Psyllid ID: psy8689

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--
Protein Sequence
MRCGRLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE
Secondary Structure (PSIPRED)
cccccccccccccHHHcccccccccccccEEEccccccccEEEEEEEccccccccEEEEEEcccccccEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHccccHHHHHcccccccccccccccEEEEEEEEEEcccccccEEEEEcccHccccccc
Coil and Loop (DISEMBL)
mrcgrlkikpkeidhvmggaaawenvdtteekcpkcehpraYFMQIqtrsadepmttfykccnikcgfrwre
Flexible Loop (DISEMBL)
mrcgrlkikpkeidhvmggaaawenvdTTEEKCPKCEHPRAYFMQIQtrsadepmttfyKCCNIKCGFRWRE
Low Complexity Region (SEG)
MRCGRLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE
Disordered region (IsUnstruct)
************IDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW**
Disordered Region (DISOPRED)
********************AAWENVDTTEEKCPKCEHPRAYFMQIQT***DEPMTTFYKCCNIKCGFRWR*
Disordered Region (DISEMBL)
MRCGRLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE
Disordered Region (DISPRO)
************IDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRCGRLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE
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	72	2.2.26 [Sep-21-2011]
Q9Y2Y1	108	DNA-directed RNA polymera	yes	N/A	0.888	0.592	0.812	1e-26
Q9CQZ7	108	DNA-directed RNA polymera	yes	N/A	0.888	0.592	0.812	2e-26
Q2M2S7	108	DNA-directed RNA polymera	yes	N/A	0.888	0.592	0.781	6e-25
Q04307	110	DNA-directed RNA polymera	yes	N/A	0.888	0.581	0.563	2e-14
O13896	109	DNA-directed RNA polymera	yes	N/A	0.930	0.614	0.521	2e-13
Q54YG9	319	Transcription elongation	yes	N/A	0.611	0.137	0.545	1e-07
Q58548	108	DNA-directed RNA polymera	yes	N/A	0.708	0.472	0.528	1e-06
Q07271	111	DNA-directed RNA polymera	yes	N/A	0.527	0.342	0.625	3e-06
P36958	129	DNA-directed RNA polymera	no	N/A	0.847	0.472	0.403	4e-06
Q56254	110	DNA-directed RNA polymera	N/A	N/A	0.902	0.590	0.388	5e-06

>sp|Q9Y2Y1|RPC10_HUMAN DNA-directed RNA polymerase III subunit RPC10 OS=Homo sapiens GN=POLR3K PE=1 SV=2

 Score =  118 bits (295), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQ+QTRSADEPMTTFYKCCN +CG 
Sbjct: 45  KLKEVDDVLGGAAAWENVDSTAESCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGH 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts, such as Epstein-Barr virus-encoded RNAs (EBERs) induce type I interferon and NF- Kappa-B through the RIG-I pathway.
Homo sapiens (taxid: 9606)

>sp|Q9CQZ7|RPC10_MOUSE DNA-directed RNA polymerase III subunit RPC10 OS=Mus musculus GN=Polr3k PE=2 SV=1

 Score =  117 bits (293), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQ+QTRSADEPMTTFYKCCN +CG 
Sbjct: 45  KLKEVDDVLGGAAAWENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGH 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway.

Mus musculus (taxid: 10090)

>sp|Q2M2S7|RPC10_BOVIN DNA-directed RNA polymerase III subunit RPC10 OS=Bos taurus GN=POLR3K PE=3 SV=1

 Score =  112 bits (280), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 50/64 (78%), Positives = 56/64 (87%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D  +GGAAAWENVD+T E CPKCEHPRAYFMQ+QTR ADEPMTTFYKCCN +CG 
Sbjct: 45  KLKEVDDELGGAAAWENVDSTAEPCPKCEHPRAYFMQLQTRYADEPMTTFYKCCNAQCGH 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway.

Bos taurus (taxid: 9913)

>sp|Q04307|RPC10_YEAST DNA-directed RNA polymerase III subunit RPC10 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPC11 PE=1 SV=1

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 40/71 (56%), Positives = 48/71 (67%), Gaps = 7/71 (9%)

Query: 5   RLKIKPKEIDHVMGGAAAWENVDTTEEKCPK---CEHPRAYFMQIQTRSADEPMTTFYKC 61
           R K+  KE+D V+GG   W+NVD T+ +CP    C    AYF Q+Q RSADEPMTTFYKC
Sbjct: 43  RKKLPRKEVDDVLGGG--WDNVDQTKTQCPNYDTCGGESAYFFQLQIRSADEPMTTFYKC 100

Query: 62  CNIKCGFRWRE 72
            N  CG RW+E
Sbjct: 101 VN--CGHRWKE 109

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Involved in Pol III transcription reinitiation and RNA cleavage during transcription termination.

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

>sp|O13896|RPC10_SCHPO DNA-directed RNA polymerase III subunit RPC10 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc11 PE=3 SV=1

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/71 (52%), Positives = 48/71 (67%), Gaps = 4/71 (5%)

Query: 4   GRLKIKPKEIDHVMGGAAAWENVDTTEEKC--PKCEHPRAYFMQIQTRSADEPMTTFYKC 61
            R +   KE+D V+GG  A+E+   TE  C   KC++ RAYF Q+Q RSADEPM+TFY+C
Sbjct: 40  SRHEFAQKEVDDVLGGEEAFESNQQTEVTCENTKCDNNRAYFFQLQIRSADEPMSTFYRC 99

Query: 62  CNIKCGFRWRE 72
              KC F+WRE
Sbjct: 100 --TKCKFQWRE 108

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.

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

>sp|Q54YG9|TCEA1_DICDI Transcription elongation factor A protein 1 OS=Dictyostelium discoideum GN=tcea1 PE=3 SV=1

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 24/44 (54%), Positives = 30/44 (68%)

Query: 28  TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
           T + +C KC+  +  + Q+QTRSADEP TTF KCC   CG RWR
Sbjct: 274 TDQFQCGKCKQRKCTYTQLQTRSADEPPTTFVKCCVKGCGNRWR 317

Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites. The arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by S-II allows the resumption of elongation from the new 3'-terminus.

Dictyostelium discoideum (taxid: 44689)

>sp|Q58548|RPOM_METJA DNA-directed RNA polymerase subunit M OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=rpoM PE=3 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/53 (52%), Positives = 32/53 (60%), Gaps = 2/53 (3%)

Query: 20  AAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
           +   E + TT  +CPKC H  AY+   QTR ADEP T FYKC   KCG  WRE
Sbjct: 56  SEGLETLPTTRIECPKCGHNEAYWWLQQTRCADEPETRFYKC--KKCGHTWRE 106

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (taxid: 243232)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q07271|RPOM_SULAC DNA-directed RNA polymerase subunit M OS=Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) GN=rpoM PE=3 SV=2

 Score = 50.8 bits (120), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/40 (62%), Positives = 27/40 (67%), Gaps = 2/40 (5%)

Query: 33  CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
           CP C +  AYF  +QTRSADEP T FYKC   KCG  WRE
Sbjct: 72  CPSCGNDEAYFWILQTRSADEPATRFYKC--TKCGKVWRE 109

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (taxid: 330779)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P36958|RPB9_DROME DNA-directed RNA polymerase II subunit RPB9 OS=Drosophila melanogaster GN=RpII15 PE=2 SV=2

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 12  EIDHVMGGAAAWENVDTTEEK-CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70
           E+ H++    +   +  TE+  CPKC H  A F Q QTR A+E M  +Y C N  C  RW
Sbjct: 68  ELTHIVPDVISDPTLPRTEDHACPKCSHREAVFFQAQTRRAEEEMRLYYVCTNQNCTHRW 127

Query: 71  RE 72
            E
Sbjct: 128 TE 129

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template.

Drosophila melanogaster (taxid: 7227)

>sp|Q56254|RPOM_THECE DNA-directed RNA polymerase subunit M OS=Thermococcus celer GN=rpoM PE=1 SV=1

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 40/67 (59%), Gaps = 2/67 (2%)

Query: 5   RLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI 64
           + ++K K  + ++      + + TT+  CPKC +  AY+ ++QTR+ DEP T FYKC   
Sbjct: 43  KQEVKHKPDEGIVVIEQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKC--T 100

Query: 65  KCGFRWR 71
           KCG  WR
Sbjct: 101 KCGHTWR 107

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Thermococcus celer (taxid: 2264)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

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	72
62751522	108	polymerase (RNA) III (DNA directed) poly	0.888	0.592	0.828	1e-25
21956651	108	POLR3K [Sphoeroides nephelus]	0.888	0.592	0.843	1e-25
50540172	108	DNA-directed RNA polymerase III subunit	0.888	0.592	0.828	2e-25
344292282	108	PREDICTED: DNA-directed RNA polymerase I	0.888	0.592	0.812	3e-25
47220062	108	unnamed protein product [Tetraodon nigro	0.888	0.592	0.828	3e-25
225717070	108	DNA-directed RNA polymerase III subunit	0.888	0.592	0.843	3e-25
432868046	108	PREDICTED: DNA-directed RNA polymerase I	0.888	0.592	0.828	4e-25
209732138	93	DNA-directed RNA polymerase III subunit	0.888	0.688	0.828	4e-25
348509155	108	PREDICTED: DNA-directed RNA polymerase I	0.888	0.592	0.828	4e-25
238231633	108	DNA-directed RNA polymerases III 12.5 kD	0.888	0.592	0.828	4e-25

>gi|62751522|ref|NP_001015803.1| polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa [Xenopus (Silurana) tropicalis] gi|62858741|ref|NP_001016313.1| uncharacterized protein LOC549067 [Xenopus (Silurana) tropicalis] gi|58477102|gb|AAH89759.1| polymerase (RNA) III (DNA directed) polypeptide K [Xenopus (Silurana) tropicalis] gi|89266864|emb|CAJ83854.1| polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa [Xenopus (Silurana) tropicalis] gi|213625552|gb|AAI70845.1| polr3k protein [Xenopus (Silurana) tropicalis]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 53/64 (82%), Positives = 59/64 (92%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GG+AAWENVD+T E CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI+CG 
Sbjct: 45  KLKEVDDVLGGSAAWENVDSTAETCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIQCGH 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|21956651|gb|AAM83406.1| POLR3K [Sphoeroides nephelus]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 54/64 (84%), Positives = 58/64 (90%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQIQTRSADEPMTTFYKCCN +CG 
Sbjct: 45  KLKEVDDVLGGAAAWENVDSTAETCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNAQCGH 104

Query: 69  RWRE 72
           RWRE
Sbjct: 105 RWRE 108

Source: Sphoeroides nephelus

Species: Sphoeroides nephelus

Genus: Sphoeroides

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|50540172|ref|NP_001002553.1| DNA-directed RNA polymerase III subunit RPC10 [Danio rerio] gi|49903001|gb|AAH76249.1| Polymerase (RNA) III (DNA directed) polypeptide K [Danio rerio]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 53/64 (82%), Positives = 59/64 (92%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GG+AAWENVD+T E CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI+CG 
Sbjct: 45  KLKEVDDVLGGSAAWENVDSTAEPCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIQCGH 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|344292282|ref|XP_003417857.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC10-like [Loxodonta africana]

 Score =  119 bits (298), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 52/64 (81%), Positives = 59/64 (92%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQ+QTRSADEPMTTFYKCCN++CG 
Sbjct: 45  KLKEVDDVLGGAAAWENVDSTAELCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNVQCGH 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

Source: Loxodonta africana

Species: Loxodonta africana

Genus: Loxodonta

Family: Elephantidae

Order: Proboscidea

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|47220062|emb|CAG12210.1| unnamed protein product [Tetraodon nigroviridis]

 Score =  119 bits (297), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 53/64 (82%), Positives = 58/64 (90%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQIQTRSADEPMTTFYKCCN +CG 
Sbjct: 45  KLKEVDDVLGGAAAWENVDSTAETCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNAQCGH 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

Source: Tetraodon nigroviridis

Species: Tetraodon nigroviridis

Genus: Tetraodon

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|225717070|gb|ACO14381.1| DNA-directed RNA polymerase III subunit RPC10 [Esox lucius]

 Score =  119 bits (297), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 54/64 (84%), Positives = 59/64 (92%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GGAAAWENVD+T EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN +CG 
Sbjct: 45  KLKEVDDVLGGAAAWENVDSTPEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNHECGH 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

Source: Esox lucius

Species: Esox lucius

Genus: Esox

Family: Esocidae

Order: Esociformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|432868046|ref|XP_004071384.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC10-like [Oryzias latipes]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 53/64 (82%), Positives = 58/64 (90%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQIQTRSADEPMTTFYKCCN +CG 
Sbjct: 45  KLKEVDDVLGGAAAWENVDSTAETCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNAQCGN 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|209732138|gb|ACI66938.1| DNA-directed RNA polymerase III subunit RPC10 [Salmo salar]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 53/64 (82%), Positives = 59/64 (92%)

Query: 9  KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
          K KE+D V+GGAAAWENVD+T EKCPKCEHPRA+FMQIQTRSADEPMTTFYKCCN +CG 
Sbjct: 30 KLKEVDDVLGGAAAWENVDSTPEKCPKCEHPRAFFMQIQTRSADEPMTTFYKCCNYECGH 89

Query: 69 RWRE 72
          RWR+
Sbjct: 90 RWRD 93

Source: Salmo salar

Species: Salmo salar

Genus: Salmo

Family: Salmonidae

Order: Salmoniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|348509155|ref|XP_003442117.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC10-like [Oreochromis niloticus]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 53/64 (82%), Positives = 58/64 (90%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQIQTRSADEPMTTFYKCCN +CG 
Sbjct: 45  KLKEVDDVLGGAAAWENVDSTPETCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNAQCGH 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|238231633|ref|NP_001154002.1| DNA-directed RNA polymerases III 12.5 kDa polypeptide [Oncorhynchus mykiss] gi|209736212|gb|ACI68975.1| DNA-directed RNA polymerase III subunit RPC10 [Salmo salar] gi|209737866|gb|ACI69802.1| DNA-directed RNA polymerase III subunit RPC10 [Salmo salar] gi|225703324|gb|ACO07508.1| DNA-directed RNA polymerases III 12.5 kDa polypeptide [Oncorhynchus mykiss]

 Score =  118 bits (296), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 53/64 (82%), Positives = 59/64 (92%)

Query: 9   KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
           K KE+D V+GGAAAWENVD+T EKCPKCEHPRA+FMQIQTRSADEPMTTFYKCCN +CG 
Sbjct: 45  KLKEVDDVLGGAAAWENVDSTPEKCPKCEHPRAFFMQIQTRSADEPMTTFYKCCNYECGH 104

Query: 69  RWRE 72
           RWR+
Sbjct: 105 RWRD 108

Source: Oncorhynchus mykiss

Species: Oncorhynchus mykiss

Genus: Oncorhynchus

Family: Salmonidae

Order: Salmoniformes

Class: Actinopterygii

Phylum: Chordata

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	72
ZFIN|ZDB-GENE-040718-291	108	polr3k "polymerase (RNA) III (	0.888	0.592	0.828	3.9e-28
UNIPROTKB|E2QZU0	108	POLR3K "DNA-directed RNA polym	0.888	0.592	0.812	8.2e-28
UNIPROTKB|Q9Y2Y1	108	POLR3K "DNA-directed RNA polym	0.888	0.592	0.812	8.2e-28
UNIPROTKB|F1N3E8	108	POLR3K "DNA-directed RNA polym	0.888	0.592	0.812	1e-27
UNIPROTKB|F2Z4X7	108	POLR3K "DNA-directed RNA polym	0.888	0.592	0.812	1e-27
MGI|MGI:1914255	108	Polr3k "polymerase (RNA) III (	0.888	0.592	0.812	1e-27
UNIPROTKB|Q5FVH1	108	Polr3k "DNA-directed RNA polym	0.888	0.592	0.812	1e-27
UNIPROTKB|Q2M2S7	108	POLR3K "DNA-directed RNA polym	0.888	0.592	0.781	1.9e-26
FB|FBgn0061362	108	CG33785 [Drosophila melanogast	0.861	0.574	0.741	2.6e-24
UNIPROTKB|E1C6D4	99	POLR3K "DNA-directed RNA polym	0.736	0.535	0.773	9.2e-20

ZFIN|ZDB-GENE-040718-291 polr3k "polymerase (RNA) III (DNA directed) polypeptide K" [Danio rerio (taxid:7955)]

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 53/64 (82%), Positives = 59/64 (92%)

Query:     9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
             K KE+D V+GG+AAWENVD+T E CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI+CG 
Sbjct:    45 KLKEVDDVLGGSAAWENVDSTAEPCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIQCGH 104

Query:    69 RWRE 72
             RWR+
Sbjct:   105 RWRD 108

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|E2QZU0 POLR3K "DNA-directed RNA polymerase subunit" [Canis lupus familiaris (taxid:9615)]

 Score = 311 (114.5 bits), Expect = 8.2e-28, P = 8.2e-28
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query:     9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
             K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQ+QTRSADEPMTTFYKCCN +CG 
Sbjct:    45 KLKEVDDVLGGAAAWENVDSTAESCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGH 104

Query:    69 RWRE 72
             RWR+
Sbjct:   105 RWRD 108

GO:0005634 "nucleus" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q9Y2Y1 POLR3K "DNA-directed RNA polymerase III subunit RPC10" [Homo sapiens (taxid:9606)]

 Score = 311 (114.5 bits), Expect = 8.2e-28, P = 8.2e-28
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query:     9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
             K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQ+QTRSADEPMTTFYKCCN +CG 
Sbjct:    45 KLKEVDDVLGGAAAWENVDSTAESCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGH 104

Query:    69 RWRE 72
             RWR+
Sbjct:   105 RWRD 108

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0005666 "DNA-directed RNA polymerase III complex" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006383 "transcription from RNA polymerase III promoter" evidence=TAS

GO:0006385 "transcription elongation from RNA polymerase III promoter" evidence=TAS

GO:0006386 "termination of RNA polymerase III transcription" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

UNIPROTKB|F1N3E8 POLR3K "DNA-directed RNA polymerase subunit" [Bos taurus (taxid:9913)]

 Score = 310 (114.2 bits), Expect = 1.0e-27, P = 1.0e-27
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query:     9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
             K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQ+QTRSADEPMTTFYKCCN +CG 
Sbjct:    45 KLKEVDDVLGGAAAWENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGH 104

Query:    69 RWRE 72
             RWR+
Sbjct:   105 RWRD 108

GO:0005634 "nucleus" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F2Z4X7 POLR3K "DNA-directed RNA polymerase subunit" [Sus scrofa (taxid:9823)]

 Score = 310 (114.2 bits), Expect = 1.0e-27, P = 1.0e-27
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query:     9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
             K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQ+QTRSADEPMTTFYKCCN +CG 
Sbjct:    45 KLKEVDDVLGGAAAWENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGH 104

Query:    69 RWRE 72
             RWR+
Sbjct:   105 RWRD 108

GO:0005634 "nucleus" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

MGI|MGI:1914255 Polr3k "polymerase (RNA) III (DNA directed) polypeptide K" [Mus musculus (taxid:10090)]

 Score = 310 (114.2 bits), Expect = 1.0e-27, P = 1.0e-27
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query:     9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
             K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQ+QTRSADEPMTTFYKCCN +CG 
Sbjct:    45 KLKEVDDVLGGAAAWENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGH 104

Query:    69 RWRE 72
             RWR+
Sbjct:   105 RWRD 108

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

UNIPROTKB|Q5FVH1 Polr3k "DNA-directed RNA polymerase subunit" [Rattus norvegicus (taxid:10116)]

 Score = 310 (114.2 bits), Expect = 1.0e-27, P = 1.0e-27
 Identities = 52/64 (81%), Positives = 58/64 (90%)

Query:     9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
             K KE+D V+GGAAAWENVD+T E CPKCEHPRAYFMQ+QTRSADEPMTTFYKCCN +CG 
Sbjct:    45 KLKEVDDVLGGAAAWENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGH 104

Query:    69 RWRE 72
             RWR+
Sbjct:   105 RWRD 108

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q2M2S7 POLR3K "DNA-directed RNA polymerase III subunit RPC10" [Bos taurus (taxid:9913)]

 Score = 298 (110.0 bits), Expect = 1.9e-26, P = 1.9e-26
 Identities = 50/64 (78%), Positives = 56/64 (87%)

Query:     9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF 68
             K KE+D  +GGAAAWENVD+T E CPKCEHPRAYFMQ+QTR ADEPMTTFYKCCN +CG 
Sbjct:    45 KLKEVDDELGGAAAWENVDSTAEPCPKCEHPRAYFMQLQTRYADEPMTTFYKCCNAQCGH 104

Query:    69 RWRE 72
             RWR+
Sbjct:   105 RWRD 108

GO:0005634 "nucleus" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

FB|FBgn0061362 CG33785 [Drosophila melanogaster (taxid:7227)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 46/62 (74%), Positives = 53/62 (85%)

Query:    11 KEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW 70
             KE+DHV+GG AAWENVD+T+ +CP C H RAYFMQIQTRSADEPMTTFYKCCN +C   W
Sbjct:    47 KEVDHVLGGKAAWENVDSTDAECPTCGHKRAYFMQIQTRSADEPMTTFYKCCNHECNHTW 106

Query:    71 RE 72
             R+
Sbjct:   107 RD 108

GO:0006359 "regulation of transcription from RNA polymerase III promoter" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0005666 "DNA-directed RNA polymerase III complex" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E1C6D4 POLR3K "DNA-directed RNA polymerase subunit" [Gallus gallus (taxid:9031)]

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 41/53 (77%), Positives = 44/53 (83%)

Query:    11 KEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN 63
             KE+D V+GGAAAWENVD+T E CPKCEH RAYFMQIQTRS D    TFYKCCN
Sbjct:    47 KEVDDVLGGAAAWENVDSTAEPCPKCEHSRAYFMQIQTRSPDSRANTFYKCCN 99

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

---

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)
Q04307	RPC10_YEAST	No assigned EC number	0.5633	0.8888	0.5818	yes	N/A
Q2M2S7	RPC10_BOVIN	No assigned EC number	0.7812	0.8888	0.5925	yes	N/A
Q54YG9	TCEA1_DICDI	No assigned EC number	0.5454	0.6111	0.1379	yes	N/A
Q07271	RPOM_SULAC	2, ., 7, ., 7, ., 6	0.625	0.5277	0.3423	yes	N/A
Q58548	RPOM_METJA	2, ., 7, ., 7, ., 6	0.5283	0.7083	0.4722	yes	N/A
Q9CQZ7	RPC10_MOUSE	No assigned EC number	0.8125	0.8888	0.5925	yes	N/A
O13896	RPC10_SCHPO	No assigned EC number	0.5211	0.9305	0.6146	yes	N/A
Q9Y2Y1	RPC10_HUMAN	No assigned EC number	0.8125	0.8888	0.5925	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	72
COG1594	113	COG1594, RPB9, DNA-directed RNA polymerase, subuni	6e-17
pfam01096	39	pfam01096, TFIIS_C, Transcription factor S-II (TFI	8e-17
smart00440	40	smart00440, ZnF_C2C2, C2C2 Zinc finger	1e-14
TIGR01384	104	TIGR01384, TFS_arch, transcription factor S, archa	8e-12
TIGR01385	299	TIGR01385, TFSII, transcription elongation factor	4e-10
PHA02998	195	PHA02998, PHA02998, RNA polymerase subunit; Provis	4e-04

>gnl|CDD|224510 COG1594, RPB9, DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

 Score = 68.3 bits (167), Expect = 6e-17
 Identities = 29/47 (61%), Positives = 36/47 (76%), Gaps = 2/47 (4%)

Query: 26  VDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
           + T +EKCPKC +  AY+ Q+QTRSADEP T FYKC   +CG+RWRE
Sbjct: 68  LPTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCT--RCGYRWRE 112

Length = 113

>gnl|CDD|201594 pfam01096, TFIIS_C, Transcription factor S-II (TFIIS)

 Score = 66.1 bits (162), Expect = 8e-17
 Identities = 27/40 (67%), Positives = 28/40 (70%), Gaps = 2/40 (5%)

Query: 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
          KCPKC H  A F Q+QTRSADEPMT FY C    CG RWR
Sbjct: 2  KCPKCGHREAVFFQLQTRSADEPMTLFYVCTK--CGHRWR 39

Length = 39

>gnl|CDD|128717 smart00440, ZnF_C2C2, C2C2 Zinc finger

 Score = 60.4 bits (147), Expect = 1e-14
 Identities = 26/41 (63%), Positives = 29/41 (70%), Gaps = 2/41 (4%)

Query: 32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
          +CPKC +  A F Q+QTRSADEPMT FY C   KCG  WRE
Sbjct: 2  ECPKCGNREATFYQLQTRSADEPMTVFYVC--TKCGHHWRE 40

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases. Length = 40

>gnl|CDD|130451 TIGR01384, TFS_arch, transcription factor S, archaeal

 Score = 55.2 bits (133), Expect = 8e-12
 Identities = 28/49 (57%), Positives = 33/49 (67%), Gaps = 2/49 (4%)

Query: 24  ENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
           E + TT  +CPKC H  AY+  +QTR ADEP T FYKC   KCG+ WRE
Sbjct: 56  ETLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKC--TKCGYVWRE 102

This model describes archaeal transcription factor S, a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae [Transcription, Transcription factors]. Length = 104

>gnl|CDD|233390 TIGR01385, TFSII, transcription elongation factor S-II

 Score = 53.3 bits (128), Expect = 4e-10
 Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 4/67 (5%)

Query: 5   RLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI 64
           R +I  + +    G     +   T    C KC+  +  + Q+QTRSADEPMTTF  C   
Sbjct: 235 REEITKENLFEAQGAKI--QKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEE- 291

Query: 65  KCGFRWR 71
            CG RW+
Sbjct: 292 -CGNRWK 297

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end. Length = 299

>gnl|CDD|222958 PHA02998, PHA02998, RNA polymerase subunit; Provisional

 Score = 36.3 bits (84), Expect = 4e-04
 Identities = 15/38 (39%), Positives = 20/38 (52%)

Query: 32  KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR 69
            CP C+      M IQTR+ADEP    + C + K  F+
Sbjct: 145 PCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182

Length = 195

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	72
KOG2906|consensus	105		99.97
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	99.92
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	99.91
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	99.9
KOG2691|consensus	113		99.87
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	99.85
PHA02998	195	RNA polymerase subunit; Provisional	99.79
TIGR01385	299	TFSII transcription elongation factor S-II. This m	99.71
KOG2907|consensus	116		99.61
KOG1105|consensus	296		99.17
PF04606	47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	98.37
PRK09678	72	DNA-binding transcriptional regulator; Provisional	98.01
COG4332	203	Uncharacterized protein conserved in bacteria [Fun	96.15
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	96.1
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	95.95
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	95.53
PHA00626	59	hypothetical protein	95.34
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	95.16
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	95.08
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	94.89
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	94.85
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	94.78
TIGR00244	147	transcriptional regulator NrdR. Members of this al	94.33
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	94.22
PF10058	54	DUF2296: Predicted integral membrane metal-binding	94.08
COG3478	68	Predicted nucleic-acid-binding protein containing	93.86
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	93.16
COG1779	201	C4-type Zn-finger protein [General function predic	93.09
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	92.83
COG1327	156	Predicted transcriptional regulator, consists of a	92.72
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	92.07
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	91.69
PF09151	36	DUF1936: Domain of unknown function (DUF1936); Int	91.15
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	91.06
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	90.43
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	90.4
PRK10220	111	hypothetical protein; Provisional	90.3
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	90.13
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	90.01
smart00661	52	RPOL9 RNA polymerase subunit 9.	89.69
PF11781	36	RRN7: RNA polymerase I-specific transcription init	89.64
TIGR00340	163	zpr1_rel ZPR1-related zinc finger protein. A model	89.08
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	88.66
COG1326	201	Uncharacterized archaeal Zn-finger protein [Genera	88.37
COG4888	104	Uncharacterized Zn ribbon-containing protein [Gene	87.07
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	86.56
PTZ00083	85	40S ribosomal protein S27; Provisional	86.51
PLN00209	86	ribosomal protein S27; Provisional	86.5
PRK00432	50	30S ribosomal protein S27ae; Validated	86.43
smart00709	160	Zpr1 Duplicated domain in the epidermal growth fac	85.47
TIGR00310	192	ZPR1_znf ZPR1 zinc finger domain.	84.72
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	83.79
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	83.43
PRK03988	138	translation initiation factor IF-2 subunit beta; V	83.31
COG5415	251	Predicted integral membrane metal-binding protein	83.29
PF14353	128	CpXC: CpXC protein	83.08
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	82.72
TIGR00311	133	aIF-2beta translation initiation factor aIF-2, bet	82.64
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	82.4
PF01873	125	eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro:	82.05
PF11792	43	Baculo_LEF5_C: Baculoviridae late expression facto	82.05
TIGR02443	59	conserved hypothetical metal-binding protein. Memb	81.61
PF03367	161	zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004	80.8
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	80.5
PF06044	254	DRP: Dam-replacing family; InterPro: IPR010324 Dam	80.19

>KOG2906|consensus

Probab=99.97  E-value=1.6e-32  Score=171.77  Aligned_cols=67  Identities=70%  Similarity=1.280  Sum_probs=64.5

Q ss_pred             ccCccCccccccccCCccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689           4 GRLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus         4 ~~~~~~~ke~~~v~~~~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      .|..++.|++|+|+||+++|++++.+...||+|||++|+|+|+|+||||||||+||.|++  |+|+|||
T Consensus        39 ~r~~~~~Kevd~vlgg~~a~~nv~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~--C~~~Wre  105 (105)
T KOG2906|consen   39 SRKYPKLKEVDDVLGGDEAWENVDQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCK--CKHRWRE  105 (105)
T ss_pred             ccccCchhhhhhhcCCcccccchhhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhc--ccccccC
Confidence            356789999999999999999999999999999999999999999999999999999999  9999997

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=99.92  E-value=1.2e-25  Score=139.49  Aligned_cols=60  Identities=47%  Similarity=0.907  Sum_probs=52.2

Q ss_pred             cccccccCCccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689          11 KEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus        11 ke~~~v~~~~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      ++.++++.+.+..+++|++.+.||+|||++|+|+|+|+||||||||+||+|++  |||+|++
T Consensus        43 ~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~--C~~~w~~  102 (104)
T TIGR01384        43 KIKETIIIREEDSETLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTK--CGYVWRE  102 (104)
T ss_pred             ccccceeeccccccCCCcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCC--CCCeeEe
Confidence            44455544445568999999999999999999999999999999999999999  9999986

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=99.91  E-value=5e-25  Score=118.20  Aligned_cols=40  Identities=65%  Similarity=1.290  Sum_probs=38.4

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      ..||+||+++|+|+|+|+||||||||+||+|++  |||+|++
T Consensus         1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~--C~~~w~~   40 (40)
T smart00440        1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTK--CGHRWRE   40 (40)
T ss_pred             CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCC--CCCEeCC
Confidence            369999999999999999999999999999999  9999986

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.90  E-value=3.6e-24  Score=114.28  Aligned_cols=39  Identities=77%  Similarity=1.476  Sum_probs=35.0

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +.||+||+++++|+|+|+||||||||+||.|.+  |||+|+
T Consensus         1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~--C~~~wr   39 (39)
T PF01096_consen    1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCN--CGHRWR   39 (39)
T ss_dssp             S--SSS-SSEEEEEEESSSSSSSSSEEEEEESS--STEEEE
T ss_pred             CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCC--CCCeeC
Confidence            479999999999999999999999999999999  999997

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>KOG2691|consensus

Probab=99.87  E-value=4.3e-23  Score=130.90  Aligned_cols=65  Identities=43%  Similarity=0.863  Sum_probs=60.4

Q ss_pred             CccCccccccccCCccccccCCcc-eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689           6 LKIKPKEIDHVMGGAAAWENVDTT-EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus         6 ~~~~~ke~~~v~~~~~~~~~~~~t-~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      ..++.+|.+.|+.+.++||++|++ ++.||+||+++|+|||.|+|.+|+.|+|||+|++  |||+|+|
T Consensus        48 ~~~e~dE~t~ii~Dl~~DPTLPrts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~--C~h~wte  113 (113)
T KOG2691|consen   48 LSHEHDELTQIIMDLASDPTLPRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCS--CGHRWTE  113 (113)
T ss_pred             cccchhhHHHHHHhhccCCCcCccccccCCccCCcceEEEecccccccceEEEEEEecc--ccccccC
Confidence            345678999999999999999996 6899999999999999999999999999999999  9999986

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=99.85  E-value=7e-22  Score=125.92  Aligned_cols=49  Identities=59%  Similarity=1.189  Sum_probs=44.0

Q ss_pred             ccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689          22 AWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus        22 ~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      ..+++++..+.||+||+++|+|||.|+||||||||+||.|+.  |||+|++
T Consensus        64 ~~~~~~~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~--Cg~~wre  112 (113)
T COG1594          64 GAKTLPTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTR--CGYRWRE  112 (113)
T ss_pred             CccccccccccCCCCCCceeEEEeeehhccCCCceEEEEecc--cCCEeec
Confidence            344555667899999999999999999999999999999999  9999985

>PHA02998 RNA polymerase subunit; Provisional

Probab=99.79  E-value=1e-19  Score=124.16  Aligned_cols=44  Identities=34%  Similarity=0.639  Sum_probs=41.6

Q ss_pred             CCc-ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          26 VDT-TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        26 ~~~-t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +|. +.+.||+|||++|+|+|+|+||||||||+||.|.+  |||+|+
T Consensus       138 lpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~--CG~~wk  182 (195)
T PHA02998        138 LDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRD--CKKHFK  182 (195)
T ss_pred             cCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCC--CCCccC
Confidence            566 67999999999999999999999999999999999  999997

>TIGR01385 TFSII transcription elongation factor S-II

Probab=99.71  E-value=8.2e-18  Score=121.54  Aligned_cols=42  Identities=52%  Similarity=0.997  Sum_probs=39.7

Q ss_pred             cceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +..+.||+||+++++|||+|+||||||||+||+|++  |||+|+
T Consensus       256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~--Cg~~w~  297 (299)
T TIGR01385       256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEE--CGNRWK  297 (299)
T ss_pred             cccccCCCCCCccceEEEecccCCCCCCeEEEEcCC--CCCeee
Confidence            345899999999999999999999999999999999  999997

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.

>KOG2907|consensus

Probab=99.61  E-value=2e-16  Score=101.13  Aligned_cols=46  Identities=39%  Similarity=0.825  Sum_probs=42.7

Q ss_pred             cCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689          25 NVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus        25 ~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      ..+..+.+||+|||.++.|..+|+|||||+.|+||.|.+  |+|++++
T Consensus        69 ~ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~k--C~~k~~e  114 (116)
T KOG2907|consen   69 DGAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPK--CKYKFTE  114 (116)
T ss_pred             cccchhccCcccCCchhhhhhhhcccccCCceEEEEcCc--cceeeec
Confidence            457778899999999999999999999999999999988  9999875

>KOG1105|consensus

Probab=99.17  E-value=2.5e-11  Score=88.02  Aligned_cols=40  Identities=55%  Similarity=1.033  Sum_probs=38.7

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .+.|-+|+.....|.|.|+||+|||||.|..|.+  ||++|+
T Consensus       255 ~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~e--cgnrWk  294 (296)
T KOG1105|consen  255 LFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNE--CGNRWK  294 (296)
T ss_pred             ceeeccccccceeEEeeccCCCCCCcceeeeecc--cCCccc
Confidence            5899999999999999999999999999999999  999996

>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr

Probab=98.37  E-value=5.4e-07  Score=49.24  Aligned_cols=38  Identities=21%  Similarity=0.514  Sum_probs=30.4

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .||.||++..+-...+  ..+.--.+||+|.|++|||+|+
T Consensus         1 ~CP~Cg~~a~ir~S~~--~s~~~~~~Y~qC~N~~Cg~tfv   38 (47)
T PF04606_consen    1 RCPHCGSKARIRTSRQ--LSPLTRELYCQCTNPECGHTFV   38 (47)
T ss_pred             CcCCCCCeeEEEEchh--hCcceEEEEEEECCCcCCCEEE
Confidence            5999999998876543  2445566999999999999996

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=98.01  E-value=6.3e-06  Score=49.13  Aligned_cols=39  Identities=21%  Similarity=0.475  Sum_probs=29.4

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      ..||.||+...+--..+  ..++-..+||.|.|++|||+|+
T Consensus         2 m~CP~Cg~~a~irtSr~--~s~~~~~~Y~qC~N~eCg~tF~   40 (72)
T PRK09678          2 FHCPLCQHAAHARTSRY--ITDTTKERYHQCQNVNCSATFI   40 (72)
T ss_pred             ccCCCCCCccEEEEChh--cChhhheeeeecCCCCCCCEEE
Confidence            47999999996554422  2344455999999999999996

>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.15  E-value=0.0051  Score=42.72  Aligned_cols=46  Identities=22%  Similarity=0.580  Sum_probs=33.2

Q ss_pred             ccCCcceeeCCCCCCCceEEEEeeccCCCCC----ceEEEEecCCCCCceec
Q psy8689          24 ENVDTTEEKCPKCEHPRAYFMQIQTRSADEP----MTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        24 ~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~----mTlfy~C~~~~Cg~~w~   71 (72)
                      .++|+.-+.|++||...++.=.-..|....+    .=++|.|++  |.++|-
T Consensus        11 ~~~pq~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~--Cd~tWN   60 (203)
T COG4332          11 VGAPQPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTH--CDYTWN   60 (203)
T ss_pred             ccCChhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeec--cCCccc
Confidence            3577778899999999987533333333333    338899999  999994

>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=96.10  E-value=0.0099  Score=31.19  Aligned_cols=31  Identities=32%  Similarity=0.780  Sum_probs=20.8

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecC-CCCCce
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN-IKCGFR   69 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~-~~Cg~~   69 (72)
                      ..||.|| ...+.  .+.+   -+  .|+.|.+ |+|.+.
T Consensus         2 ~~CP~Cg-~~lv~--r~~k---~g--~F~~Cs~yP~C~~~   33 (39)
T PF01396_consen    2 EKCPKCG-GPLVL--RRGK---KG--KFLGCSNYPECKYT   33 (39)
T ss_pred             cCCCCCC-ceeEE--EECC---CC--CEEECCCCCCcCCe
Confidence            4799999 33322  2222   23  8999998 889875

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=95.95  E-value=0.0085  Score=30.97  Aligned_cols=36  Identities=19%  Similarity=0.459  Sum_probs=22.2

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +.+.||+|+..-.+=-. +  ..  +...-..|.+  |+|.|.
T Consensus         1 M~i~Cp~C~~~y~i~d~-~--ip--~~g~~v~C~~--C~~~f~   36 (36)
T PF13717_consen    1 MIITCPNCQAKYEIDDE-K--IP--PKGRKVRCSK--CGHVFF   36 (36)
T ss_pred             CEEECCCCCCEEeCCHH-H--CC--CCCcEEECCC--CCCEeC
Confidence            45789999865432110 1  11  3335678988  999995

>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins

Probab=95.53  E-value=0.022  Score=33.17  Aligned_cols=15  Identities=33%  Similarity=0.687  Sum_probs=8.9

Q ss_pred             eCCCCCCCceEEEEe
Q psy8689          32 KCPKCEHPRAYFMQI   46 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~   46 (72)
                      .||+||+.+...-++
T Consensus         2 ~C~KCg~~~~e~~~v   16 (64)
T PF09855_consen    2 KCPKCGNEEYESGEV   16 (64)
T ss_pred             CCCCCCCcceecceE
Confidence            477777766554443

>PHA00626 hypothetical protein

Probab=95.34  E-value=0.014  Score=33.50  Aligned_cols=33  Identities=30%  Similarity=0.674  Sum_probs=21.2

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .||+||+.+.+= -...|   .+.. =|.|.+  ||+.|.
T Consensus         2 ~CP~CGS~~Ivr-cg~cr---~~sn-rYkCkd--CGY~ft   34 (59)
T PHA00626          2 SCPKCGSGNIAK-EKTMR---GWSD-DYVCCD--CGYNDS   34 (59)
T ss_pred             CCCCCCCceeee-eceec---ccCc-ceEcCC--CCCeec
Confidence            699999987762 11111   1122 488988  999875

>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues

Probab=95.16  E-value=0.0072  Score=30.41  Aligned_cols=27  Identities=33%  Similarity=0.878  Sum_probs=13.5

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +||.|++...+.           -...|+|-.  |+|.|.
T Consensus         4 ~Cp~C~se~~y~-----------D~~~~vCp~--C~~ew~   30 (30)
T PF08274_consen    4 KCPLCGSEYTYE-----------DGELLVCPE--CGHEWN   30 (30)
T ss_dssp             --TTT-----EE------------SSSEEETT--TTEEE-
T ss_pred             CCCCCCCcceec-----------cCCEEeCCc--ccccCC
Confidence            799999999872           112478966  999993

The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.

>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc

Probab=95.08  E-value=0.019  Score=30.75  Aligned_cols=28  Identities=25%  Similarity=0.691  Sum_probs=20.9

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      +.||+||+.+++.+..         ...|.|..  |+++
T Consensus        19 ~~CP~Cg~~~~~~~~~---------~~~~~C~~--C~~q   46 (46)
T PF12760_consen   19 FVCPHCGSTKHYRLKT---------RGRYRCKA--CRKQ   46 (46)
T ss_pred             CCCCCCCCeeeEEeCC---------CCeEECCC--CCCc
Confidence            5699999996655442         45789998  9874

It may be a zinc-binding beta ribbon domain that could bind DNA.

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=94.89  E-value=0.041  Score=28.04  Aligned_cols=35  Identities=20%  Similarity=0.586  Sum_probs=21.1

Q ss_pred             ceeeCCCCCCCceEEEEeec-cCCCCCceEEEEecCCCCCceec
Q psy8689          29 TEEKCPKCEHPRAYFMQIQT-RSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~-rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +.+.||.|+..-.    ++. ...+.+.  -..|.+  |++.|.
T Consensus         1 M~~~CP~C~~~~~----v~~~~~~~~~~--~v~C~~--C~~~~~   36 (38)
T TIGR02098         1 MRIQCPNCKTSFR----VVDSQLGANGG--KVRCGK--CGHVWY   36 (38)
T ss_pred             CEEECCCCCCEEE----eCHHHcCCCCC--EEECCC--CCCEEE
Confidence            3578999987522    221 1222333  567988  999885

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=94.85  E-value=0.03  Score=28.92  Aligned_cols=36  Identities=19%  Similarity=0.392  Sum_probs=21.8

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +.+.||+|+..-.+--. |  ..  .-..-..|.+  |+|.|.
T Consensus         1 M~i~CP~C~~~f~v~~~-~--l~--~~~~~vrC~~--C~~~f~   36 (37)
T PF13719_consen    1 MIITCPNCQTRFRVPDD-K--LP--AGGRKVRCPK--CGHVFR   36 (37)
T ss_pred             CEEECCCCCceEEcCHH-H--cc--cCCcEEECCC--CCcEee
Confidence            35789999865432211 1  11  2234678988  999995

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=94.78  E-value=0.042  Score=36.73  Aligned_cols=36  Identities=31%  Similarity=0.837  Sum_probs=24.0

Q ss_pred             eCCCCCCCceEEEEeeccCCCC--CceEEEEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADE--PMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE--~mTlfy~C~~~~Cg~~w~   71 (72)
                      +||.||+....-..  .|...+  ..+.+|.|.+  ||.+|.
T Consensus         2 ~cp~c~~~~~~~~~--s~~~~~~~~~~~~~~c~~--c~~~f~   39 (154)
T PRK00464          2 RCPFCGHPDTRVID--SRPAEDGNAIRRRRECLA--CGKRFT   39 (154)
T ss_pred             cCCCCCCCCCEeEe--ccccCCCCceeeeeeccc--cCCcce
Confidence            69999998742211  132334  3667899988  999874

>TIGR00244 transcriptional regulator NrdR

Probab=94.33  E-value=0.059  Score=36.05  Aligned_cols=36  Identities=22%  Similarity=0.618  Sum_probs=26.5

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEE--EEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTF--YKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlf--y~C~~~~Cg~~w~   71 (72)
                      .||.|||.+.--  +-+|+++++.++=  -.|.+  ||++|.
T Consensus         2 ~CP~C~~~dtkV--iDSR~~~dg~~IRRRReC~~--C~~RFT   39 (147)
T TIGR00244         2 HCPFCQHHNTRV--LDSRLVEDGQSIRRRRECLE--CHERFT   39 (147)
T ss_pred             CCCCCCCCCCEe--eeccccCCCCeeeecccCCc--cCCccc
Confidence            699999877644  3458888887754  45877  998885

Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=94.22  E-value=0.11  Score=28.54  Aligned_cols=34  Identities=21%  Similarity=0.688  Sum_probs=22.2

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      +.||.||.....+..   +..+..-.-+|.|..  ||..
T Consensus         2 kPCPfCGg~~~~~~~---~~~~~~~~~~~~C~~--Cga~   35 (53)
T TIGR03655         2 KPCPFCGGADVYLRR---GFDPLDLSHYFECST--CGAS   35 (53)
T ss_pred             CCCCCCCCcceeeEe---ccCCCCCEEEEECCC--CCCC
Confidence            479999997765532   123344455668988  9875

Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.

>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function []

Probab=94.08  E-value=0.058  Score=30.26  Aligned_cols=48  Identities=23%  Similarity=0.322  Sum_probs=29.3

Q ss_pred             cccccCCccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689          13 IDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF   68 (72)
Q Consensus        13 ~~~v~~~~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~   68 (72)
                      +-|+|-|++.-....+..+.|++|....-.+.      ..|+..+-|+|..  ||+
T Consensus         5 i~d~L~G~d~~~~~~r~aLIC~~C~~hNGla~------~~~~~~i~y~C~~--Cg~   52 (54)
T PF10058_consen    5 ILDVLLGDDPTSPSNRYALICSKCFSHNGLAP------KEEFEEIQYRCPY--CGA   52 (54)
T ss_pred             HHHHHhCCCCccccCceeEECcccchhhcccc------cccCCceEEEcCC--CCC
Confidence            34455454442223334578999975555332      3567777899977  986

>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=93.86  E-value=0.053  Score=31.96  Aligned_cols=35  Identities=31%  Similarity=0.710  Sum_probs=21.0

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCce--------EE--EEecCCCCCce
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMT--------TF--YKCCNIKCGFR   69 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mT--------lf--y~C~~~~Cg~~   69 (72)
                      .+||+||+++..--++  +...+...        .|  ..|.+  ||++
T Consensus         5 ~kCpKCgn~~~~ekei--~~tg~~lskifdvq~n~f~~itCk~--CgYt   49 (68)
T COG3478           5 FKCPKCGNTNYEEKEI--AATGGGLSKIFDVQNNKFIVITCKN--CGYT   49 (68)
T ss_pred             ccCCCcCCcchhhcee--eccCCCcceeEEecccEEEEEEecc--CCch
Confidence            3599999987654443  33433332        23  34888  9874

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=93.16  E-value=0.1  Score=27.46  Aligned_cols=28  Identities=36%  Similarity=0.806  Sum_probs=19.2

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW   70 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w   70 (72)
                      .||.||+...++ -        +++-.++|.+  ||...
T Consensus         2 ~Cp~Cg~~~~~~-D--------~~~g~~vC~~--CG~Vl   29 (43)
T PF08271_consen    2 KCPNCGSKEIVF-D--------PERGELVCPN--CGLVL   29 (43)
T ss_dssp             SBTTTSSSEEEE-E--------TTTTEEEETT--T-BBE
T ss_pred             CCcCCcCCceEE-c--------CCCCeEECCC--CCCEe
Confidence            699999988333 2        3455679988  99753

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>COG1779 C4-type Zn-finger protein [General function prediction only]

Probab=93.09  E-value=0.16  Score=35.51  Aligned_cols=42  Identities=19%  Similarity=0.292  Sum_probs=28.6

Q ss_pred             cceeeCCCCCCCceEEEEeeccCCCCC--ceEEEEecCCCCCceecC
Q psy8689          28 TTEEKCPKCEHPRAYFMQIQTRSADEP--MTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus        28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~--mTlfy~C~~~~Cg~~w~~   72 (72)
                      .+.+.||.||+ .....+......-.+  |-..++|.+  ||+|..+
T Consensus        12 ~~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~--CgYR~~D   55 (201)
T COG1779          12 ETRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCER--CGYRSTD   55 (201)
T ss_pred             eeeecCCcccc-eeeEEEeeecCCccceEEEEEEEccc--cCCcccc
Confidence            34689999999 555555454444444  445677999  9999764

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=92.83  E-value=0.076  Score=33.95  Aligned_cols=27  Identities=33%  Similarity=0.865  Sum_probs=20.1

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .||+|++..+|--.           -.|+|-.  |+|-|.
T Consensus         4 ~CP~C~seytY~dg-----------~~~iCpe--C~~EW~   30 (109)
T TIGR00686         4 PCPKCNSEYTYHDG-----------TQLICPS--CLYEWN   30 (109)
T ss_pred             cCCcCCCcceEecC-----------CeeECcc--cccccc
Confidence            69999998775422           1388955  999995

The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).

>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]

Probab=92.72  E-value=0.065  Score=36.17  Aligned_cols=36  Identities=33%  Similarity=0.720  Sum_probs=25.6

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEE--EEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTF--YKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlf--y~C~~~~Cg~~w~   71 (72)
                      .||.|+|...--.  -.|.++++.++=  -.|.+  ||++|.
T Consensus         2 ~CPfC~~~~tkVi--DSR~~edg~aIRRRReC~~--C~~RFT   39 (156)
T COG1327           2 KCPFCGHEDTKVI--DSRPAEEGNAIRRRRECLE--CGERFT   39 (156)
T ss_pred             CCCCCCCCCCeee--ecccccccchhhhhhcccc--cccccc
Confidence            6888888877543  457888876643  45877  888875

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=92.07  E-value=0.28  Score=27.12  Aligned_cols=34  Identities=26%  Similarity=0.577  Sum_probs=21.2

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF   68 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~   68 (72)
                      ..||-||+......+.  ...+..+..+..|.+  ||.
T Consensus         4 kPCPFCG~~~~~~~~~--~~~~~~~~~~V~C~~--Cga   37 (61)
T PF14354_consen    4 KPCPFCGSADVLIRQD--EGFDYGMYYYVECTD--CGA   37 (61)
T ss_pred             cCCCCCCCcceEeecc--cCCCCCCEEEEEcCC--CCC
Confidence            5799997666655442  222333335666988  986

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=91.69  E-value=0.13  Score=40.12  Aligned_cols=41  Identities=24%  Similarity=0.549  Sum_probs=28.5

Q ss_pred             eeeCCCCCCCceEEE-EeeccCCCCCceEEEEecCCCCCceecC
Q psy8689          30 EEKCPKCEHPRAYFM-QIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~-q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      -+.||.||+.-..-| +++--....+.+.+|+|..  ||+.|.+
T Consensus       200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~--Cg~~i~e  241 (557)
T PF05876_consen  200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPH--CGCEIEE  241 (557)
T ss_pred             EccCCCCCCCccccccceeecCCCCccceEEECCC--CcCCCCH
Confidence            479999998776644 3332111168899999966  9998753

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins

Probab=91.15  E-value=0.62  Score=23.93  Aligned_cols=33  Identities=24%  Similarity=0.525  Sum_probs=16.5

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF   68 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~   68 (72)
                      .-||+||-.-..-.-.|     .+....|.|.||.|.+
T Consensus         2 hlcpkcgvgvl~pvy~~-----kgeikvfrcsnpacdy   34 (36)
T PF09151_consen    2 HLCPKCGVGVLEPVYNQ-----KGEIKVFRCSNPACDY   34 (36)
T ss_dssp             -B-TTTSSSBEEEEE-T-----TS-EEEEEES-TT---
T ss_pred             ccCCccCceEEEEeecC-----CCcEEEEEcCCCcccc
Confidence            35999987654432222     2456678899999975

Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.

>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]

Probab=91.06  E-value=0.25  Score=29.09  Aligned_cols=29  Identities=31%  Similarity=0.734  Sum_probs=22.9

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      +++||.|||...+|--.|         ....|..  ||..
T Consensus        19 ~VkCpdC~N~q~vFshas---------t~V~C~~--CG~~   47 (67)
T COG2051          19 RVKCPDCGNEQVVFSHAS---------TVVTCLI--CGTT   47 (67)
T ss_pred             EEECCCCCCEEEEeccCc---------eEEEecc--cccE
Confidence            689999999999996644         3467888  8864

>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=90.43  E-value=0.16  Score=28.79  Aligned_cols=30  Identities=37%  Similarity=0.738  Sum_probs=19.5

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      ++++||.|++...+|-..|+         -..|..  ||..
T Consensus         6 m~VkCp~C~~~q~vFSha~t---------~V~C~~--Cg~~   35 (55)
T PF01667_consen    6 MDVKCPGCYNIQTVFSHAQT---------VVKCVV--CGTV   35 (55)
T ss_dssp             EEEE-TTT-SEEEEETT-SS----------EE-SS--STSE
T ss_pred             EEEECCCCCCeeEEEecCCe---------EEEccc--CCCE
Confidence            47899999999999966553         256877  8764

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.

>PF13453 zf-TFIIB: Transcription factor zinc-finger

Probab=90.40  E-value=0.56  Score=24.35  Aligned_cols=30  Identities=27%  Similarity=0.654  Sum_probs=18.9

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +||+|+.. ..-.+.      .. ...+.|..  |+-.|-
T Consensus         1 ~CP~C~~~-l~~~~~------~~-~~id~C~~--C~G~W~   30 (41)
T PF13453_consen    1 KCPRCGTE-LEPVRL------GD-VEIDVCPS--CGGIWF   30 (41)
T ss_pred             CcCCCCcc-cceEEE------CC-EEEEECCC--CCeEEc
Confidence            59999883 322221      12 45577977  999985

>PRK10220 hypothetical protein; Provisional

Probab=90.30  E-value=0.19  Score=32.19  Aligned_cols=27  Identities=33%  Similarity=0.947  Sum_probs=19.9

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .||+|++..+|--.        .   -|+|-.  |+|-|.
T Consensus         5 ~CP~C~seytY~d~--------~---~~vCpe--C~hEW~   31 (111)
T PRK10220          5 HCPKCNSEYTYEDN--------G---MYICPE--CAHEWN   31 (111)
T ss_pred             cCCCCCCcceEcCC--------C---eEECCc--ccCcCC
Confidence            69999988775321        1   488955  999996

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=90.13  E-value=0.39  Score=34.25  Aligned_cols=36  Identities=28%  Similarity=0.732  Sum_probs=18.6

Q ss_pred             eeeCCCCCCCceEEEEeeccCCC-CCceEEEEecCCCCCceec
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSAD-EPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsad-E~mTlfy~C~~~~Cg~~w~   71 (72)
                      ...||-||+.-..-.-..   .+ ++- .|..|.-  |++.|+
T Consensus       172 ~g~CPvCGs~P~~s~l~~---~~~~G~-R~L~Cs~--C~t~W~  208 (290)
T PF04216_consen  172 RGYCPVCGSPPVLSVLRG---GEREGK-RYLHCSL--CGTEWR  208 (290)
T ss_dssp             -SS-TTT---EEEEEEE---------E-EEEEETT--T--EEE
T ss_pred             CCcCCCCCCcCceEEEec---CCCCcc-EEEEcCC--CCCeee
Confidence            368999999876654322   22 244 8999988  999996

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=90.01  E-value=0.35  Score=27.84  Aligned_cols=30  Identities=30%  Similarity=0.728  Sum_probs=23.4

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      ++++||.|++...+|--.|+         -..|..  ||..
T Consensus        10 ~~VkCp~C~n~q~vFsha~t---------~V~C~~--Cg~~   39 (59)
T PRK00415         10 LKVKCPDCGNEQVVFSHAST---------VVRCLV--CGKT   39 (59)
T ss_pred             EEEECCCCCCeEEEEecCCc---------EEECcc--cCCC
Confidence            46899999999999976542         366877  8864

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=89.69  E-value=0.38  Score=25.60  Aligned_cols=12  Identities=25%  Similarity=0.797  Sum_probs=7.5

Q ss_pred             EEEecCCCCCceec
Q psy8689          58 FYKCCNIKCGFRWR   71 (72)
Q Consensus        58 fy~C~~~~Cg~~w~   71 (72)
                      .|+|..  ||+.+.
T Consensus        20 ~~vC~~--Cg~~~~   31 (52)
T smart00661       20 RFVCRK--CGYEEP   31 (52)
T ss_pred             EEECCc--CCCeEE
Confidence            566755  776653

>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[]

Probab=89.64  E-value=0.37  Score=24.86  Aligned_cols=26  Identities=35%  Similarity=0.961  Sum_probs=18.4

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      ..|+.|++.   +|...     +   =||.|..  |||.
T Consensus         9 ~~C~~C~~~---~~~~~-----d---G~~yC~~--cG~~   34 (36)
T PF11781_consen    9 EPCPVCGSR---WFYSD-----D---GFYYCDR--CGHQ   34 (36)
T ss_pred             CcCCCCCCe---EeEcc-----C---CEEEhhh--CceE
Confidence            469999998   44422     2   2788988  9986

>TIGR00340 zpr1_rel ZPR1-related zinc finger protein

Probab=89.08  E-value=0.8  Score=30.83  Aligned_cols=37  Identities=24%  Similarity=0.476  Sum_probs=17.0

Q ss_pred             CCCCCCCceEEEEeeccCCCCC--ceEEEEecCCCCCceec
Q psy8689          33 CPKCEHPRAYFMQIQTRSADEP--MTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        33 Cp~Cg~~~a~~~q~Q~rsadE~--mTlfy~C~~~~Cg~~w~   71 (72)
                      ||.||++...+....+...-=.  +-.-|.|-.  ||++..
T Consensus         1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~--CGyr~~   39 (163)
T TIGR00340         1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEK--CGYRST   39 (163)
T ss_pred             CCCCCCcceEeeeEeccCCCcceEEEEEEECCC--CCCchh
Confidence            6777766444422222221111  223456655  777654

A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.

>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines

Probab=88.66  E-value=1.2  Score=26.75  Aligned_cols=37  Identities=22%  Similarity=0.548  Sum_probs=19.6

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +.+.||.|||..++-..+- +.   ..+-...|..  ||..|.
T Consensus        21 ~~F~CPfC~~~~sV~v~id-kk---~~~~~~~C~~--Cg~~~~   57 (81)
T PF05129_consen   21 KVFDCPFCNHEKSVSVKID-KK---EGIGILSCRV--CGESFQ   57 (81)
T ss_dssp             S----TTT--SS-EEEEEE-TT---TTEEEEEESS--S--EEE
T ss_pred             ceEcCCcCCCCCeEEEEEE-cc---CCEEEEEecC--CCCeEE
Confidence            3589999999999887653 21   4555677999  998764

; PDB: 1WII_A.

>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]

Probab=88.37  E-value=0.22  Score=34.80  Aligned_cols=36  Identities=22%  Similarity=0.482  Sum_probs=22.4

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .+.||.||..+..---+-.|    +-..-+.|.+  ||+.|.
T Consensus         6 y~~Cp~Cg~eev~hEVik~~----g~~~lvrC~e--CG~V~~   41 (201)
T COG1326           6 YIECPSCGSEEVSHEVIKER----GREPLVRCEE--CGTVHP   41 (201)
T ss_pred             EEECCCCCcchhhHHHHHhc----CCceEEEccC--CCcEee
Confidence            47899999554411111111    2236788998  999995

>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]

Probab=87.07  E-value=1.9  Score=27.38  Aligned_cols=35  Identities=23%  Similarity=0.584  Sum_probs=25.6

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW   70 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w   70 (72)
                      .+.||.|||...+--.+-    -..+.-+..|.+  ||.++
T Consensus        22 ~FtCp~Cghe~vs~ctvk----k~~~~g~~~Cg~--CGls~   56 (104)
T COG4888          22 TFTCPRCGHEKVSSCTVK----KTVNIGTAVCGN--CGLSF   56 (104)
T ss_pred             eEecCccCCeeeeEEEEE----ecCceeEEEccc--CcceE
Confidence            489999999988744332    124666788999  99876

>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins

Probab=86.56  E-value=0.72  Score=25.95  Aligned_cols=30  Identities=33%  Similarity=0.874  Sum_probs=22.2

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW   70 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w   70 (72)
                      |...||.||+....          ......|.|.+  ||+.+
T Consensus        27 TSq~C~~CG~~~~~----------~~~~r~~~C~~--Cg~~~   56 (69)
T PF07282_consen   27 TSQTCPRCGHRNKK----------RRSGRVFTCPN--CGFEM   56 (69)
T ss_pred             CccCccCccccccc----------ccccceEEcCC--CCCEE
Confidence            45679999998774          23445788988  99875

More information about these proteins can be found at Protein of the Month: Transposase [].

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=86.51  E-value=0.91  Score=27.88  Aligned_cols=30  Identities=30%  Similarity=0.662  Sum_probs=23.8

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      ++++||.|++...+|-..|+         -..|..  ||..
T Consensus        34 m~VkCp~C~n~q~VFShA~t---------~V~C~~--Cg~~   63 (85)
T PTZ00083         34 MDVKCPGCSQITTVFSHAQT---------VVLCGG--CSSQ   63 (85)
T ss_pred             EEEECCCCCCeeEEEecCce---------EEEccc--cCCE
Confidence            47899999999999987653         366877  8764

>PLN00209 ribosomal protein S27; Provisional

Probab=86.50  E-value=0.87  Score=28.02  Aligned_cols=30  Identities=27%  Similarity=0.482  Sum_probs=23.7

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      ++++||.|++...+|-..|+         -..|..  ||..
T Consensus        35 m~VkCp~C~n~q~VFShA~t---------~V~C~~--Cg~~   64 (86)
T PLN00209         35 MDVKCQGCFNITTVFSHSQT---------VVVCGS--CQTV   64 (86)
T ss_pred             EEEECCCCCCeeEEEecCce---------EEEccc--cCCE
Confidence            46899999999999987552         366877  8764

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=86.43  E-value=0.62  Score=25.63  Aligned_cols=29  Identities=28%  Similarity=0.776  Sum_probs=18.8

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW   70 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w   70 (72)
                      ....||+||+.   |.-.. .       -.+.|-.  ||+.+
T Consensus        19 ~~~fCP~Cg~~---~m~~~-~-------~r~~C~~--Cgyt~   47 (50)
T PRK00432         19 KNKFCPRCGSG---FMAEH-L-------DRWHCGK--CGYTE   47 (50)
T ss_pred             ccCcCcCCCcc---hhecc-C-------CcEECCC--cCCEE
Confidence            44689999986   22211 1       2577988  99874

>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1

Probab=85.47  E-value=1.6  Score=29.18  Aligned_cols=37  Identities=22%  Similarity=0.473  Sum_probs=17.5

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCce--EEEEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMT--TFYKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mT--lfy~C~~~~Cg~~w~   71 (72)
                      .||.||++.. +....+....-.-.  .-|.|-.  ||++..
T Consensus         2 ~Cp~C~~~~~-~~~~~~~IP~F~evii~sf~C~~--CGyk~~   40 (160)
T smart00709        2 DCPSCGGNGT-TRMLLTSIPYFREVIIMSFECEH--CGYRNN   40 (160)
T ss_pred             cCCCCCCCCE-EEEEEecCCCcceEEEEEEECCC--CCCccc
Confidence            4777776543 33323333322222  2355655  777654

Also present in archaeal proteins.

>TIGR00310 ZPR1_znf ZPR1 zinc finger domain

Probab=84.72  E-value=1.6  Score=30.05  Aligned_cols=38  Identities=24%  Similarity=0.506  Sum_probs=18.0

Q ss_pred             eCCCCCCCceE-EEEee-ccCCCCCceEEEEecCCCCCceec
Q psy8689          32 KCPKCEHPRAY-FMQIQ-TRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~-~~q~Q-~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .||.||.+..+ ..... +---.+=+-.-|.|-.  ||++..
T Consensus         2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~--CGyr~~   41 (192)
T TIGR00310         2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEH--CGYRSN   41 (192)
T ss_pred             cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCC--CCCccc
Confidence            58888765333 22212 1111111233466766  887764

>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors []

Probab=83.79  E-value=2.2  Score=21.52  Aligned_cols=29  Identities=24%  Similarity=0.524  Sum_probs=21.5

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW   70 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w   70 (72)
                      ...|+.||++..++ +.+         -+++|..  ||..+
T Consensus         3 ~~~C~~C~~~~i~~-~~~---------~~~~C~~--Cg~~~   31 (33)
T PF08792_consen    3 LKKCSKCGGNGIVN-KED---------DYEVCIF--CGSSF   31 (33)
T ss_pred             ceEcCCCCCCeEEE-ecC---------CeEEccc--CCcEe
Confidence            36899999999765 222         2788988  99765

>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.43  E-value=0.99  Score=21.98  Aligned_cols=25  Identities=32%  Similarity=0.677  Sum_probs=10.3

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEEEEecCC-CC
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI-KC   66 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~-~C   66 (72)
                      .||.||+.-.       |..+|.   .+.|.|+ .|
T Consensus         1 ~CP~C~s~l~-------~~~~ev---~~~C~N~l~C   26 (28)
T PF03119_consen    1 TCPVCGSKLV-------REEGEV---DIRCPNPLSC   26 (28)
T ss_dssp             B-TTT--BEE-------E-CCTT---CEEE--CGC-
T ss_pred             CcCCCCCEeE-------cCCCCE---eEECCCCCcC
Confidence            4999998765       223333   4567775 45

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.

>PRK03988 translation initiation factor IF-2 subunit beta; Validated

Probab=83.31  E-value=2.2  Score=27.99  Aligned_cols=30  Identities=27%  Similarity=0.674  Sum_probs=23.9

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      +.|+.|++.+..+.- .      .-.+|..|..  ||..
T Consensus       103 VlC~~C~spdT~l~k-~------~r~~~l~C~A--CGa~  132 (138)
T PRK03988        103 VICPECGSPDTKLIK-E------GRIWVLKCEA--CGAE  132 (138)
T ss_pred             EECCCCCCCCcEEEE-c------CCeEEEEccc--CCCC
Confidence            789999999987743 2      3478889998  9974

>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]

Probab=83.29  E-value=0.54  Score=33.61  Aligned_cols=36  Identities=25%  Similarity=0.706  Sum_probs=24.9

Q ss_pred             CCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          26 VDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        26 ~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      .+.-.+.||.|.|....+     |-++-|.. =|+|.+  |+|.
T Consensus       188 ~~~~alIC~~C~hhngl~-----~~~ek~~~-efiC~~--Cn~~  223 (251)
T COG5415         188 SPFKALICPQCHHHNGLY-----RLAEKPII-EFICPH--CNHK  223 (251)
T ss_pred             Cchhhhcccccccccccc-----ccccccch-heeccc--chhh
Confidence            344458999999888766     44555555 567987  9873

>PF14353 CpXC: CpXC protein

Probab=83.08  E-value=1.7  Score=27.22  Aligned_cols=11  Identities=36%  Similarity=0.911  Sum_probs=6.1

Q ss_pred             eeCCCCCCCce
Q psy8689          31 EKCPKCEHPRA   41 (72)
Q Consensus        31 ~~Cp~Cg~~~a   41 (72)
                      +.||+||+.--
T Consensus         2 itCP~C~~~~~   12 (128)
T PF14353_consen    2 ITCPHCGHEFE   12 (128)
T ss_pred             cCCCCCCCeeE
Confidence            45666665433

>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases

Probab=82.72  E-value=2.9  Score=21.52  Aligned_cols=32  Identities=16%  Similarity=0.469  Sum_probs=20.3

Q ss_pred             cceeeCCCCCCCceEEEEeeccCCCCCceEEEEecC
Q psy8689          28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCN   63 (72)
Q Consensus        28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~   63 (72)
                      +.++.||.|++.+.++.--+.   ..+- .=|.|.+
T Consensus         3 ~i~v~CP~C~s~~~v~k~G~~---~~G~-qryrC~~   34 (36)
T PF03811_consen    3 KIDVHCPRCQSTEGVKKNGKS---PSGH-QRYRCKD   34 (36)
T ss_pred             cEeeeCCCCCCCCcceeCCCC---CCCC-EeEecCc
Confidence            346899999999977754332   1222 3366766

Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated

>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative

Probab=82.64  E-value=2.4  Score=27.69  Aligned_cols=30  Identities=23%  Similarity=0.708  Sum_probs=23.1

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      +.||.|++.+..+.- .      .-..|..|..  ||..
T Consensus        98 VlC~~C~sPdT~l~k-~------~r~~~l~C~A--CGa~  127 (133)
T TIGR00311        98 VICRECNRPDTRIIK-E------GRVSLLKCEA--CGAK  127 (133)
T ss_pred             EECCCCCCCCcEEEE-e------CCeEEEeccc--CCCC
Confidence            789999999987653 2      3355778988  9975

>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []

Probab=82.40  E-value=1.3  Score=31.58  Aligned_cols=39  Identities=23%  Similarity=0.448  Sum_probs=19.8

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .+.||.||+.+..-+.. ....+++.-..++|-.  |+.-++
T Consensus       211 R~~Cp~Cg~~~~~~l~~-~~~e~~~~~rve~C~~--C~~YlK  249 (290)
T PF04216_consen  211 RIKCPYCGNTDHEKLEY-FTVEGEPAYRVEVCES--CGSYLK  249 (290)
T ss_dssp             TTS-TTT---SS-EEE---------SEEEEEETT--TTEEEE
T ss_pred             CCCCcCCCCCCCcceee-EecCCCCcEEEEECCc--ccchHH
Confidence            46899999887764442 2235666777889988  998664

The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.

>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []

Probab=82.05  E-value=2.4  Score=27.34  Aligned_cols=30  Identities=30%  Similarity=0.714  Sum_probs=24.1

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      +.||.|++.+..+.-.       .-.+|..|..  ||..
T Consensus        94 VlC~~C~spdT~l~k~-------~r~~~l~C~a--CGa~  123 (125)
T PF01873_consen   94 VLCPECGSPDTELIKE-------GRLIFLKCKA--CGAS  123 (125)
T ss_dssp             SSCTSTSSSSEEEEEE-------TTCCEEEETT--TSCE
T ss_pred             EEcCCCCCCccEEEEc-------CCEEEEEecc--cCCc
Confidence            7899999999887653       2357889998  9975

Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....

>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain

Probab=82.05  E-value=0.053  Score=29.43  Aligned_cols=30  Identities=30%  Similarity=0.604  Sum_probs=23.9

Q ss_pred             CCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689          36 CEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF   68 (72)
Q Consensus        36 Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~   68 (72)
                      |.|.-+ ....|+|+.||..+.+-.|..  |+.
T Consensus        13 C~H~f~-~~E~Q~RAGDE~VSfI~~C~~--C~~   42 (43)
T PF11792_consen   13 CKHKFV-TIEKQLRAGDEAVSFIKYCQK--CGQ   42 (43)
T ss_pred             ceeeee-ehhhhhcccchHHHHHHHHHH--hCC
Confidence            777666 445699999999998888987  875

>TIGR02443 conserved hypothetical metal-binding protein

Probab=81.61  E-value=3.7  Score=23.60  Aligned_cols=32  Identities=25%  Similarity=0.624  Sum_probs=21.0

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW   70 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w   70 (72)
                      +.||+|+....+-+=.      |.-.-+..|+.  |||+-
T Consensus        10 A~CP~C~~~Dtl~~~~------e~~~e~vECv~--Cg~~~   41 (59)
T TIGR02443        10 AVCPACSAQDTLAMWK------ENNIELVECVE--CGYQE   41 (59)
T ss_pred             ccCCCCcCccEEEEEE------eCCceEEEecc--CCCcc
Confidence            5899999877763221      11224678998  99874

Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.

>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=80.80  E-value=2.3  Score=28.33  Aligned_cols=38  Identities=18%  Similarity=0.500  Sum_probs=17.2

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCC--ceEEEEecCCCCCceec
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEP--MTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~--mTlfy~C~~~~Cg~~w~   71 (72)
                      ..||.||++...-+ ..+....=+  +-.-|.|-+  ||++..
T Consensus         2 s~Cp~C~~~~~~~~-~~~~IP~F~evii~sf~C~~--CGyk~~   41 (161)
T PF03367_consen    2 SLCPNCGENGTTRI-LLTDIPYFKEVIIMSFECEH--CGYKNN   41 (161)
T ss_dssp             EE-TTTSSCCEEEE-EEEEETTTEEEEEEEEE-TT--T--EEE
T ss_pred             CcCCCCCCCcEEEE-EEEcCCCCceEEEEEeECCC--CCCEee
Confidence            36888887765433 222222112  223466877  888765

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=80.50  E-value=1  Score=24.12  Aligned_cols=14  Identities=21%  Similarity=0.536  Sum_probs=11.2

Q ss_pred             ceeeCCCCCCCceE
Q psy8689          29 TEEKCPKCEHPRAY   42 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~   42 (72)
                      ..+.||.||++-.+
T Consensus        18 ~~irC~~CG~rIly   31 (44)
T smart00659       18 DVVRCRECGYRILY   31 (44)
T ss_pred             CceECCCCCceEEE
Confidence            45899999998663

present in RNA polymerase I, II and III

>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements

Probab=80.19  E-value=1.1  Score=32.42  Aligned_cols=33  Identities=27%  Similarity=0.703  Sum_probs=11.5

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW   70 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w   70 (72)
                      ...||.||+....-|..-.     |..=|| |.+  |+..+
T Consensus        31 n~yCP~Cg~~~L~~f~NN~-----PVaDF~-C~~--C~eey   63 (254)
T PF06044_consen   31 NMYCPNCGSKPLSKFENNR-----PVADFY-CPN--CNEEY   63 (254)
T ss_dssp             H---TTT--SS-EE-------------EEE--TT--T--EE
T ss_pred             CCcCCCCCChhHhhccCCC-----ccceeE-CCC--CchHH
Confidence            4689999999766555433     444455 888  98765

The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	72
3qt1_I	133	Rna Polymerase Ii Variant Containing A Chimeric Rpb		2e-09
1qyp_A	57	Thermococcus Celer Rpb9, Nmr, 25 Structures Length		2e-07
1pqv_S	309	Rna Polymerase Ii-Tfiis Complex Length = 309		4e-06
1tfi_A	50	A Novel Zn Finger Motif In The Basal Transcriptiona		2e-05
1y1v_S	179	Refined Rna Polymerase Ii-tfiis Complex Length = 17		3e-05
3gtm_S	173	Co-Complex Of Backtracked Rna Polymerase Ii With Tf		1e-04

>pdb|3QT1|I Chain I, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11 Subunit Length = 133

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 26/44 (59%), Positives = 31/44 (70%), Gaps = 2/44 (4%)
Query: 29  TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
           ++ +CPKC      F Q+Q RSADEPMTTFYKC N  CG RW+E
Sbjct: 91  SDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVN--CGHRWKE 132

>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures Length = 57

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 32/49 (65%), Gaps = 2/49 (4%)
Query: 24 ENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
          + + TT+  CPKC +  AY+ ++QTR+ DEP T FYKC   KCG  WR 
Sbjct: 9  KTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKC--TKCGHTWRS 55

>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex Length = 309

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 23/52 (44%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 20  AAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
            A  E   T    C KC+  +  + Q+QTRSADEP+TTF  C    CG RW+
Sbjct: 258 GATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTC--EACGNRWK 307

>pdb|1TFI|A Chain A, A Novel Zn Finger Motif In The Basal Transcriptional Machinery: Three-Dimensional Nmr Studies Of The Nucleic- Acid Binding Domain Of Transcriptional Elongation Factor Tfiis Length = 50

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 33 CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
          C KC+     + Q+QTRSADEPMTTF  C   +CG RW+
Sbjct: 12 CGKCKKKNCTYTQVQTRSADEPMTTFVVC--NECGNRWK 48

>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex Length = 179

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/39 (51%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 33  CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
           C KC+  +  + Q+QTRSADEP+TTF  C    CG RW+
Sbjct: 141 CGKCKEKKVSYYQLQTRSADEPLTTFCTC--EACGNRWK 177

>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis Length = 173

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 33  CPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
           C KC+  +  + Q+QTRSAD P+TTF  C    CG RW+
Sbjct: 135 CGKCKEKKVSYYQLQTRSADHPLTTFCTC--EACGNRWK 171

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	72
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	3e-21
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	1e-18
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	1e-18
3po3_S	178	Transcription elongation factor S-II; RNA polymera	3e-16
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	1e-15
1tfi_A	50	Transcriptional elongation factor SII; transcripti	1e-15
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	2e-14

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1 Length = 57

 Score = 77.2 bits (190), Expect = 3e-21
 Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 2/51 (3%)

Query: 22 AWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
            + + TT+  CPKC +  AY+ ++QTR+ DEP T FYKC    CG  WR 
Sbjct: 7  DLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTK--CGHTWRS 55

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 113

 Score = 72.5 bits (177), Expect = 1e-18
 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 5   RLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI 64
            L+    E   V   A+    +  ++++CP+C    A F Q  +R  D  MT  Y C + 
Sbjct: 47  ELQSSNVENTTVSHDASTDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVH- 105

Query: 65  KCGFRWRE 72
            CGF + E
Sbjct: 106 -CGFAFEE 112

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae} Length = 133

 Score = 72.9 bits (178), Expect = 1e-18
 Identities = 29/68 (42%), Positives = 37/68 (54%), Gaps = 2/68 (2%)

Query: 5   RLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI 64
            L     E   V+    +   +  ++ +CPKC      F Q+Q RSADEPMTTFYKC N 
Sbjct: 67  ELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVN- 125

Query: 65  KCGFRWRE 72
            CG RW+E
Sbjct: 126 -CGHRWKE 132

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A Length = 178

 Score = 67.5 bits (164), Expect = 3e-16
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 2/66 (3%)

Query: 6   LKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIK 65
              +  + +      A  E   T    C KC+  +  + Q+QTRSA  P+TTF  C    
Sbjct: 113 KIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEA-- 170

Query: 66  CGFRWR 71
           CG RW+
Sbjct: 171 CGNRWK 176

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A Length = 309

 Score = 67.9 bits (164), Expect = 1e-15
 Identities = 23/51 (45%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 21  AAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
           A  E   T    C KC+  +  + Q+QTRSADEP+TTF  C    CG RW+
Sbjct: 259 ATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEA--CGNRWK 307

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1 Length = 50

 Score = 62.8 bits (153), Expect = 1e-15
 Identities = 22/44 (50%), Positives = 26/44 (59%), Gaps = 2/44 (4%)

Query: 28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
          T    C KC+     + Q+QTRSADEPMTTF  C    CG RW+
Sbjct: 7  TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNE--CGNRWK 48

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ... Length = 122

 Score = 61.8 bits (149), Expect = 2e-14
 Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 5   RLKIKPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNI 64
            L     E   V+    +   +  ++ +CPKC      F Q Q R  D  M  F+ C + 
Sbjct: 47  ELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLS- 105

Query: 65  KCGFRWRE 72
            C   +  
Sbjct: 106 -CSHIFTS 112

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	72
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	99.95
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	99.94
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	99.92
1tfi_A	50	Transcriptional elongation factor SII; transcripti	99.91
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	99.89
3po3_S	178	Transcription elongation factor S-II; RNA polymera	99.8
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	99.75
1k81_A	36	EIF-2-beta, probable translation initiation factor	94.68
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	91.8
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	90.68
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	90.17
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	89.43
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	87.6
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	87.27
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	86.52
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	84.5
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	81.23

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.95  E-value=3.3e-28  Score=153.47  Aligned_cols=62  Identities=31%  Similarity=0.628  Sum_probs=59.0

Q ss_pred             CccccccccCCccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689           9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus         9 ~~ke~~~v~~~~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      ..+|.++|++++++|+++|++.+.||+|||++|+|||+|+||||||||+||+|.+  |||+|++
T Consensus        51 ~~~e~~~v~~~~~~~~tlp~~~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~--C~~~w~~  112 (113)
T 3h0g_I           51 SNVENTTVSHDASTDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVH--CGFAFEE  112 (113)
T ss_dssp             CSCTTCTTCTTSTTCSSSCBCCSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESS--SCCCCCC
T ss_pred             ccccccceeccccccccCCCcccCCCCCCCceEEEEEEecccCCCCCeeEEEcCC--CCCEEec
Confidence            4478889999999999999999999999999999999999999999999999998  9999986

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=99.94  E-value=5.4e-27  Score=149.58  Aligned_cols=62  Identities=24%  Similarity=0.514  Sum_probs=58.5

Q ss_pred             CccccccccCCccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689           9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus         9 ~~ke~~~v~~~~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      ..++.++|++++++|+++|++++.||+|||++|+|||+|+||||||||+||+|++  |||+|++
T Consensus        51 ~~~e~~~v~~~~~~~~t~p~t~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~--C~~~w~~  112 (122)
T 1twf_I           51 NIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLS--CSHIFTS  112 (122)
T ss_dssp             CTTSSTTCCTTGGGCTTSCCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETT--TCCEEEC
T ss_pred             cccccccccccccccccccccCCCCCCCCCCEEEEEEecCccCCCCceEEEEeCC--CCCEecc
Confidence            4577789999999999999999999999999999999999999999999999999  9999985

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=99.92  E-value=2.2e-25  Score=125.71  Aligned_cols=51  Identities=45%  Similarity=0.980  Sum_probs=48.2

Q ss_pred             ccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689          20 AAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus        20 ~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      +++|+++|++.+.||+||+++++|+|+|+||||||||+||+|.+  |||+|++
T Consensus         5 e~~~~~~~~~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~--Cg~~w~~   55 (57)
T 1qyp_A            5 EQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTK--CGHTWRS   55 (57)
T ss_dssp             CCCCSSSCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESS--SCCEEEC
T ss_pred             hhhhhcCCceEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCC--CCCEecc
Confidence            45789999999999999999999999999999999999999999  9999985

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=99.91  E-value=6.5e-25  Score=121.95  Aligned_cols=42  Identities=52%  Similarity=0.967  Sum_probs=39.8

Q ss_pred             cceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        28 ~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +..+.||+||+++|+|||+|+||||||||+||+|++  |||+|+
T Consensus         7 t~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~--Cg~~w~   48 (50)
T 1tfi_A            7 TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNE--CGNRWK   48 (50)
T ss_dssp             CCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESS--SCCEEE
T ss_pred             eCccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCC--CCCeEE
Confidence            446899999999999999999999999999999999  999997

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=99.89  E-value=3.1e-25  Score=143.79  Aligned_cols=57  Identities=47%  Similarity=0.958  Sum_probs=0.0

Q ss_pred             ccccCCccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689          14 DHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus        14 ~~v~~~~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      ..|+.++..++++|++++.||+||+++|+|||+|+||||||||+||+|++  |||+|++
T Consensus        76 ~~vv~dv~~dptlp~t~~~CpkCg~~~a~f~q~Q~RsaDE~mT~fy~C~~--C~~~w~e  132 (133)
T 3qt1_I           76 AGVVQDIGSDPTLPRSDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVN--CGHRWKE  132 (133)
T ss_dssp             -----------------------------------------------------------
T ss_pred             ceeEeeccccccCCcccCCCCCCCCceEEEEEEeeecCCCCCcEEEEcCC--CCCEeCc
Confidence            34556666789999999999999999999999999999999999999999  9999986

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A

Probab=99.80  E-value=9.4e-21  Score=127.27  Aligned_cols=48  Identities=38%  Similarity=0.808  Sum_probs=42.7

Q ss_pred             ccccCCc---ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          22 AWENVDT---TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        22 ~~~~~~~---t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .++++++   +.+.||+|||++++|||+|+||||||||+||+|++  |||+|+
T Consensus       126 ~~~~~~~~~t~~~~Cp~C~~~~a~~~q~Q~rsaDE~mt~f~~C~~--C~~~w~  176 (178)
T 3po3_S          126 QGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEA--CGNRWK  176 (178)
T ss_dssp             BCCCCCCCCBSSSCCSSSCCSCEECCCCCCSCTTSCCCCCEEETT--TCCEEC
T ss_pred             hhccccCCCcCCcCCCCCCCCceEEEEeecccCCCCCcEEEEcCC--CCCeec
Confidence            3455554   35899999999999999999999999999999999  999997

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A

Probab=99.75  E-value=8e-19  Score=125.57  Aligned_cols=43  Identities=49%  Similarity=0.950  Sum_probs=40.0

Q ss_pred             CcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          27 DTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        27 ~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      +++.+.||+||+++++|||+|+||||||||+||.|++  |||+|+
T Consensus       265 ~~~~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C~~--Cg~~w~  307 (309)
T 1pqv_S          265 VTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEA--CGNRWK  307 (309)
T ss_pred             CcccccCCCCCCCeeEEEEeecccCCCCCcEEEEeCC--CCCcee
Confidence            3345799999999999999999999999999999999  999997

>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1

Probab=94.68  E-value=0.062  Score=27.01  Aligned_cols=31  Identities=23%  Similarity=0.548  Sum_probs=24.6

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW   70 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w   70 (72)
                      +.||.|++.+..+.-.       .-.+|..|..  ||+++
T Consensus         1 VlC~~C~~peT~l~~~-------~~~~~l~C~a--CG~~~   31 (36)
T 1k81_A            1 VICRECGKPDTKIIKE-------GRVHLLKCMA--CGAIR   31 (36)
T ss_dssp             CCCSSSCSCEEEEEEE-------TTEEEEEEET--TTEEE
T ss_pred             CCCcCCCCCCcEEEEe-------CCcEEEEhhc--CCCcc
Confidence            4699999999987552       2568888998  99876

>2akl_A PHNA-like protein PA0128; two domains, Zn binding protein, beta-strand protein, structural genomics, PSI; NMR {Pseudomonas aeruginosa PAO1} SCOP: b.34.11.2 g.41.3.5

Probab=91.80  E-value=0.079  Score=34.15  Aligned_cols=28  Identities=25%  Similarity=0.787  Sum_probs=20.7

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      -.||+|++..+|.-.        .   -|+|-.  |+|-|.
T Consensus        28 P~CP~C~seytYeDg--------~---l~vCPe--C~hEW~   55 (138)
T 2akl_A           28 PPCPQCNSEYTYEDG--------A---LLVCPE--CAHEWS   55 (138)
T ss_dssp             CCCTTTCCCCCEECS--------S---SEEETT--TTEEEC
T ss_pred             CCCCCCCCcceEecC--------C---eEECCc--cccccC
Confidence            479999998886421        1   288955  999995

>1qxf_A GR2, 30S ribosomal protein S27E; structural genomics, beta sheet, PSI, protein structure initiative; NMR {Archaeoglobus fulgidus} SCOP: g.41.8.4

Probab=90.68  E-value=0.14  Score=29.29  Aligned_cols=30  Identities=40%  Similarity=0.825  Sum_probs=23.5

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      ++++||.|++...+|-..|+         -..|..  ||..
T Consensus         6 m~VKCp~C~niq~VFShA~t---------vV~C~~--Cg~~   35 (66)
T 1qxf_A            6 VKVKCPDCEHEQVIFDHPST---------IVKCII--CGRT   35 (66)
T ss_dssp             EEEECTTTCCEEEEESSCSS---------CEECSS--SCCE
T ss_pred             EEEECCCCCCceEEEecCce---------EEEccc--CCCE
Confidence            47899999999999977653         256877  8764

>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1

Probab=90.17  E-value=0.35  Score=34.36  Aligned_cols=38  Identities=21%  Similarity=0.602  Sum_probs=25.4

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      ...||.||+.-..-.- ..+...++ ..|..|.-  |++.|.
T Consensus       182 ~~~CPvCGs~P~~s~l-~~~g~~~G-~R~l~Cs~--C~t~W~  219 (309)
T 2fiy_A          182 RTLCPACGSPPMAGMI-RQGGKETG-LRYLSCSL--CACEWH  219 (309)
T ss_dssp             CSSCTTTCCCEEEEEE-EC----CC-EEEEEETT--TCCEEE
T ss_pred             CCCCCCCCCcCceeEE-eecCCCCC-cEEEEeCC--CCCEEe
Confidence            4689999998876533 22223344 35899988  999996

>3j20_W 30S ribosomal protein S27E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=89.43  E-value=0.2  Score=28.32  Aligned_cols=30  Identities=27%  Similarity=0.538  Sum_probs=23.3

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      ++++||.|++...+|-..|+         -..|..  ||..
T Consensus        14 m~VkCp~C~~~q~VFSha~t---------~V~C~~--Cgt~   43 (63)
T 3j20_W           14 LRVKCIDCGNEQIVFSHPAT---------KVRCLI--CGAT   43 (63)
T ss_dssp             EEEECSSSCCEEEEESSCSS---------CEECSS--SCCE
T ss_pred             EEEECCCCCCeeEEEecCCe---------EEEccC--cCCE
Confidence            57999999999999976553         256877  8764

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=87.60  E-value=0.55  Score=24.38  Aligned_cols=31  Identities=23%  Similarity=0.629  Sum_probs=20.5

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      ...||.||+...+|-.         .+--++|..  ||..+.
T Consensus         5 ~~~CP~C~~~~l~~d~---------~~gelvC~~--CG~v~~   35 (50)
T 1pft_A            5 QKVCPACESAELIYDP---------ERGEIVCAK--CGYVIE   35 (50)
T ss_dssp             CCSCTTTSCCCEEEET---------TTTEEEESS--SCCBCC
T ss_pred             cEeCcCCCCcceEEcC---------CCCeEECcc--cCCccc
Confidence            3579999986665521         111378988  998654

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4

Probab=87.27  E-value=1.3  Score=26.05  Aligned_cols=35  Identities=23%  Similarity=0.539  Sum_probs=26.1

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW   70 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w   70 (72)
                      .+.||.|||..++-..+- +.   ..+-...|..  ||-.|
T Consensus        23 ~F~CPfCnh~~sV~vkid-k~---~~~g~l~C~~--Cg~~~   57 (85)
T 1wii_A           23 QFTCPFCNHEKSCDVKMD-RA---RNTGVISCTV--CLEEF   57 (85)
T ss_dssp             CCCCTTTCCSSCEEEEEE-TT---TTEEEEEESS--SCCEE
T ss_pred             eEcCCCCCCCCeEEEEEE-cc---CCEEEEEccc--CCCeE
Confidence            489999999988776653 21   3466778999  99766

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6

Probab=86.52  E-value=0.32  Score=28.74  Aligned_cols=30  Identities=23%  Similarity=0.554  Sum_probs=23.5

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      ++++||.|++...+|-..|+         ...|..  ||..
T Consensus        31 m~VkCp~C~n~q~VFShA~t---------~V~C~~--Cg~~   60 (81)
T 2xzm_6           31 MDVKCAQCQNIQMIFSNAQS---------TIICEK--CSAI   60 (81)
T ss_dssp             EEEECSSSCCEEEEETTCSS---------CEECSS--SCCE
T ss_pred             EEeECCCCCCeeEEEecCcc---------EEEccC--CCCE
Confidence            57899999999999976553         366887  8764

>3u5c_b RP61, YS20, 40S ribosomal protein S27-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_X 3u5g_b

Probab=84.50  E-value=0.36  Score=28.62  Aligned_cols=29  Identities=31%  Similarity=0.644  Sum_probs=22.5

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF   68 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~   68 (72)
                      ++++||.|++...+|-..|+-         ..|..  ||.
T Consensus        33 m~VkCp~C~~~q~VFSha~t~---------V~C~~--Cg~   61 (82)
T 3u5c_b           33 LDVKCPGCLNITTVFSHAQTA---------VTCES--CST   61 (82)
T ss_dssp             EEEECTTSCSCEEEESBCSSC---------CCCSS--SCC
T ss_pred             EEEECCCCCCeeEEEecCCeE---------EEccc--cCC
Confidence            479999999999999776643         45666  765

>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1

Probab=81.23  E-value=1.6  Score=30.91  Aligned_cols=40  Identities=18%  Similarity=0.502  Sum_probs=26.0

Q ss_pred             eeeCCCCCCCceE-EEEeeccC--CCCCceEEEEecCCCCCceec
Q psy8689          30 EEKCPKCEHPRAY-FMQIQTRS--ADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~-~~q~Q~rs--adE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .+.||.||+.+.. |+..-.-+  ++++....++|..  |++-++
T Consensus       222 R~~C~~Cg~~~~l~y~~~e~~~~~~~~~~~r~e~C~~--C~~YlK  264 (309)
T 2fiy_A          222 RIKCSHCEESKHLAYLSLEHDGQPAEKAVLRAETCPS--CQGYLK  264 (309)
T ss_dssp             TTSCSSSCCCSCCEEECCCC-CCCSTTCSEEEEEETT--TTEEEE
T ss_pred             CcCCcCCCCCCCeeEEEecCccccCCCcceEEEEccc--ccchHh
Confidence            4689999986554 44332100  1346678899998  998664

---

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	72
d1qypa_	57	g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {A	5e-19
d1twfi2	72	g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase	2e-15
d1tfia_	50	g.41.3.1 (A:) Transcriptional factor SII, C-termin	1e-14

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]} Length = 57

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

 Score = 70.6 bits (173), Expect = 5e-19
 Identities = 23/50 (46%), Positives = 31/50 (62%), Gaps = 2/50 (4%)

Query: 23 WENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
           + + TT+  CPKC +  AY+ ++QTR+ DEP T FYKC    CG  WR 
Sbjct: 8  LKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTK--CGHTWRS 55

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 72

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 61.8 bits (150), Expect = 2e-15
 Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 2/45 (4%)

Query: 28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE 72
           ++ +CPKC      F Q Q R  D  M  F+ C +  C   +  
Sbjct: 21 RSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLS--CSHIFTS 63

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 50

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (144), Expect = 1e-14
 Identities = 22/44 (50%), Positives = 26/44 (59%), Gaps = 2/44 (4%)

Query: 28 TTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR 71
          T    C KC+     + Q+QTRSADEPMTTF  C    CG RW+
Sbjct: 7  TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNE--CGNRWK 48

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	72
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	99.95
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	99.93
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	99.88
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	94.86
d1pvma3	36	Hypothetical protein Ta0289 C-terminal domain {Arc	92.11
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	89.69
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	88.79
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	88.46
d1wiia_	85	Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m	84.79
d1k81a_	36	Zinc-binding domain of translation initiation fact	80.63

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.95  E-value=1.9e-28  Score=143.75  Aligned_cols=62  Identities=24%  Similarity=0.514  Sum_probs=58.9

Q ss_pred             CccccccccCCccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689           9 KPKEIDHVMGGAAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus         9 ~~ke~~~v~~~~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      ..+|...|+.+.+.+|++|++++.||+||+++++|||.|+||||||||+||+|++  |||+|++
T Consensus         2 ~~~e~~~v~~d~~~DPtlp~t~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~--C~h~Wr~   63 (72)
T d1twfi2           2 NIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLS--CSHIFTS   63 (72)
T ss_dssp             CTTSSTTCCTTGGGCTTSCCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETT--TCCEEEC
T ss_pred             CcccccccccccccCCCCCccCCCCCCCCCCeEEEEEeecCccCCCceEEEEcCC--CCCCccc
Confidence            3578889999999999999999999999999999999999999999999999999  9999985

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=99.93  E-value=4.2e-27  Score=132.67  Aligned_cols=51  Identities=45%  Similarity=0.980  Sum_probs=47.8

Q ss_pred             ccccccCCcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceecC
Q psy8689          20 AAAWENVDTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWRE   72 (72)
Q Consensus        20 ~~~~~~~~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~~   72 (72)
                      +...+++|++++.||+||+++++|+|+|+||||||||+||.|.+  |||+||+
T Consensus         5 ~~~~~~~pt~~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~--Cg~~wre   55 (57)
T d1qypa_           5 EQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTK--CGHTWRS   55 (57)
T ss_dssp             CCCCSSSCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESS--SCCEEEC
T ss_pred             hhccccCCcccCCCCCCCCCceEEEEeecccccCCCeEEEEeCC--CCCccee
Confidence            44567899999999999999999999999999999999999999  9999996

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.2e-23  Score=114.61  Aligned_cols=43  Identities=51%  Similarity=0.952  Sum_probs=40.2

Q ss_pred             CcceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          27 DTTEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        27 ~~t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      ++..+.||+||++++.|+|+|+||||||||+||.|.+  |||+||
T Consensus         6 ~T~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~--Cg~~Wr   48 (50)
T d1tfia_           6 QTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNE--CGNRWK   48 (50)
T ss_dssp             ECCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESS--SCCEEE
T ss_pred             ccCCEECCCCCCCccEEEEEEccCCCCCceEEEEccc--cCCeee
Confidence            4445799999999999999999999999999999999  999997

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.86  E-value=0.0069  Score=30.09  Aligned_cols=27  Identities=26%  Similarity=0.825  Sum_probs=19.6

Q ss_pred             eCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          32 KCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        32 ~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      .||+|++.-++--.           ..|+|-.  |+|-|.
T Consensus         5 ~CP~C~seytYedg-----------~l~vCPe--C~hEW~   31 (38)
T d2akla2           5 PCPQCNSEYTYEDG-----------ALLVCPE--CAHEWS   31 (38)
T ss_dssp             CCTTTCCCCCEECS-----------SSEEETT--TTEEEC
T ss_pred             cCCCCCCcceEcCC-----------CEEECCc--ccCcCC
Confidence            69999998774311           1378955  999996

>d1pvma3 g.41.13.1 (A:143-178) Hypothetical protein Ta0289 C-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Hypothetical protein Ta0289 C-terminal domain
family: Hypothetical protein Ta0289 C-terminal domain
domain: Hypothetical protein Ta0289 C-terminal domain
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=92.11  E-value=0.18  Score=23.93  Aligned_cols=33  Identities=21%  Similarity=0.515  Sum_probs=22.1

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCc
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGF   68 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~   68 (72)
                      .-||+||-.-..-.-.|     .+....|.|.||.|.+
T Consensus         2 hlcpkcgvgvl~pvy~~-----kgeikvfrcsnpacdy   34 (36)
T d1pvma3           2 HLCPKCGVGVLEPVYNE-----KGEIKVFRCSNPACDY   34 (36)
T ss_dssp             CBCTTTSSSBEEEEECT-----TSCEEEEEESCTTCCC
T ss_pred             ccCCccCceEEEEeecC-----CCcEEEEEcCCCcccc
Confidence            35999987655432222     2456678899999975

>d1qxfa_ g.41.8.4 (A:) Ribosomal protein S27e {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27e
domain: Ribosomal protein S27e
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.69  E-value=0.089  Score=28.01  Aligned_cols=30  Identities=40%  Similarity=0.825  Sum_probs=22.9

Q ss_pred             ceeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          29 TEEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        29 t~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      ++++||.|++...+|-..|+         -..|..  ||..
T Consensus         6 ~~VkC~~C~n~~ivFsha~t---------~V~C~~--Cg~~   35 (58)
T d1qxfa_           6 VKVKCPDCEHEQVIFDHPST---------IVKCII--CGRT   35 (58)
T ss_dssp             EEEECTTTCCEEEEESSCSS---------CEECSS--SCCE
T ss_pred             EEeECCCCCCeEEEEecCce---------EEEccc--cCCE
Confidence            36899999999999966442         356877  8865

>d2fiya1 e.59.1.1 (A:19-308) FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId: 287]}

class: Multi-domain proteins (alpha and beta)
fold: FdhE-like
superfamily: FdhE-like
family: FdhE-like
domain: FdhE homolog PA4809
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.79  E-value=0.31  Score=32.68  Aligned_cols=38  Identities=21%  Similarity=0.602  Sum_probs=24.8

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCceec
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRWR   71 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w~   71 (72)
                      ...||-||+.-..-+- ......++ ..|..|.-  |++.|.
T Consensus       164 ~~~CPvCGs~P~~s~l-~~~~~~~G-~R~l~C~~--C~teW~  201 (290)
T d2fiya1         164 RTLCPACGSPPMAGMI-RQGGKETG-LRYLSCSL--CACEWH  201 (290)
T ss_dssp             CSSCTTTCCCEEEEEE-EC----CC-EEEEEETT--TCCEEE
T ss_pred             CCcCCCCCCcchhhee-eccCCCCC-ceEEECCC--CCCccc
Confidence            3579999998655433 21222233 58999988  999995

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.46  E-value=0.092  Score=27.68  Aligned_cols=29  Identities=17%  Similarity=0.260  Sum_probs=20.6

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      .++||.||+...++-.         .+--++|.+  ||..
T Consensus        11 ~~~Cp~Cgs~~ii~D~---------~~Ge~vC~~--CG~V   39 (58)
T d1dl6a_          11 RVTCPNHPDAILVEDY---------RAGDMICPE--CGLV   39 (58)
T ss_dssp             CCSBTTBSSSCCEECS---------SSCCEECTT--TCCE
T ss_pred             ccCCCCCCCCCEEEEC---------CCCcEeccc--CCCE
Confidence            4699999999866532         122478999  9974

>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Putative zinc binding domain
domain: Hypothetical UPF0222 protein MGC4549
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.79  E-value=1  Score=25.33  Aligned_cols=35  Identities=23%  Similarity=0.539  Sum_probs=26.0

Q ss_pred             eeeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCcee
Q psy8689          30 EEKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFRW   70 (72)
Q Consensus        30 ~~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~w   70 (72)
                      .+.||-|+|..++-..+- +.   ..+-...|..  ||-.+
T Consensus        23 ~F~CPfCnh~~sV~vk~d-kk---~~~g~l~C~v--Cg~~~   57 (85)
T d1wiia_          23 QFTCPFCNHEKSCDVKMD-RA---RNTGVISCTV--CLEEF   57 (85)
T ss_dssp             CCCCTTTCCSSCEEEEEE-TT---TTEEEEEESS--SCCEE
T ss_pred             eEcCCCCCCCCeEEEEEE-ec---CCEEEEEEec--CCCeE
Confidence            489999999999887654 22   2455677988  98765

>d1k81a_ g.59.1.1 (A:) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=80.63  E-value=1.3  Score=21.07  Aligned_cols=30  Identities=23%  Similarity=0.632  Sum_probs=21.8

Q ss_pred             eeCCCCCCCceEEEEeeccCCCCCceEEEEecCCCCCce
Q psy8689          31 EKCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIKCGFR   69 (72)
Q Consensus        31 ~~Cp~Cg~~~a~~~q~Q~rsadE~mTlfy~C~~~~Cg~~   69 (72)
                      +.|+.|++....... .      .=..|..|..  ||-+
T Consensus         1 V~C~~C~spDT~l~k-e------~R~~~l~C~a--CGa~   30 (36)
T d1k81a_           1 VICRECGKPDTKIIK-E------GRVHLLKCMA--CGAI   30 (36)
T ss_dssp             CCCSSSCSCEEEEEE-E------TTEEEEEEET--TTEE
T ss_pred             CCCCCCCCCCCEEEE-c------CCEEEEEecc--CCCC
Confidence            469999999876644 2      2367788988  9853