	5e-73
Q9CTH6	198	rRNA-processing protein F	yes	no	0.989	0.989	0.675	9e-72
Q05498	189	rRNA-processing protein F	yes	no	0.934	0.978	0.611	2e-64
O13610	192	rRNA-processing protein f	yes	no	0.964	0.994	0.575	3e-61
Q55GM5	194	rRNA-processing protein F	yes	no	0.924	0.943	0.532	8e-56
Q9BRU9	249	rRNA-processing protein U	no	no	0.707	0.562	0.274	2e-12
O74862	260	rRNA-processing protein u	no	no	0.691	0.526	0.308	2e-12
Q08DU1	248	rRNA-processing protein U	no	no	0.666	0.532	0.294	3e-12

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

 Score =  273 bits (699), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 138/200 (69%), Positives = 160/200 (80%), Gaps = 4/200 (2%)

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 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYIT 178
           LRIAKDPRFERLPCTHKGTYADDCLV+RVTQHKC+IVAT DRDLKRRIRK+PGVPIMYI+
Sbjct: 121 LRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYIS 180

Query: 179 RHKYSIERLPEATVGGAPRI 198
            H+Y+IER+P+    GAPR 
Sbjct: 181 NHRYNIERMPDDY--GAPRF 198

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 =  273 bits (699), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 138/200 (69%), Positives = 160/200 (80%), Gaps = 4/200 (2%)

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 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYIT 178
           LRIAKDPRFERLPCTHKGTYADDCLV+RVTQHKC+IVAT DRDLKRRIRK+PGVPIMYI+
Sbjct: 121 LRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYIS 180

Query: 179 RHKYSIERLPEATVGGAPRI 198
            H+Y+IER+P+    GAPR 
Sbjct: 181 NHRYNIERMPDDY--GAPRF 198

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 =  273 bits (699), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 138/200 (69%), Positives = 160/200 (80%), Gaps = 4/200 (2%)

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 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYIT 178
           LRIAKDPRFERLPCTHKGTYADDCLV+RVTQHKC+IVAT DRDLKRRIRK+PGVPIMYI+
Sbjct: 121 LRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYIS 180

Query: 179 RHKYSIERLPEATVGGAPRI 198
            H+Y+IER+P+    GAPR 
Sbjct: 181 NHRYNIERMPDDY--GAPRF 198

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 =  269 bits (688), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 135/200 (67%), Positives = 160/200 (80%), Gaps = 4/200 (2%)

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 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYIT 178
           LRIAKDPRF+RLPCTHKGTYADDCLV+RVTQHKC+IVAT DRDLKRRIRK+PGVPIMY++
Sbjct: 121 LRIAKDPRFDRLPCTHKGTYADDCLVQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYLS 180

Query: 179 RHKYSIERLPEATVGGAPRI 198
            H+Y+IER+P+    GAPR 
Sbjct: 181 NHRYNIERMPDDY--GAPRF 198

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 =  244 bits (623), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 118/193 (61%), Positives = 149/193 (77%), Gaps = 8/193 (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 ALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYI 177
           AL++A+DPR +RL C+HKGTYADDCLV RV QHKC+IVAT D  LK+RIRK+PG+P+M +
Sbjct: 116 ALKLARDPRIKRLSCSHKGTYADDCLVHRVLQHKCYIVATNDAGLKQRIRKIPGIPLMSV 175

Query: 178 TRHKYSIERLPEA 190
             H Y IE+LP+ 
Sbjct: 176 GGHAYVIEKLPDV 188

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 =  234 bits (597), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 110/191 (57%), Positives = 145/191 (75%)

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 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH 180
           IAKD RFERLPCTHKGTYADDC+V+RV QHKC++VAT D++LK+RIRK+PG+PI+ +  H
Sbjct: 121 IAKDERFERLPCTHKGTYADDCIVQRVMQHKCYLVATNDKNLKQRIRKIPGIPILSVANH 180

Query: 181 KYSIERLPEAT 191
           K  +ERL +  
Sbjct: 181 KIRVERLVDVV 191

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 =  216 bits (550), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 98/184 (53%), Positives = 140/184 (76%), Gaps = 1/184 (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 RFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIE 185
           RF+RL C+HKGTYADDC++ R+T H+ FIVATCD DL+RRIRK+PGVPI+Y+   KY++E
Sbjct: 128 RFQRLTCSHKGTYADDCIINRITMHRMFIVATCDADLRRRIRKIPGVPIVYLKGKKYTVE 187

Query: 186 RLPE 189
           R+P+
Sbjct: 188 RMPD 191

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 = 72.4 bits (176), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 39/142 (27%), Positives = 73/142 (51%), Gaps = 2/142 (1%)

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

Query: 114 KYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHK--CFIVATCDRDLKRRIRKVPG 171
               A  IA+  +    P         +CL+  V +     + VAT D++L  +++K PG
Sbjct: 75  DLYGAKLIAQKCQVRNCPHFKNAVSGSECLLSMVEEGNPHHYFVATQDQNLSVKVKKKPG 134

Query: 172 VPIMYITRHKYSIERLPEATVG 193
           VP+M+I ++   +++    T+ 
Sbjct: 135 VPLMFIIQNTMVLDKPSPKTIA 156

Involved in rRNA-processing and ribosome biogenesis.

Homo sapiens (taxid: 9606)

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

 Score = 72.0 bits (175), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 46/149 (30%), Positives = 76/149 (51%), Gaps = 12/149 (8%)

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 RRIRKVPGVPIMYITRHKYSIERLPEATV 192
           + +R VPGVP++Y+ R    +E    AT+
Sbjct: 129 QALRSVPGVPLIYMKRSVVILEPASRATL 157

Involved in rRNA-processing and ribosome biogenesis.

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

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

 Score = 71.6 bits (174), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 72/136 (52%), Gaps = 4/136 (2%)

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---VERVTQHKCFIVATCDRDLKRRIRKVP 170
               A  IA+  +    P         +CL   VE    H  F+ AT D++L  +++K P
Sbjct: 75  DLYGAKLIAQKCQVRNCPHFKNAVSGSECLLSMVEDGNPHHYFL-ATQDQNLSMKVKKKP 133

Query: 171 GVPIMYITRHKYSIER 186
           G+P+M+I ++   +++
Sbjct: 134 GIPLMFIIQNTIVLDK 149

Involved in rRNA-processing and ribosome biogenesis.

Bos taurus (taxid: 9913)

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	198
449437727	198	PREDICTED: rRNA-processing protein FCF1	1.0	1.0	0.898	1e-103
356543662	198	PREDICTED: rRNA-processing protein FCF1	1.0	1.0	0.888	1e-101
294461424	198	unknown [Picea sitchensis]	1.0	1.0	0.878	1e-100
115466536	199	Os06g0158600 [Oryza sativa Japonica Grou	1.0	0.994	0.884	1e-100
388522413	198	unknown [Lotus japonicus]	1.0	1.0	0.873	1e-100
224130438	198	predicted protein [Populus trichocarpa]	0.994	0.994	0.873	1e-99
226529278	199	uncharacterized protein LOC100272977 [Ze	1.0	0.994	0.884	2e-99
413953095	199	nucleolar protein [Zea mays]	1.0	0.994	0.884	3e-99
255638538	198	unknown [Glycine max]	1.0	1.0	0.878	4e-99
242094750	199	hypothetical protein SORBIDRAFT_10g00403	1.0	0.994	0.884	5e-99

>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 =  380 bits (975), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 178/198 (89%), Positives = 191/198 (96%)

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 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH 180
           IAKDPRFERLPCTHKGTYADDCLVERVTQHKC+IVATCDRDLKRRIRKVPGVPIMYITRH
Sbjct: 121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCYIVATCDRDLKRRIRKVPGVPIMYITRH 180

Query: 181 KYSIERLPEATVGGAPRI 198
           +YSIERLPEAT+GGAPR+
Sbjct: 181 QYSIERLPEATIGGAPRM 198

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 =  371 bits (953), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 176/198 (88%), Positives = 188/198 (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 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH 180
           IAKDPRFER+ CTHKGTYADDCLVERVTQHKC+IVATCDRDLKRRIRK+PGVPIMYIT+ 
Sbjct: 121 IAKDPRFERILCTHKGTYADDCLVERVTQHKCYIVATCDRDLKRRIRKIPGVPIMYITKR 180

Query: 181 KYSIERLPEATVGGAPRI 198
           KYSIERLPEAT+GGAPRI
Sbjct: 181 KYSIERLPEATIGGAPRI 198

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 =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 174/198 (87%), Positives = 187/198 (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 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH 180
           IAKDPRFERLPCTH+GTYADDCLVERVTQHKC+IVATCDRDLKRRIRK+PGVPIMYIT+H
Sbjct: 121 IAKDPRFERLPCTHEGTYADDCLVERVTQHKCYIVATCDRDLKRRIRKIPGVPIMYITQH 180

Query: 181 KYSIERLPEATVGGAPRI 198
           KYSIERLPEAT+GGAPR 
Sbjct: 181 KYSIERLPEATIGGAPRF 198

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

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 =  368 bits (945), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 176/199 (88%), Positives = 189/199 (94%), Gaps = 1/199 (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 RIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITR 179
           RIAKDPRF+RL CTHKGTYADDC+VERVTQHKC+IVATCDRDLKRRIRKVPGVPIMYITR
Sbjct: 121 RIAKDPRFQRLACTHKGTYADDCIVERVTQHKCYIVATCDRDLKRRIRKVPGVPIMYITR 180

Query: 180 HKYSIERLPEATVGGAPRI 198
           H+YSIERLPEAT+GGAPRI
Sbjct: 181 HRYSIERLPEATIGGAPRI 199

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  368 bits (945), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 173/198 (87%), Positives = 187/198 (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 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH 180
           IAKDPRFER+ CTHKGTYADDCLVERVTQHKC+IVATCDRDLKRRIRK+PGVPIMYI +H
Sbjct: 121 IAKDPRFERILCTHKGTYADDCLVERVTQHKCYIVATCDRDLKRRIRKIPGVPIMYIIKH 180

Query: 181 KYSIERLPEATVGGAPRI 198
           KYSIERLPEAT+GGAPRI
Sbjct: 181 KYSIERLPEATIGGAPRI 198

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

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 =  367 bits (943), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 172/197 (87%), Positives = 188/197 (95%)

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 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH 180
           IAKDPRFERLPC HKGTYADDC+VERVT+HKC+IVATCDRDLKRRIRK+PGVPIMYIT+H
Sbjct: 121 IAKDPRFERLPCIHKGTYADDCIVERVTKHKCYIVATCDRDLKRRIRKIPGVPIMYITQH 180

Query: 181 KYSIERLPEATVGGAPR 197
           KYSIERLPEATVGGAPR
Sbjct: 181 KYSIERLPEATVGGAPR 197

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 =  366 bits (940), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 176/199 (88%), Positives = 188/199 (94%), Gaps = 1/199 (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 RIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITR 179
           RIAKDPRF+RL CTHKGTYADDC+VERVTQHKC+IVATCDRDLKRRIRKVPGVPIMYITR
Sbjct: 121 RIAKDPRFQRLACTHKGTYADDCIVERVTQHKCYIVATCDRDLKRRIRKVPGVPIMYITR 180

Query: 180 HKYSIERLPEATVGGAPRI 198
           H+YSIERLPEAT+GGAPRI
Sbjct: 181 HRYSIERLPEATIGGAPRI 199

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413953095|gb|AFW85744.1| nucleolar protein [Zea mays]

 Score =  366 bits (939), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 176/199 (88%), Positives = 187/199 (93%), Gaps = 1/199 (0%)

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

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

Query: 120 RIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITR 179
           RIAKDPRF+RL CTHKGTYADDC+VERVTQHKC+IVATCDRDLKRRIRKVPGVPIMYITR
Sbjct: 121 RIAKDPRFQRLACTHKGTYADDCIVERVTQHKCYIVATCDRDLKRRIRKVPGVPIMYITR 180

Query: 180 HKYSIERLPEATVGGAPRI 198
           H+YSIERLPEAT+GGAPRI
Sbjct: 181 HRYSIERLPEATIGGAPRI 199

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  365 bits (938), Expect = 4e-99,   Method: Compositional matrix adjust.
 Identities = 174/198 (87%), Positives = 186/198 (93%)

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 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH 180
           IAKDPRFER+ CTHKGTYADDCLVERVTQHKC+IVATCDRDLKRRIRK+PGVPIMYI + 
Sbjct: 121 IAKDPRFERILCTHKGTYADDCLVERVTQHKCYIVATCDRDLKRRIRKIPGVPIMYIPKR 180

Query: 181 KYSIERLPEATVGGAPRI 198
           KYSIE LPEAT+GGAPRI
Sbjct: 181 KYSIEGLPEATIGGAPRI 198

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242094750|ref|XP_002437865.1| hypothetical protein SORBIDRAFT_10g004030 [Sorghum bicolor] gi|241916088|gb|EER89232.1| hypothetical protein SORBIDRAFT_10g004030 [Sorghum bicolor]

 Score =  365 bits (937), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 176/199 (88%), Positives = 187/199 (93%), Gaps = 1/199 (0%)

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

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

Query: 120 RIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITR 179
           RIAKDPRF+RL CTHKGTYADDC+VERVTQHKC+IVATCDRDLKRRIRKVPGVPIMYITR
Sbjct: 121 RIAKDPRFQRLACTHKGTYADDCIVERVTQHKCYIVATCDRDLKRRIRKVPGVPIMYITR 180

Query: 180 HKYSIERLPEATVGGAPRI 198
           H+YSIERLPEAT+GGAPRI
Sbjct: 181 HRYSIERLPEATIGGAPRI 199

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

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	198
TAIR|locus:2062902	196	AT2G46230 "AT2G46230" [Arabido	0.909	0.918	0.824	4.5e-82
UNIPROTKB|Q32PD0	198	FCF1 "rRNA-processing protein	0.858	0.858	0.735	1.3e-66
UNIPROTKB|Q9Y324	198	FCF1 "rRNA-processing protein	0.858	0.858	0.735	1.3e-66
MGI|MGI:1920986	198	Fcf1 "FCF1 small subunit (SSU)	0.858	0.858	0.718	1.2e-65
TAIR|locus:2197885	178	AT1G26530 "AT1G26530" [Arabido	0.388	0.432	0.883	3.7e-64
ZFIN|ZDB-GENE-050417-67	198	fcf1 "FCF1 small subunit (SSU)	0.813	0.813	0.731	5.4e-63
FB|FBgn0010520	200	Bka "Bekka" [Drosophila melano	0.712	0.705	0.773	1.7e-59
SGD|S000002747	189	FCF1 "Putative PINc domain nuc	0.873	0.915	0.625	1.2e-58
CGD|CAL0003244	201	orf19.3220 [Candida albicans (	0.752	0.741	0.691	5.3e-56
UNIPROTKB|Q59MK3	201	CaO19.10731 "Potential essenti	0.752	0.741	0.691	5.3e-56

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

 Score = 823 (294.8 bits), Expect = 4.5e-82, P = 4.5e-82
 Identities = 150/182 (82%), Positives = 169/182 (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 GTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEATVGGA 195
             GTYADDCLV+RVTQHKCFIVATCDRDLKRRIRK+PGVPIMY+T  KYSIE+LPEAT+GGA
Sbjct:   134 GTYADDCLVDRVTQHKCFIVATCDRDLKRRIRKIPGVPIMYVTNRKYSIEKLPEATLGGA 193

Query:   196 PR 197
             PR
Sbjct:   194 PR 195

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 = 677 (243.4 bits), Expect = 1.3e-66, P = 1.3e-66
 Identities = 128/174 (73%), Positives = 144/174 (82%)

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 VERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEATVGGAPR 197
             V+RVTQHKC+IVAT DRDLKRRIRK+PGVPIMYI+ H+Y+IER+P+    GAPR
Sbjct:   146 VQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDY--GAPR 197

GO:0005730 "nucleolus" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

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

 Score = 677 (243.4 bits), Expect = 1.3e-66, P = 1.3e-66
 Identities = 128/174 (73%), Positives = 144/174 (82%)

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 VERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEATVGGAPR 197
             V+RVTQHKC+IVAT DRDLKRRIRK+PGVPIMYI+ H+Y+IER+P+    GAPR
Sbjct:   146 VQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDY--GAPR 197

GO:0006364 "rRNA processing" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

 Score = 668 (240.2 bits), Expect = 1.2e-65, P = 1.2e-65
 Identities = 125/174 (71%), Positives = 144/174 (82%)

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 VERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEATVGGAPR 197
             V+RVTQHKC+IVAT DRDLKRRIRK+PGVPIMY++ H+Y+IER+P+    GAPR
Sbjct:   146 VQRVTQHKCYIVATVDRDLKRRIRKIPGVPIMYLSNHRYNIERMPDDY--GAPR 197

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0042254 "ribosome biogenesis" evidence=IEA

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

 Score = 380 (138.8 bits), Expect = 3.7e-64, Sum P(2) = 3.7e-64
 Identities = 68/77 (88%), Positives = 74/77 (96%)

Query:   121 IAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH 180
             IAKDPRFERLPC  KGTYADDCLV+RVTQHKCFIVATCDRDLKRRIRK+PGVPIMY+T+ 
Sbjct:   101 IAKDPRFERLPCVLKGTYADDCLVDRVTQHKCFIVATCDRDLKRRIRKIPGVPIMYVTQR 160

Query:   181 KYSIERLPEATVGGAPR 197
             KYSIE+LPEAT+GGAPR
Sbjct:   161 KYSIEKLPEATIGGAPR 177

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

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

 Score = 643 (231.4 bits), Expect = 5.4e-63, P = 5.4e-63
 Identities = 120/164 (73%), Positives = 139/164 (84%)

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 IVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEATVGGAPR 197
             IVAT DRDLKRRIRK+PGVPIMYI+ H+Y+IER+P+    GAPR
Sbjct:   156 IVATVDRDLKRRIRKIPGVPIMYISNHRYNIERMPDDY--GAPR 197

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

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

 Score = 610 (219.8 bits), Expect = 1.7e-59, P = 1.7e-59
 Identities = 109/141 (77%), Positives = 125/141 (88%)

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 PGVPIMYITRHKYSIERLPEA 190
             PGVPIMY+  HKY+IER+PEA
Sbjct:   175 PGVPIMYVAAHKYAIERMPEA 195

GO:0005634 "nucleus" evidence=NAS

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

GO:0048812 "neuron projection morphogenesis" evidence=IMP

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

 Score = 602 (217.0 bits), Expect = 1.2e-58, P = 1.2e-58
 Identities = 110/176 (62%), Positives = 141/176 (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 HKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPE 189
             HKGTYADDCLV RV QHKC+IVAT D  LK+RIRK+PG+P+M +  H Y IE+LP+
Sbjct:   132 HKGTYADDCLVHRVLQHKCYIVATNDAGLKQRIRKIPGIPLMSVGGHAYVIEKLPD 187

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

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

 Score = 577 (208.2 bits), Expect = 5.3e-56, P = 5.3e-56
 Identities = 103/149 (69%), Positives = 126/149 (84%)

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 DLKRRIRKVPGVPIMYITRHKYSIERLPE 189
             DLKRRIRK+PG+PIM +  H Y IERLP+
Sbjct:   171 DLKRRIRKIPGIPIMSVGGHSYVIERLPD 199

GO:0003674 "molecular_function" evidence=ND

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

GO:0005730 "nucleolus" evidence=IEA

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

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

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

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

 Score = 577 (208.2 bits), Expect = 5.3e-56, P = 5.3e-56
 Identities = 103/149 (69%), Positives = 126/149 (84%)

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 DLKRRIRKVPGVPIMYITRHKYSIERLPE 189
             DLKRRIRK+PG+PIM +  H Y IERLP+
Sbjct:   171 DLKRRIRKIPGIPIMSVGGHSYVIERLPD 199

GO:0003674 "molecular_function" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q55GM5	FCF1_DICDI	No assigned EC number	0.5326	0.9242	0.9432	yes	no
Q9Y324	FCF1_HUMAN	No assigned EC number	0.69	0.9898	0.9898	yes	no
Q9CTH6	FCF1_MOUSE	No assigned EC number	0.675	0.9898	0.9898	yes	no
Q32PD0	FCF1_BOVIN	No assigned EC number	0.69	0.9898	0.9898	yes	no
Q05498	FCF1_YEAST	No assigned EC number	0.6113	0.9343	0.9788	yes	no
O13610	FCF1_SCHPO	No assigned EC number	0.5759	0.9646	0.9947	yes	no
Q5RFQ0	FCF1_PONAB	No assigned EC number	0.69	0.9898	0.9898	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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	198
cd09864	143	cd09864, PIN_Fcf1, PIN domain of rRNA-processing p	1e-104
pfam04900	101	pfam04900, Fcf1, Fcf1	3e-53
cd08553	120	cd08553, PIN_Fcf1-like, PIN domain of rRNA-process	1e-50
COG1412	136	COG1412, COG1412, Uncharacterized proteins of PilT	3e-47
cd09854	125	cd09854, PIN_VapC-Smg6_family, PIN domains of VapC	8e-33
cd09866	147	cd09866, PIN_Fcf1-Utp23-H, PIN domain of rRNA-proc	3e-29
cd09852	120	cd09852, PIN_SF, PIN (PilT N terminus) domain: Sup	6e-18
cd09865	148	cd09865, PIN_Utp23, PIN domain of rRNA-processing	2e-17
cd09879	117	cd09879, PIN_AF0591, PIN domain of Archaeoglobus f	8e-15
smart00670	111	smart00670, PINc, Large family of predicted nucleo	2e-10

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

 Score =  295 bits (757), Expect = e-104
 Identities = 121/135 (89%), Positives = 128/135 (94%)

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

Query: 113 QKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGV 172
           QKYRVAL+IAKDPRFERLPC HKGTYADDCLVERVTQH+C+IVATCDRDLKRRIRK+PGV
Sbjct: 69  QKYRVALKIAKDPRFERLPCDHKGTYADDCLVERVTQHRCYIVATCDRDLKRRIRKIPGV 128

Query: 173 PIMYITRHKYSIERL 187
           PIMYI  HKYSIERL
Sbjct: 129 PIMYIRNHKYSIERL 143

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

>gnl|CDD|218319 pfam04900, Fcf1, Fcf1

 Score =  165 bits (419), Expect = 3e-53
 Identities = 65/101 (64%), Positives = 80/101 (79%), Gaps = 2/101 (1%)

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 VTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERL 187
           V +H C+IVAT DR+L+RR+RK+PGVPI+YI R+   +E  
Sbjct: 61  VGKHNCYIVATQDRELRRRLRKIPGVPIIYINRNVMVLEPP 101

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

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

 Score =  159 bits (403), Expect = 1e-50
 Identities = 60/122 (49%), Positives = 85/122 (69%), Gaps = 5/122 (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--KCFIVATCDRDLKRRIRKVPGVPIMYITRHKYS 183
            ERL C HK    AD+CL++ V +H    + VAT D+DL+ ++RK+PGVP++YI ++K  
Sbjct: 60  -ERLNCNHKEGASADECLLDIVKKHNNHRYFVATQDQDLRVKLRKIPGVPLVYILQNKMI 118

Query: 184 IE 185
           +E
Sbjct: 119 LE 120

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

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

 Score =  150 bits (382), Expect = 3e-47
 Identities = 62/137 (45%), Positives = 85/137 (62%), Gaps = 3/137 (2%)

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-KDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVP 173
           +R   RIA      ERL C HKG YAD+CL+E   +H  +IVAT D++LKRR+R+  G+P
Sbjct: 61  HRGKARIAIALKYAERLECIHKGRYADECLLEAALKHGRYIVATNDKELKRRLREN-GIP 119

Query: 174 IMYIT-RHKYSIERLPE 189
           ++ +  R    IERL +
Sbjct: 120 VITLRQRKLLIIERLSD 136

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

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

 Score =  113 bits (285), Expect = 8e-33
 Identities = 53/125 (42%), Positives = 69/125 (55%), Gaps = 16/125 (12%)

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---------------YADDCLVERVTQHKCFIVATCDRDLKRRIRKVPG 171
            +R  C HK                  ADDC + +   H+ FIVATCD DL+   RK PG
Sbjct: 61  HKRFICFHKEFSEHTFVERLPNETINDADDCAINKTCMHRMFIVATCDADLREAARKEPG 120

Query: 172 VPIMY 176
           V I  
Sbjct: 121 VIIKS 125

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

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

 Score =  105 bits (265), Expect = 3e-29
 Identities = 46/128 (35%), Positives = 75/128 (58%), Gaps = 6/128 (4%)

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

Query: 170 PGVPIMYI 177
           PGVP++Y+
Sbjct: 132 PGVPLLYL 139

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

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

 Score = 75.6 bits (186), Expect = 6e-18
 Identities = 30/122 (24%), Positives = 52/122 (42%), Gaps = 15/122 (12%)

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-KCFIVATCDRDLKRRIRKVPGVPI 174
           + +D        +P  H     Y  D  +  + +      + T D DL+++ +  PGV +
Sbjct: 61  LLRDLELLDLMGIPVVHAPGDLYEADAQIAALAKKGHVVALITNDSDLRQKAK--PGVKV 118

Query: 175 MY 176
             
Sbjct: 119 FS 120

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

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

 Score = 75.1 bits (185), Expect = 2e-17
 Identities = 46/124 (37%), Positives = 68/124 (54%), Gaps = 11/124 (8%)

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-----TQHKCFIVATCDRDLKRRIRKVPGVPIM 175
              FER  C H+   A   D+CL   V      +H+ +IVAT D  L+  +R +PGVP++
Sbjct: 82  --TFERRRCNHRDADALSPDECLKSVVDPKGKNKHR-YIVATQDPPLRTDLRSIPGVPLI 138

Query: 176 YITR 179
           +I R
Sbjct: 139 HINR 142

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

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

 Score = 67.2 bits (165), Expect = 8e-15
 Identities = 36/124 (29%), Positives = 64/124 (51%), Gaps = 16/124 (12%)

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

Query: 119 LRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYIT 178
           L++A+      +  +  G  ADD ++E   +     V T DR+LK+R+    G+P++Y+ 
Sbjct: 59  LQLAERC---EVVESEGG-PADDAILELAKELGA-AVVTNDRELKKRLLDA-GIPVIYLR 112

Query: 179 RHKY 182
           + K 
Sbjct: 113 QKKK 116

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

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

 Score = 55.5 bits (134), Expect = 2e-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	198
KOG3165	195	consensus Predicted nucleic-acid-binding protein,	100.0
KOG3164	236	consensus Uncharacterized proteins of PilT N-term.	100.0
COG1412	136	Uncharacterized proteins of PilT N-term./Vapc supe	100.0
PF04900	101	Fcf1: Fcf1; InterPro: IPR006984 This family is com	99.97
smart00670	111	PINc Large family of predicted nucleotide-binding	98.48
PF13638	133	PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_	98.21
PRK13764	602	ATPase; Provisional	97.82
TIGR00305	114	probable toxin-antitoxin system toxin component, P	97.25
PF01850	121	PIN: PIN domain; InterPro: IPR002716 The PilT prot	96.91
TIGR00028	142	Mtu_PIN_fam Mycobacterium tuberculosis PIN domain	96.81
PRK00124	151	hypothetical protein; Validated	95.72
PF13470	119	PIN_3: PIN domain	95.7
PF02639	130	DUF188: Uncharacterized BCR, YaiI/YqxD family COG1	94.9
COG1848	140	Predicted nucleic acid-binding protein, contains P	94.37
COG1569	142	Predicted nucleic acid-binding protein, contains P	93.77
COG2402	135	Predicted nucleic acid-binding protein, contains P	92.88
COG4956	356	Integral membrane protein (PIN domain superfamily)	90.7
PRK12496	164	hypothetical protein; Provisional	89.84
PF05991	166	NYN_YacP: YacP-like NYN domain; InterPro: IPR01029	88.71
PRK13725	132	plasmid maintenance protein; Provisional	88.61
COG1487	133	VapC Predicted nucleic acid-binding protein, conta	86.58
COG1671	150	Uncharacterized protein conserved in bacteria [Fun	85.33

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

Probab=100.00  E-value=2.3e-81  Score=510.48  Aligned_cols=193  Identities=75%  Similarity=1.228  Sum_probs=183.4

Q ss_pred             CCccccchhhHHhhhccCccccccccccccCCCCcCCCCCCCCcccCCCchhhhHHhhhCCCCCeEEEeehHHHHHHHHc
Q 029148            1 MGKAKKAPKFAAMKKIITKRAIKNYKEDVLNPNKKDLTKEKMPRNVPNVSSALFFTHNTALGPPYRVLVDTNFINFSIQN   80 (198)
Q Consensus         1 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~fy~~n~~~~~PY~VLvDtNFl~~~i~~   80 (198)
                      |||+|||||||.||+||+.+ .|++++++.+.++++.+.+..++++||+||++||+||++|+|||+|||||||||+|+++
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            99999999999999999887 88888887665544444556899999999999999999999999999999999999999


Q ss_pred             CCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHHhccCCCeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCH
Q 029148           81 KLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDR  160 (198)
Q Consensus        81 kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak~~r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~  160 (198)
                      |+|++++||+||+++|+||||+|||+|||+||.+|+.||++|+||+|+|++|.|+|+||||||+++|.+|+||||||||+
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             HHHHHHhcCCCccEEEEeCceEEEecCCCcccCC
Q 029148          161 DLKRRIRKVPGVPIMYITRHKYSIERLPEATVGG  194 (198)
Q Consensus       161 ~LrrrLRkipGVPIiyi~~~~~~lE~~s~~~~~~  194 (198)
                      +|++|||+||||||||+.++++.||++|+++.||
T Consensus       160 dLK~RIrkIPGVPim~v~~hk~~IEr~pda~~g~  193 (195)
T KOG3165|consen  160 DLKQRIRKIPGVPIMYVANHKYSIERLPDATLGG  193 (195)
T ss_pred             HHHHHHhcCCCCceEEEecceeeeeeCCcccccC
Confidence            9999999999999999999999999999998443

>KOG3164 consensus Uncharacterized proteins of PilT N-term

Probab=100.00  E-value=6e-43  Score=296.38  Aligned_cols=138  Identities=36%  Similarity=0.637  Sum_probs=132.1

Q ss_pred             hhhHHhhhCCCCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHHhccCCCeeeee
Q 029148           52 ALFFTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLP  131 (198)
Q Consensus        52 ~~fy~~n~~~~~PY~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak~~r~e~~~  131 (198)
                      -.||++|||||+|||||||++|+.++++++|++.++|.++|.+.++++||+|||.||+++|..+.+|+.+|+  +|+++.
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-CHHHHHHHHHhc--CCeEEEEecCHHHHHHHhcCCCccEEEEeCceEEEecCCCcc
Q 029148          132 CTHKGT-YADDCLVERVTQ--HKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLPEAT  191 (198)
Q Consensus       132 C~H~g~-~aDdCIv~~v~~--~~~yiVATnD~~LrrrLRkipGVPIiyi~~~~~~lE~~s~~~  191 (198)
                      |+|+.. +|++||.++++.  .++|||||||.+|++.||++||||+||+.++.++||.||+++
T Consensus        91 C~H~~~~s~seCl~svv~~~Nk~~YvvATQD~el~~kLr~~pgvPli~~~r~t~vld~~S~at  153 (236)
T KOG3164|consen   91 CNHKDARSPSECLRSVVRISNKHHYVVATQDQELRRKLRKEPGVPLIYLKRNTLVLDAPSQAT  153 (236)
T ss_pred             CCCCCCCCHHHHHHHHHhccCCceEEEecCCHHHHHHHhcCCCCceEEEecceEEecCcchhh
Confidence            999643 899999999974  467999999999999999999999999999999999999998

/Vapc superfamily [General function prediction only]

>COG1412 Uncharacterized proteins of PilT N-term

Probab=100.00  E-value=2.9e-41  Score=269.47  Aligned_cols=133  Identities=46%  Similarity=0.744  Sum_probs=123.5

Q ss_pred             HHhhhCCCCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHH--hccCCCeeeeec
Q 029148           55 FTHNTALGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALR--IAKDPRFERLPC  132 (198)
Q Consensus        55 y~~n~~~~~PY~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~--iak~~r~e~~~C  132 (198)
                      |++|++|++||+||+|||||+++.++++|++++|+++++++++|+||+||++||++|+..++.+++  +|.. .+++++|
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            678999999999999999999999999999999999999999999999999999999998777666  4442 5888999


Q ss_pred             CCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeC-ceEEEecCCC
Q 029148          133 THKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITR-HKYSIERLPE  189 (198)
Q Consensus       133 ~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~-~~~~lE~~s~  189 (198)
                      .|.+++|||||.++|.+++||+|||||++|++|||+. |||+||+++ +.+.+|++++
T Consensus        80 ~~~~~~aDe~i~~~a~~~~~~iVaTnD~eLk~rlr~~-GIPvi~lr~r~~~~ie~~~~  136 (136)
T COG1412          80 IHKGRYADECLLEAALKHGRYIVATNDKELKRRLREN-GIPVITLRQRKLLIIERLSD  136 (136)
T ss_pred             cccCCChHHHHHHHHHHcCCEEEEeCCHHHHHHHHHc-CCCEEEEeCCeEEEeeCCCC
Confidence            9999999999999999999999999999999999996 999999995 5899998874

/Vapc superfamily [General function prediction only]

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

Probab=99.97  E-value=1.2e-31  Score=202.47  Aligned_cols=99  Identities=45%  Similarity=0.813  Sum_probs=92.5

Q ss_pred             HHhhcccceEeecHHHHHHHHHhhhhhHHHHHhccCCCeeeeecCCCCC--CHHHHHHHHHhcCCeEEEEecCHHHHHHH
Q 029148           89 MDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKDPRFERLPCTHKGT--YADDCLVERVTQHKCFIVATCDRDLKRRI  166 (198)
Q Consensus        89 ~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak~~r~e~~~C~H~g~--~aDdCIv~~v~~~~~yiVATnD~~LrrrL  166 (198)
                      +++|+++++|+||+||++||++||+.++.+..+|+...+++++|+|.+.  +|||||++++++++.|||||||++||++|
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            3689999999999999999999999999999999954499999999965  99999999999887799999999999999


Q ss_pred             hcCCCccEEEEeCceEEEecC
Q 029148          167 RKVPGVPIMYITRHKYSIERL  187 (198)
Q Consensus       167 RkipGVPIiyi~~~~~~lE~~  187 (198)
                      |++|||||||+++++++||+|
T Consensus        81 r~~~GvPvi~l~~~~~~le~p  101 (101)
T PF04900_consen   81 RKIPGVPVIYLRRNVLILEPP  101 (101)
T ss_pred             hcCCCCCEEEEECCEEEecCC
Confidence            988999999999999999987

>smart00670 PINc Large family of predicted nucleotide-binding domains

Probab=98.48  E-value=5e-07  Score=66.89  Aligned_cols=93  Identities=24%  Similarity=0.255  Sum_probs=59.5

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhh--hhHHHHHhcc----------CCC-eeeeecC
Q 029148           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ--KYRVALRIAK----------DPR-FERLPCT  133 (198)
Q Consensus        67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~--k~~~Al~iak----------~~r-~e~~~C~  133 (198)
                      +++|||+++..+..  ++.+.   +...+..++||.+|++||..+..  .++.--.++.          +.. +....+.
T Consensus         1 ~vlDTnvli~~~~~--~~~~~---~~~~~~~~~i~~~v~~El~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~   75 (111)
T smart00670        1 VVLDTNVLIDGLIG--KALEK---LLEKKGEVYIPPTVLEELEYLAKLRSLKKLEELALEGKIKLKVLKEERKLEEEILE   75 (111)
T ss_pred             CEeeHHHHHHHHHH--HHHHH---HHcCCCcEEECHHHHHHHHHHHHHHHHhhHHHHHHhcccccceeecCCCeEEEecc
Confidence            58999999998766  33333   33447889999999999999772  1111111111          000 1112233


Q ss_pred             CCCC-----CHHHHHHHHHhcCCeEEEEecCHHHHH
Q 029148          134 HKGT-----YADDCLVERVTQHKCFIVATCDRDLKR  164 (198)
Q Consensus       134 H~g~-----~aDdCIv~~v~~~~~yiVATnD~~Lrr  164 (198)
                      +.+.     ..|.+|+..+...++.+++|+|.+|++
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=98.21  E-value=1.9e-05  Score=60.86  Aligned_cols=101  Identities=19%  Similarity=0.262  Sum_probs=60.2

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhh-----------hHHHHHhccC---CCeeeeec
Q 029148           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK-----------YRVALRIAKD---PRFERLPC  132 (198)
Q Consensus        67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k-----------~~~Al~iak~---~r~e~~~C  132 (198)
                      +++|||+++...       +.+.++  ....++||.+|+.||..+...           .+.|.++...   ..-..+..
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            589999999763       223332  788899999999999887432           2334333321   00001111


Q ss_pred             CCC-----------CCCHHHHHHHHHhc------CCeEEEEecCHHHHHHHhcCCCccEEEE
Q 029148          133 THK-----------GTYADDCLVERVTQ------HKCFIVATCDRDLKRRIRKVPGVPIMYI  177 (198)
Q Consensus       133 ~H~-----------g~~aDdCIv~~v~~------~~~yiVATnD~~LrrrLRkipGVPIiyi  177 (198)
                      ...           ....|+.|++.+..      ....++.|+|..|+-+++. -|||...+
T Consensus        72 q~~~~~~~~~~~~~~~~~D~~Il~~a~~~~~~~~~~~vvLvT~D~~l~~~A~~-~gi~~~~~  132 (133)
T PF13638_consen   72 QTSDEEIDEDLNLDAQRNDDRILNCALYLQEENPGRKVVLVTNDKNLRLKARA-EGIPAVSY  132 (133)
T ss_dssp             CTTTS-EES--S----HHHHHHHHHHHHHHHHCGCEEEEEEE--HHHHHHHHH-TT--EE--
T ss_pred             chhhhhcchhhhccccccHHHHHHHHHHHHHhcCCCeEEEEeCCHHHHHHHhh-cccccccC
Confidence            111           12578888888742      3457999999999999999 79998865

>PRK13764 ATPase; Provisional

Probab=97.82  E-value=3.5e-05  Score=74.92  Aligned_cols=115  Identities=21%  Similarity=0.218  Sum_probs=75.4

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhh----hHHHHHhccC-------CCeeeeecCC
Q 029148           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK----YRVALRIAKD-------PRFERLPCTH  134 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k----~~~Al~iak~-------~r~e~~~C~H  134 (198)
                      .+++|||.|+.--     +.+.+..-+.-...++||.-|++||+.+...    -+.|++.++.       -.++..-.++
T Consensus         2 ~yVlDTSVIIDGr-----i~~~i~~g~~~~~~IiIP~~Vl~ELe~~A~~~r~~G~~gLeeL~~L~~l~~~g~i~ie~~~~   76 (602)
T PRK13764          2 KIVPDTSVVIDGR-----VSELIEKGEYIGGTIIIPEAVVAELEAQANQGREIGFSGLEELKKLRELAEEGLIELEFVGE   76 (602)
T ss_pred             eEEccceEEEech-----HHHHHHcCCccCCEEEeehHHHHHHHHHhhccchhhHHHHHHHHHHHHhhccCceEEEEecc
Confidence            4677777776531     2222222221245799999999999998653    2334444431       0121111111


Q ss_pred             C----------CCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCc-e-EEEecC
Q 029148          135 K----------GTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH-K-YSIERL  187 (198)
Q Consensus       135 ~----------g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~-~-~~lE~~  187 (198)
                      .          +...|+-|++++.+++ .++.|||..|+..++. -|||++|++.. . +.||..
T Consensus        77 ~p~~~~~~~~~~gevD~~I~~~A~~~~-~~lvT~D~~l~~~A~~-~GI~V~~l~~~~~~L~ie~~  139 (602)
T PRK13764         77 RPTLEQIKLAKGGEIDALIREVAKELG-ATLVTSDRVQAEVARA-KGIDVIYLKPEREPLEIEKF  139 (602)
T ss_pred             ccchhhcccccCCCHHHHHHHHHHHcC-CEEEeCCHHHHHHHHH-cCCEEEEeCCCCCccchHHH
Confidence            1          1468999999999887 5999999999999998 69999999985 3 567764

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

Probab=97.25  E-value=0.0046  Score=46.86  Aligned_cols=96  Identities=18%  Similarity=0.119  Sum_probs=61.0

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHH-hhcccceEeecHHHHHHH-HHhh-hhh---------HHHHHhccCCCeeeeecC
Q 029148           66 RVLVDTNFINFSIQNKLDLEKGMMD-CLYAKCTPCITDCVMAEL-EKLG-QKY---------RVALRIAKDPRFERLPCT  133 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kldl~~~L~~-~L~~k~~~~iT~CVi~EL-ekLg-~k~---------~~Al~iak~~r~e~~~C~  133 (198)
                      +|++|||.++.++-.+-. ...+.+ +..+.+.++++..++.|+ +.|. +++         +..+..... .++...-.
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            489999999998877654 334443 356889999999999999 4443 111         111211111 22222211


Q ss_pred             C----CCCCHHHHHHHHHhcCCeEEEEecCHHHH
Q 029148          134 H----KGTYADDCLVERVTQHKCFIVATCDRDLK  163 (198)
Q Consensus       134 H----~g~~aDdCIv~~v~~~~~yiVATnD~~Lr  163 (198)
                      .    -..+.|+.+++.+...++=++.|.|++|-
T Consensus        79 ~~~~~~~D~~D~~~l~~A~~~~ad~iVT~Dkdll  112 (114)
T TIGR00305        79 PEFDDCRDKKDNKFLNTAYASKANALITGDTDLL  112 (114)
T ss_pred             CCCCCCCCchhHHHHHHHHhcCCCEEEECCHHHh
Confidence            1    12356888889888777668889999874

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=0.0068  Score=44.59  Aligned_cols=99  Identities=22%  Similarity=0.273  Sum_probs=61.7

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhh-----h---HHHHHhccCCCeeeeecCCC---
Q 029148           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK-----Y---RVALRIAKDPRFERLPCTHK---  135 (198)
Q Consensus        67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k-----~---~~Al~iak~~r~e~~~C~H~---  135 (198)
                      |+||||++...+ ..=.-.+...+++.....++++.-++.|+-..-.+     .   ....... .+.++.++.+..   
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            799999999988 33344456666666558899999999999776433     1   1111111 235666664321   


Q ss_pred             ---------CCCHHHHH-HHHHhcCCeEEEEecCHHHHHHHh
Q 029148          136 ---------GTYADDCL-VERVTQHKCFIVATCDRDLKRRIR  167 (198)
Q Consensus       136 ---------g~~aDdCI-v~~v~~~~~yiVATnD~~LrrrLR  167 (198)
                               +....||+ +..+..+++-+|.|+|+++++-.+
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                     12445554 466777787788899999887543

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=96.81  E-value=0.0035  Score=47.89  Aligned_cols=104  Identities=17%  Similarity=0.162  Sum_probs=56.2

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhc---ccceEeecHHHHHHHHHh-hhh-----------hHHHHHhc-cCCCeeee
Q 029148           67 VLVDTNFINFSIQNKLDLEKGMMDCLY---AKCTPCITDCVMAELEKL-GQK-----------YRVALRIA-KDPRFERL  130 (198)
Q Consensus        67 VLvDtNFl~~~i~~kldl~~~L~~~L~---~k~~~~iT~CVi~ELekL-g~k-----------~~~Al~ia-k~~r~e~~  130 (198)
                      +++|||++++.+...=...+...+.+.   ....++++.-|+.|+... ...           ....++-. ..+.+...
T Consensus         2 i~lDTnvli~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vl~E~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   81 (142)
T TIGR00028         2 LLLDVNVLLAAVNRDHPHHDAARAWLDRFAAGGDWATCPLTLAGFVRLLTNPRVLPAPLSPAEAIAVVAAFLATPRHRLL   81 (142)
T ss_pred             ccchhhHHHHhcCCCCcchHHHHHHHHHHhcCCCceechhhhhhheeeeccCCcCCCCCCHHHHHHHHHHHHhCCCeeec
Confidence            689999999988654322223333332   344567788999998552 211           11112111 11112111


Q ss_pred             ec--------------CC-CCC-CHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEE
Q 029148          131 PC--------------TH-KGT-YADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIM  175 (198)
Q Consensus       131 ~C--------------~H-~g~-~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIi  175 (198)
                      .-              .. .+. ++|..|+..+..+++ .+.|.|+++    .+.+|+.++
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              00 112 455556678888876 555999864    456777765

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.

>PRK00124 hypothetical protein; Validated

Probab=95.72  E-value=0.0094  Score=48.79  Aligned_cols=81  Identities=15%  Similarity=0.160  Sum_probs=58.2

Q ss_pred             HHHHHHHhhhhhHHHHHhcc-------CC---CeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCcc
Q 029148          104 VMAELEKLGQKYRVALRIAK-------DP---RFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVP  173 (198)
Q Consensus       104 Vi~ELekLg~k~~~Al~iak-------~~---r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVP  173 (198)
                      |.+|+.+++.++..-+-+.-       .|   ..+.+-.+.....||+-|++.+.+..  +|.|||-.|-.++-. .|.-
T Consensus        12 Vk~~i~r~a~r~~i~v~~Vas~n~~~~~~~~~~v~~v~V~~g~D~AD~~Iv~~~~~gD--iVIT~Di~LAa~~l~-Kga~   88 (151)
T PRK00124         12 VKDIIIRVAERHGIPVTLVASFNHFLRVPYSPFIRTVYVDAGFDAADNEIVQLAEKGD--IVITQDYGLAALALE-KGAI   88 (151)
T ss_pred             HHHHHHHHHHHHCCeEEEEEeCCcccCCCCCCceEEEEeCCCCChHHHHHHHhCCCCC--EEEeCCHHHHHHHHH-CCCE
Confidence            88899988877643322211       11   12223333333479999999998886  999999999999999 7999


Q ss_pred             EEEEeCceEEEecC
Q 029148          174 IMYITRHKYSIERL  187 (198)
Q Consensus       174 Iiyi~~~~~~lE~~  187 (198)
                      +|.-++..|.=|.+
T Consensus        89 vl~prG~~yt~~nI  102 (151)
T PRK00124         89 VLNPRGYIYTNDNI  102 (151)
T ss_pred             EECCCCcCCCHHHH
Confidence            99999888766554

>PF13470 PIN_3: PIN domain

Probab=95.70  E-value=0.11  Score=38.93  Aligned_cols=46  Identities=22%  Similarity=0.363  Sum_probs=36.0

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhh-cccceEeecHHHHHHHHHh
Q 029148           66 RVLVDTNFINFSIQNKLDLEKGMMDCL-YAKCTPCITDCVMAELEKL  111 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kldl~~~L~~~L-~~k~~~~iT~CVi~ELekL  111 (198)
                      +|++|||.++.++-..=.....+.+.+ .+.+.++++.-++.|++..
T Consensus         1 RVvlDTNVli~~ll~~~~~~~~l~~~~~~~~~~~~~s~~~l~E~~~v   47 (119)
T PF13470_consen    1 RVVLDTNVLISALLSREPAARKLLDLAEDGRIELYISPEILDELERV   47 (119)
T ss_pred             CEEEEechhHHHHhCCCchHHHHHHHHHcCCCeEEecHHHHHHHHHH
Confidence            589999999998875543444454444 6889999999999999864

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

Probab=94.90  E-value=0.026  Score=44.96  Aligned_cols=61  Identities=21%  Similarity=0.211  Sum_probs=51.7

Q ss_pred             CCeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCceEEEecCC
Q 029148          125 PRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLP  188 (198)
Q Consensus       125 ~r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~~~~lE~~s  188 (198)
                      +..+.+-|+.....||.-|++.+.+..  +|.|||-.|-.++-. .|+.+|.-++..|.-|.+.
T Consensus        27 ~~~~~i~Vd~g~DaaD~~I~~~~~~gD--iVITqDigLA~~~l~-Kga~vl~~rG~~yt~~nI~   87 (130)
T PF02639_consen   27 PYVEMIVVDSGFDAADFYIVNHAKPGD--IVITQDIGLASLLLA-KGAYVLNPRGKEYTKENID   87 (130)
T ss_pred             CCeEEEEECCCCChHHHHHHHcCCCCC--EEEECCHHHHHHHHH-CCCEEECCCCCCCCHHHHH
Confidence            456666677666689999999999887  999999999999998 7999999999888777653

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

Probab=94.37  E-value=0.31  Score=37.83  Aligned_cols=100  Identities=20%  Similarity=0.283  Sum_probs=58.9

Q ss_pred             EEEeehHHHHHHHHcCC----ChHHhHHHhhcccceEeecHHHHHHHHHhhhh----h--HHHHHhc----cCCCe----
Q 029148           66 RVLVDTNFINFSIQNKL----DLEKGMMDCLYAKCTPCITDCVMAELEKLGQK----Y--RVALRIA----KDPRF----  127 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kl----dl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k----~--~~Al~ia----k~~r~----  127 (198)
                      .+++|||++.+.+-..-    ...+.+.....+....+++.-|+.|+-.+-.+    +  ..+....    ..+.+    
T Consensus         1 ~i~~Dtnvlv~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~v~~e~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (140)
T COG1848           1 MIVIDTNVLVYALFRDHPHHDRARELLERLEAGDIRVYTPELVLAELLRVLTRRRRPLSLAEAIEVVAALLALPRFELLL   80 (140)
T ss_pred             CeeeehHHHHHHHHccChhHHHHHHHHHHHhcCCCceeecHHHHHHHHHHHhhcccCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            37899999999887763    23455555666677899999999999665332    1  1111111    00011    


Q ss_pred             eeee--cC----------CCCCCHHHHHH-HHHhcCCeEEEEecCHHHHHH
Q 029148          128 ERLP--CT----------HKGTYADDCLV-ERVTQHKCFIVATCDRDLKRR  165 (198)
Q Consensus       128 e~~~--C~----------H~g~~aDdCIv-~~v~~~~~yiVATnD~~Lrrr  165 (198)
                      +.++  ..          +.+-.+.|||. ..+..++.--++|.|+++++-
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            1110  00          11123566655 566666667899999977763

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

Probab=93.77  E-value=0.56  Score=38.13  Aligned_cols=95  Identities=25%  Similarity=0.288  Sum_probs=63.8

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhc-ccceEeecHHHHHHHHH-hhh-hhH------------HHHH-----hccCC
Q 029148           66 RVLVDTNFINFSIQNKLDLEKGMMDCLY-AKCTPCITDCVMAELEK-LGQ-KYR------------VALR-----IAKDP  125 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~-~k~~~~iT~CVi~ELek-Lg~-k~~------------~Al~-----iak~~  125 (198)
                      +|++|||-++.++=.+=.+...+.+++. .+...|++.-.++||+. ++. +++            .++.     ++-.|
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            7999999999998887766667776665 56889999999999943 331 211            0111     11112


Q ss_pred             CeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCHHHH
Q 029148          126 RFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLK  163 (198)
Q Consensus       126 r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~~Lr  163 (198)
                      .++...|.   .+-|.-++++|-..+..++.|-|.+|-
T Consensus        82 ~~~f~~~R---Dp~Dn~~L~~A~~~kA~~lvTgD~dLL  116 (142)
T COG1569          82 LEKFNICR---DPKDNKLLALAYESKADYLVTGDQDLL  116 (142)
T ss_pred             cccccccC---CchHHHHHHHHHhccCCEEEEcchhhh
Confidence            22222342   245778899998877779999999774

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

Probab=92.88  E-value=0.44  Score=38.26  Aligned_cols=95  Identities=18%  Similarity=0.156  Sum_probs=55.0

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccc-----eEeecHHHHHHHHHhhhh-hHHHH----HhccCCCeeeeecCC--
Q 029148           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKC-----TPCITDCVMAELEKLGQK-YRVAL----RIAKDPRFERLPCTH--  134 (198)
Q Consensus        67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~-----~~~iT~CVi~ELekLg~k-~~~Al----~iak~~r~e~~~C~H--  134 (198)
                      |||||||+.+....+=.--+.-..++.+..     .+++++|++.|.--|.++ +..|.    ..+....+.+..|.-  
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            899999998876655443333333444433     789999999999988652 22221    122223455555542  


Q ss_pred             --------------CCCC-HHHHHHHHHhcCCeEEEEecCHH
Q 029148          135 --------------KGTY-ADDCLVERVTQHKCFIVATCDRD  161 (198)
Q Consensus       135 --------------~g~~-aDdCIv~~v~~~~~yiVATnD~~  161 (198)
                                    .+-+ +|-|.+-++.+.++-=+-|.|.+
T Consensus        82 ~~~~a~~~~k~~d~~~~df~Da~~~ala~k~g~~~ilSfD~d  123 (135)
T COG2402          82 LEEAAEAVFKRQDDLGLDFVDATSVALAEKLGILKILSFDSD  123 (135)
T ss_pred             HHHHHHHHHHhhcccCCCHHHHHHHHHHHHcCCCcEEEeccc
Confidence                          2223 44444455566665556677664

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

Probab=90.70  E-value=0.38  Score=43.95  Aligned_cols=81  Identities=22%  Similarity=0.241  Sum_probs=55.7

Q ss_pred             eEeecHHHHHHHHHhhhh--------hHHHHHhccC------CCeeeeecCCCC-CCHHHHHHHHHhcCCeEEEEecCHH
Q 029148           97 TPCITDCVMAELEKLGQK--------YRVALRIAKD------PRFERLPCTHKG-TYADDCLVERVTQHKCFIVATCDRD  161 (198)
Q Consensus        97 ~~~iT~CVi~ELekLg~k--------~~~Al~iak~------~r~e~~~C~H~g-~~aDdCIv~~v~~~~~yiVATnD~~  161 (198)
                      .++||+-|++||..++..        -|..|.+.-.      ++.+...-+-.. ...|.-|+.+++..+ -.|.|||-+
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            589999999999999642        2445555421      123333322111 147889999999876 599999999


Q ss_pred             HHHHHhcCCCccEEEEeC
Q 029148          162 LKRRIRKVPGVPIMYITR  179 (198)
Q Consensus       162 LrrrLRkipGVPIiyi~~  179 (198)
                      |-+=.. +-|||++.++.
T Consensus       266 LnKVae-~qgV~vLNIND  282 (356)
T COG4956         266 LNKVAE-LQGVQVLNIND  282 (356)
T ss_pred             HHHHHh-hcCCceecHHH
Confidence            976554 47999998764

>PRK12496 hypothetical protein; Provisional

Probab=89.84  E-value=2.1  Score=35.23  Aligned_cols=97  Identities=13%  Similarity=0.086  Sum_probs=62.1

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHHhccC-CCeeeeecCC----------
Q 029148           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKD-PRFERLPCTH----------  134 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak~-~r~e~~~C~H----------  134 (198)
                      .+++||+.+++-..           .+++  .++||.-|++|+..-...  ..+..+.. ..++...=+.          
T Consensus         3 ~~VlDtS~~I~~~~-----------~~~~--~i~tp~~V~~Ev~d~~~~--~~~~~l~~~~~i~v~~p~~~~i~~v~~~a   67 (164)
T PRK12496          3 IKVLDASAFIHGYN-----------PEDG--EHYTTPSVVEEVKDKESR--LILESAISAGKLKILEPSPESIEKVEEAA   67 (164)
T ss_pred             EEEEEChHHHccch-----------hhCC--CEEecHHHHHHHhCHHHH--HHHHHhcccCCeEEECCCHHHHHHHHHHH
Confidence            47999999986422           1233  479999999999873322  22222221 0122221110          


Q ss_pred             --CC-----CCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeC
Q 029148          135 --KG-----TYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITR  179 (198)
Q Consensus       135 --~g-----~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~  179 (198)
                        .|     ..+|.-++.++.+.+ ..+.|.|..+++-++. -|++++.+++
T Consensus        68 ~~tgd~~~Ls~~D~~~iaLA~el~-~~lvtDD~~~~~vA~~-lgi~v~~~~~  117 (164)
T PRK12496         68 IKTGDLMRLSNTDIEVLALALELN-GTLYTDDYGIQNVAKK-LNIKFENIKT  117 (164)
T ss_pred             HhcCCccccchhhHHHHHHHHHhC-CcEECcHHHHHHHHHH-cCCeEecccc
Confidence              01     135666777777766 4899999999999998 6999999883

>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=88.71  E-value=1.2  Score=36.52  Aligned_cols=42  Identities=29%  Similarity=0.423  Sum_probs=33.7

Q ss_pred             CCCCCHHHHHHHHHhc----CCeEEEEecCHHHHHHHhcCCCccEEE
Q 029148          134 HKGTYADDCLVERVTQ----HKCFIVATCDRDLKRRIRKVPGVPIMY  176 (198)
Q Consensus       134 H~g~~aDdCIv~~v~~----~~~yiVATnD~~LrrrLRkipGVPIiy  176 (198)
                      ..|..||+.|.+++..    +...+|+|.|..+++.++. -|.-.|.
T Consensus        74 ~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~-~GA~~is  119 (166)
T PF05991_consen   74 KEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARG-RGAKRIS  119 (166)
T ss_pred             CCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhh-CCCEEEc
Confidence            3456899999999964    3467999999999999988 5765554

The function of this family is unknown.

>PRK13725 plasmid maintenance protein; Provisional

Probab=88.61  E-value=3.9  Score=31.90  Aligned_cols=42  Identities=29%  Similarity=0.445  Sum_probs=29.1

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHH
Q 029148           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEK  110 (198)
Q Consensus        67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELek  110 (198)
                      .|+|||.+.+.++.+-.......+ . ..-.++|+.-++.||..
T Consensus         4 yLLDTni~i~~~~~~~~~v~~~~~-~-~~~~~~iS~It~~EL~~   45 (132)
T PRK13725          4 FMLDTNICIFTIKNKPEHVRERFN-L-NTGRMCISSVTLMELIY   45 (132)
T ss_pred             hhhhHHHHHHHHhCCcHHHHHHHh-C-CCcceeehHHHHHHHHH
Confidence            589999999998866433222222 1 23458899999999975

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

Probab=86.58  E-value=4.2  Score=31.30  Aligned_cols=43  Identities=19%  Similarity=0.073  Sum_probs=29.1

Q ss_pred             eEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHH
Q 029148           65 YRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEK  110 (198)
Q Consensus        65 Y~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELek  110 (198)
                      ...++|||.+.......-.-.  +...+.. ...+++.-++.||..
T Consensus         2 ~~~llDTnv~i~l~~~~~~~~--~~~~~~~-~~~~~s~it~~El~~   44 (133)
T COG1487           2 MMYLLDTSVIIALLRGEPKEL--LELRLAE-FEIYLSSITVAELLL   44 (133)
T ss_pred             CceeeeHHHHHHHHhcCChHH--HHHHHhc-CCeeecHHHHHHHHH
Confidence            357999999999877655432  1112222 567889899999864

>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=85.33  E-value=1.4  Score=36.26  Aligned_cols=48  Identities=23%  Similarity=0.311  Sum_probs=42.4

Q ss_pred             CHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCceEEEecCC
Q 029148          138 YADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKYSIERLP  188 (198)
Q Consensus       138 ~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~~~~lE~~s  188 (198)
                      -||+-|++++....  +|.|+|-.|-.++-. .|+-+|.=++..|.-|.+.
T Consensus        55 aaD~~Iv~~a~~gD--lVVT~Di~LA~~ll~-kg~~v~~prGr~y~~~nI~  102 (150)
T COG1671          55 AADDWIVNLAEKGD--LVVTADIPLASLLLD-KGAAVLNPRGRLYTEENIG  102 (150)
T ss_pred             hHHHHHHHhCCCCC--EEEECchHHHHHHHh-cCCEEECCCCcccCHhHHH
Confidence            58999999998876  999999999999999 7999998888888777654

---

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	198
1o4w_A	147	PIN (PILT N-terminus) domain; structural genomics,	3e-48

>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 =  153 bits (388), Expect = 3e-48
 Identities = 33/127 (25%), Positives = 58/127 (45%), Gaps = 7/127 (5%)

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

Query: 125 --PRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKY 182
                E        +  D  L+E   ++ C I+ T D++LKR+ ++  G+P+ Y+   K 
Sbjct: 83  ALKLLEHFEVVETESEGDPSLIEAAEKYGC-ILITNDKELKRKAKQ-RGIPVGYLKEDKR 140

Query: 183 SIERLPE 189
               L +
Sbjct: 141 VFVELLD 147

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	198
1o4w_A	147	PIN (PILT N-terminus) domain; structural genomics,	99.88
3ix7_A	134	Uncharacterized protein TTHA0540; unknown function	98.99
2dok_A	186	Telomerase-binding protein EST1A; telomerase-assoc	98.77
3i8o_A	142	KH domain-containing protein MJ1533; APC89320.5, m	98.69
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	97.0
3zvk_A	134	VAPC2, toxin of toxin-antitoxin system; antitoxin-	96.39
3tnd_A	132	TRNA(FMet)-specific endonuclease VAPC; PIN domain,	96.08
1v96_A	149	Hypothetical protein PH0500; rossmann fold, tRNA s	95.43
2fe1_A	156	Conserved hypothetical protein PAE0151; PIN domain	94.73
1w8i_A	156	Putative VAPC ribonuclease AF_1683; structural gen	94.69
3h87_A	156	Putative uncharacterized protein; toxin antitoxin	94.44
2hwy_A	164	Protein SMG5; RNA degradation, decay, NMD, EST1A,	93.53
2h1c_A	139	Trafficking protein B; DNA binding, PIN domain, RH	93.24
3dbo_B	150	Uncharacterized protein; toxin antitoxin complex,	91.1

>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=99.88  E-value=1.1e-22  Score=160.24  Aligned_cols=119  Identities=29%  Similarity=0.409  Sum_probs=96.8

Q ss_pred             HHhhhCCCCCeE-EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhh--------hhHHHHHhccCC
Q 029148           55 FTHNTALGPPYR-VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ--------KYRVALRIAKDP  125 (198)
Q Consensus        55 y~~n~~~~~PY~-VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~--------k~~~Al~iak~~  125 (198)
                      ...|||||+||+ +|+|||++++++..+.++.+.+.+++.  ..++||.||+.||+.+..        ..+.++.++.  
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            457999999999 999999999999999999999999876  789999999999999863        3456677777  


Q ss_pred             CeeeeecCCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCceE
Q 029148          126 RFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKY  182 (198)
Q Consensus       126 r~e~~~C~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~~~  182 (198)
                      .++.+.|+ .+ + |+||++.+..++ ++|+|+|++|+++++.. |||+++++++++
T Consensus        89 ~~~vv~~~-~~-~-D~~Ila~A~~~~-~~LvT~D~~l~~~a~~~-Gv~vi~~~~~~~  140 (147)
T 1o4w_A           89 HFEVVETE-SE-G-DPSLIEAAEKYG-CILITNDKELKRKAKQR-GIPVGYLKEDKR  140 (147)
T ss_dssp             TSEEECCS-SC-S-HHHHHHHHHHHT-CEEECCCHHHHHHHHHT-TCCEECCCCCCC
T ss_pred             cCcEeeCC-CC-c-hHHHHHHHHHhC-CEEEECCHHHHHHHHHC-CCeEEEecCCcE
Confidence            47778887 44 7 999999998887 79999999999999996 999999999754

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

Probab=98.99  E-value=2.3e-09  Score=84.52  Aligned_cols=104  Identities=21%  Similarity=0.206  Sum_probs=74.3

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhh--------hhHHHHHhccC----CCeeeeecCC
Q 029148           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ--------KYRVALRIAKD----PRFERLPCTH  134 (198)
Q Consensus        67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~--------k~~~Al~iak~----~r~e~~~C~H  134 (198)
                      .++|||+|+..-     +.+.+..-+.. -.++||.+|++||+.+..        +.+.+|++.+.    ..++... +.
T Consensus         8 ~vlDTSviIdGr-----i~~~~~~gf~e-g~liIP~~Vl~ELq~lA~s~d~~~r~rGr~gL~iL~~L~~~~~vei~~-~~   80 (134)
T 3ix7_A            8 KVLDTSVLVDGR-----VAEVAAVGFLE-GPLWVPHFVLKELQHFADSQDPLRRAKGRRGLETLERLREAAPLEVLE-TT   80 (134)
T ss_dssp             EEECHHHHHHCH-----HHHHHTTTCCC-SCEEEEHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHSCEEEEC-CC
T ss_pred             eEcccceEEecH-----HHHHHHhcccc-CceecHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHhcCCEEEeC-CC
Confidence            477999998541     22222222211 269999999999999972        34567766652    1144443 22


Q ss_pred             -CCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeC
Q 029148          135 -KGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITR  179 (198)
Q Consensus       135 -~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~  179 (198)
                       .+..+|+.|++++.+.++ +|.|||..|++.++. -|||++|++.
T Consensus        81 ~~~~~vD~~ll~lA~~~~~-~lvTnD~~L~kvA~~-~GI~Vl~l~~  124 (134)
T 3ix7_A           81 PKGESVDEKLLFLARDLEA-ALVTNDHALLQMARI-YGVKALSIQA  124 (134)
T ss_dssp             CSCSSHHHHHHHHHHHTTC-EEEESCHHHHHHHHH-TTCCEEEHHH
T ss_pred             CCcccHHHHHHHHHHHhCC-EEEeCCHHHHHHHHH-CCCeEEehHH
Confidence             235799999999999885 999999999999998 7999999864

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

Probab=98.77  E-value=1.3e-08  Score=83.08  Aligned_cols=107  Identities=20%  Similarity=0.233  Sum_probs=72.3

Q ss_pred             CeEEEeehHHHHHHHHcCCChHHhHHHhhc-ccceEeecHHHHHHHHHhhh-----------------hhHHHHHhccC-
Q 029148           64 PYRVLVDTNFINFSIQNKLDLEKGMMDCLY-AKCTPCITDCVMAELEKLGQ-----------------KYRVALRIAKD-  124 (198)
Q Consensus        64 PY~VLvDtNFl~~~i~~kldl~~~L~~~L~-~k~~~~iT~CVi~ELekLg~-----------------k~~~Al~iak~-  124 (198)
                      |..+++|||+|+...       +.|.++.. +...++||..|++||+.|..                 ..|.|+++..+ 
T Consensus        12 ~~~~VlDTNvLl~~~-------~~l~~~~~~~~~~viIP~~VleELd~lk~~~~~~~~~~~~~~~~~~~AR~a~~~L~~~   84 (186)
T 2dok_A           12 PLFLVPDTNGFIDHL-------ASLARLLESRKYILVVPLIVINELDGLAKGQETDHRAGGYARVVQEKARKSIEFLEQR   84 (186)
T ss_dssp             EEEEEECHHHHHHHH-------HHHHHHHHHTSSEEEEEHHHHHHHHHHHC-------CCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEhHHHHcCH-------HHHHHHHcCCCeEEEECHHHHHHHHHhccCCCccccccchhHHHHHHHHHHHHHHHHH
Confidence            456899999997753       34444332 45789999999999999843                 34555555432 


Q ss_pred             -----CCeee----------eecCCC-----CCCHHHHHHHHHhcC--------------------CeEEEEecCHHHHH
Q 029148          125 -----PRFER----------LPCTHK-----GTYADDCLVERVTQH--------------------KCFIVATCDRDLKR  164 (198)
Q Consensus       125 -----~r~e~----------~~C~H~-----g~~aDdCIv~~v~~~--------------------~~yiVATnD~~Lrr  164 (198)
                           +.+..          +...+.     ...+|+.|++.|...                    ...++.|+|.+||.
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     246899999999631                    14689999999999


Q ss_pred             HHhcCCCccEEEEe
Q 029148          165 RIRKVPGVPIMYIT  178 (198)
Q Consensus       165 rLRkipGVPIiyi~  178 (198)
                      +++. -|||++.++
T Consensus       165 KA~~-~Gi~~~~~~  177 (186)
T 2dok_A          165 KALT-RNVPVRDIP  177 (186)
T ss_dssp             HHHH-TTCCEECHH
T ss_pred             HHHH-CCCeeCcHH
Confidence            9999 799988654

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

Probab=98.69  E-value=6.4e-08  Score=77.05  Aligned_cols=108  Identities=16%  Similarity=0.112  Sum_probs=76.9

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhh----hHHHHHhccC---------CCeeeeec
Q 029148           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK----YRVALRIAKD---------PRFERLPC  132 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k----~~~Al~iak~---------~r~e~~~C  132 (198)
                      .+++|||.|+.--     +.+.+..-+.....++||..|++||+.+...    -+.+|.+++.         -.++...-
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            6899999998632     3444443343345799999999999999643    3456665541         01222110


Q ss_pred             C-------C-CCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCc
Q 029148          133 T-------H-KGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH  180 (198)
Q Consensus       133 ~-------H-~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~  180 (198)
                      .       + .+..+|+-|+++|.+.++ .+.|||..|++.++. -|||++|+++.
T Consensus        80 r~~~~~i~~~~~~~vD~~l~~lA~~~~a-~lvTnD~~l~kvA~~-~GI~V~~l~~~  133 (142)
T 3i8o_A           80 RPTREEIFLAKSGEIDAMIRKVAKETNS-ILLTSDWIQYNLAKA-QGIEAYFLEAA  133 (142)
T ss_dssp             CCCHHHHHSCCSSSHHHHHHHHHHHTTC-EEEESCHHHHHHHHH-TTCCEEECCCC
T ss_pred             cCchhhhccccCCcHHHHHHHHHHHhCC-EEEcCCHHHHHHHHH-cCCEEEEeccc
Confidence            0       0 124789999999999884 899999999999999 79999999875

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

Probab=97.00  E-value=0.00032  Score=55.69  Aligned_cols=93  Identities=14%  Similarity=0.141  Sum_probs=63.4

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHHhcc-CCCeeeeecC-----------
Q 029148           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAK-DPRFERLPCT-----------  133 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak-~~r~e~~~C~-----------  133 (198)
                      .+|+|||.|+...    ++            .++||..|++||....  .+..+.... ...++...=.           
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            4699999999843    21            7899999999996432  222232221 1112221100           


Q ss_pred             -CCC-----CCHHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEe
Q 029148          134 -HKG-----TYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYIT  178 (198)
Q Consensus       134 -H~g-----~~aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~  178 (198)
                       ..|     ..+|..++.++.+.+. .|.|+|..|++.++. -||+++.+.
T Consensus        74 ~~~gd~~~Ls~~D~~lIaLA~~l~~-~lvT~D~~l~~vA~~-~Gv~v~~~~  122 (165)
T 2lcq_A           74 KETGEVNELSKADIEVLALAYELKG-EIFSDDYNVQNIASL-LGLRFRTLK  122 (165)
T ss_dssp             HHHSCSSCSCHHHHHHHHHHHHHTC-CEECCCHHHHHHHHH-TTCCEECCS
T ss_pred             HHcCCcccCCHHHHHHHHhHHHhCC-eEEcCcHHHHHHHHH-CCCeEEchh
Confidence             011     2488999999988774 888999999999999 699999887

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

Probab=96.39  E-value=0.015  Score=43.06  Aligned_cols=102  Identities=17%  Similarity=0.198  Sum_probs=61.6

Q ss_pred             EEEeehHHHHHHHHcCCC-hHHhHHHhhcccceEeecHHHHHHHHHhhhh------hHHHHH-hccCCCeeeeecC----
Q 029148           66 RVLVDTNFINFSIQNKLD-LEKGMMDCLYAKCTPCITDCVMAELEKLGQK------YRVALR-IAKDPRFERLPCT----  133 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kld-l~~~L~~~L~~k~~~~iT~CVi~ELekLg~k------~~~Al~-iak~~r~e~~~C~----  133 (198)
                      .+|+|||.++..+...-. +.+.+..+.. .-.++|+.-++.|+...-.+      ....+. +..  .++.++.+    
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            589999999999887643 3344444332 24789999999999754221      111111 122  35444432    


Q ss_pred             --------------CCCCCHHHHHHHHHhcCCeEEEEecC-HHHHHHHhcCCCccEE
Q 029148          134 --------------HKGTYADDCLVERVTQHKCFIVATCD-RDLKRRIRKVPGVPIM  175 (198)
Q Consensus       134 --------------H~g~~aDdCIv~~v~~~~~yiVATnD-~~LrrrLRkipGVPIi  175 (198)
                                    |.-..+|--|...+..+++ .+.|.| +++    ..+||+.++
T Consensus        79 ~~a~~l~~~~~~~g~~~~~~D~lIaA~A~~~~~-~lvT~d~~df----~~~~gl~~~  130 (134)
T 3zvk_A           79 FYYGELRTELEQKGLIIGNNDLLIASHAIAENA-TLVTNNIKEF----KRIPNLILE  130 (134)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTC-EEEESSTTTS----CSCTTCEEE
T ss_pred             HHHHHHHHHHHHcCCCCCccHHHHHHHHHHCCC-EEEECCHHHh----cCCCCCeee
Confidence                          1112344445566777886 788999 655    457888765

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

Probab=96.08  E-value=0.068  Score=39.35  Aligned_cols=100  Identities=21%  Similarity=0.317  Sum_probs=61.3

Q ss_pred             EEEeehHHHHHHHHcCCC-hHHhHHHhhcccceEeecHHHHHHHHHhhhh------hHHHHH-hccCCCeeeeecC----
Q 029148           66 RVLVDTNFINFSIQNKLD-LEKGMMDCLYAKCTPCITDCVMAELEKLGQK------YRVALR-IAKDPRFERLPCT----  133 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kld-l~~~L~~~L~~k~~~~iT~CVi~ELekLg~k------~~~Al~-iak~~r~e~~~C~----  133 (198)
                      ++|+|||.++..+...-. +.+.+....   -.++|+.-++.|+...-.+      ....+. +..  .++.++-+    
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            479999999999887644 344444432   3689999999999764221      111111 112  34444422    


Q ss_pred             -----------CCC--CC-HHHHHHHHHhcCCeEEEEecC-HHHHHHHhcCCCccEE
Q 029148          134 -----------HKG--TY-ADDCLVERVTQHKCFIVATCD-RDLKRRIRKVPGVPIM  175 (198)
Q Consensus       134 -----------H~g--~~-aDdCIv~~v~~~~~yiVATnD-~~LrrrLRkipGVPIi  175 (198)
                                 |.|  .. .|--|...+..+++ .+.|.| +++    ..+||+.+.
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  23 44445566777886 788998 776    457899875

>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=95.43  E-value=0.039  Score=41.55  Aligned_cols=104  Identities=13%  Similarity=0.102  Sum_probs=59.1

Q ss_pred             eEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhh----hHHHH-HhccCCCeeeeecC------
Q 029148           65 YRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK----YRVAL-RIAKDPRFERLPCT------  133 (198)
Q Consensus        65 Y~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k----~~~Al-~iak~~r~e~~~C~------  133 (198)
                      -.+++|||.++..+.   +-...+.+.+.....++++.-++.|+...-.+    -...+ .+..  .++.+..+      
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   22234444443445689999999999853211    01111 1111  12233322      


Q ss_pred             -------C--CC--CCHHHHH-HHHHhcCCeEEEEecCH-HHHHHHhcCCCccEEE
Q 029148          134 -------H--KG--TYADDCL-VERVTQHKCFIVATCDR-DLKRRIRKVPGVPIMY  176 (198)
Q Consensus       134 -------H--~g--~~aDdCI-v~~v~~~~~yiVATnD~-~LrrrLRkipGVPIiy  176 (198)
                             +  .|  .+..||+ ...+..+++ .+.|+|. ++.+ +.. .|++++.
T Consensus        80 a~~l~~~~~~~g~~~~~~D~lIaA~A~~~~~-~lvT~D~kdf~~-i~~-~~i~~i~  132 (149)
T 1v96_A           80 AAQIEANLIKKEITLDMEDIITATTAIYTNS-LLVTDDPKRYEP-IRR-FGLDTMP  132 (149)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHHHTC-EEEESCHHHHGG-GGG-GTCCEEE
T ss_pred             HHHHHHHHHHCCCCCCHhHHHHHHHHHHcCC-EEEECCHHHHhh-hhh-CCeeecC
Confidence                   0  12  2445555 466777787 6889995 6643 555 3677664

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

Probab=94.73  E-value=0.029  Score=43.28  Aligned_cols=104  Identities=15%  Similarity=0.078  Sum_probs=62.6

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhh-h----------hhHHHHHh----ccCCCeeee
Q 029148           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLG-Q----------KYRVALRI----AKDPRFERL  130 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg-~----------k~~~Al~i----ak~~r~e~~  130 (198)
                      .+++|||.++..+... +..+.+.+.+.....++++.-++.|+...- .          ....++..    .....+...
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            5899999999987553 223555666654457899999999996421 1          11222222    221011111


Q ss_pred             e----------cCCCCCC-HHHHHHHHHhcCCeEEEEecCHHHHHHHhcCCCcc
Q 029148          131 P----------CTHKGTY-ADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVP  173 (198)
Q Consensus       131 ~----------C~H~g~~-aDdCIv~~v~~~~~yiVATnD~~LrrrLRkipGVP  173 (198)
                      .          -.| +-. .|.-++..+..+++- ++|.|++|.+..++ -|+|
T Consensus       106 ~~~~~~A~~l~~~~-~l~~~Dal~lA~A~~~~~~-LvT~D~~l~~~a~~-~Gi~  156 (156)
T 2fe1_A          106 AEVLKDAFALALKH-GVTVYDAAYVALAEKIGGK-LLTLDRQLAEKFPA-LVTP  156 (156)
T ss_dssp             GGTHHHHHHHHHHH-TCCHHHHHHHHHHHHHTCE-EECSCHHHHHHCTT-TBC-
T ss_pred             hHHHHHHHHHHHHh-CcCHHHHHHHHHHHHcCCC-EEeCCHHHHHHHHH-cCCC
Confidence            1          011 223 344456777777764 99999999999888 5775

>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=94.69  E-value=0.11  Score=39.70  Aligned_cols=98  Identities=12%  Similarity=-0.071  Sum_probs=58.4

Q ss_pred             EEEeehHHHHHHHHcCCChHH----hHH-HhhcccceEeecHHHHHHHHHhhh----hhHHHHHhc-cCCCeeeeec---
Q 029148           66 RVLVDTNFINFSIQNKLDLEK----GMM-DCLYAKCTPCITDCVMAELEKLGQ----KYRVALRIA-KDPRFERLPC---  132 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kldl~~----~L~-~~L~~k~~~~iT~CVi~ELekLg~----k~~~Al~ia-k~~r~e~~~C---  132 (198)
                      .++||||++++.+...=...+    .+. .+..+...++|+.-|+.|+...-.    .....++.. ..+.++.+..   
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            489999999998865433222    233 333446789999999999976422    122222221 1123443332   


Q ss_pred             -----------CCC--CCC-HHHHHHHHHhcCCeEEEEecCHHHHH
Q 029148          133 -----------THK--GTY-ADDCLVERVTQHKCFIVATCDRDLKR  164 (198)
Q Consensus       133 -----------~H~--g~~-aDdCIv~~v~~~~~yiVATnD~~Lrr  164 (198)
                                 .+.  +.. +|-.|...+..+++ .++|.|+++.+
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                       121  233 44445567778888 99999988765

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

Probab=94.44  E-value=0.16  Score=39.94  Aligned_cols=111  Identities=15%  Similarity=0.071  Sum_probs=66.0

Q ss_pred             CCCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhh---hhHHHHHh--ccCCCeeeeecC--
Q 029148           61 LGPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ---KYRVALRI--AKDPRFERLPCT--  133 (198)
Q Consensus        61 ~~~PY~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~---k~~~Al~i--ak~~r~e~~~C~--  133 (198)
                      ...+..+|||||.++..++..  ..+.+.+.+... .++|+.-++.||..-..   .......+  ..  .|+.++.+  
T Consensus        15 ~~~~~~~LLDTnvli~~l~~~--~~~~l~~~~~~~-~l~iS~it~~El~~G~~~~~~~~~l~~~~~L~--~~~vlp~d~~   89 (156)
T 3h87_A           15 MVTDQRWLIDKSALVRLTDSP--DMEIWSNRIERG-LVHITGVTRLEVGFSAECGEIARREFREPPLS--AMPVEYLTPR   89 (156)
T ss_dssp             --CCCCEEECHHHHTTGGGCT--THHHHHHHHHTT-CEEEEHHHHHHHHHHSSSHHHHHHHHHSTTGG--GSCEECCCHH
T ss_pred             hhcCCCEEEEHHHHHHHHcCH--HHHHHHHhccCC-CEEEccccHHHHhhhhhCchHHHHHHHhhccc--CCCeecCCHH
Confidence            455678999999999988553  445666665433 47899999999986311   12222222  22  34444422  


Q ss_pred             -------------CC----CCCHHHHHH-HHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEe
Q 029148          134 -------------HK----GTYADDCLV-ERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYIT  178 (198)
Q Consensus       134 -------------H~----g~~aDdCIv-~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~  178 (198)
                                   .+    +...-||++ ..+..++ ..+.|+|+++.+- ..+.|.|+-.+.
T Consensus        90 ~a~~a~~i~~~l~~~G~~~~i~~~D~lIAAtA~~~g-l~LvT~d~dF~~i-~~~~~l~~~~~~  150 (156)
T 3h87_A           90 IEDRALEVQTLLADRGHHRGPSIPDLLIAATAELSG-LTVLHVDKDFDAI-AALTGQKTERLT  150 (156)
T ss_dssp             HHHHHHHHHHHHHHTTCTTSSCHHHHHHHHHHHHHT-CEEEESCTHHHHH-HHHHCCCEEECC
T ss_pred             HHHHHHHHHHHHHhcCCCCCCChhHHHHHHHHHHCC-CEEEEeChhhhhh-hhcCCCceEEec
Confidence                         11    224455554 5566677 4677999887654 444777766544

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

Probab=93.53  E-value=0.092  Score=42.38  Aligned_cols=50  Identities=18%  Similarity=0.222  Sum_probs=37.0

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhh---hhHHHHHhc
Q 029148           67 VLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ---KYRVALRIA  122 (198)
Q Consensus        67 VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~---k~~~Al~ia  122 (198)
                      .++|||+|+.-    +++...|.+  ..+..++||.-|+.||..|..   .+|.|+++.
T Consensus         5 lVlDTN~Li~~----l~~i~~l~~--~~~~~IvIP~~Vi~ELD~LK~~~~~AR~Air~L   57 (164)
T 2hwy_A            5 LVPDTQALCHH----LPVIRQLAT--SGRFIVIIPRTVIDGLDLLKKEHPGARDGIRYL   57 (164)
T ss_dssp             EEECHHHHHHC----HHHHHHHHH--HSSSEEEECHHHHHHHHHHC-CCHHHHHHHHHH
T ss_pred             EEechHHHHhC----HHHHHHHHh--CCCcEEEEcHHHHHHHHHhccCCHHHHHHHHHH
Confidence            57899999883    444455533  357899999999999999965   467777665

>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=93.24  E-value=0.44  Score=34.58  Aligned_cols=99  Identities=23%  Similarity=0.261  Sum_probs=56.6

Q ss_pred             EEeehHHHHHHHHcCCChHHhHHHhhc--ccceEeecHHHHHHHHHh-hhh--------hHHHHHh--ccCCCe--eeee
Q 029148           67 VLVDTNFINFSIQNKLDLEKGMMDCLY--AKCTPCITDCVMAELEKL-GQK--------YRVALRI--AKDPRF--ERLP  131 (198)
Q Consensus        67 VLvDtNFl~~~i~~kldl~~~L~~~L~--~k~~~~iT~CVi~ELekL-g~k--------~~~Al~i--ak~~r~--e~~~  131 (198)
                      +++|||.++..+...-+  ....+.|.  ..-.++|+.-++.|+... ...        ....+.-  ..  .+  +.++
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            68999999998875532  22333332  234689999999999863 221        1112211  12  23  3343


Q ss_pred             cCC---------------CC--CC-HHHHHHHHHhcCCeEEEEecC-HHHHHHHhcCCCccEE
Q 029148          132 CTH---------------KG--TY-ADDCLVERVTQHKCFIVATCD-RDLKRRIRKVPGVPIM  175 (198)
Q Consensus       132 C~H---------------~g--~~-aDdCIv~~v~~~~~yiVATnD-~~LrrrLRkipGVPIi  175 (198)
                      .+.               .|  .. +|--|...+..+++ .+.|.| +++.+    + |++++
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            321               11  23 44445566777786 899999 77753    3 77654

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

Probab=91.10  E-value=0.24  Score=38.38  Aligned_cols=104  Identities=19%  Similarity=0.152  Sum_probs=56.0

Q ss_pred             CCCeEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhh----h--hHHHHH---hccCCCeeeeec
Q 029148           62 GPPYRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQ----K--YRVALR---IAKDPRFERLPC  132 (198)
Q Consensus        62 ~~PY~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~----k--~~~Al~---iak~~r~e~~~C  132 (198)
                      .+|-++|+|||.++..++..-.. .    .+ ..-.++|+.-++.||..--.    .  ....++   +..  .|+.++.
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            46778999999999887755322 2    22 34578999999999865311    1  112222   222  4655553


Q ss_pred             CC---------------CC--CCHHHH-HHHHHhcCCeEEEEecCHHHHHHHhcCCCccEE
Q 029148          133 TH---------------KG--TYADDC-LVERVTQHKCFIVATCDRDLKRRIRKVPGVPIM  175 (198)
Q Consensus       133 ~H---------------~g--~~aDdC-Iv~~v~~~~~yiVATnD~~LrrrLRkipGVPIi  175 (198)
                      +.               .|  ...-|| |...+..+++ .+.|+|+++. ++-.+-|.+++
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-PVITQDDDFA-ALDGAASVEII  148 (150)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCCCBHHHHHHHHHHHHTTC-CEEESSSSGG-GGTTSTTCCEE
T ss_pred             CHHHHHHHHHHHHHHHHcCCCCCCchHHHHHHHHHCCC-EEEECChhhh-hCCCccCceee
Confidence            31               11  123344 4566677774 7899997553 34444455554

---

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	198
d1o4wa_	125	c.120.1.1 (A:) Hypothetical protein AF0591 {Archae	1e-37

>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 =  124 bits (313), Expect = 1e-37
 Identities = 34/126 (26%), Positives = 59/126 (46%), Gaps = 8/126 (6%)

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

Query: 125 --PRFERLPCTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRHKY 182
                E        +  D  L+E   ++ C I+ T D++LKR+ ++  G+P+ Y+   K 
Sbjct: 62  ALKLLEHFEVVETESEGDPSLIEAAEKYGC-ILITNDKELKRKAKQ-RGIPVGYLKEDKR 119

Query: 183 -SIERL 187
             +E L
Sbjct: 120 VFVELL 125

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	198
d1o4wa_	125	Hypothetical protein AF0591 {Archaeon Archaeoglobu	99.95
d2fe1a1	130	Conserved hypothetical protein PAE0151 {Pyrobaculu	96.49
d1v96a1	148	Hypothetical protein PH0500 {Pyrococcus horikoshii	96.16
d1w8ia_	155	Hypothetical protein AF1683 {Archaeoglobus fulgidu	94.74
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=6e-29  Score=191.32  Aligned_cols=118  Identities=26%  Similarity=0.363  Sum_probs=95.1

Q ss_pred             eEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhhhHHHHHhccC---CCeeeeecCCCCCCHHH
Q 029148           65 YRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQKYRVALRIAKD---PRFERLPCTHKGTYADD  141 (198)
Q Consensus        65 Y~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k~~~Al~iak~---~r~e~~~C~H~g~~aDd  141 (198)
                      ..||+|||||++++++++|+.++|.++  +..+++||.||+.||++|+++.+.+.+.++.   ..++..++.+.+.++||
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            469999999999999999999999985  4577999999999999998765433332221   01222334455778999


Q ss_pred             HHHHHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEeCc-eEEEec
Q 029148          142 CLVERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYITRH-KYSIER  186 (198)
Q Consensus       142 CIv~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~~~-~~~lE~  186 (198)
                      ||++.+.+++ |+|||||++||++++. +||||||++++ .+.||.
T Consensus        81 ~il~~a~~~~-~iv~T~D~~Lr~~~~~-~GVpvi~l~~~~~l~~~~  124 (125)
T d1o4wa_          81 SLIEAAEKYG-CILITNDKELKRKAKQ-RGIPVGYLKEDKRVFVEL  124 (125)
T ss_dssp             HHHHHHHHHT-CEEECCCHHHHHHHHH-TTCCEECCCCCCCCCCCC
T ss_pred             HHHHHHhhCC-eEEEecCHHHHHHHHH-cCCcEEEEeCCceEEEEe
Confidence            9999999887 8999999999999998 99999999997 447764

>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=96.49  E-value=0.002  Score=45.55  Aligned_cols=100  Identities=15%  Similarity=0.026  Sum_probs=61.0

Q ss_pred             EEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHhhhh-----------hHHHHHhccC-CCeeeee--
Q 029148           66 RVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKLGQK-----------YRVALRIAKD-PRFERLP--  131 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekLg~k-----------~~~Al~iak~-~r~e~~~--  131 (198)
                      +|++|||+++..+... +-.+...+.+...-.++++..++.|+.....+           ...++..... .......  
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            6899999999877554 34566667777677899999999999643211           1111111100 0000011  


Q ss_pred             -----------cCCCCCCHHHHHHHHHhcCCeEEEEecCHHHHHHHh
Q 029148          132 -----------CTHKGTYADDCLVERVTQHKCFIVATCDRDLKRRIR  167 (198)
Q Consensus       132 -----------C~H~g~~aDdCIv~~v~~~~~yiVATnD~~LrrrLR  167 (198)
                                 ..|.-...|--++..+..+++ -++|.|+.|.+++.
T Consensus        81 ~~~~~~a~~l~~~~~l~~~Da~i~A~A~~~~~-~l~T~D~~l~~~~~  126 (130)
T d2fe1a1          81 AEVLKDAFALALKHGVTVYDAAYVALAEKIGG-KLLTLDRQLAEKFP  126 (130)
T ss_dssp             GGTHHHHHHHHHHHTCCHHHHHHHHHHHHHTC-EEECSCHHHHHHCT
T ss_pred             HHHHHHHHHHHHHcCCCccHHHHHHHHHHcCC-EEEECCHHHHHhcC
Confidence                       122222456666788888886 69999998887743

>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=96.16  E-value=0.0037  Score=47.13  Aligned_cols=108  Identities=16%  Similarity=0.150  Sum_probs=68.8

Q ss_pred             eEEEeehHHHHHHHHcCCChHHhHHHhhcccceEeecHHHHHHHHHh----hhhhHHHHHhccCCCeeeeecC-------
Q 029148           65 YRVLVDTNFINFSIQNKLDLEKGMMDCLYAKCTPCITDCVMAELEKL----GQKYRVALRIAKDPRFERLPCT-------  133 (198)
Q Consensus        65 Y~VLvDtNFl~~~i~~kldl~~~L~~~L~~k~~~~iT~CVi~ELekL----g~k~~~Al~iak~~r~e~~~C~-------  133 (198)
                      =++|+|||.++.-.+.+   .+.+.+.+.++..++++..++.|+..-    ++.....++...+ .++.++.+       
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            48999999999865433   245555666778899999999998631    2222222222221 23333322       


Q ss_pred             --------CCC--CCHHHHHH-HHHhcCCeEEEEecCHHHHHHHhcCCCccEEEEe
Q 029148          134 --------HKG--TYADDCLV-ERVTQHKCFIVATCDRDLKRRIRKVPGVPIMYIT  178 (198)
Q Consensus       134 --------H~g--~~aDdCIv-~~v~~~~~yiVATnD~~LrrrLRkipGVPIiyi~  178 (198)
                              +.|  ....||++ ..+..++ +.++|+|..--+++.+ -|+-++.+.
T Consensus        80 ~~i~a~l~~~g~~i~~~D~lIAAtAi~~~-~~LVT~n~kdF~~i~~-~Gl~vi~~~  133 (148)
T d1v96a1          80 AQIEANLIKKEITLDMEDIITATTAIYTN-SLLVTDDPKRYEPIRR-FGLDTMPLD  133 (148)
T ss_dssp             HHHHHHHHHTTCCCCHHHHHHHHHHHHHT-CEEEESCHHHHGGGGG-GTCCEEEHH
T ss_pred             HHHHHHHHhccCCCChhHHHHHHHHHHcC-CEEEeCCHHHhhHHHH-CCceEecHH
Confidence                    122  24555554 5666777 5999999988888877 699888653

>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=94.74  E-value=0.1  Score=38.65  Aligned_cols=96  Identities=14%  Similarity=0.012  Sum_probs=56.1

Q ss_pred             EEEeehHHHHHHHHcCCC----hHHhHHHhhcc-cceEeecHHHHHHHHHh-hhh----hHHHHHhccCCCeeeeecCC-
Q 029148           66 RVLVDTNFINFSIQNKLD----LEKGMMDCLYA-KCTPCITDCVMAELEKL-GQK----YRVALRIAKDPRFERLPCTH-  134 (198)
Q Consensus        66 ~VLvDtNFl~~~i~~kld----l~~~L~~~L~~-k~~~~iT~CVi~ELekL-g~k----~~~Al~iak~~r~e~~~C~H-  134 (198)
                      .+|||||++.+.+..+=.    ..+.+.+++.+ ...++||..|+.|+-.+ +..    ......+...+.++.+.++. 
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            689999999998754422    23444445554 45789999999997554 332    12222333334566665532 


Q ss_pred             ---------------CCCCHHHH-HHHHHhcCCeEEEEecCHHH
Q 029148          135 ---------------KGTYADDC-LVERVTQHKCFIVATCDRDL  162 (198)
Q Consensus       135 ---------------~g~~aDdC-Iv~~v~~~~~yiVATnD~~L  162 (198)
                                     ++-+-.|| ++.++.+.+. =|+|-|.++
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                           11232444 4556666665 467888754

>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=0.053  Score=38.42  Aligned_cols=42  Identities=19%  Similarity=0.176  Sum_probs=28.9

Q ss_pred             EEeehHHHHHHHHcCCCh--HHhHHHhhcccceEeecHHHHHHHHH
Q 029148           67 VLVDTNFINFSIQNKLDL--EKGMMDCLYAKCTPCITDCVMAELEK  110 (198)
Q Consensus        67 VLvDtNFl~~~i~~kldl--~~~L~~~L~~k~~~~iT~CVi~ELek  110 (198)
                      +|+|||.+...++.+-+-  ...+..  ...-.++|+.-++.||..
T Consensus         2 iLlDTnvli~~~r~~~~~~v~~~l~~--~~~~~~~iS~it~~El~~   45 (138)
T d2h1ca1           2 ILLDTNVISEPLRPQPNERVVAWLDS--LILEDVYLSAITVAELRL   45 (138)
T ss_dssp             EEECHHHHTGGGSSSCCHHHHHHHHH--SCGGGEEEEHHHHHHHHH
T ss_pred             EEEecHHHHHHHccCCCHHHHHHHHh--cCccceeecHHHHHHHHH
Confidence            689999999987765542  222222  233457899999999964