Citrus Sinensis ID: 033869

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110
Protein Sequence
MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE
Secondary Structure (PSIPRED)
ccccccccccccccccccccccEEEccccccEEEEcccEEEEEEccccccccccEEEccccccccccEEEccccccccEEEEEEcccccccccEEEEEccccccccEEcc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEEccccccEEEEEEccccEEEEccccEEEEEEEEcccccEcEEEccccccccccccccccccccccEEEEEEEEccccccccEEEEEccccccccccc
Coil and Loop (DISEMBL)
mefcptcgtmlqyelphmdrpsrfscpacpyvcnmesrvkikrkqplskkeiqpiftqdammegpqtevtcpackhgkAVYHElqtrsadepmSIFYMCANknckhrwne
Flexible Loop (DISEMBL)
MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESrvkikrkqplskkeiqPIFTQDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKnckhrwne
Low Complexity Region (SEG)
MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE
Disordered region (IsUnstruct)
***CPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVK***************************EVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCK*****
Disordered Region (DISOPRED)
MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM*********************TQDAMMEGPQTEVTCPACKHGKAVYHELQT***DEPMSIFYMCANKNCKHRW**
Disordered Region (DISEMBL)
MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE
Disordered Region (DISPRO)
MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCK*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE
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	110	2.2.26 [Sep-21-2011]
Q9Y2Y1	108	DNA-directed RNA polymera	yes	no	0.963	0.981	0.441	7e-17
Q9CQZ7	108	DNA-directed RNA polymera	yes	no	0.963	0.981	0.432	4e-16
Q2M2S7	108	DNA-directed RNA polymera	yes	no	0.972	0.990	0.409	4e-15
O13896	109	DNA-directed RNA polymera	yes	no	0.954	0.963	0.371	1e-12
Q04307	110	DNA-directed RNA polymera	yes	no	0.954	0.954	0.345	3e-10
Q56254	110	DNA-directed RNA polymera	N/A	no	0.927	0.927	0.348	2e-09
P36958	129	DNA-directed RNA polymera	no	no	0.981	0.837	0.333	2e-09
O27369	104	DNA-directed RNA polymera	yes	no	0.909	0.961	0.357	2e-08
Q58548	108	DNA-directed RNA polymera	yes	no	0.927	0.944	0.327	3e-08
Q07271	111	DNA-directed RNA polymera	yes	no	0.954	0.945	0.333	3e-08

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

 Score = 85.9 bits (211), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 49/111 (44%), Positives = 61/111 (54%), Gaps = 5/111 (4%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           + FCP CG  L  E     R  RFSC  CPYV N+  +V   RK P   KE+  +    A
Sbjct: 2   LLFCPGCGNGLIVE--EGQRCHRFSCNTCPYVHNITRKV-TNRKYP-KLKEVDDVLGGAA 57

Query: 61  MMEG-PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             E    T  +CP C+H +A + +LQTRSADEPM+ FY C N  C HRW +
Sbjct: 58  AWENVDSTAESCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD 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 = 83.6 bits (205), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 48/111 (43%), Positives = 60/111 (54%), Gaps = 5/111 (4%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           + FCP CG  L  E     R  RF+C  CPYV N+  +V   RK P   KE+  +    A
Sbjct: 2   LLFCPGCGNGLIVE--EGQRCHRFACNTCPYVHNITRKV-TNRKYP-KLKEVDDVLGGAA 57

Query: 61  MMEG-PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             E    T   CP C+H +A + +LQTRSADEPM+ FY C N  C HRW +
Sbjct: 58  AWENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD 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 = 80.1 bits (196), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 45/110 (40%), Positives = 57/110 (51%), Gaps = 3/110 (2%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           + FCP CG  L  E     R  RF+C  CPYV N+  +V   RK P  K+    +    A
Sbjct: 2   LLFCPGCGNGLIVE--EGQRCHRFACNTCPYVHNVTRKV-TNRKYPKLKEVDDELGGAAA 58

Query: 61  MMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
                 T   CP C+H +A + +LQTR ADEPM+ FY C N  C HRW +
Sbjct: 59  WENVDSTAEPCPKCEHPRAYFMQLQTRYADEPMTTFYKCCNAQCGHRWRD 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|O13896|RPC10_SCHPO DNA-directed RNA polymerase III subunit RPC10 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc11 PE=3 SV=1

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 42/113 (37%), Positives = 59/113 (52%), Gaps = 8/113 (7%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFT-QD 59
           M+FCPTCG  L   +    R + F C  CPY  +      +  +   ++KE+  +   ++
Sbjct: 1   MQFCPTCGNHLIVAVDEEGRNA-FDCRTCPY--HFPISTFLYSRHEFAQKEVDDVLGGEE 57

Query: 60  AMMEGPQTEVTC--PACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           A     QTEVTC    C + +A + +LQ RSADEPMS FY C    CK +W E
Sbjct: 58  AFESNQQTEVTCENTKCDNNRAYFFQLQIRSADEPMSTFYRCT--KCKFQWRE 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|Q04307|RPC10_YEAST DNA-directed RNA polymerase III subunit RPC10 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPC11 PE=1 SV=1

 Score = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 39/113 (34%), Positives = 56/113 (49%), Gaps = 8/113 (7%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           + FCP+C  ML          +  +C +CPY   +E  ++I  ++ L +KE+  +     
Sbjct: 2   LSFCPSCNNMLLITSGDSGVYT-LACRSCPYEFPIEG-IEIYDRKKLPRKEVDDVLGG-G 58

Query: 61  MMEGPQTEVTCP---ACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
                QT+  CP    C    A + +LQ RSADEPM+ FY C   NC HRW E
Sbjct: 59  WDNVDQTKTQCPNYDTCGGESAYFFQLQIRSADEPMTTFYKCV--NCGHRWKE 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|Q56254|RPOM_THECE DNA-directed RNA polymerase subunit M OS=Thermococcus celer GN=rpoM PE=1 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 39/112 (34%), Positives = 57/112 (50%), Gaps = 10/112 (8%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPY---VCNMESRVKIKRKQPLSKKEIQPIFT 57
           M+FCP CG ++   LP   R   + C +C Y       + R K   KQ +  K  + I  
Sbjct: 1   MKFCPKCGNLM---LPDRKRKV-WVCRSCGYEEPFDEEKDREKTVIKQEVKHKPDEGIVV 56

Query: 58  QDAMMEG-PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108
            +  ++  P T++TCP C +  A + E+QTR+ DEP +IFY C    C H W
Sbjct: 57  IEQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCT--KCGHTW 106

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

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

 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 38/114 (33%), Positives = 55/114 (48%), Gaps = 6/114 (5%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKE---IQPIFT 57
           + FC  C  ML  +    ++   ++C  C Y    +S      K      E   I P   
Sbjct: 18  IRFCQECNNMLYPKEDKENKILLYACRNCDYKQEADSNCIYVNKIMHEIDELTHIVPDVI 77

Query: 58  QDAMMEGPQTEV-TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
            D  +  P+TE   CP C H +AV+ + QTR A+E M ++Y+C N+NC HRW E
Sbjct: 78  SDPTL--PRTEDHACPKCSHREAVFFQAQTRRAEEEMRLYYVCTNQNCTHRWTE 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|O27369|RPOM_METTH DNA-directed RNA polymerase subunit M OS=Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) GN=rpoM PE=3 SV=2

 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/112 (35%), Positives = 56/112 (50%), Gaps = 12/112 (10%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRK--QPLSKKEIQPIFTQ 58
           MEFCP CG ++    P      +F C  C Y  ++  ++K K +  + +  KE   IFT 
Sbjct: 1   MEFCPKCGAVM---FPS---EGKFKC-QCGYEKDITDKLKDKYRVSEEVEAKET-IIFTG 52

Query: 59  DAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           D +   P T V CP C + +A +   QTR ADE  + F+ C    CKH W E
Sbjct: 53  DDVNTLPTTRVECPKCGNMEAFWWLQQTRRADESETRFFRCT--RCKHTWRE 102

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

Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (taxid: 187420)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>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 = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 37/113 (32%), Positives = 54/113 (47%), Gaps = 11/113 (9%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV--CNMESRVKIKRKQPL-SKKEIQPIFT 57
           ++FCP C  ++   LP   +  +  C  C Y      E   + + K+ L +KKE   +  
Sbjct: 2   VKFCPKCNNLM---LP---KDGKLKCAVCGYEEETTAEGSKEYEYKEHLENKKEKITVIE 55

Query: 58  QDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
            + +   P T + CP C H +A +   QTR ADEP + FY C  K C H W E
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 = 57.4 bits (137), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 38/114 (33%), Positives = 55/114 (48%), Gaps = 9/114 (7%)

Query: 1   MEFCPTCGTMLQYELPHMDRP-SRFSCPACPYV-CNMESRVKIKRKQPLSKKEIQPIFTQ 58
           M+FCP CG+M+   +P  +   + + C  C Y+    +   KI      S KE   +   
Sbjct: 1   MKFCPKCGSMM---MPRKENGKTVYKCSKCGYIDTENQKEAKITTVIKHSAKEKTLVLES 57

Query: 59  DAMMEGPQTE--VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           D    G Q    ++CP+C + +A +  LQTRSADEP + FY C    C   W E
Sbjct: 58  DMPKTGVQLTRGISCPSCGNDEAYFWILQTRSADEPATRFYKCT--KCGKVWRE 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

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	110
297745506	175	unnamed protein product [Vitis vinifera]	1.0	0.628	0.681	1e-40
225470966	111	PREDICTED: DNA-directed RNA polymerase I	1.0	0.990	0.681	1e-39
356567921	111	PREDICTED: DNA-directed RNA polymerase I	1.0	0.990	0.654	2e-38
351725003	111	uncharacterized protein LOC100527062 [Gl	1.0	0.990	0.645	1e-36
449446776	111	PREDICTED: DNA-directed RNA polymerase I	1.0	0.990	0.6	8e-34
255565039	112	DNA-directed RNA polymerase III, putativ	1.0	0.982	0.603	1e-33
449489530	112	PREDICTED: DNA-directed RNA polymerase I	1.0	0.982	0.594	2e-32
388510306	111	unknown [Lotus japonicus]	1.0	0.990	0.581	5e-32
224120828	112	predicted protein [Populus trichocarpa]	1.0	0.982	0.558	6e-31
294462028	110	unknown [Picea sitchensis]	0.981	0.981	0.504	1e-23

>gi|297745506|emb|CBI40586.3| unnamed protein product [Vitis vinifera]

 Score =  170 bits (430), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 75/110 (68%), Positives = 88/110 (80%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           MEFCPTCG  LQYELPHM RP+RF CP CPYVC++E++VKIKRKQ L KKEI+PIF++D 
Sbjct: 65  MEFCPTCGNFLQYELPHMGRPARFFCPTCPYVCHIETKVKIKRKQRLVKKEIEPIFSKDD 124

Query: 61  MMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           M  GP T+ TCP C  GKAV+ +LQTRSADEPMS FY C N+NC  +W E
Sbjct: 125 MKNGPTTDATCPHCNFGKAVFQQLQTRSADEPMSTFYWCLNENCGRQWRE 174

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225470966|ref|XP_002267122.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC10-like [Vitis vinifera]

 Score =  167 bits (422), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 75/110 (68%), Positives = 88/110 (80%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           MEFCPTCG  LQYELPHM RP+RF CP CPYVC++E++VKIKRKQ L KKEI+PIF++D 
Sbjct: 1   MEFCPTCGNFLQYELPHMGRPARFFCPTCPYVCHIETKVKIKRKQRLVKKEIEPIFSKDD 60

Query: 61  MMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           M  GP T+ TCP C  GKAV+ +LQTRSADEPMS FY C N+NC  +W E
Sbjct: 61  MKNGPTTDATCPHCNFGKAVFQQLQTRSADEPMSTFYWCLNENCGRQWRE 110

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356567921|ref|XP_003552163.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC10-like [Glycine max]

 Score =  162 bits (410), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 72/110 (65%), Positives = 87/110 (79%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           MEFCP+CG MLQYELP+M RPSRF C ACPYVC++E+RV+IKRKQ L +KEI+PIF++D 
Sbjct: 1   MEFCPSCGNMLQYELPYMGRPSRFFCSACPYVCHIENRVEIKRKQRLVRKEIEPIFSEDD 60

Query: 61  MMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           M   P TE TCP C HGKA + E QTRSADEP ++FY C N +CK +W E
Sbjct: 61  MTNAPSTEATCPFCGHGKAAFKEFQTRSADEPATLFYKCLNNDCKKQWRE 110

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725003|ref|NP_001238101.1| uncharacterized protein LOC100527062 [Glycine max] gi|255631470|gb|ACU16102.1| unknown [Glycine max]

 Score =  157 bits (396), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 71/110 (64%), Positives = 82/110 (74%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           MEFCPTCG MLQYELP+M RPSRF C ACPYVC +E+RV+IKRKQ L  KEI+PIF++D 
Sbjct: 1   MEFCPTCGNMLQYELPYMGRPSRFFCSACPYVCLIENRVEIKRKQRLVSKEIEPIFSEDD 60

Query: 61  MMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           M     TE TCP C HGKA + E QTRSAD P ++FY C N  CK +W E
Sbjct: 61  MTNAASTEATCPFCGHGKAAFKEFQTRSADGPATLFYKCLNNECKKQWRE 110

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446776|ref|XP_004141147.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC10-like [Cucumis sativus]

 Score =  147 bits (371), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 66/110 (60%), Positives = 80/110 (72%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           MEFCPTCG MLQ+ELP+M + SRF CP CPYV  +E+RVKIKRKQ L KKE++PI + D 
Sbjct: 1   MEFCPTCGNMLQFELPNMGKSSRFFCPTCPYVSYLENRVKIKRKQHLVKKELEPIISDDD 60

Query: 61  MMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           M    QTE TCP C  GKA + ++Q RSADEP + FY C N+NC+  W E
Sbjct: 61  MKNAAQTEATCPNCAFGKAAFIQIQLRSADEPATTFYKCMNENCRQNWRE 110

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255565039|ref|XP_002523512.1| DNA-directed RNA polymerase III, putative [Ricinus communis] gi|223537219|gb|EEF38851.1| DNA-directed RNA polymerase III, putative [Ricinus communis]

 Score =  146 bits (369), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 67/111 (60%), Positives = 82/111 (73%), Gaps = 1/111 (0%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           MEFCPTCG +L+YELP+M + +RF C  CPYVC++ESRVKIKRKQ L KKEI+P+FT D 
Sbjct: 1   MEFCPTCGVLLRYELPNMGQSARFYCSTCPYVCSIESRVKIKRKQQLIKKEIEPVFTLDD 60

Query: 61  MME-GPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           MM+ G +TE TCP C  G+A +  LQ RSADEP + FY C N+ C   W E
Sbjct: 61  MMKGGSETEATCPHCNFGRARFQSLQIRSADEPATTFYFCLNEKCSRVWRE 111

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449489530|ref|XP_004158339.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC10-like [Cucumis sativus]

 Score =  142 bits (358), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 66/111 (59%), Positives = 80/111 (72%), Gaps = 1/111 (0%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRV-KIKRKQPLSKKEIQPIFTQD 59
           MEFCPTCG MLQ+ELP+M + SRF CP CPYV  +E+RV KIKRKQ L KKE++PI + D
Sbjct: 1   MEFCPTCGNMLQFELPNMGKSSRFFCPTCPYVSYLENRVCKIKRKQHLVKKELEPIISDD 60

Query: 60  AMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
            M    QTE TCP C  GKA + ++Q RSADEP + FY C N+NC+  W E
Sbjct: 61  DMKNAAQTEATCPNCAFGKAAFIQIQLRSADEPATTFYKCMNENCRQNWRE 111

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388510306|gb|AFK43219.1| unknown [Lotus japonicus]

 Score =  141 bits (355), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 64/110 (58%), Positives = 77/110 (70%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
           MEFCP+C  ML++ELP+M   SR  C  CPYVC +E  VKIKRKQ L +KEI P+ + D 
Sbjct: 1   MEFCPSCSNMLKFELPNMGHNSRLFCQTCPYVCYIEKGVKIKRKQRLVRKEIDPVISYDD 60

Query: 61  MMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           M  GP TEV CP C H KA Y E+Q RSADEP +IFY C N+ C+H+W E
Sbjct: 61  MKNGPTTEVRCPNCSHDKAAYTEMQIRSADEPATIFYWCLNEKCRHQWRE 110

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224120828|ref|XP_002318427.1| predicted protein [Populus trichocarpa] gi|222859100|gb|EEE96647.1| predicted protein [Populus trichocarpa]

 Score =  137 bits (346), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 62/111 (55%), Positives = 80/111 (72%), Gaps = 1/111 (0%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFT-QD 59
           MEFCPTCG +L+YE P+M + +RF CP CPY  ++ESRVKIKRKQ L+KKEI+PIFT +D
Sbjct: 1   MEFCPTCGMLLRYETPNMGQAARFYCPTCPYFASIESRVKIKRKQKLAKKEIEPIFTLED 60

Query: 60  AMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
               G +T+ TCP C  G+A + ++Q RSADEP + FY C N+ C   W E
Sbjct: 61  MKTGGAETDATCPHCNFGRACFQQIQIRSADEPATTFYFCLNEKCGRMWRE 111

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|294462028|gb|ADE76569.1| unknown [Picea sitchensis]

 Score =  113 bits (283), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 56/111 (50%), Positives = 71/111 (63%), Gaps = 3/111 (2%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFT-QD 59
           MEFCPTCG +LQ E P+M +  RF CP CPYV  +E   KI +K  L KKE+  +F  ++
Sbjct: 1   MEFCPTCGNLLQIEHPYMSQSLRFFCPTCPYVFPIER--KISKKLQLKKKEVDDVFGGEE 58

Query: 60  AMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           A     +TE TCP C  GKA + ++Q RSADEPMS FY C N  C+ RW +
Sbjct: 59  AWKNVDRTEATCPKCSFGKAFFMQIQIRSADEPMSTFYKCCNNQCQFRWRQ 109

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	110
TAIR|locus:2120527	106	AT4G07950 [Arabidopsis thalian	0.954	0.990	0.509	1.1e-25
TAIR|locus:2035322	106	AT1G01210 [Arabidopsis thalian	0.954	0.990	0.472	3.8e-23
WB|WBGene00022309	108	rpc-11 [Caenorhabditis elegans	0.963	0.981	0.459	4.3e-22
ZFIN|ZDB-GENE-040718-291	108	polr3k "polymerase (RNA) III (	0.945	0.962	0.440	5.7e-20
UNIPROTKB|Q9Y2Y1	108	POLR3K "DNA-directed RNA polym	0.945	0.962	0.449	1.5e-19
UNIPROTKB|E2QZU0	108	POLR3K "DNA-directed RNA polym	0.945	0.962	0.440	3.1e-19
UNIPROTKB|F1N3E8	108	POLR3K "DNA-directed RNA polym	0.945	0.962	0.440	5.1e-19
UNIPROTKB|F2Z4X7	108	POLR3K "DNA-directed RNA polym	0.945	0.962	0.440	5.1e-19
MGI|MGI:1914255	108	Polr3k "polymerase (RNA) III (	0.945	0.962	0.440	5.1e-19
UNIPROTKB|Q5FVH1	108	Polr3k "DNA-directed RNA polym	0.945	0.962	0.440	5.1e-19

TAIR|locus:2120527 AT4G07950 [Arabidopsis thaliana (taxid:3702)]

 Score = 291 (107.5 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 56/110 (50%), Positives = 69/110 (62%)

Query:     1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
             MEFCPTCG +L+YE       SRF C  CPYV N+E RV+IK+KQ L KK I+P+ T+D 
Sbjct:     1 MEFCPTCGNLLRYE---GGGSSRFFCSTCPYVANIERRVEIKKKQLLVKKSIEPVVTKDD 57

Query:    61 MMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             +    +TE  CP C H KA +  +Q RSADEP S FY C    C+  W E
Sbjct:    58 IPTAAETEAPCPRCGHDKAYFKSMQIRSADEPESRFYRCLK--CEFTWRE 105

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;ISS;IDA

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

GO:0006354 "DNA-dependent transcription, elongation" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

TAIR|locus:2035322 AT1G01210 [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 3.8e-23, P = 3.8e-23
 Identities = 52/110 (47%), Positives = 67/110 (60%)

Query:     1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
             MEFCPTCG +L+YE       SRF C  CPYV  ++ +V+IK+KQ L KK I+ + T+D 
Sbjct:     1 MEFCPTCGNLLRYE---GGGNSRFFCSTCPYVAYIQRQVEIKKKQLLVKKSIEAVVTKDD 57

Query:    61 MMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             +    +TE  CP C H KA +  +Q RSADEP S FY C    C+  W E
Sbjct:    58 IPTAAETEAPCPRCGHDKAYFKSMQIRSADEPESRFYRCLK--CEFTWRE 105

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;ISS

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

GO:0006354 "DNA-dependent transcription, elongation" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

WB|WBGene00022309 rpc-11 [Caenorhabditis elegans (taxid:6239)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 51/111 (45%), Positives = 65/111 (58%)

Query:     1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
             + FCP CG +LQ E    ++  RFSCPACPYVC +   V   R  P   K+I  +     
Sbjct:     2 LTFCPECGCVLQIESG--EQCMRFSCPACPYVCPVTQTVT-SRIYP-KLKDIDDVLGGPG 57

Query:    61 MMEGPQ-TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
                  Q T+ TCP C HG+A + +LQTRSADEP +IFY CA+  C HRW +
Sbjct:    58 AWANAQVTDETCPVCSHGRAYFMQLQTRSADEPSTIFYRCADNACAHRWKD 108

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

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

 Score = 237 (88.5 bits), Expect = 5.7e-20, P = 5.7e-20
 Identities = 48/109 (44%), Positives = 61/109 (55%)

Query:     3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMM 62
             FCPTCG +L  E     R  RF+C  CPYV N+  +V   RK P   KE+  +    A  
Sbjct:     4 FCPTCGNVLIVE--EGQRCFRFACNTCPYVHNITRKVN-NRKYP-KLKEVDDVLGGSAAW 59

Query:    63 EG-PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             E    T   CP C+H +A + ++QTRSADEPM+ FY C N  C HRW +
Sbjct:    60 ENVDSTAEPCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIQCGHRWRD 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|Q9Y2Y1 POLR3K "DNA-directed RNA polymerase III subunit RPC10" [Homo sapiens (taxid:9606)]

 Score = 233 (87.1 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 49/109 (44%), Positives = 60/109 (55%)

Query:     3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMM 62
             FCP CG  L  E     R  RFSC  CPYV N+  +V   RK P   KE+  +    A  
Sbjct:     4 FCPGCGNGLIVE--EGQRCHRFSCNTCPYVHNITRKVT-NRKYP-KLKEVDDVLGGAAAW 59

Query:    63 EG-PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             E    T  +CP C+H +A + +LQTRSADEPM+ FY C N  C HRW +
Sbjct:    60 ENVDSTAESCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD 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|E2QZU0 POLR3K "DNA-directed RNA polymerase subunit" [Canis lupus familiaris (taxid:9615)]

 Score = 230 (86.0 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 48/109 (44%), Positives = 60/109 (55%)

Query:     3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMM 62
             FCP CG  L  E     R  RF+C  CPYV N+  +V   RK P   KE+  +    A  
Sbjct:     4 FCPGCGNGLIVE--EGQRCHRFACNTCPYVHNITRKVT-NRKYP-KLKEVDDVLGGAAAW 59

Query:    63 EG-PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             E    T  +CP C+H +A + +LQTRSADEPM+ FY C N  C HRW +
Sbjct:    60 ENVDSTAESCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD 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|F1N3E8 POLR3K "DNA-directed RNA polymerase subunit" [Bos taurus (taxid:9913)]

 Score = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 48/109 (44%), Positives = 59/109 (54%)

Query:     3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMM 62
             FCP CG  L  E     R  RF+C  CPYV N+  +V   RK P   KE+  +    A  
Sbjct:     4 FCPGCGNGLIVE--EGQRCHRFACNTCPYVHNVTRKVT-NRKYP-KLKEVDDVLGGAAAW 59

Query:    63 EG-PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             E    T   CP C+H +A + +LQTRSADEPM+ FY C N  C HRW +
Sbjct:    60 ENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD 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 = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 48/109 (44%), Positives = 59/109 (54%)

Query:     3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMM 62
             FCP CG  L  E     R  RF+C  CPYV N+  +V   RK P   KE+  +    A  
Sbjct:     4 FCPGCGNGLIVE--EGQRCHRFACNTCPYVHNITRKVT-NRKYP-KLKEVDDVLGGAAAW 59

Query:    63 EG-PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             E    T   CP C+H +A + +LQTRSADEPM+ FY C N  C HRW +
Sbjct:    60 ENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD 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 = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 48/109 (44%), Positives = 59/109 (54%)

Query:     3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMM 62
             FCP CG  L  E     R  RF+C  CPYV N+  +V   RK P   KE+  +    A  
Sbjct:     4 FCPGCGNGLIVE--EGQRCHRFACNTCPYVHNITRKVT-NRKYP-KLKEVDDVLGGAAAW 59

Query:    63 EG-PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             E    T   CP C+H +A + +LQTRSADEPM+ FY C N  C HRW +
Sbjct:    60 ENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD 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 = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 48/109 (44%), Positives = 59/109 (54%)

Query:     3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMM 62
             FCP CG  L  E     R  RF+C  CPYV N+  +V   RK P   KE+  +    A  
Sbjct:     4 FCPGCGNGLIVE--EGQRCHRFACNTCPYVHNITRKVT-NRKYP-KLKEVDDVLGGAAAW 59

Query:    63 EG-PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             E    T   CP C+H +A + +LQTRSADEPM+ FY C N  C HRW +
Sbjct:    60 ENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD 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

---

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	0.3451	0.9545	0.9545	yes	no
Q2M2S7	RPC10_BOVIN	No assigned EC number	0.4090	0.9727	0.9907	yes	no
Q07271	RPOM_SULAC	2, ., 7, ., 7, ., 6	0.3333	0.9545	0.9459	yes	no
Q58548	RPOM_METJA	2, ., 7, ., 7, ., 6	0.3274	0.9272	0.9444	yes	no
O27369	RPOM_METTH	2, ., 7, ., 7, ., 6	0.3571	0.9090	0.9615	yes	no
Q9CQZ7	RPC10_MOUSE	No assigned EC number	0.4324	0.9636	0.9814	yes	no
O13896	RPC10_SCHPO	No assigned EC number	0.3716	0.9545	0.9633	yes	no
Q9Y2Y1	RPC10_HUMAN	No assigned EC number	0.4414	0.9636	0.9814	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	110
COG1594	113	COG1594, RPB9, DNA-directed RNA polymerase, subuni	3e-20
TIGR01384	104	TIGR01384, TFS_arch, transcription factor S, archa	1e-17
pfam01096	39	pfam01096, TFIIS_C, Transcription factor S-II (TFI	3e-14
smart00440	40	smart00440, ZnF_C2C2, C2C2 Zinc finger	4e-12
TIGR01385	299	TIGR01385, TFSII, transcription elongation factor	2e-09
smart00661	52	smart00661, RPOL9, RNA polymerase subunit 9	2e-06
PHA02998	195	PHA02998, PHA02998, RNA polymerase subunit; Provis	3e-04

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

 Score = 78.3 bits (193), Expect = 3e-20
 Identities = 32/115 (27%), Positives = 47/115 (40%), Gaps = 9/115 (7%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV-----CNMESRVKIKRKQPLSKKEIQPI 55
           M FCP CG++L  +        +  C  C Y        +      +  +   +  +   
Sbjct: 2   MRFCPKCGSLLYPKKDDEGG--KLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVLVVE 59

Query: 56  FTQDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
                    P  +  CP C + +A Y +LQTRSADEP + FY C    C +RW E
Sbjct: 60  DETQGAKTLPTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKC--TRCGYRWRE 112

Length = 113

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

 Score = 71.4 bits (175), Expect = 1e-17
 Identities = 38/111 (34%), Positives = 51/111 (45%), Gaps = 11/111 (9%)

Query: 2   EFCPTCGTMLQYELPHMDRPSRFSCPACPY--VCNMESRVKIKRKQPLSKKEIQPIFTQD 59
           +FCP CG+++        +   + CP+C Y      E   K+  K     KE   I  ++
Sbjct: 1   KFCPKCGSLM------TPKNGVYVCPSCGYEKEKKPEDDYKVTEKVKHKIKETI-IIREE 53

Query: 60  AMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
                P T V CP C H +A Y  LQTR ADEP + FY C    C + W E
Sbjct: 54  DSETLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKC--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|201594 pfam01096, TFIIS_C, Transcription factor S-II (TFIIS)

 Score = 60.7 bits (148), Expect = 3e-14
 Identities = 23/40 (57%), Positives = 30/40 (75%), Gaps = 2/40 (5%)

Query: 69  VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108
           + CP C H +AV+ +LQTRSADEPM++FY+C    C HRW
Sbjct: 1   IKCPKCGHREAVFFQLQTRSADEPMTLFYVC--TKCGHRW 38

Length = 39

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

 Score = 55.8 bits (135), Expect = 4e-12
 Identities = 21/42 (50%), Positives = 29/42 (69%), Gaps = 2/42 (4%)

Query: 69  VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             CP C + +A +++LQTRSADEPM++FY+C    C H W E
Sbjct: 1   AECPKCGNREATFYQLQTRSADEPMTVFYVC--TKCGHHWRE 40

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

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

 Score = 52.5 bits (126), Expect = 2e-09
 Identities = 27/69 (39%), Positives = 40/69 (57%), Gaps = 4/69 (5%)

Query: 42  KRKQPLSKKEIQPIF-TQDAMMEGPQTEV-TCPACKHGKAVYHELQTRSADEPMSIFYMC 99
           + KQ   +   + +F  Q A ++   T++ TC  CK  K  Y++LQTRSADEPM+ F  C
Sbjct: 230 ELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTC 289

Query: 100 ANKNCKHRW 108
             + C +RW
Sbjct: 290 --EECGNRW 296

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|197822 smart00661, RPOL9, RNA polymerase subunit 9

 Score = 41.2 bits (97), Expect = 2e-06
 Identities = 18/50 (36%), Positives = 20/50 (40%), Gaps = 2/50 (4%)

Query: 2  EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKE 51
          +FCP CG ML           RF C  C Y    E +   K K   SK E
Sbjct: 1  KFCPKCGNMLYPR--EGKEKRRFVCRKCGYEEPAEQKYVYKEKLKHSKDE 48

Length = 52

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

 Score = 37.4 bits (87), Expect = 3e-04
 Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%)

Query: 71  CPACKHGKAVYHELQTRSADEPMSIFYMCANKNCK 105
           CP CK        +QTR+ADEP  + + C  ++CK
Sbjct: 146 CPNCKSKNTTPMMIQTRAADEPPLVRHAC--RDCK 178

Length = 195

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	110
KOG2906	105	consensus RNA polymerase III subunit C11 [Transcri	100.0
KOG2691	113	consensus RNA polymerase II subunit 9 [Transcripti	100.0
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	100.0
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	100.0
KOG2907	116	consensus RNA polymerase I transcription factor TF	99.97
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	99.93
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	99.92
PHA02998	195	RNA polymerase subunit; Provisional	99.84
TIGR01385	299	TFSII transcription elongation factor S-II. This m	99.71
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	99.51
smart00661	52	RPOL9 RNA polymerase subunit 9.	99.14
KOG1105	296	consensus Transcription elongation factor TFIIS/Co	98.97
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	98.46
PRK00432	50	30S ribosomal protein S27ae; Validated	98.18
PF04606	47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	97.58
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	97.35
PRK09678	72	DNA-binding transcriptional regulator; Provisional	97.31
PHA00626	59	hypothetical protein	96.85
PF13248	26	zf-ribbon_3: zinc-ribbon domain	96.7
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	96.63
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	96.57
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	96.56
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	96.4
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	96.39
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	96.24
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	96.21
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	96.18
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	95.9
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	95.88
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	95.87
PHA00626	59	hypothetical protein	95.8
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	95.8
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	95.76
COG1773	55	Rubredoxin [Energy production and conversion]	95.74
cd00730	50	rubredoxin Rubredoxin; nonheme iron binding domain	95.66
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	95.53
PF00301	47	Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubred	95.48
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	95.47
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	95.41
PF12773	50	DZR: Double zinc ribbon	95.38
PF14353	128	CpXC: CpXC protein	95.17
COG3478	68	Predicted nucleic-acid-binding protein containing	95.09
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	94.97
PRK14973	936	DNA topoisomerase I; Provisional	94.8
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	94.7
TIGR00244	147	transcriptional regulator NrdR. Members of this al	94.62
KOG3084	345	consensus NADH pyrophosphatase I of the Nudix fami	94.61
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	94.59
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	94.49
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	94.45
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	94.34
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	94.24
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.15
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	94.12
COG2816	279	NPY1 NTP pyrophosphohydrolases containing a Zn-fin	94.09
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	94.07
smart00661	52	RPOL9 RNA polymerase subunit 9.	94.06
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	94.04
TIGR00595	505	priA primosomal protein N'. All proteins in this f	94.02
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	93.83
PRK00241	256	nudC NADH pyrophosphatase; Reviewed	93.79
PRK07220	740	DNA topoisomerase I; Validated	93.63
PRK09678	72	DNA-binding transcriptional regulator; Provisional	93.63
PF10058	54	DUF2296: Predicted integral membrane metal-binding	93.62
PF04606	47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	93.6
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	93.56
PF09151	36	DUF1936: Domain of unknown function (DUF1936); Int	93.56
PRK07219	822	DNA topoisomerase I; Validated	93.54
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	93.46
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	93.44
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	93.43
COG1779	201	C4-type Zn-finger protein [General function predic	93.39
PRK10220	111	hypothetical protein; Provisional	93.37
COG4332	203	Uncharacterized protein conserved in bacteria [Fun	93.29
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	93.25
PRK07219	822	DNA topoisomerase I; Validated	93.15
COG2023	105	RPR2 RNase P subunit RPR2 [Translation, ribosomal	92.97
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	92.85
TIGR00340	163	zpr1_rel ZPR1-related zinc finger protein. A model	92.79
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	92.78
PRK14559	645	putative protein serine/threonine phosphatase; Pro	92.71
PF14353	128	CpXC: CpXC protein	92.58
PRK14892	99	putative transcription elongation factor Elf1; Pro	92.55
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	92.45
smart00647	64	IBR In Between Ring fingers. the domains occurs be	92.37
PRK14714	1337	DNA polymerase II large subunit; Provisional	92.1
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	91.83
PRK05580	679	primosome assembly protein PriA; Validated	91.66
PF11781	36	RRN7: RNA polymerase I-specific transcription init	91.65
PRK04023	1121	DNA polymerase II large subunit; Validated	91.62
COG1327	156	Predicted transcriptional regulator, consists of a	91.52
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	91.48
PF12773	50	DZR: Double zinc ribbon	91.37
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	91.22
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	91.15
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	91.1
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	91.07
PRK14873	665	primosome assembly protein PriA; Provisional	90.94
COG1592	166	Rubrerythrin [Energy production and conversion]	90.87
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	90.78
PF09526	71	DUF2387: Probable metal-binding protein (DUF2387);	90.57
COG0551	140	TopA Zn-finger domain associated with topoisomeras	90.53
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	90.53
PRK00420	112	hypothetical protein; Validated	90.46
KOG2907	116	consensus RNA polymerase I transcription factor TF	90.18
TIGR02443	59	conserved hypothetical metal-binding protein. Memb	90.13
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	89.92
PF07295	146	DUF1451: Protein of unknown function (DUF1451); In	89.89
smart00709	160	Zpr1 Duplicated domain in the epidermal growth fac	89.81
PF13408	58	Zn_ribbon_recom: Recombinase zinc beta ribbon doma	89.63
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	89.52
PF06827	30	zf-FPG_IleRS: Zinc finger found in FPG and IleRS;	89.4
TIGR00515	285	accD acetyl-CoA carboxylase, carboxyl transferase,	89.34
COG4640	465	Predicted membrane protein [Function unknown]	89.27
PRK05452	479	anaerobic nitric oxide reductase flavorubredoxin;	89.21
CHL00174	296	accD acetyl-CoA carboxylase beta subunit; Reviewed	89.11
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	89.08
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	88.99
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	88.9
COG0777	294	AccD Acetyl-CoA carboxylase beta subunit [Lipid me	88.83
PF10058	54	DUF2296: Predicted integral membrane metal-binding	88.54
TIGR01031	55	rpmF_bact ribosomal protein L32. This protein desc	88.53
PF11792	43	Baculo_LEF5_C: Baculoviridae late expression facto	88.35
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	88.34
PF12172	37	DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35	88.3
PF04032	85	Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; Inte	88.26
PF08772	73	NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon lik	88.19
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	87.92
KOG3507	62	consensus DNA-directed RNA polymerase, subunit RPB	87.9
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	87.76
PRK05654	292	acetyl-CoA carboxylase subunit beta; Validated	87.52
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	87.41
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	87.28
PRK11032	160	hypothetical protein; Provisional	87.09
COG0675	364	Transposase and inactivated derivatives [DNA repli	87.08
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	86.83
PF14205	55	Cys_rich_KTR: Cysteine-rich KTR	86.2
COG1326	201	Uncharacterized archaeal Zn-finger protein [Genera	85.93
PHA02942	383	putative transposase; Provisional	85.82
PF01780	90	Ribosomal_L37ae: Ribosomal L37ae protein family; I	85.6
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	85.16
TIGR00310	192	ZPR1_znf ZPR1 zinc finger domain.	85.01
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	84.89
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	84.87
PF09082	68	DUF1922: Domain of unknown function (DUF1922); Int	84.66
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	84.65
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	84.54
PF09986	214	DUF2225: Uncharacterized protein conserved in bact	84.53
PRK11827	60	hypothetical protein; Provisional	84.45
TIGR00311	133	aIF-2beta translation initiation factor aIF-2, bet	83.77
COG3809	88	Uncharacterized protein conserved in bacteria [Fun	83.68
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	83.61
PF04810	40	zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro:	83.27
PRK04136	48	rpl40e 50S ribosomal protein L40e; Provisional	82.95
PRK03988	138	translation initiation factor IF-2 subunit beta; V	82.79
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	82.38
COG2176	1444	PolC DNA polymerase III, alpha subunit (gram-posit	82.33
PF06839	45	zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc	82.11
PRK05582	650	DNA topoisomerase I; Validated	82.11
PF03367	161	zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004	81.8
PF01783	56	Ribosomal_L32p: Ribosomal L32p protein family; Int	81.67
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	81.62
PF01599	47	Ribosomal_S27: Ribosomal protein S27a; InterPro: I	81.5
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	81.23
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	81.22
COG1571	421	Predicted DNA-binding protein containing a Zn-ribb	81.17
COG1545	140	Predicted nucleic-acid-binding protein containing	81.14
PF06044	254	DRP: Dam-replacing family; InterPro: IPR010324 Dam	81.12
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	80.84
PHA02998	195	RNA polymerase subunit; Provisional	80.56
PRK03954	121	ribonuclease P protein component 4; Validated	80.11
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	80.03

>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]

Probab=100.00  E-value=1.5e-46  Score=236.93  Aligned_cols=104  Identities=49%  Similarity=0.940  Sum_probs=97.8

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCce
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKA   79 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a   79 (110)
                      |.|||.|||||.++  ++....+|.|++|+|..++..  .|.++..+..|++++|++++.+|+ .+.+++.||+|||++|
T Consensus         1 m~FCP~Cgn~Live--~g~~~~rf~C~tCpY~~~I~~--ei~~r~~~~~Kevd~vlgg~~a~~nv~~t~~~Cp~Cgh~ra   76 (105)
T KOG2906|consen    1 MLFCPTCGNMLIVE--SGESCNRFSCRTCPYVFPISR--EISSRKYPKLKEVDDVLGGDEAWENVDQTEATCPTCGHERA   76 (105)
T ss_pred             CcccCCCCCEEEEe--cCCeEeeEEcCCCCceeeEee--eeeccccCchhhhhhhcCCcccccchhhccCcCCCCCCCce
Confidence            89999999999999  555578999999999999987  788888889999999999988898 8899999999999999


Q ss_pred             EEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           80 VYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        80 ~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      +|+|+|+||||||||+||.|++  |+|+|||
T Consensus        77 yF~qlQtRSADEPmT~FYkC~~--C~~~Wre  105 (105)
T KOG2906|consen   77 YFMQLQTRSADEPMTTFYKCCK--CKHRWRE  105 (105)
T ss_pred             EEEEeeeccCCCcHhHhhhhhc--ccccccC
Confidence            9999999999999999999999  9999997

>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]

Probab=100.00  E-value=2.9e-41  Score=216.02  Aligned_cols=108  Identities=34%  Similarity=0.682  Sum_probs=94.0

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCC-CcccCCCCCCCc
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQ-TEVTCPACKHGK   78 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~-~~~~CpkCg~~~   78 (110)
                      ++||++|||||||+||+.++.+.|+||+|.|++.++++...+.....+.++.+.++.+...+| +|+ .++.||+|||++
T Consensus         4 ~rfC~eCNNmLYPkEDked~~L~laCrnCd~ve~A~s~~vY~~~~~~e~dE~t~ii~Dl~~DPTLPrts~~~C~~C~~~e   83 (113)
T KOG2691|consen    4 IRFCRECNNMLYPKEDKEDRILLLACRNCDYVEEADSSRVYVNELSHEHDELTQIIMDLASDPTLPRTSDKHCPKCGHRE   83 (113)
T ss_pred             cchhhhhhccccccccccccEEEEEecCCcceEecCCcceEcCCcccchhhHHHHHHhhccCCCcCccccccCCccCCcc
Confidence            589999999999999999999999999999999999943333334445567666665556678 998 589999999999


Q ss_pred             eEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           79 AVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        79 a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      |+|||.|+|.||++|++||+|++  |+|+|+|
T Consensus        84 avffQ~~~~r~d~~m~l~yvC~~--C~h~wte  113 (113)
T KOG2691|consen   84 AVFFQAQTRRADEAMRLFYVCCS--CGHRWTE  113 (113)
T ss_pred             eEEEecccccccceEEEEEEecc--ccccccC
Confidence            99999999999999999999999  9999986

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

Probab=100.00  E-value=7.4e-39  Score=210.38  Aligned_cols=104  Identities=35%  Similarity=0.726  Sum_probs=78.1

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEeccc----C-ccccccccc-cccccC-CCCCcccCCC
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPL----S-KKEIQPIFT-QDAMME-GPQTEVTCPA   73 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~----~-~~~~~~~~~-~~~~~~-~~~~~~~Cpk   73 (110)
                      |+|||+|||||+|+  ++..+..++|++|||..++...  .+++...    . .+.+..+.. .....+ +++..+.||+
T Consensus         2 m~FCp~Cgsll~p~--~~~~~~~l~C~kCgye~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cpk   77 (113)
T COG1594           2 MRFCPKCGSLLYPK--KDDEGGKLVCRKCGYEEEASNK--KVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPK   77 (113)
T ss_pred             ccccCCccCeeEEe--EcCCCcEEECCCCCcchhcccc--ceeEEEEeeccCCcceeeeeecccccCccccccccccCCC
Confidence            89999999999999  4333559999999999999872  2222221    1 111111111 111223 5566889999


Q ss_pred             CCCCceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           74 CKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        74 Cg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      ||+++|+|||+|+||||||||+||+|++  |||+||+
T Consensus        78 Cg~~ea~y~~~QtRsaDEp~T~Fy~C~~--Cg~~wre  112 (113)
T COG1594          78 CGNKEAYYWQLQTRSADEPETRFYKCTR--CGYRWRE  112 (113)
T ss_pred             CCCceeEEEeeehhccCCCceEEEEecc--cCCEeec
Confidence            9999999999999999999999999999  9999996

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=100.00  E-value=1e-38  Score=206.81  Aligned_cols=101  Identities=36%  Similarity=0.755  Sum_probs=80.1

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceE
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAV   80 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~   80 (110)
                      .|||+||+||++.  .    ..+.|+.|+|.+.......++++..++.+..++++..++..+ +|++++.||+|||++|+
T Consensus         1 ~fC~~Cg~~l~~~--~----~~~~C~~C~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a~   74 (104)
T TIGR01384         1 KFCPKCGSLMTPK--N----GVYVCPSCGYEKEKKPEDDYKVTEKVKHKIKETIIIREEDSETLPTTRVECPKCGHKEAY   74 (104)
T ss_pred             CCCcccCcccccC--C----CeEECcCCCCccccccccccEEEEEeccccccceeeccccccCCCcccCCCCCCCCCeeE
Confidence            5999999999887  2    389999999998875222455555554443333322333336 89999999999999999


Q ss_pred             EEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           81 YHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        81 ~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      |||+|+||||||||+||+|++  |+|+||+
T Consensus        75 f~~~Q~RsadE~~T~fy~C~~--C~~~w~~  102 (104)
T TIGR01384        75 YWLLQTRRADEPETRFYKCTK--CGYVWRE  102 (104)
T ss_pred             EEEeccCCCCCCcEEEEEeCC--CCCeeEe
Confidence            999999999999999999999  9999996

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.

>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12

Probab=99.97  E-value=3.5e-33  Score=180.26  Aligned_cols=104  Identities=28%  Similarity=0.578  Sum_probs=76.2

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCce-EEE-EecccCccccccccc-cccccC-CCCCcccCCCCCC
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRV-KIK-RKQPLSKKEIQPIFT-QDAMME-GPQTEVTCPACKH   76 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~-~~~-~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~CpkCg~   76 (110)
                      +.||+.||+||+.+  .  ......|..|+..++.+... ..+ .+..+.......... ...... +|+++++||||||
T Consensus         7 ~~FC~~CG~ll~~~--~--~~~~~~C~~Ck~~~~v~~~~~~~v~~~~~~~~~~~A~~~~ve~~~~~~ga~I~~kCpkCgh   82 (116)
T KOG2907|consen    7 LDFCSDCGSLLEEP--S--AQSTVLCIRCKIEYPVSQFSGLVVETKSLFDEFTSALAEKVENESSADGAVIKHKCPKCGH   82 (116)
T ss_pred             cchhhhhhhhcccc--c--ccCceEeccccccCCHHHhCCeeEEEEEeecccchhhhhhhcccccccccchhccCcccCC
Confidence            46999999999998  3  35577899999988876521 222 222222211111111 111223 8999999999999


Q ss_pred             CceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           77 GKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        77 ~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      ++|.|.++|+||||||+|+||+|++  |+|++++
T Consensus        83 e~m~Y~T~QlRSADEGQTVFYTC~k--C~~k~~e  114 (116)
T KOG2907|consen   83 EEMSYHTLQLRSADEGQTVFYTCPK--CKYKFTE  114 (116)
T ss_pred             chhhhhhhhcccccCCceEEEEcCc--cceeeec
Confidence            9999999999999999999999999  9999875

2/RPA12 [Transcription]

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=99.93  E-value=9.2e-27  Score=127.11  Aligned_cols=40  Identities=55%  Similarity=1.262  Sum_probs=38.5

Q ss_pred             ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      .+||+|||++|+|||+|+||||||||+||+|++  |+|+|++
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            379999999999999999999999999999999  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=99.92  E-value=2e-25  Score=121.22  Aligned_cols=39  Identities=59%  Similarity=1.382  Sum_probs=35.0

Q ss_pred             ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      .+||+|||++|+|+|+|+||||||||+||+|.+  |+|+||
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 ....

>PHA02998 RNA polymerase subunit; Provisional

Probab=99.84  E-value=1.8e-21  Score=135.08  Aligned_cols=44  Identities=32%  Similarity=0.613  Sum_probs=42.6

Q ss_pred             CCC-CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           64 GPQ-TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        64 ~~~-~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      +|+ +++.||+|||++|+|||+|+||||||||+||.|.+  |||+|+
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            777 89999999999999999999999999999999999  999997

>TIGR01385 TFSII transcription elongation factor S-II

Probab=99.71  E-value=7.3e-18  Score=126.68  Aligned_cols=41  Identities=51%  Similarity=1.005  Sum_probs=39.3

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      ....||+||+++++|||+|+||||||||+||+|++  |||+|+
T Consensus       257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~--Cg~~w~  297 (299)
T TIGR01385       257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEE--CGNRWK  297 (299)
T ss_pred             ccccCCCCCCccceEEEecccCCCCCCeEEEEcCC--CCCeee
Confidence            35799999999999999999999999999999999  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.

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=99.51  E-value=4.8e-15  Score=78.49  Aligned_cols=34  Identities=32%  Similarity=0.764  Sum_probs=25.7

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      |+|||+|||||+|++++...  . +|++|||++++++
T Consensus         1 m~FCp~C~nlL~p~~~~~~~--~-~C~~C~Y~~~~~~   34 (35)
T PF02150_consen    1 MRFCPECGNLLYPKEDKEKR--V-ACRTCGYEEPISQ   34 (35)
T ss_dssp             --BETTTTSBEEEEEETTTT--E-EESSSS-EEE-SS
T ss_pred             CeeCCCCCccceEcCCCccC--c-CCCCCCCccCCCC
Confidence            89999999999999666543  4 9999999999875

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=99.14  E-value=9.5e-11  Score=66.59  Aligned_cols=41  Identities=37%  Similarity=0.721  Sum_probs=32.1

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEecc
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQP   46 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~   46 (110)
                      .|||+||+||+++++.  ...+++|+.|||...+..  .++++..
T Consensus         1 ~FCp~Cg~~l~~~~~~--~~~~~vC~~Cg~~~~~~~--~~~~~~~   41 (52)
T smart00661        1 KFCPKCGNMLIPKEGK--EKRRFVCRKCGYEEPIEQ--KYVYKEK   41 (52)
T ss_pred             CCCCCCCCccccccCC--CCCEEECCcCCCeEECCC--cEEEEEE
Confidence            5999999999999433  235999999999999887  5555433

>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]

Probab=98.97  E-value=4.6e-10  Score=84.15  Aligned_cols=40  Identities=48%  Similarity=0.998  Sum_probs=38.5

Q ss_pred             cccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      ..+|.+|+.....|+|+|+||||||||.|-.|..  ||++|+
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            4799999999999999999999999999999999  999996

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=98.46  E-value=1e-07  Score=49.89  Aligned_cols=33  Identities=39%  Similarity=1.007  Sum_probs=21.4

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      +|||.||..|..+++.++...+++|+.||++..
T Consensus         1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~IhY   33 (34)
T PF14803_consen    1 KFCPQCGGPLERRIPEGDDRERLVCPACGFIHY   33 (34)
T ss_dssp             -B-TTT--B-EEE--TT-SS-EEEETTTTEEE-
T ss_pred             CccccccChhhhhcCCCCCccceECCCCCCEEe
Confidence            599999999999988888899999999998753

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=98.18  E-value=1.3e-06  Score=49.57  Aligned_cols=27  Identities=33%  Similarity=0.942  Sum_probs=23.2

Q ss_pred             CCCcCCCC-CcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGT-MLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~n-lL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      +|||.||+ +|.+.  .    .++.|..|||++.
T Consensus        21 ~fCP~Cg~~~m~~~--~----~r~~C~~Cgyt~~   48 (50)
T PRK00432         21 KFCPRCGSGFMAEH--L----DRWHCGKCGYTEF   48 (50)
T ss_pred             CcCcCCCcchhecc--C----CcEECCCcCCEEe
Confidence            59999999 88887  2    4899999999864

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

Probab=97.58  E-value=9.9e-05  Score=41.14  Aligned_cols=38  Identities=21%  Similarity=0.553  Sum_probs=27.2

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      .||.||+.-..--..++  .++--.++|.|.|+.|||+|.
T Consensus         1 ~CP~Cg~~a~ir~S~~~--s~~~~~~Y~qC~N~~Cg~tfv   38 (47)
T PF04606_consen    1 RCPHCGSKARIRTSRQL--SPLTRELYCQCTNPECGHTFV   38 (47)
T ss_pred             CcCCCCCeeEEEEchhh--CcceEEEEEEECCCcCCCEEE
Confidence            59999986544433332  334455899999999999985

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

>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]

Probab=97.35  E-value=0.00018  Score=40.48  Aligned_cols=28  Identities=32%  Similarity=0.895  Sum_probs=22.1

Q ss_pred             CCCcCCC--CCcccccCCCCCCceEEcCCCCCeeee
Q 033869            2 EFCPTCG--TMLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         2 ~FCp~C~--nlL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      +|||.||  .+|---      ..+++|-.|||++-.
T Consensus        20 ~~CPrCG~gvfmA~H------~dR~~CGkCgyTe~~   49 (51)
T COG1998          20 RFCPRCGPGVFMADH------KDRWACGKCGYTEFK   49 (51)
T ss_pred             ccCCCCCCcchhhhc------CceeEeccccceEee
Confidence            5999999  555444      459999999998754

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=97.31  E-value=0.00024  Score=43.18  Aligned_cols=38  Identities=24%  Similarity=0.594  Sum_probs=27.7

Q ss_pred             ccCCCCCCCceEEEEeccCCCCCCce-EEEEecCCCCCcccc
Q 033869           69 VTCPACKHGKAVYHELQTRSADEPMS-IFYMCANKNCKHRWN  109 (110)
Q Consensus        69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T-~fY~C~~~~C~~~wr  109 (110)
                      ..||.||+.-.   ..-+|..+++.. ++|.|.|..|||+|.
T Consensus         2 m~CP~Cg~~a~---irtSr~~s~~~~~~Y~qC~N~eCg~tF~   40 (72)
T PRK09678          2 FHCPLCQHAAH---ARTSRYITDTTKERYHQCQNVNCSATFI   40 (72)
T ss_pred             ccCCCCCCccE---EEEChhcChhhheeeeecCCCCCCCEEE
Confidence            37999999763   233455555543 899999888999985

>PHA00626 hypothetical protein

Probab=96.85  E-value=0.001  Score=38.42  Aligned_cols=36  Identities=22%  Similarity=0.480  Sum_probs=24.9

Q ss_pred             CCCcCCCCCcccccCCCC-CCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMD-RPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~-~~~~~~C~~C~y~~~~~~   37 (110)
                      +.||+||+--..+..... ....|.|+.|||....+.
T Consensus         1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~   37 (59)
T PHA00626          1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDA   37 (59)
T ss_pred             CCCCCCCCceeeeeceecccCcceEcCCCCCeechhh
Confidence            479999995444412222 267999999999876553

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=96.70  E-value=0.00075  Score=33.00  Aligned_cols=24  Identities=33%  Similarity=0.843  Sum_probs=18.4

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      +++||.||..+...        .-.|+.||..
T Consensus         2 ~~~Cp~Cg~~~~~~--------~~fC~~CG~~   25 (26)
T PF13248_consen    2 EMFCPNCGAEIDPD--------AKFCPNCGAK   25 (26)
T ss_pred             cCCCcccCCcCCcc--------cccChhhCCC
Confidence            46999999965444        5689999963

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=96.63  E-value=0.0016  Score=33.25  Aligned_cols=28  Identities=25%  Similarity=0.497  Sum_probs=18.0

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      +||+.||.-+.+.  ..  .-...|+.|+...
T Consensus         4 rfC~~CG~~t~~~--~~--g~~r~C~~Cg~~~   31 (32)
T PF09297_consen    4 RFCGRCGAPTKPA--PG--GWARRCPSCGHEH   31 (32)
T ss_dssp             SB-TTT--BEEE---SS--SS-EEESSSS-EE
T ss_pred             cccCcCCccccCC--CC--cCEeECCCCcCEe
Confidence            6999999999998  33  4689999999764

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

>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=96.57  E-value=0.0032  Score=33.67  Aligned_cols=34  Identities=26%  Similarity=0.626  Sum_probs=27.8

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCC---CCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPA---CPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~---C~y~~~~~~   37 (110)
                      ..||.||..|..+  ....+..+.|.+   |.|+..+..
T Consensus         2 ~~CP~Cg~~lv~r--~~k~g~F~~Cs~yP~C~~~~~~~~   38 (39)
T PF01396_consen    2 EKCPKCGGPLVLR--RGKKGKFLGCSNYPECKYTEPLPK   38 (39)
T ss_pred             cCCCCCCceeEEE--ECCCCCEEECCCCCCcCCeEeCCC
Confidence            4699999999999  555568999997   999887653

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

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=96.56  E-value=0.0011  Score=32.55  Aligned_cols=24  Identities=33%  Similarity=0.820  Sum_probs=19.9

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      =||+|+..+...        .-.|+.|||...
T Consensus         2 ~CP~C~~~V~~~--------~~~Cp~CG~~F~   25 (26)
T PF10571_consen    2 TCPECGAEVPES--------AKFCPHCGYDFE   25 (26)
T ss_pred             cCCCCcCCchhh--------cCcCCCCCCCCc
Confidence            499999998666        678999999764

Several members are annotated as putative helicases.

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=96.40  E-value=0.0015  Score=31.16  Aligned_cols=22  Identities=32%  Similarity=0.970  Sum_probs=17.2

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      |||.||+-+...        .-.|+.||..
T Consensus         1 ~Cp~CG~~~~~~--------~~fC~~CG~~   22 (23)
T PF13240_consen    1 YCPNCGAEIEDD--------AKFCPNCGTP   22 (23)
T ss_pred             CCcccCCCCCCc--------CcchhhhCCc
Confidence            899999988654        4459999863

>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=96.39  E-value=0.0042  Score=33.24  Aligned_cols=32  Identities=34%  Similarity=0.720  Sum_probs=22.7

Q ss_pred             cccCCCCCCCceEEEEeccCCCCCCceEEEEecC-CCCCcc
Q 033869           68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN-KNCKHR  107 (110)
Q Consensus        68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~-~~C~~~  107 (110)
                      ++.||+|| ..++.     |.+--|  .||-|.+ |.|.++
T Consensus         1 ~~~CP~Cg-~~lv~-----r~~k~g--~F~~Cs~yP~C~~~   33 (39)
T PF01396_consen    1 VEKCPKCG-GPLVL-----RRGKKG--KFLGCSNYPECKYT   33 (39)
T ss_pred             CcCCCCCC-ceeEE-----EECCCC--CEEECCCCCCcCCe
Confidence            36899999 44433     444445  9999998 689875

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

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=96.24  E-value=0.0049  Score=29.66  Aligned_cols=24  Identities=29%  Similarity=1.003  Sum_probs=19.6

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPY   31 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y   31 (110)
                      |..||-.|.++    .+...|.|++||+
T Consensus         1 C~sC~~~i~~r----~~~v~f~CPnCG~   24 (24)
T PF07754_consen    1 CTSCGRPIAPR----EQAVPFPCPNCGF   24 (24)
T ss_pred             CccCCCcccCc----ccCceEeCCCCCC
Confidence            67899999988    2356999999995

It is likely to bind zinc via its four well-conserved cysteine residues.

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=96.21  E-value=0.022  Score=43.46  Aligned_cols=72  Identities=22%  Similarity=0.558  Sum_probs=41.2

Q ss_pred             CCCcCCCCCcccc---cCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCC-
Q 033869            2 EFCPTCGTMLQYE---LPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHG-   77 (110)
Q Consensus         2 ~FCp~C~nlL~~~---~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~-   77 (110)
                      .+||-||+.=...   ....++.-++.|..|+..+...                               ...||.||+. 
T Consensus       188 ~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~-------------------------------R~~C~~Cg~~~  236 (309)
T PRK03564        188 QFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVV-------------------------------RVKCSNCEQSG  236 (309)
T ss_pred             CCCCCCCCcchhheeeccCCCCceEEEcCCCCCccccc-------------------------------CccCCCCCCCC
Confidence            4788888762111   0012334577888888655432                               3468888864 


Q ss_pred             ceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           78 KAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        78 ~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      +..||.+-   .+++-...++|..  |+.-++
T Consensus       237 ~l~y~~~~---~~~~~~r~e~C~~--C~~YlK  263 (309)
T PRK03564        237 KLHYWSLD---SEQAAVKAESCGD--CGTYLK  263 (309)
T ss_pred             ceeeeeec---CCCcceEeeeccc--ccccce
Confidence            55565552   1224457788887  876543

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=96.18  E-value=0.0042  Score=31.96  Aligned_cols=15  Identities=27%  Similarity=0.685  Sum_probs=11.9

Q ss_pred             cccCCCCCCCceEEE
Q 033869           68 EVTCPACKHGKAVYH   82 (110)
Q Consensus        68 ~~~CpkCg~~~a~~~   82 (110)
                      +..||.||..+..|.
T Consensus        17 ~~~CP~Cg~~~~~F~   31 (33)
T cd00350          17 PWVCPVCGAPKDKFE   31 (33)
T ss_pred             CCcCcCCCCcHHHcE
Confidence            458999999877664

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

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

Probab=95.90  E-value=0.002  Score=32.65  Aligned_cols=27  Identities=33%  Similarity=0.966  Sum_probs=14.3

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      +||+||....+        .|   ...|+|..  |+|.|.
T Consensus         4 ~Cp~C~se~~y--------~D---~~~~vCp~--C~~ew~   30 (30)
T PF08274_consen    4 KCPLCGSEYTY--------ED---GELLVCPE--CGHEWN   30 (30)
T ss_dssp             --TTT-----E--------E----SSSEEETT--TTEEE-
T ss_pred             CCCCCCCccee--------cc---CCEEeCCc--ccccCC
Confidence            79999998877        22   22489999  999994

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.

>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=95.88  E-value=0.0093  Score=44.74  Aligned_cols=72  Identities=21%  Similarity=0.489  Sum_probs=30.5

Q ss_pred             CCCcCCCCC-----cccccCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCC
Q 033869            2 EFCPTCGTM-----LQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKH   76 (110)
Q Consensus         2 ~FCp~C~nl-----L~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~   76 (110)
                      .+||-||+.     |...++  .+.-++.|..|+..+...                               ...||.||+
T Consensus       173 g~CPvCGs~P~~s~l~~~~~--~G~R~L~Cs~C~t~W~~~-------------------------------R~~Cp~Cg~  219 (290)
T PF04216_consen  173 GYCPVCGSPPVLSVLRGGER--EGKRYLHCSLCGTEWRFV-------------------------------RIKCPYCGN  219 (290)
T ss_dssp             SS-TTT---EEEEEEE--------EEEEEETTT--EEE---------------------------------TTS-TTT--
T ss_pred             CcCCCCCCcCceEEEecCCC--CccEEEEcCCCCCeeeec-------------------------------CCCCcCCCC
Confidence            368888875     222211  123577888888765532                               336999998


Q ss_pred             CceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           77 GKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        77 ~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      .+..=+.. ....+++.-..++|-+  |+.-++
T Consensus       220 ~~~~~l~~-~~~e~~~~~rve~C~~--C~~YlK  249 (290)
T PF04216_consen  220 TDHEKLEY-FTVEGEPAYRVEVCES--CGSYLK  249 (290)
T ss_dssp             -SS-EEE---------SEEEEEETT--TTEEEE
T ss_pred             CCCcceee-EecCCCCcEEEEECCc--ccchHH
Confidence            65432222 2245667888899999  987654

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.

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=95.87  E-value=0.012  Score=32.34  Aligned_cols=31  Identities=23%  Similarity=0.673  Sum_probs=23.2

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      =|+.||..+...  ...  ..+.|+.||.......
T Consensus         5 ~C~~CG~~~~~~--~~~--~~~~Cp~CG~~~~~~~   35 (46)
T PRK00398          5 KCARCGREVELD--EYG--TGVRCPYCGYRILFKE   35 (46)
T ss_pred             ECCCCCCEEEEC--CCC--CceECCCCCCeEEEcc
Confidence            399999998887  322  2799999998665544

>PHA00626 hypothetical protein

Probab=95.80  E-value=0.0095  Score=34.41  Aligned_cols=33  Identities=30%  Similarity=0.631  Sum_probs=22.3

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      .||+||+.+.+ -....|    .+..-|+|..  |||.++
T Consensus         2 ~CP~CGS~~Iv-rcg~cr----~~snrYkCkd--CGY~ft   34 (59)
T PHA00626          2 SCPKCGSGNIA-KEKTMR----GWSDDYVCCD--CGYNDS   34 (59)
T ss_pred             CCCCCCCceee-eeceec----ccCcceEcCC--CCCeec
Confidence            69999997764 211112    2345599998  999875

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=95.80  E-value=0.046  Score=41.67  Aligned_cols=72  Identities=21%  Similarity=0.482  Sum_probs=41.7

Q ss_pred             CCcCCCCCccc---cc-CCCCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCC-
Q 033869            3 FCPTCGTMLQY---EL-PHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHG-   77 (110)
Q Consensus         3 FCp~C~nlL~~---~~-~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~-   77 (110)
                      +||-||+.=..   .. ...++.-++.|..|+..+...                               ...||.||+. 
T Consensus       186 ~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~-------------------------------R~~C~~Cg~~~  234 (305)
T TIGR01562       186 LCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV-------------------------------RVKCSHCEESK  234 (305)
T ss_pred             cCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccccc-------------------------------CccCCCCCCCC
Confidence            78888876322   10 012334578888888665432                               3468888865 


Q ss_pred             ceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869           78 KAVYHELQTRSADEPMSIFYMCANKNCKHRW  108 (110)
Q Consensus        78 ~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w  108 (110)
                      +..||.+-. ..+++-....+|..  |+.-+
T Consensus       235 ~l~y~~~e~-~~~~~~~r~e~C~~--C~~Yl  262 (305)
T TIGR01562       235 HLAYLSLEH-DAEKAVLKAETCDS--CQGYL  262 (305)
T ss_pred             ceeeEeecC-CCCCcceEEeeccc--cccch
Confidence            344665532 11234567788887  87644

The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).

>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=95.76  E-value=0.019  Score=34.09  Aligned_cols=11  Identities=27%  Similarity=0.809  Sum_probs=6.8

Q ss_pred             cCCCCCCCceE
Q 033869           70 TCPACKHGKAV   80 (110)
Q Consensus        70 ~CpkCg~~~a~   80 (110)
                      .|||||+.+..
T Consensus         2 ~C~KCg~~~~e   12 (64)
T PF09855_consen    2 KCPKCGNEEYE   12 (64)
T ss_pred             CCCCCCCccee
Confidence            57777775543

>COG1773 Rubredoxin [Energy production and conversion]

Probab=95.74  E-value=0.014  Score=33.55  Aligned_cols=49  Identities=29%  Similarity=0.572  Sum_probs=30.1

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEe
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHEL   84 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~   84 (110)
                      .|.|+.|||+++....           .....|-.+. .+. +| .+..||.||-.+..|..+
T Consensus         3 ~~~C~~CG~vYd~e~G-----------dp~~gi~pgT-~fedlP-d~w~CP~Cg~~K~~F~~~   52 (55)
T COG1773           3 RWRCSVCGYVYDPEKG-----------DPRCGIAPGT-PFEDLP-DDWVCPECGVGKKDFEMI   52 (55)
T ss_pred             ceEecCCceEeccccC-----------CccCCCCCCC-chhhCC-CccCCCCCCCCHhHeeec
Confidence            6899999998876541           1111222111 122 22 478999999888877654

>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center

Probab=95.66  E-value=0.0079  Score=34.00  Aligned_cols=47  Identities=23%  Similarity=0.572  Sum_probs=27.3

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEE
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYH   82 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~   82 (110)
                      .|.|+.|||+++....           .....|..+. .+. ||. +..||.||..+..|-
T Consensus         1 ~y~C~~CgyiYd~~~G-----------d~~~~i~pGt-~f~~Lp~-~w~CP~C~a~K~~F~   48 (50)
T cd00730           1 KYECRICGYIYDPAEG-----------DPDEGIPPGT-PFEDLPD-DWVCPVCGAGKDDFE   48 (50)
T ss_pred             CcCCCCCCeEECCCCC-----------CcccCcCCCC-CHhHCCC-CCCCCCCCCcHHHcE
Confidence            3789999998875431           0001122111 122 443 789999998876653

Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.

>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=95.53  E-value=0.013  Score=32.24  Aligned_cols=28  Identities=25%  Similarity=0.599  Sum_probs=20.8

Q ss_pred             ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869           69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR  107 (110)
Q Consensus        69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~  107 (110)
                      ..||+||+.+++....         ...|.|.+  |+++
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            5699999995555432         45699999  9874

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

>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []

Probab=95.48  E-value=0.017  Score=32.18  Aligned_cols=46  Identities=28%  Similarity=0.622  Sum_probs=23.8

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEE
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVY   81 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~   81 (110)
                      .|.|+.|||+.+....           +....|..+. .+. || .+..||.||..+..|
T Consensus         1 ky~C~~CgyvYd~~~G-----------d~~~~i~pGt-~F~~Lp-~~w~CP~C~a~K~~F   47 (47)
T PF00301_consen    1 KYQCPVCGYVYDPEKG-----------DPENGIPPGT-PFEDLP-DDWVCPVCGAPKSDF   47 (47)
T ss_dssp             EEEETTTSBEEETTTB-----------BGGGTB-TT---GGGS--TT-B-TTTSSBGGGE
T ss_pred             CcCCCCCCEEEcCCcC-----------CcccCcCCCC-CHHHCC-CCCcCcCCCCccccC
Confidence            4899999998875441           1111222211 122 43 368999999876433

The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....

>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase

Probab=95.47  E-value=0.016  Score=30.06  Aligned_cols=12  Identities=33%  Similarity=1.115  Sum_probs=10.1

Q ss_pred             eEEcCCCCCeee
Q 033869           23 RFSCPACPYVCN   34 (110)
Q Consensus        23 ~~~C~~C~y~~~   34 (110)
                      .|.|+.|||+..
T Consensus         2 ~~~C~~CG~i~~   13 (34)
T cd00729           2 VWVCPVCGYIHE   13 (34)
T ss_pred             eEECCCCCCEeE
Confidence            689999999754

In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=95.41  E-value=0.0091  Score=34.87  Aligned_cols=26  Identities=31%  Similarity=0.885  Sum_probs=15.1

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      -|.-||-.|.|.    .+...|.|++||.+
T Consensus        11 ~CtSCg~~i~p~----e~~v~F~CPnCGe~   36 (61)
T COG2888          11 VCTSCGREIAPG----ETAVKFPCPNCGEV   36 (61)
T ss_pred             eeccCCCEeccC----CceeEeeCCCCCce
Confidence            356666666665    22346677777743

>PF12773 DZR: Double zinc ribbon

Probab=95.38  E-value=0.008  Score=33.36  Aligned_cols=27  Identities=41%  Similarity=0.833  Sum_probs=18.7

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      .||+.||..|...     ....+.|+.||+..
T Consensus        13 ~fC~~CG~~l~~~-----~~~~~~C~~Cg~~~   39 (50)
T PF12773_consen   13 KFCPHCGTPLPPP-----DQSKKICPNCGAEN   39 (50)
T ss_pred             cCChhhcCChhhc-----cCCCCCCcCCcCCC
Confidence            6888888888822     13467888888753

>PF14353 CpXC: CpXC protein

Probab=95.17  E-value=0.018  Score=38.10  Aligned_cols=45  Identities=22%  Similarity=0.440  Sum_probs=25.2

Q ss_pred             EEcCCCCCeeeeCCceEEEEeccc--CccccccccccccccCCCCCcccCCCCCCCc
Q 033869           24 FSCPACPYVCNMESRVKIKRKQPL--SKKEIQPIFTQDAMMEGPQTEVTCPACKHGK   78 (110)
Q Consensus        24 ~~C~~C~y~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~~   78 (110)
                      +.|+.|+....++-.    ..+..  ...-.+.++.++      --...||+||+.-
T Consensus         2 itCP~C~~~~~~~v~----~~I~~~~~p~l~e~il~g~------l~~~~CP~Cg~~~   48 (128)
T PF14353_consen    2 ITCPHCGHEFEFEVW----TSINADEDPELKEKILDGS------LFSFTCPSCGHKF   48 (128)
T ss_pred             cCCCCCCCeeEEEEE----eEEcCcCCHHHHHHHHcCC------cCEEECCCCCCce
Confidence            579999998776542    11221  121122344322      2367999999854

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

Probab=95.09  E-value=0.018  Score=34.11  Aligned_cols=34  Identities=26%  Similarity=0.696  Sum_probs=20.9

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceEEE----------EecCCCCCcc
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSIFY----------MCANKNCKHR  107 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY----------~C~~~~C~~~  107 (110)
                      +|||||+++  |.+.+++...++..-||          .|.+  |||+
T Consensus         6 kCpKCgn~~--~~ekei~~tg~~lskifdvq~n~f~~itCk~--CgYt   49 (68)
T COG3478           6 KCPKCGNTN--YEEKEIAATGGGLSKIFDVQNNKFIVITCKN--CGYT   49 (68)
T ss_pred             cCCCcCCcc--hhhceeeccCCCcceeEEecccEEEEEEecc--CCch
Confidence            488888765  35555556656655443          4667  7764

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

Probab=94.97  E-value=0.015  Score=29.42  Aligned_cols=26  Identities=35%  Similarity=0.821  Sum_probs=15.1

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      =||.|++-.... |    +..|+|+.|+++.
T Consensus         4 ~Cp~C~se~~y~-D----~~~~vCp~C~~ew   29 (30)
T PF08274_consen    4 KCPLCGSEYTYE-D----GELLVCPECGHEW   29 (30)
T ss_dssp             --TTT-----EE------SSSEEETTTTEEE
T ss_pred             CCCCCCCcceec-c----CCEEeCCcccccC
Confidence            499999887775 2    4599999999875

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.

>PRK14973 DNA topoisomerase I; Provisional

Probab=94.80  E-value=0.057  Score=46.74  Aligned_cols=33  Identities=24%  Similarity=0.415  Sum_probs=21.8

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR  107 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~  107 (110)
                      ++..||+||.+.    .+.+|...-|+  |.-|..  |+|.
T Consensus       634 ~~~~Cp~CG~p~----~~~~r~Gr~g~--fl~CP~--C~~~  666 (936)
T PRK14973        634 TDEVCPIHHLNH----VRLIRKGARPW--DIGCPL--CSHI  666 (936)
T ss_pred             CCCCCCCCCCCc----eEEeecCCCcc--cccCcc--ccch
Confidence            356899999862    22235555566  778966  9884

>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=94.70  E-value=0.018  Score=34.22  Aligned_cols=15  Identities=27%  Similarity=0.476  Sum_probs=12.0

Q ss_pred             CcccCCCCCCCceEE
Q 033869           67 TEVTCPACKHGKAVY   81 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~   81 (110)
                      +-+.|++||+.|.+-
T Consensus        35 ~~v~C~~CGYTE~Y~   49 (64)
T PF09855_consen   35 TTVSCTNCGYTEFYK   49 (64)
T ss_pred             EEEECCCCCCEEEEe
Confidence            456899999998755

>TIGR00244 transcriptional regulator NrdR

Probab=94.62  E-value=0.044  Score=37.58  Aligned_cols=36  Identities=31%  Similarity=0.704  Sum_probs=28.5

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceEE--EEecCCCCCcccc
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSIF--YMCANKNCKHRWN  109 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~f--Y~C~~~~C~~~wr  109 (110)
                      +||.|||.+-.-  +-+|++++|.++=  -.|.+  |+++|.
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            699999976644  4579999997764  68998  999885

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.

>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]

Probab=94.61  E-value=0.048  Score=41.82  Aligned_cols=40  Identities=28%  Similarity=0.585  Sum_probs=27.2

Q ss_pred             CCCcCCCCCcccccCCCCCCce-EEcCCCCCeeeeCCceEE
Q 033869            2 EFCPTCGTMLQYELPHMDRPSR-FSCPACPYVCNMESRVKI   41 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~-~~C~~C~y~~~~~~~~~~   41 (110)
                      +|||.||+-+.|++........ -.|+.|++.++..++.+|
T Consensus       151 kFCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yPr~dPvVI  191 (345)
T KOG3084|consen  151 KFCPGCGSPTKPEEAGTKLQCSDETCPSCNVIYPRTDPVVI  191 (345)
T ss_pred             ccCcccCCCcccccCCccceeecccCCcCCeeccCCCCeEE
Confidence            6999999999999544322222 346666778887776443

>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=94.59  E-value=0.023  Score=30.78  Aligned_cols=30  Identities=27%  Similarity=0.668  Sum_probs=20.1

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      .||.||+-. +..|.  ....++|+.||.+..-
T Consensus         2 ~Cp~Cg~~~-~~~D~--~~g~~vC~~CG~Vl~e   31 (43)
T PF08271_consen    2 KCPNCGSKE-IVFDP--ERGELVCPNCGLVLEE   31 (43)
T ss_dssp             SBTTTSSSE-EEEET--TTTEEEETTT-BBEE-
T ss_pred             CCcCCcCCc-eEEcC--CCCeEECCCCCCEeec
Confidence            699999865 33233  3568899999987553

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.

>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated

Probab=94.49  E-value=0.11  Score=44.73  Aligned_cols=32  Identities=25%  Similarity=0.530  Sum_probs=22.9

Q ss_pred             CCcCCCC-CcccccCCCCCCceEEcCC---CCCeeeeC
Q 033869            3 FCPTCGT-MLQYELPHMDRPSRFSCPA---CPYVCNME   36 (110)
Q Consensus         3 FCp~C~n-lL~~~~~~~~~~~~~~C~~---C~y~~~~~   36 (110)
                      =||.||. .|..+  .+..+..+.|.+   |.|..++.
T Consensus       594 ~CP~Cg~~~L~~k--~gr~G~Fl~Cs~yP~C~~t~~~~  629 (860)
T PRK06319        594 DCPKCHKGKLVKI--WAKNRYFYGCSEYPECDYKTSEE  629 (860)
T ss_pred             ccCCCCCcceeEE--ecCCCceeeccCCccccccCCcc
Confidence            4999964 77766  445567999976   88876554

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=94.45  E-value=0.035  Score=29.04  Aligned_cols=33  Identities=21%  Similarity=0.489  Sum_probs=23.5

Q ss_pred             CCcCCCCCcccccCCC-CCCceEEcCCCCCeeee
Q 033869            3 FCPTCGTMLQYELPHM-DRPSRFSCPACPYVCNM   35 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~-~~~~~~~C~~C~y~~~~   35 (110)
                      =||.|+....+..+.. ..+..+.|++|+....+
T Consensus         4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~   37 (38)
T TIGR02098         4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA   37 (38)
T ss_pred             ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence            3999999887774332 23348999999987653

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.

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=94.34  E-value=0.031  Score=32.62  Aligned_cols=26  Identities=31%  Similarity=0.857  Sum_probs=18.1

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      .|.-||-.|.+.    ++...|.|++||..
T Consensus         9 ~CtSCg~~i~~~----~~~~~F~CPnCG~~   34 (59)
T PRK14890          9 KCTSCGIEIAPR----EKAVKFLCPNCGEV   34 (59)
T ss_pred             cccCCCCcccCC----CccCEeeCCCCCCe
Confidence            577788777776    22457888888864

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=94.24  E-value=0.043  Score=28.85  Aligned_cols=32  Identities=25%  Similarity=0.606  Sum_probs=24.2

Q ss_pred             CCcCCCCCcccccCCC-CCCceEEcCCCCCeee
Q 033869            3 FCPTCGTMLQYELPHM-DRPSRFSCPACPYVCN   34 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~-~~~~~~~C~~C~y~~~   34 (110)
                      =||.|+..+.++.++- ..+..+.|+.|+..+.
T Consensus         4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence            3999999988874431 3456899999998764

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=94.15  E-value=0.014  Score=49.18  Aligned_cols=25  Identities=20%  Similarity=0.331  Sum_probs=16.2

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCC
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADE   91 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE   91 (110)
                      +-..||+||....+++-.-|....|
T Consensus       474 ~p~~Cp~Cgs~~L~~~G~Gteriee  498 (730)
T COG1198         474 IPQSCPECGSEHLRAVGPGTERIEE  498 (730)
T ss_pred             CCCCCCCCCCCeeEEecccHHHHHH
Confidence            3457999988877776655444333

>PF13453 zf-TFIIB: Transcription factor zinc-finger

Probab=94.12  E-value=0.033  Score=29.82  Aligned_cols=29  Identities=31%  Similarity=0.655  Sum_probs=23.0

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ||.|++.|...  .........|+.|+-...
T Consensus         2 CP~C~~~l~~~--~~~~~~id~C~~C~G~W~   30 (41)
T PF13453_consen    2 CPRCGTELEPV--RLGDVEIDVCPSCGGIWF   30 (41)
T ss_pred             cCCCCcccceE--EECCEEEEECCCCCeEEc
Confidence            99999988877  434467889999997654

>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]

Probab=94.09  E-value=0.066  Score=40.32  Aligned_cols=38  Identities=24%  Similarity=0.334  Sum_probs=29.5

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee-eCCceEEEE
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN-MESRVKIKR   43 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~-~~~~~~~~~   43 (110)
                      +||+.||.-+++.    .......|+.||+... ..++.+|+-
T Consensus       112 RFCg~CG~~~~~~----~~g~~~~C~~cg~~~fPR~dP~vIv~  150 (279)
T COG2816         112 RFCGRCGTKTYPR----EGGWARVCPKCGHEHFPRIDPCVIVA  150 (279)
T ss_pred             cCCCCCCCcCccc----cCceeeeCCCCCCccCCCCCCeEEEE
Confidence            7999999999999    3356899999998754 455655543

>PF13453 zf-TFIIB: Transcription factor zinc-finger

Probab=94.07  E-value=0.085  Score=28.19  Aligned_cols=30  Identities=23%  Similarity=0.534  Sum_probs=20.9

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      .||+|+. .+.=..+       +-...+.|.+  |+-.|=
T Consensus         1 ~CP~C~~-~l~~~~~-------~~~~id~C~~--C~G~W~   30 (41)
T PF13453_consen    1 KCPRCGT-ELEPVRL-------GDVEIDVCPS--CGGIWF   30 (41)
T ss_pred             CcCCCCc-ccceEEE-------CCEEEEECCC--CCeEEc
Confidence            5999998 4432222       3367799999  999884

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=94.06  E-value=0.059  Score=29.89  Aligned_cols=12  Identities=17%  Similarity=0.517  Sum_probs=9.1

Q ss_pred             EEEecCCCCCcccc
Q 033869           96 FYMCANKNCKHRWN  109 (110)
Q Consensus        96 fY~C~~~~C~~~wr  109 (110)
                      .|+|..  |||.++
T Consensus        20 ~~vC~~--Cg~~~~   31 (52)
T smart00661       20 RFVCRK--CGYEEP   31 (52)
T ss_pred             EEECCc--CCCeEE
Confidence            778887  888764

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=94.04  E-value=0.077  Score=36.67  Aligned_cols=36  Identities=25%  Similarity=0.636  Sum_probs=24.5

Q ss_pred             cCCCCCCCceEEEEeccCCCCCC--ceEEEEecCCCCCcccc
Q 033869           70 TCPACKHGKAVYHELQTRSADEP--MSIFYMCANKNCKHRWN  109 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~--~T~fY~C~~~~C~~~wr  109 (110)
                      +||-||+....-  .-.|...+|  -+.||.|.+  ||.+|.
T Consensus         2 ~cp~c~~~~~~~--~~s~~~~~~~~~~~~~~c~~--c~~~f~   39 (154)
T PRK00464          2 RCPFCGHPDTRV--IDSRPAEDGNAIRRRRECLA--CGKRFT   39 (154)
T ss_pred             cCCCCCCCCCEe--EeccccCCCCceeeeeeccc--cCCcce
Confidence            799999976211  123334465  567899999  999874

>TIGR00595 priA primosomal protein N'

Probab=94.02  E-value=0.075  Score=42.95  Aligned_cols=27  Identities=30%  Similarity=0.816  Sum_probs=12.8

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ||.|+.-|...  +.  ...+.|..|||...
T Consensus       225 C~~C~~~l~~h--~~--~~~l~Ch~Cg~~~~  251 (505)
T TIGR00595       225 CPNCDVSLTYH--KK--EGKLRCHYCGYQEP  251 (505)
T ss_pred             CCCCCCceEEe--cC--CCeEEcCCCcCcCC
Confidence            45555444444  21  23555555555444

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=93.83  E-value=0.088  Score=28.19  Aligned_cols=30  Identities=23%  Similarity=0.496  Sum_probs=19.6

Q ss_pred             CcCCCCCc------ccccCCCCCCceEEcCCCCCee
Q 033869            4 CPTCGTML------QYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         4 Cp~C~nlL------~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      ||.||+--      ..+...+...+.|.|.+|++..
T Consensus         3 Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w   38 (40)
T smart00440        3 CPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW   38 (40)
T ss_pred             CCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence            89999752      1221122346789999999865

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

>PRK00241 nudC NADH pyrophosphatase; Reviewed

Probab=93.79  E-value=0.1  Score=38.65  Aligned_cols=32  Identities=22%  Similarity=0.480  Sum_probs=25.2

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      .+|||.||+-|...  .+  .....|..|+......
T Consensus        99 ~~fC~~CG~~~~~~--~~--~~~~~C~~c~~~~yp~  130 (256)
T PRK00241         99 HRFCGYCGHPMHPS--KT--EWAMLCPHCRERYYPR  130 (256)
T ss_pred             CccccccCCCCeec--CC--ceeEECCCCCCEECCC
Confidence            47999999999876  32  4578999999877643

>PRK07220 DNA topoisomerase I; Validated

Probab=93.63  E-value=0.25  Score=41.79  Aligned_cols=32  Identities=19%  Similarity=0.357  Sum_probs=19.0

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKH  106 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~  106 (110)
                      ++..||+||......    .+....+  -||.|.+  |.+
T Consensus       634 ~~~~Cp~Cg~~~~k~----~~~g~~~--~~~~Cp~--C~~  665 (740)
T PRK07220        634 TDKVCEAHGLNHIRI----INGGKRP--WDLGCPQ--CNF  665 (740)
T ss_pred             CCCCCCCCCCceEEE----EecCCcc--ceeeCCC--CCC
Confidence            356899999754311    1222122  2889977  986

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=93.63  E-value=0.12  Score=31.29  Aligned_cols=37  Identities=16%  Similarity=0.354  Sum_probs=27.5

Q ss_pred             CCCCcCCCCCcccccCC----CCCCceEEcC--CCCCeeeeCC
Q 033869            1 MEFCPTCGTMLQYELPH----MDRPSRFSCP--ACPYVCNMES   37 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~----~~~~~~~~C~--~C~y~~~~~~   37 (110)
                      |+.||.||+-..+...+    ....+++.|.  .||+..-...
T Consensus         1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~e   43 (72)
T PRK09678          1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYE   43 (72)
T ss_pred             CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEE
Confidence            89999999988665222    1347899999  7999876544

>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=93.62  E-value=0.062  Score=30.78  Aligned_cols=33  Identities=24%  Similarity=0.491  Sum_probs=24.1

Q ss_pred             CCCcccCCCCC-CCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869           65 PQTEVTCPACK-HGKAVYHELQTRSADEPMSIFYMCANKNCKH  106 (110)
Q Consensus        65 ~~~~~~CpkCg-~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~  106 (110)
                      .+.-..|++|. |++++.       ..|...+-|+|..  |++
T Consensus        19 ~r~aLIC~~C~~hNGla~-------~~~~~~i~y~C~~--Cg~   52 (54)
T PF10058_consen   19 NRYALICSKCFSHNGLAP-------KEEFEEIQYRCPY--CGA   52 (54)
T ss_pred             CceeEECcccchhhcccc-------cccCCceEEEcCC--CCC
Confidence            34567899999 455543       4566777899999  986

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

Probab=93.60  E-value=0.081  Score=29.22  Aligned_cols=34  Identities=21%  Similarity=0.523  Sum_probs=25.4

Q ss_pred             CcCCCCCcccccCC----CCCCceEEcCC--CCCeeeeCC
Q 033869            4 CPTCGTMLQYELPH----MDRPSRFSCPA--CPYVCNMES   37 (110)
Q Consensus         4 Cp~C~nlL~~~~~~----~~~~~~~~C~~--C~y~~~~~~   37 (110)
                      ||.||+.+..+...    ....+++.|.+  ||+...+..
T Consensus         2 CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~~   41 (47)
T PF04606_consen    2 CPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVANL   41 (47)
T ss_pred             cCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEEE
Confidence            99999988876222    23478899999  999876543

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

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=93.56  E-value=0.058  Score=35.12  Aligned_cols=30  Identities=30%  Similarity=0.816  Sum_probs=24.1

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      .=||.|++-...+  .   +..|.|+.|+|++...
T Consensus         3 p~CP~C~seytY~--d---g~~~iCpeC~~EW~~~   32 (109)
T TIGR00686         3 PPCPKCNSEYTYH--D---GTQLICPSCLYEWNEN   32 (109)
T ss_pred             CcCCcCCCcceEe--c---CCeeECcccccccccc
Confidence            4599999988887  2   3479999999998654

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).

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

Probab=93.56  E-value=0.23  Score=25.29  Aligned_cols=32  Identities=28%  Similarity=0.718  Sum_probs=18.1

Q ss_pred             ccCCCCCCC--ceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869           69 VTCPACKHG--KAVYHELQTRSADEPMSIFYMCANKNCKHR  107 (110)
Q Consensus        69 ~~CpkCg~~--~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~  107 (110)
                      ..|||||-.  +.+|-+       .|....|.|.||.|.+.
T Consensus         2 hlcpkcgvgvl~pvy~~-------kgeikvfrcsnpacdye   35 (36)
T PF09151_consen    2 HLCPKCGVGVLEPVYNQ-------KGEIKVFRCSNPACDYE   35 (36)
T ss_dssp             -B-TTTSSSBEEEEE-T-------TS-EEEEEES-TT---E
T ss_pred             ccCCccCceEEEEeecC-------CCcEEEEEcCCCccccC
Confidence            469999986  445532       37788899999999763

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

>PRK07219 DNA topoisomerase I; Validated

Probab=93.54  E-value=0.28  Score=41.92  Aligned_cols=33  Identities=21%  Similarity=0.385  Sum_probs=19.0

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCCCceEEEEec-CCCCCcc
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCA-NKNCKHR  107 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~-~~~C~~~  107 (110)
                      +...||+||..-.   ....+.   |  .|+.|. .+.|++.
T Consensus       732 ~~~~CpkCg~~l~---~~k~~~---g--~~~~Cs~~p~C~~~  765 (822)
T PRK07219        732 TDEKCPECGLPLL---RVKGGF---G--DELGCCNNPKCNYT  765 (822)
T ss_pred             ccCCCCCCCCeEE---EEecCC---C--ceeeeCCCCCCCcc
Confidence            5679999997522   222222   2  378883 2448764

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

Probab=93.46  E-value=0.068  Score=43.71  Aligned_cols=42  Identities=24%  Similarity=0.560  Sum_probs=29.7

Q ss_pred             CcccCCCCCCC-ceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           67 TEVTCPACKHG-KAVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        67 ~~~~CpkCg~~-~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      -.+.||.||+. ...|-.++--....+.+..|+|..  ||+.|.+
T Consensus       199 ~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~--Cg~~i~e  241 (557)
T PF05876_consen  199 YYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPH--CGCEIEE  241 (557)
T ss_pred             EEccCCCCCCCccccccceeecCCCCccceEEECCC--CcCCCCH
Confidence            36799999985 444444544111168999999998  9998864

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 [].

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=93.44  E-value=0.12  Score=29.64  Aligned_cols=31  Identities=23%  Similarity=0.555  Sum_probs=24.6

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      =||.||.-+.++  ....+..+.|+.||....+
T Consensus         4 ~CP~CG~~iev~--~~~~GeiV~Cp~CGaeleV   34 (54)
T TIGR01206         4 ECPDCGAEIELE--NPELGELVICDECGAELEV   34 (54)
T ss_pred             CCCCCCCEEecC--CCccCCEEeCCCCCCEEEE
Confidence            599999999887  3333678999999987664

This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=93.43  E-value=0.079  Score=35.68  Aligned_cols=27  Identities=37%  Similarity=0.824  Sum_probs=22.2

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      -||.||.-|.-+      ....+|+.|||....
T Consensus        30 hCp~Cg~PLF~K------dG~v~CPvC~~~~~~   56 (131)
T COG1645          30 HCPKCGTPLFRK------DGEVFCPVCGYREVV   56 (131)
T ss_pred             hCcccCCcceee------CCeEECCCCCceEEE
Confidence            499999999886      448999999986543

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

Probab=93.39  E-value=0.12  Score=37.17  Aligned_cols=42  Identities=19%  Similarity=0.323  Sum_probs=33.7

Q ss_pred             CCcccCCCCCCCceEEEEeccCCCCCC--ceEEEEecCCCCCccccC
Q 033869           66 QTEVTCPACKHGKAVYHELQTRSADEP--MSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        66 ~~~~~CpkCg~~~a~~~~~Q~RsaDE~--~T~fY~C~~~~C~~~wre  110 (110)
                      .....||-||+ ..+..+.+..-.-.|  +-..+.|-+  |||+.++
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            35789999999 777777777776666  566789999  9999864

>PRK10220 hypothetical protein; Provisional

Probab=93.37  E-value=0.073  Score=34.73  Aligned_cols=31  Identities=29%  Similarity=0.749  Sum_probs=24.6

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      .=||.|++-..+.  .   +..|.|+.|+|++...+
T Consensus         4 P~CP~C~seytY~--d---~~~~vCpeC~hEW~~~~   34 (111)
T PRK10220          4 PHCPKCNSEYTYE--D---NGMYICPECAHEWNDAE   34 (111)
T ss_pred             CcCCCCCCcceEc--C---CCeEECCcccCcCCccc
Confidence            4599999988877  1   34799999999987654

>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=93.29  E-value=0.085  Score=37.46  Aligned_cols=44  Identities=25%  Similarity=0.566  Sum_probs=31.9

Q ss_pred             CCCCcccCCCCCCCceEEEEeccCCCCCCc----eEEEEecCCCCCcccc
Q 033869           64 GPQTEVTCPACKHGKAVYHELQTRSADEPM----SIFYMCANKNCKHRWN  109 (110)
Q Consensus        64 ~~~~~~~CpkCg~~~a~~~~~Q~RsaDE~~----T~fY~C~~~~C~~~wr  109 (110)
                      +|..-..|++||..+++--.--.|---.|-    =++|.|++  |.++|-
T Consensus        13 ~pq~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~--Cd~tWN   60 (203)
T COG4332          13 APQPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTH--CDYTWN   60 (203)
T ss_pred             CChhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeec--cCCccc
Confidence            567778999999988865444444444442    36899999  999994

>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=93.25  E-value=0.082  Score=28.99  Aligned_cols=27  Identities=30%  Similarity=0.834  Sum_probs=18.6

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      .||.||+. ...  .......|.|..|++.
T Consensus        20 ~CP~Cg~~-~~~--~~~~~~~~~C~~C~~q   46 (46)
T PF12760_consen   20 VCPHCGST-KHY--RLKTRGRYRCKACRKQ   46 (46)
T ss_pred             CCCCCCCe-eeE--EeCCCCeEECCCCCCc
Confidence            49999987 222  2223579999999863

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

>PRK07219 DNA topoisomerase I; Validated

Probab=93.15  E-value=0.36  Score=41.31  Aligned_cols=31  Identities=26%  Similarity=0.611  Sum_probs=21.5

Q ss_pred             CcCCCCCcccccCCCCCC-ceEEcCC---CCCeeeeC
Q 033869            4 CPTCGTMLQYELPHMDRP-SRFSCPA---CPYVCNME   36 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~-~~~~C~~---C~y~~~~~   36 (110)
                      ||.||.-|..+  +...+ ..+.|.+   |++..+..
T Consensus       605 CP~Cg~~l~~r--~~~~g~~F~gCs~yp~C~~t~~lp  639 (822)
T PRK07219        605 CPECGGDLIII--RTDKGSRFVGCSGYPDCRNTFPLP  639 (822)
T ss_pred             CCCCCCcceee--eccCCceeeecCCCcCCCCeeecC
Confidence            99999866555  22223 4689987   99887654

>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]

Probab=92.97  E-value=0.079  Score=34.36  Aligned_cols=34  Identities=18%  Similarity=0.276  Sum_probs=25.4

Q ss_pred             CCCcCCCCCcccccCC----CCCCceEEcCCCCCeeee
Q 033869            2 EFCPTCGTMLQYELPH----MDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~----~~~~~~~~C~~C~y~~~~   35 (110)
                      .||+.|+++|.|-..-    ..+.+.+.|..||++.-.
T Consensus        57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~   94 (105)
T COG2023          57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRY   94 (105)
T ss_pred             HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEe
Confidence            4899999999996221    133589999999987543

>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=92.85  E-value=0.092  Score=30.88  Aligned_cols=31  Identities=26%  Similarity=0.730  Sum_probs=23.9

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      =||.||..+.-.  .  ..-.|.|+.||+..+++-
T Consensus        30 ~C~~CG~~~~~~--~--~~r~~~C~~Cg~~~~rD~   60 (69)
T PF07282_consen   30 TCPRCGHRNKKR--R--SGRVFTCPNCGFEMDRDV   60 (69)
T ss_pred             CccCcccccccc--c--ccceEEcCCCCCEECcHH
Confidence            499999988773  2  244899999999877653

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

>TIGR00340 zpr1_rel ZPR1-related zinc finger protein

Probab=92.79  E-value=0.21  Score=34.85  Aligned_cols=38  Identities=21%  Similarity=0.385  Sum_probs=22.8

Q ss_pred             CCCCCCCceEEEEeccCCCCCC--ceEEEEecCCCCCccccC
Q 033869           71 CPACKHGKAVYHELQTRSADEP--MSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        71 CpkCg~~~a~~~~~Q~RsaDE~--~T~fY~C~~~~C~~~wre  110 (110)
                      ||.||+..+.+.+..+.-.-=+  .-.-|.|.+  |||+..|
T Consensus         1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~--CGyr~~e   40 (163)
T TIGR00340         1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEK--CGYRSTD   40 (163)
T ss_pred             CCCCCCcceEeeeEeccCCCcceEEEEEEECCC--CCCchhh
Confidence            7888877555544444433333  233478887  8887654

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

>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=92.78  E-value=0.077  Score=28.65  Aligned_cols=28  Identities=29%  Similarity=0.710  Sum_probs=19.0

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW  108 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w  108 (110)
                      +||.||+...++ -        ..+-.++|.+  ||...
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            699999988322 2        3444579999  98754

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.

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=92.71  E-value=0.092  Score=43.79  Aligned_cols=24  Identities=25%  Similarity=0.506  Sum_probs=18.3

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      |.+||.||.-....        .-.|..||..
T Consensus         1 M~~Cp~Cg~~n~~~--------akFC~~CG~~   24 (645)
T PRK14559          1 MLICPQCQFENPNN--------NRFCQKCGTS   24 (645)
T ss_pred             CCcCCCCCCcCCCC--------CccccccCCC
Confidence            88999999876444        4578888874

>PF14353 CpXC: CpXC protein

Probab=92.58  E-value=0.2  Score=32.96  Aligned_cols=39  Identities=23%  Similarity=0.612  Sum_probs=27.3

Q ss_pred             ccCCCCCCC-ceEEEEeccCCCC--------CCceEEEEecCCCCCcccc
Q 033869           69 VTCPACKHG-KAVYHELQTRSAD--------EPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        69 ~~CpkCg~~-~a~~~~~Q~RsaD--------E~~T~fY~C~~~~C~~~wr  109 (110)
                      ..||+||+. ++..|+.=.-+.|        +|.--.|+|.+  ||+..+
T Consensus         2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~--Cg~~~~   49 (128)
T PF14353_consen    2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPS--CGHKFR   49 (128)
T ss_pred             cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCC--CCCcee
Confidence            579999985 6777776443333        34445799999  999764

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=92.55  E-value=0.1  Score=33.48  Aligned_cols=31  Identities=19%  Similarity=0.613  Sum_probs=22.3

Q ss_pred             CCcCCCC-CcccccCCCCCCceEEcCCCCCeeee
Q 033869            3 FCPTCGT-MLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         3 FCp~C~n-lL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      -||.||+ .|..+.++  +....+|++||+....
T Consensus        23 ~CP~Cge~~v~v~~~k--~~~h~~C~~CG~y~~~   54 (99)
T PRK14892         23 ECPRCGKVSISVKIKK--NIAIITCGNCGLYTEF   54 (99)
T ss_pred             ECCCCCCeEeeeecCC--CcceEECCCCCCccCE
Confidence            4999994 34445333  5789999999987553

>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ]

Probab=92.45  E-value=0.072  Score=30.15  Aligned_cols=33  Identities=18%  Similarity=0.468  Sum_probs=25.5

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      =|+.||.+|---  .+-..+.+.|+.|+....+..
T Consensus         6 RC~~CnklLa~~--g~~~~leIKCpRC~tiN~~~a   38 (51)
T PF10122_consen    6 RCGHCNKLLAKA--GEVIELEIKCPRCKTINHVRA   38 (51)
T ss_pred             eccchhHHHhhh--cCccEEEEECCCCCccceEec
Confidence            499999999875  334468999999998766544

>smart00647 IBR In Between Ring fingers

Probab=92.37  E-value=0.19  Score=28.59  Aligned_cols=30  Identities=23%  Similarity=0.834  Sum_probs=21.6

Q ss_pred             CCCCc--CCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            1 MEFCP--TCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         1 M~FCp--~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      +.+||  .|+.++...  .+.....+.|+.|++.
T Consensus        18 ~~~CP~~~C~~~~~~~--~~~~~~~v~C~~C~~~   49 (64)
T smart00647       18 LKWCPAPDCSAAIIVT--EEEGCNRVTCPKCGFS   49 (64)
T ss_pred             ccCCCCCCCcceEEec--CCCCCCeeECCCCCCe
Confidence            35799  999888776  2234568888888875

the domains occurs between pairs og RING fingers

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=92.10  E-value=0.14  Score=45.57  Aligned_cols=12  Identities=33%  Similarity=0.830  Sum_probs=8.2

Q ss_pred             cccCCCCCCCce
Q 033869           68 EVTCPACKHGKA   79 (110)
Q Consensus        68 ~~~CpkCg~~~a   79 (110)
                      ...||+||.+-.
T Consensus       709 a~~CP~CGtplv  720 (1337)
T PRK14714        709 RVECPRCDVELT  720 (1337)
T ss_pred             cccCCCCCCccc
Confidence            347999987543

>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=91.83  E-value=0.11  Score=29.60  Aligned_cols=30  Identities=20%  Similarity=0.698  Sum_probs=15.1

Q ss_pred             CCCCcC--CCCCcccccCCCCCCceEEcCCCCCe
Q 033869            1 MEFCPT--CGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         1 M~FCp~--C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      +++||.  |+.++...  .......+.|+.|++.
T Consensus        18 ~~~Cp~~~C~~~~~~~--~~~~~~~~~C~~C~~~   49 (64)
T PF01485_consen   18 IRWCPNPDCEYIIEKD--DGCNSPIVTCPSCGTE   49 (64)
T ss_dssp             CC--TTSST---ECS---SSTTS--CCTTSCCSE
T ss_pred             ccCCCCCCCcccEEec--CCCCCCeeECCCCCCc
Confidence            358977  99998887  3332224888888875

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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.

>PRK05580 primosome assembly protein PriA; Validated

Probab=91.66  E-value=0.25  Score=41.37  Aligned_cols=10  Identities=30%  Similarity=0.919  Sum_probs=5.7

Q ss_pred             ccCCCCCCCc
Q 033869           69 VTCPACKHGK   78 (110)
Q Consensus        69 ~~CpkCg~~~   78 (110)
                      ..||+||...
T Consensus       422 ~~Cp~Cg~~~  431 (679)
T PRK05580        422 KACPECGSTD  431 (679)
T ss_pred             CCCCCCcCCe
Confidence            3566666654

>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=91.65  E-value=0.14  Score=26.89  Aligned_cols=25  Identities=28%  Similarity=0.777  Sum_probs=19.8

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      |+.|++.+...  .   ...+.|..||.+.
T Consensus        11 C~~C~~~~~~~--~---dG~~yC~~cG~~~   35 (36)
T PF11781_consen   11 CPVCGSRWFYS--D---DGFYYCDRCGHQS   35 (36)
T ss_pred             CCCCCCeEeEc--c---CCEEEhhhCceEc
Confidence            99999996666  2   3499999999763

>PRK04023 DNA polymerase II large subunit; Validated

Probab=91.62  E-value=0.13  Score=44.90  Aligned_cols=21  Identities=33%  Similarity=0.752  Sum_probs=16.9

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      +|||.||..+          ..+.|+.||..
T Consensus       627 RfCpsCG~~t----------~~frCP~CG~~  647 (1121)
T PRK04023        627 RKCPSCGKET----------FYRRCPFCGTH  647 (1121)
T ss_pred             ccCCCCCCcC----------CcccCCCCCCC
Confidence            6999999874          25789999965

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

Probab=91.52  E-value=0.13  Score=35.49  Aligned_cols=36  Identities=31%  Similarity=0.694  Sum_probs=25.0

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceE--EEEecCCCCCcccc
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSI--FYMCANKNCKHRWN  109 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~--fY~C~~~~C~~~wr  109 (110)
                      .||.|+|++-..  +-.|.+++|.++  =-.|.+  |+++|.
T Consensus         2 ~CPfC~~~~tkV--iDSR~~edg~aIRRRReC~~--C~~RFT   39 (156)
T COG1327           2 KCPFCGHEDTKV--IDSRPAEEGNAIRRRRECLE--CGERFT   39 (156)
T ss_pred             CCCCCCCCCCee--eecccccccchhhhhhcccc--cccccc
Confidence            588888876544  446788887664  357877  887764

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=91.48  E-value=0.17  Score=26.48  Aligned_cols=30  Identities=20%  Similarity=0.625  Sum_probs=20.2

Q ss_pred             CcCCCCCcccccCCC-CCCceEEcCCCCCee
Q 033869            4 CPTCGTMLQYELPHM-DRPSRFSCPACPYVC   33 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~-~~~~~~~C~~C~y~~   33 (110)
                      ||.|+.-..+++++. ..+..+.|++|+.++
T Consensus         5 Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    5 CPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             CCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence            888887766663322 345678888888754

>PF12773 DZR: Double zinc ribbon

Probab=91.37  E-value=0.13  Score=28.40  Aligned_cols=21  Identities=33%  Similarity=0.874  Sum_probs=15.9

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACP   30 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~   30 (110)
                      .+||.||..+.+.        .-.|..||
T Consensus        30 ~~C~~Cg~~~~~~--------~~fC~~CG   50 (50)
T PF12773_consen   30 KICPNCGAENPPN--------AKFCPNCG   50 (50)
T ss_pred             CCCcCCcCCCcCC--------cCccCccc
Confidence            5899999986665        55777776

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=91.22  E-value=0.47  Score=26.68  Aligned_cols=34  Identities=18%  Similarity=0.470  Sum_probs=21.9

Q ss_pred             ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869           69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR  107 (110)
Q Consensus        69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~  107 (110)
                      +.||.||.....+. .  +..|.+-.-+|.|.+  |+..
T Consensus         2 kPCPfCGg~~~~~~-~--~~~~~~~~~~~~C~~--Cga~   35 (53)
T TIGR03655         2 KPCPFCGGADVYLR-R--GFDPLDLSHYFECST--CGAS   35 (53)
T ss_pred             CCCCCCCCcceeeE-e--ccCCCCCEEEEECCC--CCCC
Confidence            47999998554342 1  233455566668998  9874

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.

>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=91.15  E-value=0.13  Score=25.52  Aligned_cols=21  Identities=38%  Similarity=0.842  Sum_probs=10.7

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCP   27 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~   27 (110)
                      +||.||+-|.-.++    .-.+.|.
T Consensus         1 ~CP~C~s~l~~~~~----ev~~~C~   21 (28)
T PF03119_consen    1 TCPVCGSKLVREEG----EVDIRCP   21 (28)
T ss_dssp             B-TTT--BEEE-CC----TTCEEE-
T ss_pred             CcCCCCCEeEcCCC----CEeEECC
Confidence            69999999996522    2266665

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.

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=91.10  E-value=0.17  Score=29.27  Aligned_cols=24  Identities=33%  Similarity=0.741  Sum_probs=18.2

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ..||+||++..+         ..+|..|||-..
T Consensus        28 ~~C~~CG~~~~~---------H~vC~~CG~Y~g   51 (57)
T PRK12286         28 VECPNCGEPKLP---------HRVCPSCGYYKG   51 (57)
T ss_pred             eECCCCCCccCC---------eEECCCCCcCCC
Confidence            469999988766         578999997543

>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]

Probab=91.07  E-value=0.22  Score=35.49  Aligned_cols=28  Identities=21%  Similarity=0.514  Sum_probs=23.6

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      -|++|+..|..+      ...+.|++||+++..+
T Consensus       151 ~CsrC~~~L~~~------~~~l~Cp~Cg~tEkRK  178 (188)
T COG1096         151 RCSRCRAPLVKK------GNMLKCPNCGNTEKRK  178 (188)
T ss_pred             EccCCCcceEEc------CcEEECCCCCCEEeee
Confidence            499999999986      4599999999987653

>PRK14873 primosome assembly protein PriA; Provisional

Probab=90.94  E-value=0.31  Score=40.88  Aligned_cols=14  Identities=21%  Similarity=0.508  Sum_probs=7.4

Q ss_pred             ccCCCCCCCceEEE
Q 033869           69 VTCPACKHGKAVYH   82 (110)
Q Consensus        69 ~~CpkCg~~~a~~~   82 (110)
                      ..||+||+....++
T Consensus       423 ~~Cp~Cgs~~l~~~  436 (665)
T PRK14873        423 WRCPRCGSDRLRAV  436 (665)
T ss_pred             ccCCCCcCCcceee
Confidence            35666666544433

>COG1592 Rubrerythrin [Energy production and conversion]

Probab=90.87  E-value=0.14  Score=35.91  Aligned_cols=29  Identities=28%  Similarity=0.746  Sum_probs=22.0

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCCceEE
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVY   81 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~~a~~   81 (110)
                      .|+|+.|||...- .                             ....||-||+.+..|
T Consensus       134 ~~vC~vCGy~~~g-e-----------------------------~P~~CPiCga~k~~F  162 (166)
T COG1592         134 VWVCPVCGYTHEG-E-----------------------------APEVCPICGAPKEKF  162 (166)
T ss_pred             EEEcCCCCCcccC-C-----------------------------CCCcCCCCCChHHHh
Confidence            8999999996442 1                             134799999987766

>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]

Probab=90.78  E-value=0.24  Score=31.10  Aligned_cols=29  Identities=21%  Similarity=0.579  Sum_probs=21.5

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      -||.|+.- ..+  +. ...+|.|+.||++.--
T Consensus        37 ~Cp~C~~~-~Vk--R~-a~GIW~C~kCg~~fAG   65 (89)
T COG1997          37 VCPFCGRT-TVK--RI-ATGIWKCRKCGAKFAG   65 (89)
T ss_pred             cCCCCCCc-cee--ee-ccCeEEcCCCCCeecc
Confidence            59999998 444  22 2469999999998653

>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 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

Probab=90.57  E-value=0.21  Score=30.14  Aligned_cols=35  Identities=20%  Similarity=0.441  Sum_probs=24.9

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      -||.|+.|=.+.--.+++.....|-.|||.....+
T Consensus        10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~   44 (71)
T PF09526_consen   10 VCPKCQAMDTIMMWRENGVEYVECVECGYTERQPD   44 (71)
T ss_pred             cCCCCcCccEEEEEEeCCceEEEecCCCCeeccCC
Confidence            39999988333211334467999999999987766

Members are found in various proteobacteria.

>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]

Probab=90.53  E-value=1.2  Score=29.69  Aligned_cols=37  Identities=30%  Similarity=0.609  Sum_probs=21.1

Q ss_pred             CCcccCCCCCCCceEEEEeccCCCCCCceEEEEecC-CCCCccc
Q 033869           66 QTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN-KNCKHRW  108 (110)
Q Consensus        66 ~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~-~~C~~~w  108 (110)
                      .+.+.||+||....+.     |.+.-+ ..||.|.+ |.|.+.+
T Consensus        58 ~~~~~Cp~C~~~~~~~-----k~~~~~-~~f~~~~~~Pkc~~~~   95 (140)
T COG0551          58 KTGVKCPKCGKGLLVL-----KKGRFG-KNFLGCSNYPKCRFTE   95 (140)
T ss_pred             cCceeCCCCCCCceEE-----EeccCC-ceEEeecCCCcCceee
Confidence            3577899999744433     222222 67887754 2355544

>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=90.53  E-value=0.16  Score=31.41  Aligned_cols=31  Identities=19%  Similarity=0.523  Sum_probs=18.7

Q ss_pred             CcCCCC--CcccccCCCCCCceEEcCCCCCeee
Q 033869            4 CPTCGT--MLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         4 Cp~C~n--lL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ||.||+  -+..+.++......+.|+.||....
T Consensus        25 CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~   57 (81)
T PF05129_consen   25 CPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQ   57 (81)
T ss_dssp             -TTT--SS-EEEEEETTTTEEEEEESSS--EEE
T ss_pred             CCcCCCCCeEEEEEEccCCEEEEEecCCCCeEE
Confidence            888883  3666666667778899999987654

; PDB: 1WII_A.

>PRK00420 hypothetical protein; Validated

Probab=90.46  E-value=0.3  Score=32.08  Aligned_cols=30  Identities=30%  Similarity=0.538  Sum_probs=22.8

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      -||.||.-|.--  +   .....|++||....+.+
T Consensus        25 ~CP~Cg~pLf~l--k---~g~~~Cp~Cg~~~~v~~   54 (112)
T PRK00420         25 HCPVCGLPLFEL--K---DGEVVCPVHGKVYIVKS   54 (112)
T ss_pred             CCCCCCCcceec--C---CCceECCCCCCeeeecc
Confidence            599999888763  1   34899999998766544

>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12

Probab=90.18  E-value=0.31  Score=31.99  Aligned_cols=32  Identities=31%  Similarity=0.780  Sum_probs=22.4

Q ss_pred             CCcCCCCC------cccccCCCCCCceEEcCCCCCeee
Q 033869            3 FCPTCGTM------LQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         3 FCp~C~nl------L~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      -||.||+-      |..+...++....|.|.+|+|.+.
T Consensus        76 kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~  113 (116)
T KOG2907|consen   76 KCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT  113 (116)
T ss_pred             cCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence            49999963      445533345567899999999764

2/RPA12 [Transcription]

>TIGR02443 conserved hypothetical metal-binding protein

Probab=90.13  E-value=0.24  Score=28.88  Aligned_cols=35  Identities=17%  Similarity=0.441  Sum_probs=24.8

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      -||.|+.|=.+.--.++......|-.|||.+..++
T Consensus        11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~~   45 (59)
T TIGR02443        11 VCPACSAQDTLAMWKENNIELVECVECGYQEQQKD   45 (59)
T ss_pred             cCCCCcCccEEEEEEeCCceEEEeccCCCccccCC
Confidence            39999987333222344556899999999987665

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.

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=89.92  E-value=0.57  Score=31.51  Aligned_cols=16  Identities=13%  Similarity=0.449  Sum_probs=13.4

Q ss_pred             CceEEcCCCCCeeeeC
Q 033869           21 PSRFSCPACPYVCNME   36 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~   36 (110)
                      ...+.|+.||+.....
T Consensus        68 p~~~~C~~CG~~~~~~   83 (135)
T PRK03824         68 EAVLKCRNCGNEWSLK   83 (135)
T ss_pred             ceEEECCCCCCEEecc
Confidence            4689999999988765

>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length

Probab=89.89  E-value=0.32  Score=33.34  Aligned_cols=16  Identities=19%  Similarity=0.584  Sum_probs=12.4

Q ss_pred             CCceEEcCCCCCeeee
Q 033869           20 RPSRFSCPACPYVCNM   35 (110)
Q Consensus        20 ~~~~~~C~~C~y~~~~   35 (110)
                      +...|+|.+||+....
T Consensus       109 g~G~l~C~~Cg~~~~~  124 (146)
T PF07295_consen  109 GPGTLVCENCGHEVEL  124 (146)
T ss_pred             cCceEecccCCCEEEe
Confidence            3568999999987544

Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.

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

Probab=89.81  E-value=0.57  Score=32.49  Aligned_cols=38  Identities=29%  Similarity=0.467  Sum_probs=22.7

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceE--EEEecCCCCCccccC
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSI--FYMCANKNCKHRWNE  110 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~--fY~C~~~~C~~~wre  110 (110)
                      .||.||++ ...-...+.-..-+-.+  -|.|.+  |||+..|
T Consensus         2 ~Cp~C~~~-~~~~~~~~~IP~F~evii~sf~C~~--CGyk~~e   41 (160)
T smart00709        2 DCPSCGGN-GTTRMLLTSIPYFREVIIMSFECEH--CGYRNNE   41 (160)
T ss_pred             cCCCCCCC-CEEEEEEecCCCcceEEEEEEECCC--CCCccce
Confidence            48888865 34444445444444333  478887  8887654

Also present in archaeal proteins.

>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain

Probab=89.63  E-value=0.25  Score=27.66  Aligned_cols=31  Identities=13%  Similarity=0.337  Sum_probs=22.8

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      +.||+.||+-|.....+ ....+|.|++....
T Consensus         5 ~l~C~~CG~~m~~~~~~-~~~~yy~C~~~~~~   35 (58)
T PF13408_consen    5 LLRCGHCGSKMTRRKRK-GKYRYYRCSNRRRK   35 (58)
T ss_pred             cEEcccCCcEeEEEECC-CCceEEEcCCCcCC
Confidence            46899999999987333 44578999877643

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=89.52  E-value=0.46  Score=24.11  Aligned_cols=26  Identities=35%  Similarity=0.740  Sum_probs=21.1

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      -|..|+++|..+  .+  ...+.|..|...
T Consensus         3 ~C~~C~t~L~yP--~g--A~~vrCs~C~~v   28 (31)
T TIGR01053         3 VCGGCRTLLMYP--RG--ASSVRCALCQTV   28 (31)
T ss_pred             CcCCCCcEeecC--CC--CCeEECCCCCeE
Confidence            489999999888  44  458999999865

This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC

>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.40  E-value=0.16  Score=25.21  Aligned_cols=27  Identities=26%  Similarity=0.698  Sum_probs=17.3

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPY   31 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y   31 (110)
                      =||.|++.+...  ..+....+.|+.|..
T Consensus         3 ~C~rC~~~~~~~--~~~~r~~~~C~rCq~   29 (30)
T PF06827_consen    3 KCPRCWNYIEDI--GINGRSTYLCPRCQK   29 (30)
T ss_dssp             B-TTT--BBEEE--EETTEEEEE-TTTCC
T ss_pred             cCccCCCcceEe--EecCCCCeECcCCcC
Confidence            389999998776  445677899999963

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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....

>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit

Probab=89.34  E-value=0.074  Score=40.18  Aligned_cols=30  Identities=30%  Similarity=0.605  Sum_probs=23.4

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      =||.|+.+|+.++-   ..+.++|+.|||-...
T Consensus        28 ~c~~c~~~~~~~~l---~~~~~vc~~c~~h~rl   57 (285)
T TIGR00515        28 KCPKCGQVLYTKEL---ERNLEVCPKCDHHMRM   57 (285)
T ss_pred             ECCCCcchhhHHHH---HhhCCCCCCCCCcCcC
Confidence            49999999999832   2346899999997654

The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.

>COG4640 Predicted membrane protein [Function unknown]

Probab=89.27  E-value=0.2  Score=39.58  Aligned_cols=26  Identities=31%  Similarity=0.806  Sum_probs=17.8

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      |+|||.||+-=.-        ..+.|..||....
T Consensus         1 M~fC~kcG~qk~E--------d~~qC~qCG~~~t   26 (465)
T COG4640           1 MKFCPKCGSQKAE--------DDVQCTQCGHKFT   26 (465)
T ss_pred             CCccccccccccc--------ccccccccCCcCC
Confidence            9999999953111        1333999998643

>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional

Probab=89.21  E-value=0.37  Score=38.71  Aligned_cols=52  Identities=25%  Similarity=0.604  Sum_probs=32.1

Q ss_pred             CCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEe
Q 033869           20 RPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHEL   84 (110)
Q Consensus        20 ~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~   84 (110)
                      ....|.|+.|||+++....           +....|..+ ..+. +|- ++.||.||..+..|-.+
T Consensus       422 ~~~~~~c~~c~~~yd~~~g-----------~~~~~~~~g-t~~~~lp~-~~~cp~c~~~k~~f~~~  474 (479)
T PRK05452        422 LGPRMQCSVCQWIYDPAKG-----------EPMQDVAPG-TPWSEVPD-NFLCPECSLGKDVFDEL  474 (479)
T ss_pred             CCCeEEECCCCeEECCCCC-----------CcccCCCCC-CChhhCCC-CCcCcCCCCcHHHhEec
Confidence            3568999999998875431           001112211 1223 553 88999999998876544

>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed

Probab=89.11  E-value=0.072  Score=40.49  Aligned_cols=31  Identities=19%  Similarity=0.399  Sum_probs=23.8

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      =||.|+.+|+.++-.   .+.++|+.|+|-...+
T Consensus        40 kc~~C~~~~~~~~l~---~~~~vcp~c~~h~rlt   70 (296)
T CHL00174         40 QCENCYGLNYKKFLK---SKMNICEQCGYHLKMS   70 (296)
T ss_pred             ECCCccchhhHHHHH---HcCCCCCCCCCCcCCC
Confidence            499999999998322   4579999999965443

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=89.08  E-value=0.21  Score=26.20  Aligned_cols=28  Identities=25%  Similarity=0.541  Sum_probs=17.1

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPY   31 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y   31 (110)
                      .|++||+.......... .....|+.||.
T Consensus         7 ~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~   34 (41)
T smart00834        7 RCEDCGHTFEVLQKISD-DPLATCPECGG   34 (41)
T ss_pred             EcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence            48888885544321211 45677888886

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

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

Probab=88.99  E-value=0.3  Score=29.15  Aligned_cols=30  Identities=27%  Similarity=0.665  Sum_probs=22.6

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR  107 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~  107 (110)
                      .+++||.|||...+|--.|+         --.|..  ||..
T Consensus        18 l~VkCpdC~N~q~vFshast---------~V~C~~--CG~~   47 (67)
T COG2051          18 LRVKCPDCGNEQVVFSHAST---------VVTCLI--CGTT   47 (67)
T ss_pred             EEEECCCCCCEEEEeccCce---------EEEecc--cccE
Confidence            37899999999999955443         257877  8753

>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=88.90  E-value=0.51  Score=24.72  Aligned_cols=33  Identities=21%  Similarity=0.539  Sum_probs=22.1

Q ss_pred             CCCcccCCCCCCCceEEEEeccCCCCCCceEEEEecC
Q 033869           65 PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN  101 (110)
Q Consensus        65 ~~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~  101 (110)
                      +++++.||.|+..+.++-.=+.   ..|-. =|.|..
T Consensus         2 a~i~v~CP~C~s~~~v~k~G~~---~~G~q-ryrC~~   34 (36)
T PF03811_consen    2 AKIDVHCPRCQSTEGVKKNGKS---PSGHQ-RYRCKD   34 (36)
T ss_pred             CcEeeeCCCCCCCCcceeCCCC---CCCCE-eEecCc
Confidence            4578999999999977744332   22333 377776

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

>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]

Probab=88.83  E-value=0.13  Score=38.86  Aligned_cols=31  Identities=29%  Similarity=0.623  Sum_probs=24.5

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      =||.|+.|||-++-   ..+.++|++|+|-..+.
T Consensus        30 KCp~c~~~~y~~eL---~~n~~vcp~c~~h~ri~   60 (294)
T COG0777          30 KCPSCGEMLYRKEL---ESNLKVCPKCGHHMRIS   60 (294)
T ss_pred             ECCCccceeeHHHH---HhhhhcccccCcccccC
Confidence            49999999999832   35689999999965543

>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=88.54  E-value=0.43  Score=27.23  Aligned_cols=27  Identities=22%  Similarity=0.519  Sum_probs=17.8

Q ss_pred             CcCCC--CCcccccCCCCCCceEEcCCCCCe
Q 033869            4 CPTCG--TMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         4 Cp~C~--nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      |+.|.  |=|.++  .+.....|.|+.||+.
T Consensus        25 C~~C~~hNGla~~--~~~~~i~y~C~~Cg~~   53 (54)
T PF10058_consen   25 CSKCFSHNGLAPK--EEFEEIQYRCPYCGAL   53 (54)
T ss_pred             Ccccchhhccccc--ccCCceEEEcCCCCCc
Confidence            67776  446665  3444568888888863

>TIGR01031 rpmF_bact ribosomal protein L32

Probab=88.53  E-value=0.3  Score=27.99  Aligned_cols=23  Identities=35%  Similarity=0.883  Sum_probs=16.4

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      ..||+||++..+         ..+|..|||-.
T Consensus        27 ~~C~~cG~~~~~---------H~vc~~cG~Y~   49 (55)
T TIGR01031        27 VVCPNCGEFKLP---------HRVCPSCGYYK   49 (55)
T ss_pred             eECCCCCCcccC---------eeECCccCeEC
Confidence            358888886554         57888888643

This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.

>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=88.35  E-value=0.019  Score=31.38  Aligned_cols=30  Identities=40%  Similarity=0.674  Sum_probs=23.3

Q ss_pred             CCCCceEEEEeccCCCCCCceEEEEecCCCCCc
Q 033869           74 CKHGKAVYHELQTRSADEPMSIFYMCANKNCKH  106 (110)
Q Consensus        74 Cg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~  106 (110)
                      |.|.= +.-..|+|+.||.-+.+=.|.+  |+.
T Consensus        13 C~H~f-~~~E~Q~RAGDE~VSfI~~C~~--C~~   42 (43)
T PF11792_consen   13 CKHKF-VTIEKQLRAGDEAVSFIKYCQK--CGQ   42 (43)
T ss_pred             ceeee-eehhhhhcccchHHHHHHHHHH--hCC
Confidence            65543 3556899999999888888888  875

>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated

Probab=88.34  E-value=1.1  Score=38.75  Aligned_cols=33  Identities=30%  Similarity=0.715  Sum_probs=19.3

Q ss_pred             CcccCCC--CCCCceEEEEeccCCCCCCceEEEEecC-CCCCc
Q 033869           67 TEVTCPA--CKHGKAVYHELQTRSADEPMSIFYMCAN-KNCKH  106 (110)
Q Consensus        67 ~~~~Cpk--Cg~~~a~~~~~Q~RsaDE~~T~fY~C~~-~~C~~  106 (110)
                      +...||+  ||..   ...   |..--| ..||.|.+ +.|.+
T Consensus       692 ~~~~CP~~~C~g~---l~~---r~gr~G-~~f~~Cs~yp~C~~  727 (860)
T PRK06319        692 ETVPCPAIGCTGH---IVK---RRSRFN-KMFYSCSEYPACSV  727 (860)
T ss_pred             cCCCCCCcCCCCc---EEE---EecCCC-CeeeccCCCCCCce
Confidence            4568997  5642   222   333334 45888975 66875

>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins

Probab=88.30  E-value=0.15  Score=26.52  Aligned_cols=21  Identities=33%  Similarity=0.719  Sum_probs=12.4

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPY   31 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y   31 (110)
                      -|+.||.+..|+        ...|+.|+-
T Consensus        13 rC~~Cg~~~~pP--------r~~Cp~C~s   33 (37)
T PF12172_consen   13 RCRDCGRVQFPP--------RPVCPHCGS   33 (37)
T ss_dssp             E-TTT--EEES----------SEETTTT-
T ss_pred             EcCCCCCEecCC--------CcCCCCcCc
Confidence            588999998888        568888873

The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.

>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast

Probab=88.26  E-value=0.2  Score=30.50  Aligned_cols=29  Identities=21%  Similarity=0.564  Sum_probs=14.3

Q ss_pred             CCCcCCCCCcccccCC---------CCCCceEEcCCCC
Q 033869            2 EFCPTCGTMLQYELPH---------MDRPSRFSCPACP   30 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~---------~~~~~~~~C~~C~   30 (110)
                      .||..||++|.|-...         ....+.+.|..||
T Consensus        47 ~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~   84 (85)
T PF04032_consen   47 TICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCG   84 (85)
T ss_dssp             TB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTT
T ss_pred             ccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccC
Confidence            4899999998886221         1335566777776

Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.

>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1

Probab=88.19  E-value=0.19  Score=30.56  Aligned_cols=9  Identities=56%  Similarity=1.693  Sum_probs=4.5

Q ss_pred             CCCcCCCCC
Q 033869            2 EFCPTCGTM   10 (110)
Q Consensus         2 ~FCp~C~nl   10 (110)
                      .|||.|||-
T Consensus        25 ~FCp~CGn~   33 (73)
T PF08772_consen   25 QFCPKCGNA   33 (73)
T ss_dssp             -S-SSS--S
T ss_pred             eeCcccCCC
Confidence            599999986

; PDB: 2CON_A.

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=87.92  E-value=0.48  Score=25.60  Aligned_cols=23  Identities=35%  Similarity=0.892  Sum_probs=17.5

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACP   30 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~   30 (110)
                      .||.||..|.-.  ++   ....|..|+
T Consensus        19 ~Cp~C~~PL~~~--k~---g~~~Cv~C~   41 (41)
T PF06677_consen   19 HCPDCGTPLMRD--KD---GKIYCVSCG   41 (41)
T ss_pred             ccCCCCCeeEEe--cC---CCEECCCCC
Confidence            699999888874  32   367899885

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7

Probab=87.90  E-value=0.32  Score=28.36  Aligned_cols=25  Identities=24%  Similarity=0.664  Sum_probs=16.1

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      -|-+||.-+.++  +   +..+.||-|||.
T Consensus        22 iCgdC~~en~lk--~---~D~irCReCG~R   46 (62)
T KOG3507|consen   22 ICGDCGQENTLK--R---GDVIRCRECGYR   46 (62)
T ss_pred             Eecccccccccc--C---CCcEehhhcchH
Confidence            367777666665  2   346777777774

0 [Transcription]

>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=87.76  E-value=0.53  Score=27.55  Aligned_cols=30  Identities=30%  Similarity=0.692  Sum_probs=23.2

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW  108 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w  108 (110)
                      +-..||.||+....          ......|.|.+  ||+.+
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            67789999986553          24556799999  99876

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

>PRK05654 acetyl-CoA carboxylase subunit beta; Validated

Probab=87.52  E-value=0.13  Score=39.04  Aligned_cols=31  Identities=26%  Similarity=0.596  Sum_probs=23.8

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      =||.|+.+++.++-.   .+.++|+.|||-....
T Consensus        29 ~c~~c~~~~~~~~l~---~~~~vc~~c~~h~rl~   59 (292)
T PRK05654         29 KCPSCGQVLYRKELE---ANLNVCPKCGHHMRIS   59 (292)
T ss_pred             ECCCccchhhHHHHH---hcCCCCCCCCCCeeCC
Confidence            499999999998322   3468999999976543

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=87.41  E-value=0.59  Score=30.72  Aligned_cols=23  Identities=39%  Similarity=0.989  Sum_probs=20.4

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ||-||.-|.+.        .+.|..|+....
T Consensus         1 CPvCg~~l~vt--------~l~C~~C~t~i~   23 (113)
T PF09862_consen    1 CPVCGGELVVT--------RLKCPSCGTEIE   23 (113)
T ss_pred             CCCCCCceEEE--------EEEcCCCCCEEE
Confidence            99999999998        899999998643

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=87.28  E-value=0.57  Score=25.60  Aligned_cols=25  Identities=24%  Similarity=0.636  Sum_probs=19.3

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      |.+||.-..++  .   ...+.|+.||+..
T Consensus         5 C~~Cg~~~~~~--~---~~~irC~~CG~rI   29 (44)
T smart00659        5 CGECGRENEIK--S---KDVVRCRECGYRI   29 (44)
T ss_pred             CCCCCCEeecC--C---CCceECCCCCceE
Confidence            88999877665  2   3579999999853

present in RNA polymerase I, II and III

>PRK11032 hypothetical protein; Provisional

Probab=87.09  E-value=0.59  Score=32.53  Aligned_cols=16  Identities=13%  Similarity=0.314  Sum_probs=12.0

Q ss_pred             CCceEEcCCCCCeeee
Q 033869           20 RPSRFSCPACPYVCNM   35 (110)
Q Consensus        20 ~~~~~~C~~C~y~~~~   35 (110)
                      +...++|.+||+...+
T Consensus       121 g~G~LvC~~Cg~~~~~  136 (160)
T PRK11032        121 GLGNLVCEKCHHHLAF  136 (160)
T ss_pred             ecceEEecCCCCEEEe
Confidence            3568999999986543

>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=87.08  E-value=0.44  Score=35.19  Aligned_cols=26  Identities=38%  Similarity=1.016  Sum_probs=20.8

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      =||.||. |.        .-.+.|+.||++.+++-
T Consensus       311 ~C~~cg~-~~--------~r~~~C~~cg~~~~rD~  336 (364)
T COG0675         311 TCPCCGH-LS--------GRLFKCPRCGFVHDRDV  336 (364)
T ss_pred             cccccCC-cc--------ceeEECCCCCCeehhhH
Confidence            4999999 22        23899999999988875

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

Probab=86.83  E-value=0.87  Score=23.36  Aligned_cols=27  Identities=19%  Similarity=0.252  Sum_probs=20.0

Q ss_pred             CCcCCCCCccc-ccCCCCCCceEEcCCCCCeee
Q 033869            3 FCPTCGTMLQY-ELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         3 FCp~C~nlL~~-~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      -|+.||.-+.. +   +  +.++.|..||.+++
T Consensus         5 ~C~~C~~~~i~~~---~--~~~~~C~~Cg~~~~   32 (33)
T PF08792_consen    5 KCSKCGGNGIVNK---E--DDYEVCIFCGSSFP   32 (33)
T ss_pred             EcCCCCCCeEEEe---c--CCeEEcccCCcEee
Confidence            48889866655 4   1  45999999998764

>PF14205 Cys_rich_KTR: Cysteine-rich KTR

Probab=86.20  E-value=0.69  Score=26.53  Aligned_cols=34  Identities=24%  Similarity=0.614  Sum_probs=26.1

Q ss_pred             CCcCCCCC--cccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTM--LQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nl--L~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      .||-|||-  +.+++|..-...-+.|+.|..+.-++
T Consensus         6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~   41 (55)
T PF14205_consen    6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLID   41 (55)
T ss_pred             ECCCCCCccceeeecCceeccccccCCCCCceEEEE
Confidence            69999964  67776666667789999999876544

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

Probab=85.93  E-value=0.26  Score=35.32  Aligned_cols=37  Identities=19%  Similarity=0.497  Sum_probs=24.3

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      +...||.||..+. -+.+ ++.  .|....+.|.+  ||+.|+
T Consensus         5 iy~~Cp~Cg~eev-~hEV-ik~--~g~~~lvrC~e--CG~V~~   41 (201)
T COG1326           5 IYIECPSCGSEEV-SHEV-IKE--RGREPLVRCEE--CGTVHP   41 (201)
T ss_pred             EEEECCCCCcchh-hHHH-HHh--cCCceEEEccC--CCcEee
Confidence            4578999994443 1111 121  34558899999  999995

>PHA02942 putative transposase; Provisional

Probab=85.82  E-value=0.7  Score=36.22  Aligned_cols=31  Identities=29%  Similarity=0.712  Sum_probs=23.0

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      +-||.||......   .  .-.|.|..||+..+.+-
T Consensus       326 q~Cs~CG~~~~~l---~--~r~f~C~~CG~~~drD~  356 (383)
T PHA02942        326 VSCPKCGHKMVEI---A--HRYFHCPSCGYENDRDV  356 (383)
T ss_pred             ccCCCCCCccCcC---C--CCEEECCCCCCEeCcHH
Confidence            4699999876421   1  23799999999987764

>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=85.60  E-value=0.43  Score=30.16  Aligned_cols=29  Identities=21%  Similarity=0.449  Sum_probs=22.0

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      .+||.||..-.-+  .  ...+|.|+.|++..-
T Consensus        36 y~Cp~Cgk~~vkR--~--a~GIW~C~~C~~~~A   64 (90)
T PF01780_consen   36 YTCPFCGKTSVKR--V--ATGIWKCKKCGKKFA   64 (90)
T ss_dssp             BEESSSSSSEEEE--E--ETTEEEETTTTEEEE
T ss_pred             CcCCCCCCceeEE--e--eeEEeecCCCCCEEe
Confidence            3799999988555  2  245899999998754

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 [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=85.16  E-value=0.85  Score=26.66  Aligned_cols=10  Identities=20%  Similarity=0.434  Sum_probs=5.4

Q ss_pred             EEcCCCCCee
Q 033869           24 FSCPACPYVC   33 (110)
Q Consensus        24 ~~C~~C~y~~   33 (110)
                      -+|..||-..
T Consensus        10 ~~CtSCg~~i   19 (61)
T COG2888          10 PVCTSCGREI   19 (61)
T ss_pred             ceeccCCCEe
Confidence            3566666544

>TIGR00310 ZPR1_znf ZPR1 zinc finger domain

Probab=85.01  E-value=1.7  Score=31.04  Aligned_cols=39  Identities=23%  Similarity=0.527  Sum_probs=21.5

Q ss_pred             cCCCCCCC-ceEEEEec-cCCCCCCceEEEEecCCCCCccccC
Q 033869           70 TCPACKHG-KAVYHELQ-TRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        70 ~CpkCg~~-~a~~~~~Q-~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      .||.||.+ ........ +=--.|=+-.-|.|.+  |||+.+|
T Consensus         2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~--CGyr~~e   42 (192)
T TIGR00310         2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEH--CGYRSND   42 (192)
T ss_pred             cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCC--CCCccce
Confidence            58999864 33333333 1111222334588888  9888764

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=84.89  E-value=1.1  Score=28.43  Aligned_cols=13  Identities=31%  Similarity=0.851  Sum_probs=7.6

Q ss_pred             CceEEcCCCCCee
Q 033869           21 PSRFSCPACPYVC   33 (110)
Q Consensus        21 ~~~~~C~~C~y~~   33 (110)
                      .+.|.|.+|+|.+
T Consensus        88 T~fy~C~~C~~~w  100 (104)
T TIGR01384        88 TRFYKCTKCGYVW  100 (104)
T ss_pred             EEEEEeCCCCCee
Confidence            4556666666654

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.

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=84.87  E-value=0.28  Score=25.10  Aligned_cols=25  Identities=24%  Similarity=0.676  Sum_probs=17.0

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      |.+||.....+  ..   ..+.|+.|||..
T Consensus         3 C~~Cg~~~~~~--~~---~~irC~~CG~RI   27 (32)
T PF03604_consen    3 CGECGAEVELK--PG---DPIRCPECGHRI   27 (32)
T ss_dssp             ESSSSSSE-BS--TS---STSSBSSSS-SE
T ss_pred             CCcCCCeeEcC--CC---CcEECCcCCCeE
Confidence            78999887766  22   357999999853

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus

Probab=84.66  E-value=0.66  Score=27.81  Aligned_cols=28  Identities=21%  Similarity=0.534  Sum_probs=18.9

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      | .||+.||.+++    .-.=.| .||+.-.++.
T Consensus         6 C-~Cgr~lya~e~----~kTkkC-~CG~~l~vk~   33 (68)
T PF09082_consen    6 C-DCGRYLYAKEG----AKTKKC-VCGKTLKVKE   33 (68)
T ss_dssp             E-TTS--EEEETT-----SEEEE-TTTEEEE--S
T ss_pred             e-cCCCEEEecCC----cceeEe-cCCCeeeeee
Confidence            7 79999999933    337899 9999887766

The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=84.65  E-value=1.2  Score=25.89  Aligned_cols=8  Identities=25%  Similarity=0.758  Sum_probs=4.3

Q ss_pred             EEcCCCCC
Q 033869           24 FSCPACPY   31 (110)
Q Consensus        24 ~~C~~C~y   31 (110)
                      .+|..||-
T Consensus         8 ~~CtSCg~   15 (59)
T PRK14890          8 PKCTSCGI   15 (59)
T ss_pred             ccccCCCC
Confidence            35556654

>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=84.54  E-value=1.1  Score=21.70  Aligned_cols=25  Identities=32%  Similarity=0.755  Sum_probs=19.1

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      |..|..+|..+  .+  .....|..|+++
T Consensus         1 C~~Cr~~L~yp--~G--A~sVrCa~C~~V   25 (25)
T PF06943_consen    1 CGGCRTLLMYP--RG--APSVRCACCHTV   25 (25)
T ss_pred             CCCCCceEEcC--CC--CCCeECCccCcC
Confidence            67899888887  44  458999999863

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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].

>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function

Probab=84.53  E-value=0.88  Score=32.83  Aligned_cols=15  Identities=20%  Similarity=0.689  Sum_probs=12.0

Q ss_pred             eEEcCCCCCeeeeCC
Q 033869           23 RFSCPACPYVCNMES   37 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~   37 (110)
                      .+.|+.|+.+.....
T Consensus         5 ~~~CPvC~~~F~~~~   19 (214)
T PF09986_consen    5 KITCPVCGKEFKTKK   19 (214)
T ss_pred             ceECCCCCCeeeeeE
Confidence            589999999877654

>PRK11827 hypothetical protein; Provisional

Probab=84.45  E-value=1.3  Score=25.93  Aligned_cols=31  Identities=19%  Similarity=0.466  Sum_probs=24.9

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      -||.|+.-|...  .+  ...+.|..|+-.+++.+
T Consensus        10 aCP~ckg~L~~~--~~--~~~Lic~~~~laYPI~d   40 (60)
T PRK11827         10 ACPVCNGKLWYN--QE--KQELICKLDNLAFPLRD   40 (60)
T ss_pred             ECCCCCCcCeEc--CC--CCeEECCccCeeccccC
Confidence            499999988876  32  34789999999888876

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

Probab=83.77  E-value=0.71  Score=31.15  Aligned_cols=33  Identities=21%  Similarity=0.415  Sum_probs=21.4

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      -||.|+|-=.--+ ++++...+.|..||...++.
T Consensus        99 lC~~C~sPdT~l~-k~~r~~~l~C~ACGa~~~v~  131 (133)
T TIGR00311        99 ICRECNRPDTRII-KEGRVSLLKCEACGAKAPLR  131 (133)
T ss_pred             ECCCCCCCCcEEE-EeCCeEEEecccCCCCCccC
Confidence            3999998522111 22344567999999987764

>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.68  E-value=1  Score=27.81  Aligned_cols=35  Identities=29%  Similarity=0.461  Sum_probs=27.4

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      |.-||.||--|.++  ...+.-+-.|+.|+-++....
T Consensus         1 ~llCP~C~v~l~~~--~rs~vEiD~CPrCrGVWLDrG   35 (88)
T COG3809           1 MLLCPICGVELVMS--VRSGVEIDYCPRCRGVWLDRG   35 (88)
T ss_pred             CcccCcCCceeeee--eecCceeeeCCccccEeecch
Confidence            67899999999888  333456789999998876544

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=83.61  E-value=0.79  Score=29.84  Aligned_cols=31  Identities=26%  Similarity=0.610  Sum_probs=24.1

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      +.||.||.-.|=-    + +.-++|+.||..+....
T Consensus        10 R~Cp~CG~kFYDL----n-k~PivCP~CG~~~~~~~   40 (108)
T PF09538_consen   10 RTCPSCGAKFYDL----N-KDPIVCPKCGTEFPPEP   40 (108)
T ss_pred             ccCCCCcchhccC----C-CCCccCCCCCCccCccc
Confidence            5799999887755    1 24688999999988763

The function of members of this family is unknown.

>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.27  E-value=0.8  Score=24.32  Aligned_cols=35  Identities=17%  Similarity=0.260  Sum_probs=19.1

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      .-|..|+..|-|-..=+.....|.|.-|+...++.
T Consensus         3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp   37 (40)
T PF04810_consen    3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLP   37 (40)
T ss_dssp             -B-TTT--BS-TTSEEETTTTEEEETTT--EEE--
T ss_pred             cccCCCCCEECCcceEcCCCCEEECcCCCCcCCCC
Confidence            35899999998863233445699999999876654

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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....

>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional

Probab=82.95  E-value=0.78  Score=25.60  Aligned_cols=23  Identities=22%  Similarity=0.677  Sum_probs=19.3

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      ..|-.|+-.+.+.        .-.||.|||.
T Consensus        15 ~ICrkC~ARnp~~--------A~~CRKCg~~   37 (48)
T PRK04136         15 KICMRCNARNPWR--------ATKCRKCGYK   37 (48)
T ss_pred             cchhcccCCCCcc--------ccccccCCCC
Confidence            4789999999998        5579999984

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

Probab=82.79  E-value=0.85  Score=30.94  Aligned_cols=33  Identities=24%  Similarity=0.444  Sum_probs=22.3

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      -||+|+|.=.-- -++++...+.|..||...++.
T Consensus       104 lC~~C~spdT~l-~k~~r~~~l~C~ACGa~~~V~  136 (138)
T PRK03988        104 ICPECGSPDTKL-IKEGRIWVLKCEACGAETPVK  136 (138)
T ss_pred             ECCCCCCCCcEE-EEcCCeEEEEcccCCCCCcCC
Confidence            499999852211 123456789999999887654

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=82.38  E-value=1.4  Score=31.00  Aligned_cols=28  Identities=25%  Similarity=0.634  Sum_probs=23.2

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      +|+.||..|.|.  .   ...+.|+.|+..+..
T Consensus       151 ~~~~~g~~~~~~--~---~~~~~c~~~~~~e~r  178 (189)
T PRK09521        151 MCSRCRTPLVKK--G---ENELKCPNCGNIETR  178 (189)
T ss_pred             EccccCCceEEC--C---CCEEECCCCCCEEee
Confidence            699999999887  2   258999999988774

>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]

Probab=82.33  E-value=1.6  Score=39.14  Aligned_cols=17  Identities=29%  Similarity=0.940  Sum_probs=13.9

Q ss_pred             CceEEcCCCCCeeeeCC
Q 033869           21 PSRFSCPACPYVCNMES   37 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~~   37 (110)
                      ...|.|+.|.|.+-.++
T Consensus       912 ~PHY~Cp~Cky~Ef~~d  928 (1444)
T COG2176         912 PPHYLCPECKYSEFIDD  928 (1444)
T ss_pred             CccccCCCCceeeeecC
Confidence            34799999999987765

>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=82.11  E-value=3.9  Score=22.06  Aligned_cols=30  Identities=33%  Similarity=0.727  Sum_probs=18.9

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceEEEEecCC
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANK  102 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~  102 (110)
                      .|+ || ..++-+++. +..+.+=-+||.|.+.
T Consensus         2 ~C~-Cg-~~~~~~~s~-k~~~N~GR~Fy~C~~~   31 (45)
T PF06839_consen    2 KCP-CG-EPAVRRTSK-KTGPNPGRRFYKCPNY   31 (45)
T ss_pred             CCC-CC-CEeEEEEEe-CCCCCCCCcceECCCC
Confidence            366 66 445544443 2466677799999863

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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding

>PRK05582 DNA topoisomerase I; Validated

Probab=82.11  E-value=2.7  Score=35.15  Aligned_cols=32  Identities=31%  Similarity=0.723  Sum_probs=18.1

Q ss_pred             cccCCCCCCCceEEEEeccCCCCCCceEEEEecC-CCCCc
Q 033869           68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN-KNCKH  106 (110)
Q Consensus        68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~-~~C~~  106 (110)
                      ...||+|+.. +..     |....+ ..|+.|.+ +.|++
T Consensus       611 ~~~CP~C~~~-l~l-----~k~k~g-k~f~~Cs~~p~C~~  643 (650)
T PRK05582        611 GVKCPKCGGQ-IVE-----RKSKKG-RKFYGCSRYPECDF  643 (650)
T ss_pred             CCCCCCCCCc-eEE-----EcCCCC-ceeeccCCCCCCCc
Confidence            4679999864 221     222223 25888865 34764

>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=81.80  E-value=1.2  Score=30.88  Aligned_cols=39  Identities=26%  Similarity=0.481  Sum_probs=17.7

Q ss_pred             ccCCCCCCCceEEEEeccCCCC--CCceEEEEecCCCCCccccC
Q 033869           69 VTCPACKHGKAVYHELQTRSAD--EPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        69 ~~CpkCg~~~a~~~~~Q~RsaD--E~~T~fY~C~~~~C~~~wre  110 (110)
                      ..||.||+....-. +.+.--.  |=.-.-|.|.+  ||++.+|
T Consensus         2 s~Cp~C~~~~~~~~-~~~~IP~F~evii~sf~C~~--CGyk~~e   42 (161)
T PF03367_consen    2 SLCPNCGENGTTRI-LLTDIPYFKEVIIMSFECEH--CGYKNNE   42 (161)
T ss_dssp             EE-TTTSSCCEEEE-EEEEETTTEEEEEEEEE-TT--T--EEEE
T ss_pred             CcCCCCCCCcEEEE-EEEcCCCCceEEEEEeECCC--CCCEeee
Confidence            36888887643221 2222211  22334478888  8887653

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.

>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=81.67  E-value=0.49  Score=27.09  Aligned_cols=21  Identities=38%  Similarity=0.921  Sum_probs=14.1

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      .||.||.+-.+.         .+|..|||.
T Consensus        28 ~c~~cg~~~~~H---------~vc~~cG~y   48 (56)
T PF01783_consen   28 KCPNCGEPKLPH---------RVCPSCGYY   48 (56)
T ss_dssp             ESSSSSSEESTT---------SBCTTTBBS
T ss_pred             eeccCCCEeccc---------EeeCCCCeE
Confidence            588888655443         568888764

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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=81.62  E-value=1  Score=34.23  Aligned_cols=30  Identities=23%  Similarity=0.597  Sum_probs=20.5

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ..||+||+- .+-+|.  ....++|..||++-.
T Consensus        12 ~~Cp~Cg~~-~iv~d~--~~Ge~vC~~CG~Vl~   41 (310)
T PRK00423         12 LVCPECGSD-KLIYDY--ERGEIVCADCGLVIE   41 (310)
T ss_pred             CcCcCCCCC-CeeEEC--CCCeEeecccCCccc
Confidence            479999973 222222  356999999999643

>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=81.50  E-value=0.93  Score=25.24  Aligned_cols=27  Identities=30%  Similarity=0.784  Sum_probs=16.8

Q ss_pred             CCCc--CCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            2 EFCP--TCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         2 ~FCp--~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      +.||  +||.-...-    .+..++.|-.|+|+
T Consensus        19 k~CP~~~CG~GvFMA----~H~dR~~CGKCg~T   47 (47)
T PF01599_consen   19 KECPSPRCGAGVFMA----EHKDRHYCGKCGYT   47 (47)
T ss_dssp             EE-TSTTTTSSSEEE----E-SSEEEETTTSS-
T ss_pred             hcCCCcccCCceEee----ecCCCccCCCcccC
Confidence            3688  999843332    23459999999974

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 [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=81.23  E-value=0.75  Score=24.66  Aligned_cols=10  Identities=30%  Similarity=0.906  Sum_probs=5.1

Q ss_pred             ceEEcCCCCC
Q 033869           22 SRFSCPACPY   31 (110)
Q Consensus        22 ~~~~C~~C~y   31 (110)
                      ....|+.||-
T Consensus        25 ~~~~CP~Cg~   34 (42)
T PF09723_consen   25 DPVPCPECGS   34 (42)
T ss_pred             CCCcCCCCCC
Confidence            3455555554

The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=81.22  E-value=1  Score=26.29  Aligned_cols=30  Identities=27%  Similarity=0.678  Sum_probs=22.9

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR  107 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~  107 (110)
                      .+++||.|++...+|--.|+         --.|..  ||..
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            47899999999999966542         257877  8764

>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=81.17  E-value=0.87  Score=36.25  Aligned_cols=30  Identities=27%  Similarity=0.661  Sum_probs=24.2

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      -||.||.-|...    .+. -|.|+.||+...-+.
T Consensus       352 ~Cp~Cg~~m~S~----G~~-g~rC~kCg~~~~~~~  381 (421)
T COG1571         352 VCPRCGGRMKSA----GRN-GFRCKKCGTRARETL  381 (421)
T ss_pred             CCCccCCchhhc----CCC-CcccccccccCCccc
Confidence            599999999877    223 899999999876554

>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]

Probab=81.14  E-value=0.79  Score=31.02  Aligned_cols=22  Identities=32%  Similarity=0.701  Sum_probs=19.8

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      =|++||++..|+        +-.|+.|+..
T Consensus        31 kC~~CG~v~~PP--------r~~Cp~C~~~   52 (140)
T COG1545          31 KCKKCGRVYFPP--------RAYCPKCGSE   52 (140)
T ss_pred             EcCCCCeEEcCC--------cccCCCCCCC
Confidence            399999999999        7789999987

>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=81.12  E-value=1  Score=33.50  Aligned_cols=35  Identities=29%  Similarity=0.663  Sum_probs=14.8

Q ss_pred             CCCcCCCCC-cccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTM-LQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nl-L~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      .+||.||+. |.--+ .....--|.|..|+-..+.++
T Consensus        32 ~yCP~Cg~~~L~~f~-NN~PVaDF~C~~C~eeyELKS   67 (254)
T PF06044_consen   32 MYCPNCGSKPLSKFE-NNRPVADFYCPNCNEEYELKS   67 (254)
T ss_dssp             ---TTT--SS-EE---------EEE-TTT--EEEEEE
T ss_pred             CcCCCCCChhHhhcc-CCCccceeECCCCchHHhhhh
Confidence            489999998 54431 233466799999999887665

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

>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=80.84  E-value=1.8  Score=32.43  Aligned_cols=36  Identities=22%  Similarity=0.485  Sum_probs=17.6

Q ss_pred             cccCCCCCCC-ceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           68 EVTCPACKHG-KAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        68 ~~~CpkCg~~-~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      .-.||-||.. .+.......+   +|. +|..|.-  |++.|+
T Consensus       172 ~g~CPvCGs~P~~s~l~~~~~---~G~-R~L~Cs~--C~t~W~  208 (290)
T PF04216_consen  172 RGYCPVCGSPPVLSVLRGGER---EGK-RYLHCSL--CGTEWR  208 (290)
T ss_dssp             -SS-TTT---EEEEEEE---------E-EEEEETT--T--EEE
T ss_pred             CCcCCCCCCcCceEEEecCCC---Ccc-EEEEcCC--CCCeee
Confidence            4699999976 3333222211   476 9999998  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.

>PHA02998 RNA polymerase subunit; Provisional

Probab=80.56  E-value=1.5  Score=31.22  Aligned_cols=34  Identities=21%  Similarity=0.421  Sum_probs=21.8

Q ss_pred             CCcCCCCC------cccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTM------LQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nl------L~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      =||.||+-      |..+...+.....|.|..||+.+...
T Consensus       145 ~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkpp  184 (195)
T PHA02998        145 PCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPP  184 (195)
T ss_pred             CCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCc
Confidence            38899874      44442222335678999999876544

>PRK03954 ribonuclease P protein component 4; Validated

Probab=80.11  E-value=1.4  Score=29.26  Aligned_cols=33  Identities=15%  Similarity=0.447  Sum_probs=23.7

Q ss_pred             CCCcCCCCCcccccCCC----C---CCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHM----D---RPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~----~---~~~~~~C~~C~y~~~   34 (110)
                      .||..|+++|.|-....    .   ..+.+.|-.||++.-
T Consensus        65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR  104 (121)
T PRK03954         65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMR  104 (121)
T ss_pred             HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEe
Confidence            48999999999852211    1   137889999998754

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=80.03  E-value=0.76  Score=29.96  Aligned_cols=23  Identities=22%  Similarity=0.706  Sum_probs=14.5

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPY   31 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y   31 (110)
                      +|+.||..-.+.      ...+.|+.||-
T Consensus        72 ~C~~Cg~~~~~~------~~~~~CP~Cgs   94 (113)
T PRK12380         72 WCWDCSQVVEIH------QHDAQCPHCHG   94 (113)
T ss_pred             EcccCCCEEecC------CcCccCcCCCC
Confidence            577888555444      23556888883

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	110
3qt1_I	133	Rna Polymerase Ii Variant Containing A Chimeric Rpb		1e-09
1qyp_A	57	Thermococcus Celer Rpb9, Nmr, 25 Structures Length		3e-07
3h0g_I	113	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		3e-06
1y1v_S	179	Refined Rna Polymerase Ii-tfiis Complex Length = 17		6e-06
1tfi_A	50	A Novel Zn Finger Motif In The Basal Transcriptiona		7e-06
1pqv_S	309	Rna Polymerase Ii-Tfiis Complex Length = 309		8e-06
3gtm_S	173	Co-Complex Of Backtracked Rna Polymerase Ii With Tf		2e-05
3po3_S	178	Arrested Rna Polymerase Ii Reactivation Intermediat		2e-04

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 39/117 (33%), Positives = 55/117 (47%), Gaps = 15/117 (12%)
Query: 1   MEFCPTCGTMLQYELPHMDRPSR---FSCPACPYVCNMESRVKIKRKQPLSKKE----IQ 53
             FC  C  ML    P  D+ +    F C  C YV    S +  + +   +  E    +Q
Sbjct: 24  FRFCRDCNNML---YPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ 80
Query: 54  PIFTQDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
            I +   +   P+++  CP C   + V+ +LQ RSADEPM+ FY C   NC HRW E
Sbjct: 81  DIGSDPTL---PRSDRECPKCHSRENVFFQLQIRSADEPMTTFYKCV--NCGHRWKE 132

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 28/44 (63%), Gaps = 2/44 (4%)
Query: 65  PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108
           P T++TCP C +  A + E+QTR+ DEP +IFY C    C H W
Sbjct: 12  PTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCT--KCGHTW 53

>pdb|3H0G|I Chain I, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 113

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 3/103 (2%)
Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
            ++C  C  ML      +DR  R +C  C Y   + +  K+ R +  S        + DA
Sbjct: 4   FQYCIECNNMLYPREDKVDRVLRLACRNCDYS-EIAATSKVYRHELQSSNVENTTVSHDA 62
Query: 61  MME--GPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101
             +   P+++  CP C   +AV+++  +R  D  M++ Y+C +
Sbjct: 63  STDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVH 105

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

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 4/67 (5%)
Query: 44  KQPLSKKEIQPIFT-QDAMMEGPQTE-VTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101
           KQ + +   Q ++  Q A +E   T+  TC  CK  K  Y++LQTRSADEP++ F  C  
Sbjct: 112 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTC-- 169
Query: 102 KNCKHRW 108
           + C +RW
Sbjct: 170 EACGNRW 176

>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 = 45.4 bits (106), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 29/46 (63%), Gaps = 3/46 (6%)
Query: 64  GPQTEV-TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108
           G QT++ TC  CK     Y ++QTRSADEPM+ F +C    C +RW
Sbjct: 4   GTQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVC--NECGNRW 47

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 4/67 (5%)
Query: 44  KQPLSKKEIQPIFT-QDAMMEGPQTE-VTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101
           KQ + +   Q ++  Q A +E   T+  TC  CK  K  Y++LQTRSADEP++ F  C  
Sbjct: 242 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTC-- 299
Query: 102 KNCKHRW 108
           + C +RW
Sbjct: 300 EACGNRW 306

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 38/67 (56%), Gaps = 4/67 (5%)
Query: 44  KQPLSKKEIQPIFT-QDAMMEGPQTE-VTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101
           KQ + +   Q ++  Q A +E   T+  TC  CK  K  Y++LQTRSAD P++ F  C  
Sbjct: 106 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSADHPLTTFCTC-- 163
Query: 102 KNCKHRW 108
           + C +RW
Sbjct: 164 EACGNRW 170

>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate Length = 178

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 37/67 (55%), Gaps = 4/67 (5%)
Query: 44  KQPLSKKEIQPIFT-QDAMMEGPQTE-VTCPACKHGKAVYHELQTRSADEPMSIFYMCAN 101
           KQ + +   Q ++  Q A +E   T+  TC  CK  K  Y++LQTRSA  P++ F  C  
Sbjct: 111 KQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTC-- 168
Query: 102 KNCKHRW 108
           + C +RW
Sbjct: 169 EACGNRW 175

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	110
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	3e-26
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	6e-26
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	5e-21
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	3e-17
1tfi_A	50	Transcriptional elongation factor SII; transcripti	7e-13
3po3_S	178	Transcription elongation factor S-II; RNA polymera	2e-12
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	1e-11
3cng_A	189	Nudix hydrolase; structural genomics, APC7497, PSI	7e-04

>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 = 93.7 bits (232), Expect = 3e-26
 Identities = 35/111 (31%), Positives = 48/111 (43%), Gaps = 3/111 (2%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
             FC  C  ML       +    F C  C YV    S +  + +   +  E   +     
Sbjct: 24  FRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIG 83

Query: 61  -MMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
                P+++  CP C   + V+ +LQ RSADEPM+ FY C   NC HRW E
Sbjct: 84  SDPTLPRSDRECPKCHSRENVFFQLQIRSADEPMTTFYKC--VNCGHRWKE 132

>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 = 92.5 bits (229), Expect = 6e-26
 Identities = 25/111 (22%), Positives = 47/111 (42%), Gaps = 3/111 (2%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDA 60
            ++C  C  ML      +DR  R +C  C Y     +    + +   S  E   +    +
Sbjct: 4   FQYCIECNNMLYPREDKVDRVLRLACRNCDYSEIAATSKVYRHELQSSNVENTTVSHDAS 63

Query: 61  M-MEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
                P+++  CP C   +AV+++  +R  D  M++ Y+C   +C   + E
Sbjct: 64  TDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVC--VHCGFAFEE 112

>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 = 80.3 bits (197), Expect = 5e-21
 Identities = 25/111 (22%), Positives = 43/111 (38%), Gaps = 3/111 (2%)

Query: 1   MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIF-TQD 59
             FC  C  ML       +    F C  C YV    S +  + +   +  E   +     
Sbjct: 4   FRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIG 63

Query: 60  AMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           +    P+++  CP C   + V+ + Q R  D  M +F++C   +C H +  
Sbjct: 64  SDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVC--LSCSHIFTS 112

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

 Score = 68.7 bits (168), Expect = 3e-17
 Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 2/52 (3%)

Query: 59  DAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
             +   P T++TCP C +  A + E+QTR+ DEP +IFY C    C H W  
Sbjct: 6   QDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKC--TKCGHTWRS 55

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

 Score = 57.1 bits (138), Expect = 7e-13
 Identities = 19/42 (45%), Positives = 24/42 (57%), Gaps = 2/42 (4%)

Query: 67  TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108
              TC  CK     Y ++QTRSADEPM+ F +C    C +RW
Sbjct: 8   DLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVC--NECGNRW 47

>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 = 59.0 bits (142), Expect = 2e-12
 Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 40  KIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMC 99
            +K+K     K+         +        TC  CK  K  Y++LQTRSA  P++ F  C
Sbjct: 109 PLKQKIEEIAKQNLYNAQGATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTC 168

Query: 100 ANKNCKHRW 108
             + C +RW
Sbjct: 169 --EACGNRW 175

>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 = 58.6 bits (140), Expect = 1e-11
 Identities = 24/88 (27%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 21  PSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAV 80
           P   +      +     + KI+     +    Q    + +         TC  CK  K  
Sbjct: 225 PEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGATIERS----VTDRFTCGKCKEKKVS 280

Query: 81  YHELQTRSADEPMSIFYMCANKNCKHRW 108
           Y++LQTRSADEP++ F  C  + C +RW
Sbjct: 281 YYQLQTRSADEPLTTFCTC--EACGNRW 306

>3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protei structure initiative; 2.00A {Nitrosomonas europaea atcc 19718} Length = 189

 Score = 36.2 bits (84), Expect = 7e-04
 Identities = 11/32 (34%), Positives = 16/32 (50%)

Query: 1  MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV 32
          M+FC  CG  +   +P  D   R+ CP C  +
Sbjct: 3  MKFCSQCGGEVILRIPEGDTLPRYICPKCHTI 34

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	110
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	100.0
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	100.0
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	100.0
1tfi_A	50	Transcriptional elongation factor SII; transcripti	99.93
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	99.92
3po3_S	178	Transcription elongation factor S-II; RNA polymera	99.81
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	99.74
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	98.38
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	97.67
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	97.06
2kn9_A	81	Rubredoxin; metalloprotein, ssgcid, structural gen	96.32
3cng_A	189	Nudix hydrolase; structural genomics, APC7497, PSI	96.26
1yk4_A	52	Rubredoxin, RD; electron transport; 0.69A {Pyrococ	96.05
2v3b_B	55	Rubredoxin 2, rubredoxin; alkane degradation, iron	96.01
1e8j_A	52	Rubredoxin; iron-sulfur-protein, zinc-substitution	95.86
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	95.59
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	95.58
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	95.51
1s24_A	87	Rubredoxin 2; electron transport; NMR {Pseudomonas	95.33
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	94.65
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	94.32
1k81_A	36	EIF-2-beta, probable translation initiation factor	93.76
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	93.61
1lko_A	191	Rubrerythrin all-iron(II) form; reduced form, DIIR	93.57
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	93.53
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	93.47
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	92.86
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	92.75
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	92.63
1vk6_A	269	NADH pyrophosphatase; 1790429, structural genomics	92.54
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	92.16
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	92.04
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	92.04
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	91.91
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	91.91
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	91.88
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	91.8
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	91.8
1tfi_A	50	Transcriptional elongation factor SII; transcripti	91.56
1x0t_A	120	Ribonuclease P protein component 4; pyrococcus hor	91.35
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	90.82
1yuz_A	202	Nigerythrin; rubrythrin, rubredoxin, hemerythrin,	90.48
4esj_A	257	Type-2 restriction enzyme DPNI; restriction endonu	90.46
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	90.24
2k3r_A	123	Ribonuclease P protein component 4; PFU RPP21, RNA	90.1
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	90.09
2con_A	79	RUH-035 protein, NIN one binding protein; ribosome	88.15
2fnf_X	72	Putative RAS effector NORE1; zinc, signal transduc	86.35
2kv1_A	124	Methionine-R-sulfoxide reductase B1; MSRB1, SELR,	86.04
3iz5_m	92	60S ribosomal protein L43 (L37AE); eukaryotic ribo	84.68
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	84.64
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	84.37
2kao_A	124	Methionine-R-sulfoxide reductase B1; mouse reduced	84.2
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	83.92
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	83.59
2zjr_Z	60	50S ribosomal protein L32; ribosome, large ribosom	83.54
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	82.78
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	82.73
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	82.67
1rfh_A	59	RAS association (ralgds/AF-6) domain family 5; zin	82.38
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	82.29
3izc_m	92	60S ribosomal protein RPL43 (L37AE); eukaryotic ri	81.42
1ffk_W	73	Ribosomal protein L37AE; ribosome assembly, RNA-RN	80.85
1faq_A	52	RAF-1; transferase, serine/threonine-protein kinas	80.2

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

Probab=100.00  E-value=2e-45  Score=240.89  Aligned_cols=106  Identities=25%  Similarity=0.558  Sum_probs=92.9

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEeccc--CccccccccccccccC-CCCCcccCCCCCCC
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPL--SKKEIQPIFTQDAMME-GPQTEVTCPACKHG   77 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~   77 (110)
                      |.|||+|||||+|+++.+++.++|+|++|||++++++  ..+++..+  +.++..+|++++.+|+ +|++++.||+|||+
T Consensus         4 m~FCp~Cgn~L~~~~~~~~~~~~~~C~~C~y~~~~~~--~~v~~~~~~~~~~e~~~v~~~~~~~~tlp~~~~~Cp~C~~~   81 (113)
T 3h0g_I            4 FQYCIECNNMLYPREDKVDRVLRLACRNCDYSEIAAT--SKVYRHELQSSNVENTTVSHDASTDPTLPRSDKECPRCHQH   81 (113)
T ss_dssp             CCCCSSSCCCCEECCCTTTCCCCEECSSSCCEECCSC--SEEEECCCCSCSCTTCTTCTTSTTCSSSCBCCSCCSSSCCS
T ss_pred             ceeCcCCCCEeeEcccCCCCeeEEECCCCCCeEEcCC--CeEEEEEEecccccccceeccccccccCCCcccCCCCCCCc
Confidence            7899999999999987777889999999999999987  34444333  3456667787777788 99999999999999


Q ss_pred             ceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           78 KAVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        78 ~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      +|+|||+|+||||||||+||+|++  |+|+|++
T Consensus        82 ~a~~~q~q~rsade~mt~fy~C~~--C~~~w~~  112 (113)
T 3h0g_I           82 EAVFYQTHSRRGDTMMTLIYVCVH--CGFAFEE  112 (113)
T ss_dssp             CEEEECCCCSSCCCCCCCEEEESS--SCCCCCC
T ss_pred             eEEEEEEecccCCCCCeeEEEcCC--CCCEEec
Confidence            999999999999999999999999  9999996

>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=100.00  E-value=1.6e-43  Score=234.53  Aligned_cols=106  Identities=25%  Similarity=0.557  Sum_probs=91.5

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEeccc--CccccccccccccccC-CCCCcccCCCCCCC
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPL--SKKEIQPIFTQDAMME-GPQTEVTCPACKHG   77 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~   77 (110)
                      |.|||+|||||+|++++..+.+.|+|++|||++.++.  .++++..+  ..++..+|++++.+|+ +|++++.||+|||+
T Consensus         4 ~~FCp~CgnlL~~~~~~~~~~~~~~C~~C~y~~~~~~--~~v~~~~~~~~~~e~~~v~~~~~~~~t~p~t~~~Cp~C~~~   81 (122)
T 1twf_I            4 FRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGS--PLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSR   81 (122)
T ss_dssp             CCBCSSSCCBCEEEEETTTTEEEEECSSSSCEEECSC--SEEEEEESSCCTTSSTTCCTTGGGCTTSCCCCCCCTTTCCC
T ss_pred             CCcccccCccCcccccCcCCCCEEECCcCCCeeecCc--cEEEEEeecccccccccccccccccccccccCCCCCCCCCC
Confidence            7899999999999987667789999999999999887  55555444  2344556666656678 99999999999999


Q ss_pred             ceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           78 KAVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        78 ~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      +|+|||+|+||||||||+||+|++  |||+|++
T Consensus        82 ~a~~~q~q~rsade~~t~fy~C~~--C~~~w~~  112 (122)
T 1twf_I           82 ENVFFQSQQRRKDTSMVLFFVCLS--CSHIFTS  112 (122)
T ss_dssp             CEEEEECSSCCTTCCCCEEEEETT--TCCEEEC
T ss_pred             EEEEEEecCccCCCCceEEEEeCC--CCCEecc
Confidence            999999999999999999999999  9999985

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

Probab=100.00  E-value=5.9e-44  Score=239.40  Aligned_cols=106  Identities=33%  Similarity=0.682  Sum_probs=39.8

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEecccCccc--cccccccccccC-CCCCcccCCCCCCC
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKE--IQPIFTQDAMME-GPQTEVTCPACKHG   77 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~-~~~~~~~CpkCg~~   77 (110)
                      |+|||+|||||+|+++++.+.+.|+|++|||++++++  .++++..++.+.  ...++.+...++ +|++++.||+||++
T Consensus        24 ~~FCPeCgNmL~pked~~~~~l~~~CrtCgY~~~~~~--~~v~r~~~~~~~~e~~~vv~dv~~dptlp~t~~~CpkCg~~  101 (133)
T 3qt1_I           24 FRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGS--PLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSR  101 (133)
T ss_dssp             CCBCTTTCCBCBCCBCTTTCCBCCBCSSSCCBCCCSC--SEEEECCC---------------------------------
T ss_pred             CeeCCCCCCEeeECccCCCceeEEECCCCCCcEEcCC--ceEEEEEeeccccccceeEeeccccccCCcccCCCCCCCCc
Confidence            7899999999999988777889999999999999988  577766654432  222333333456 99999999999999


Q ss_pred             ceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           78 KAVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        78 ~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      +|+|||+|+||||||||+||+|++  |+|+|++
T Consensus       102 ~a~f~q~Q~RsaDE~mT~fy~C~~--C~~~w~e  132 (133)
T 3qt1_I          102 ENVFFQLQIRSADEPMTTFYKCVN--CGHRWKE  132 (133)
T ss_dssp             ---------------------------------
T ss_pred             eEEEEEEeeecCCCCCcEEEEcCC--CCCEeCc
Confidence            999999999999999999999999  9999986

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

Probab=99.93  E-value=3.6e-26  Score=129.43  Aligned_cols=42  Identities=45%  Similarity=0.970  Sum_probs=40.0

Q ss_pred             CCcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           66 QTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        66 ~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      +.++.||+|||++|+|||+|+||||||||+||+|++  |+|+|+
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            456899999999999999999999999999999999  999997

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

Probab=99.92  E-value=6.8e-26  Score=131.67  Aligned_cols=48  Identities=44%  Similarity=0.997  Sum_probs=45.4

Q ss_pred             ccC-CCCCcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           61 MME-GPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        61 ~~~-~~~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      +++ +|++.+.||+||+++|+|+|+|+||||||||+||+|++  |+|+|++
T Consensus         7 ~~~~~~~~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~--Cg~~w~~   55 (57)
T 1qyp_A            7 DLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTK--CGHTWRS   55 (57)
T ss_dssp             CCSSSCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESS--SCCEEEC
T ss_pred             hhhcCCceEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCC--CCCEecc
Confidence            556 88889999999999999999999999999999999999  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=99.81  E-value=5.5e-21  Score=133.41  Aligned_cols=42  Identities=43%  Similarity=0.904  Sum_probs=39.9

Q ss_pred             CCcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           66 QTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        66 ~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      ++...||+|||++|+|||+|+||||||||+||+|++  |||+|+
T Consensus       135 t~~~~Cp~C~~~~a~~~q~Q~rsaDE~mt~f~~C~~--C~~~w~  176 (178)
T 3po3_S          135 TDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEA--CGNRWK  176 (178)
T ss_dssp             BSSSCCSSSCCSCEECCCCCCSCTTSCCCCCEEETT--TCCEEC
T ss_pred             cCCcCCCCCCCCceEEEEeecccCCCCCcEEEEcCC--CCCeec
Confidence            346899999999999999999999999999999999  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=99.74  E-value=7.7e-19  Score=131.50  Aligned_cols=41  Identities=49%  Similarity=0.996  Sum_probs=39.2

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      ....||+|||++|+|||+|+||||||||+||+|++  |||+|+
T Consensus       267 ~~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C~~--Cg~~w~  307 (309)
T 1pqv_S          267 DRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEA--CGNRWK  307 (309)
T ss_pred             ccccCCCCCCCeeEEEEeecccCCCCCcEEEEeCC--CCCcee
Confidence            35799999999999999999999999999999999  999997

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=98.38  E-value=1.9e-07  Score=53.20  Aligned_cols=30  Identities=33%  Similarity=0.843  Sum_probs=24.3

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      |.|||.||+++...    .+..++.|..|||++.
T Consensus        18 ~~fCPkCG~~~~ma----~~~dr~~C~kCgyt~~   47 (55)
T 2k4x_A           18 HRFCPRCGPGVFLA----EHADRYSCGRCGYTEF   47 (55)
T ss_dssp             SCCCTTTTTTCCCE----ECSSEEECTTTCCCEE
T ss_pred             cccCcCCCCceeEe----ccCCEEECCCCCCEEE
Confidence            68999999987755    2245999999999864

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=97.67  E-value=1.9e-05  Score=43.92  Aligned_cols=28  Identities=32%  Similarity=0.878  Sum_probs=21.6

Q ss_pred             CCCCcCCCC--CcccccCCCCCCceEEcCCCCCeee
Q 033869            1 MEFCPTCGT--MLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         1 M~FCp~C~n--lL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      .+|||.||+  +|.+.      ..++.|..|||++.
T Consensus        19 ~k~CP~CG~~~fm~~~------~~R~~C~kCG~t~~   48 (50)
T 3j20_Y           19 NKFCPRCGPGVFMADH------GDRWACGKCGYTEW   48 (50)
T ss_dssp             SEECSSSCSSCEEEEC------SSEEECSSSCCEEE
T ss_pred             cccCCCCCCceEEecC------CCeEECCCCCCEEE
Confidence            369999998  44443      35999999999864

>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=97.06  E-value=0.0011  Score=49.42  Aligned_cols=75  Identities=17%  Similarity=0.471  Sum_probs=47.5

Q ss_pred             CCCcCCCCCcccccCC----CCCCceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCC
Q 033869            2 EFCPTCGTMLQYELPH----MDRPSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHG   77 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~----~~~~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~   77 (110)
                      .+||-||+.=....-.    .++.-++.|..|+..+...                               ..+||.||+.
T Consensus       183 ~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~t~W~~~-------------------------------R~~C~~Cg~~  231 (309)
T 2fiy_A          183 TLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYV-------------------------------RIKCSHCEES  231 (309)
T ss_dssp             SSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECC-------------------------------TTSCSSSCCC
T ss_pred             CCCCCCCCcCceeEEeecCCCCCcEEEEeCCCCCEEeec-------------------------------CcCCcCCCCC
Confidence            4899999764332111    1223378899998776532                               3479999984


Q ss_pred             -ceEEEEeccCCC--CCCceEEEEecCCCCCcccc
Q 033869           78 -KAVYHELQTRSA--DEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        78 -~a~~~~~Q~Rsa--DE~~T~fY~C~~~~C~~~wr  109 (110)
                       +..||++-.-++  +++....++|.+  |++.++
T Consensus       232 ~~l~y~~~e~~~~~~~~~~~r~e~C~~--C~~YlK  264 (309)
T 2fiy_A          232 KHLAYLSLEHDGQPAEKAVLRAETCPS--CQGYLK  264 (309)
T ss_dssp             SCCEEECCCC-CCCSTTCSEEEEEETT--TTEEEE
T ss_pred             CCeeEEEecCccccCCCcceEEEEccc--ccchHh
Confidence             566665532111  457789999999  987654

>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis}

Probab=96.32  E-value=0.017  Score=34.94  Aligned_cols=52  Identities=17%  Similarity=0.364  Sum_probs=32.3

Q ss_pred             CceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEec
Q 033869           21 PSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHELQ   85 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~Q   85 (110)
                      ...|.|+.|||+++-...           +....|..+ ..+. +| .++.||.||..+..|..+.
T Consensus        25 m~~y~C~vCGyvYD~~~G-----------dp~~gI~pG-T~fedlP-ddW~CPvCga~K~~F~~i~   77 (81)
T 2kn9_A           25 YKLFRCIQCGFEYDEALG-----------WPEDGIAAG-TRWDDIP-DDWSCPDCGAAKSDFEMVE   77 (81)
T ss_dssp             CCEEEETTTCCEEETTTC-----------BTTTTBCTT-CCTTTSC-TTCCCTTTCCCGGGEEEEC
T ss_pred             cceEEeCCCCEEEcCCcC-----------CcccCcCCC-CChhHCC-CCCcCCCCCCCHHHcEEcc
Confidence            458999999998764331           011112211 1222 33 4789999999999887763

>3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protei structure initiative; 2.00A {Nitrosomonas europaea atcc 19718}

Probab=96.26  E-value=0.0046  Score=41.91  Aligned_cols=34  Identities=32%  Similarity=0.835  Sum_probs=27.2

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ++|||.||..|....+.+.......|+.|++...
T Consensus         3 ~~~C~~CG~~~~~~~~~G~~~~~~~~~~~~~~~~   36 (189)
T 3cng_A            3 MKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHY   36 (189)
T ss_dssp             CCBCTTTCCBCEEECCTTCSSCEEEETTTTEEEC
T ss_pred             cccCchhCCccccccccCCCCcceECCCCCCccC
Confidence            5899999999988754555567899999996554

>1yk4_A Rubredoxin, RD; electron transport; 0.69A {Pyrococcus abyssi} PDB: 2pya_A 1yk5_A 1bq8_A 1bq9_A* 3kyu_A 3kyv_A 3kyw_A 3kyx_A 3kyy_A 3ryg_A 3rz6_A 3rzt_A 3ss2_A 1brf_A 1caa_A 1cad_A 1vcx_A 1zrp_A 1iu5_A 1iu6_A ...

Probab=96.05  E-value=0.0095  Score=33.07  Aligned_cols=48  Identities=23%  Similarity=0.535  Sum_probs=28.6

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEE
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHE   83 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~   83 (110)
                      .|.|+.|||+++-...           .....|..+ ..+. +| .+..||.||..+..|..
T Consensus         2 ~~~C~~CGyvYd~~~G-----------dp~~gi~pG-t~f~~lP-~dw~CP~Cg~~K~~F~~   50 (52)
T 1yk4_A            2 KLSCKICGYIYDEDEG-----------DPDNGISPG-TKFEDLP-DDWVCPLCGAPKSEFER   50 (52)
T ss_dssp             EEEESSSSCEEETTTC-----------BGGGTBCTT-CCGGGSC-TTCBCTTTCCBGGGEEE
T ss_pred             cEEeCCCCeEECCCcC-----------CcccCcCCC-CCHhHCC-CCCcCCCCCCCHHHcEE
Confidence            6899999998764431           001112111 1122 32 46799999999887754

>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, ELE transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa}

Probab=96.01  E-value=0.01  Score=33.29  Aligned_cols=49  Identities=20%  Similarity=0.480  Sum_probs=29.9

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEe
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHEL   84 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~   84 (110)
                      .|.|+.|||+++-...           .....|..+ ..+. +| .+..||.||..+..|..+
T Consensus         3 ~y~C~~CGyvYd~~~G-----------dp~~gi~pG-t~f~~lP-~dw~CP~Cga~K~~F~~~   52 (55)
T 2v3b_B            3 KWQCVVCGFIYDEALG-----------LPEEGIPAG-TRWEDIP-ADWVCPDCGVGKIDFEMI   52 (55)
T ss_dssp             EEEETTTCCEEETTTC-----------BTTTTBCTT-CCGGGSC-TTCCCTTTCCCGGGEEEC
T ss_pred             cEEeCCCCeEECCCcC-----------CcccCcCCC-CChhHCC-CCCcCCCCCCCHHHceec
Confidence            6999999998764331           001112111 1122 33 478999999999888654

>1e8j_A Rubredoxin; iron-sulfur-protein, zinc-substitution, thermostability; NMR {Desulfovibrio gigas} SCOP: g.41.5.1 PDB: 1rdg_A 2dsx_A 1spw_A

Probab=95.86  E-value=0.0076  Score=33.47  Aligned_cols=47  Identities=21%  Similarity=0.485  Sum_probs=27.6

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEE
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYH   82 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~   82 (110)
                      .|.|+.|||+++-...           .....|..+ ..+. +| .+..||.||..+..|.
T Consensus         3 ~y~C~~CGyvYd~~~G-----------dp~~gi~pG-t~f~~lP-~dw~CP~Cg~~K~~F~   50 (52)
T 1e8j_A            3 IYVCTVCGYEYDPAKG-----------DPDSGIKPG-TKFEDLP-DDWACPVCGASKDAFE   50 (52)
T ss_dssp             CEECSSSCCCCCTTTC-----------CTTTTCCSS-CCTTSSC-TTCCCSSSCCCTTSCE
T ss_pred             cEEeCCCCeEEcCCcC-----------CcccCcCCC-CchHHCC-CCCcCCCCCCcHHHcE
Confidence            6999999998764320           000112111 1122 32 4789999999887664

>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1

Probab=95.59  E-value=0.0078  Score=32.64  Aligned_cols=40  Identities=20%  Similarity=0.587  Sum_probs=25.7

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEE
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYH   82 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~   82 (110)
                      .|.|+.|||+.+......                   ..+. +| .+..||.||+.+..|-
T Consensus         4 ~y~C~vCGyvyd~~~Gd~-------------------t~f~~lP-~dw~CP~Cg~~k~~F~   44 (46)
T 6rxn_A            4 KYVCNVCGYEYDPAEHDN-------------------VPFDQLP-DDWCCPVCGVSKDQFS   44 (46)
T ss_dssp             CEEETTTCCEECGGGGTT-------------------CCGGGSC-TTCBCTTTCCBGGGEE
T ss_pred             EEECCCCCeEEeCCcCCC-------------------cchhhCC-CCCcCcCCCCcHHHcE
Confidence            689999999876432000                   1111 22 3579999999887664

>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A

Probab=95.58  E-value=0.013  Score=34.56  Aligned_cols=50  Identities=22%  Similarity=0.541  Sum_probs=30.9

Q ss_pred             ceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEe
Q 033869           22 SRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHEL   84 (110)
Q Consensus        22 ~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~   84 (110)
                      ..|.|+.|||+++-...           +....|..+ ..+. +| .++.||.||..+..|..+
T Consensus         6 ~~y~C~vCGyiYd~~~G-----------dp~~gi~pG-T~f~~lP-ddw~CP~Cga~K~~F~~~   56 (70)
T 1dx8_A            6 GKYECEACGYIYEPEKG-----------DKFAGIPPG-TPFVDLS-DSFMCPACRSPKNQFKSI   56 (70)
T ss_dssp             SCEEETTTCCEECTTTC-----------CTTTTCCSS-CCGGGSC-TTCBCTTTCCBGGGEEEC
T ss_pred             ceEEeCCCCEEEcCCCC-----------CcccCcCCC-CchhhCC-CCCcCCCCCCCHHHceEc
Confidence            47999999998764331           011112111 1122 33 478999999999888765

>4rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.20A {Clostridium pasteurianum} SCOP: g.41.5.1 PDB: 5rxn_A 1bfy_A 1fhh_A 1fhm_A 1irn_A 1iro_A 1r0f_A 1r0g_A 1r0h_A 1r0i_A 1r0j_A 1t9q_A 1c09_A 1b2j_A 1b13_A 1smm_A 1smu_A 1smw_A 1be7_A 1t9o_A ...

Probab=95.51  E-value=0.016  Score=32.39  Aligned_cols=49  Identities=22%  Similarity=0.594  Sum_probs=29.1

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEe
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHEL   84 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~   84 (110)
                      .|.|+.|||+++-...           +....|..+ ..+. +| .++.||.||..+..|..+
T Consensus         3 ~y~C~vCGyvYd~~~G-----------dp~~gi~pG-t~fe~lP-~dw~CP~Cg~~K~~F~~~   52 (54)
T 4rxn_A            3 KYTCTVCGYIYDPEDG-----------DPDDGVNPG-TDFKDIP-DDWVCPLCGVGKDEFEEV   52 (54)
T ss_dssp             CEEETTTCCEECTTTC-----------BGGGTBCTT-CCGGGSC-TTCBCTTTCCBGGGEEEC
T ss_pred             ceECCCCCeEECCCcC-----------CcccCcCCC-CChhHCC-CCCcCcCCCCcHHHceEc
Confidence            6899999998874331           001112111 1222 33 468999999988777543

>1s24_A Rubredoxin 2; electron transport; NMR {Pseudomonas oleovorans} SCOP: g.41.5.1

Probab=95.33  E-value=0.017  Score=35.37  Aligned_cols=51  Identities=20%  Similarity=0.360  Sum_probs=30.9

Q ss_pred             CceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEe
Q 033869           21 PSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHEL   84 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~   84 (110)
                      ...|.|+.|||+++-...           +....|..+ ..+. +| .++.||.||..+..|..+
T Consensus        33 m~~y~C~vCGyvYD~~~G-----------dp~~gI~pG-T~fedlP-ddW~CPvCga~K~~F~~i   84 (87)
T 1s24_A           33 YLKWICITCGHIYDEALG-----------DEAEGFTPG-TRFEDIP-DDWCCPDCGATKEDYVLY   84 (87)
T ss_dssp             CCEEEETTTTEEEETTSC-----------CTTTTCCSC-CCGGGCC-TTCCCSSSCCCGGGEEEC
T ss_pred             CceEECCCCCeEecCCcC-----------CcccCcCCC-CChhHCC-CCCCCCCCCCCHHHhhhc
Confidence            458999999998764320           001112111 1122 33 478999999999888664

>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE] hydrogenase maturation, zinc-finger, nickel binding, metal-binding; HET: FME; 2.30A {Pyrococcus kodakaraensis} PDB: 3a44_A*

Probab=94.65  E-value=0.038  Score=36.41  Aligned_cols=17  Identities=24%  Similarity=0.716  Sum_probs=13.8

Q ss_pred             CceEEcCCCCCeeeeCC
Q 033869           21 PSRFSCPACPYVCNMES   37 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~~   37 (110)
                      ...+.|++|||....+.
T Consensus        68 p~~~~C~~CG~~~~~~~   84 (139)
T 3a43_A           68 EAVFKCRNCNYEWKLKE   84 (139)
T ss_dssp             CCEEEETTTCCEEEGGG
T ss_pred             CCcEECCCCCCEEeccc
Confidence            45899999999887644

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=94.32  E-value=0.0078  Score=33.36  Aligned_cols=22  Identities=27%  Similarity=0.753  Sum_probs=18.7

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      -||.||..+.+.        .+.|+.|||+
T Consensus        16 iCpkC~a~~~~g--------aw~CrKCG~~   37 (51)
T 3j21_g           16 VCLRCGATNPWG--------AKKCRKCGYK   37 (51)
T ss_dssp             ECTTTCCEECTT--------CSSCSSSSSC
T ss_pred             cCCCCCCcCCCC--------ceecCCCCCc
Confidence            599999985554        8999999997

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

Probab=93.76  E-value=0.086  Score=26.88  Aligned_cols=32  Identities=19%  Similarity=0.349  Sum_probs=25.8

Q ss_pred             ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      +.||.||+.+..+.-       +.-.+|-.|..  ||+++.
T Consensus         1 VlC~~C~~peT~l~~-------~~~~~~l~C~a--CG~~~~   32 (36)
T 1k81_A            1 VICRECGKPDTKIIK-------EGRVHLLKCMA--CGAIRP   32 (36)
T ss_dssp             CCCSSSCSCEEEEEE-------ETTEEEEEEET--TTEEEE
T ss_pred             CCCcCCCCCCcEEEE-------eCCcEEEEhhc--CCCccc
Confidence            469999999988755       24789999999  998763

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=93.61  E-value=0.088  Score=33.52  Aligned_cols=32  Identities=16%  Similarity=0.514  Sum_probs=22.9

Q ss_pred             CceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcc-cCCCCCCCceEE
Q 033869           21 PSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEV-TCPACKHGKAVY   81 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~CpkCg~~~a~~   81 (110)
                      ...+.|+.||+....+.                             ... .||.||+....+
T Consensus        71 p~~~~C~~CG~~~e~~~-----------------------------~~~~~CP~Cgs~~~~i  103 (119)
T 2kdx_A           71 KVELECKDCSHVFKPNA-----------------------------LDYGVCEKCHSKNVII  103 (119)
T ss_dssp             CCEEECSSSSCEECSCC-----------------------------STTCCCSSSSSCCCEE
T ss_pred             cceEEcCCCCCEEeCCC-----------------------------CCCCcCccccCCCcEE
Confidence            45899999998765422                             134 699999987655

>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix bundle, rubre like, electron transport; 1.63A {Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB: 1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A 1ryt_A

Probab=93.57  E-value=0.03  Score=38.63  Aligned_cols=32  Identities=38%  Similarity=0.892  Sum_probs=23.3

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCCceEEEE
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHE   83 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~~a~~~~   83 (110)
                      .|.|+.|||+...++                          +|.   .||.||+++..|-.
T Consensus       155 ~~~C~~CG~~~~g~~--------------------------~p~---~CP~C~~~k~~f~~  186 (191)
T 1lko_A          155 KWRCRNCGYVHEGTG--------------------------APE---LCPACAHPKAHFEL  186 (191)
T ss_dssp             EEEETTTCCEEEEEE--------------------------CCS---BCTTTCCBGGGEEE
T ss_pred             eEEECCCCCEeeCCC--------------------------CCC---CCCCCcCCHHHHHh
Confidence            799999999765210                          121   79999999887743

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=93.53  E-value=0.038  Score=32.57  Aligned_cols=28  Identities=25%  Similarity=0.568  Sum_probs=23.2

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      || ||++++.+  ..  .-.-.|+ ||....++.
T Consensus         7 C~-C~~~~~~~--~~--~kT~~C~-CG~~~~~~k   34 (71)
T 1gh9_A            7 CD-CGRALYSR--EG--AKTRKCV-CGRTVNVKD   34 (71)
T ss_dssp             ET-TSCCEEEE--TT--CSEEEET-TTEEEECCS
T ss_pred             CC-CCCEEEEc--CC--CcEEECC-CCCeeeece
Confidence            99 99999999  32  3488999 999888776

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

Probab=93.47  E-value=0.059  Score=29.13  Aligned_cols=29  Identities=31%  Similarity=0.838  Sum_probs=21.3

Q ss_pred             CCCcCCCC-CcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGT-MLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~n-lL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ..||.|++ -|...  ..  ...++|..||...+
T Consensus         6 ~~CP~C~~~~l~~d--~~--~gelvC~~CG~v~~   35 (50)
T 1pft_A            6 KVCPACESAELIYD--PE--RGEIVCAKCGYVIE   35 (50)
T ss_dssp             CSCTTTSCCCEEEE--TT--TTEEEESSSCCBCC
T ss_pred             EeCcCCCCcceEEc--CC--CCeEECcccCCccc
Confidence            46999998 66554  32  34799999998654

>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress, oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A 3pza_A 3qvd_A 1nnq_A 2hr5_A

Probab=92.86  E-value=0.075  Score=36.13  Aligned_cols=33  Identities=27%  Similarity=0.732  Sum_probs=23.7

Q ss_pred             CceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCCceEEEE
Q 033869           21 PSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHE   83 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~~a~~~~   83 (110)
                      ...|.|+.|||+..  +                     +    +|   ..||-||+++..|-.
T Consensus       136 ~~~~~C~~CG~i~~--~---------------------~----~p---~~CP~Cg~~~~~F~~  168 (170)
T 3pwf_A          136 KKVYICPICGYTAV--D---------------------E----AP---EYCPVCGAPKEKFVV  168 (170)
T ss_dssp             SCEEECTTTCCEEE--S---------------------C----CC---SBCTTTCCBGGGCEE
T ss_pred             CCeeEeCCCCCeeC--C---------------------C----CC---CCCCCCCCCHHHcee
Confidence            35899999999754  1                     0    11   279999998887643

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=92.75  E-value=0.07  Score=36.42  Aligned_cols=28  Identities=29%  Similarity=0.656  Sum_probs=23.6

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      .|++||+.|.|.  +    ..+.|+.||..+..+
T Consensus       142 ~~~~~g~~m~~~--~----~~~~cp~~g~~e~RK  169 (179)
T 3m7n_A          142 LCSNCKTEMVRE--G----DILKCPECGRVEKRK  169 (179)
T ss_dssp             BCTTTCCBCEEC--S----SSEECSSSCCEECCC
T ss_pred             cccccCCceEEC--C----CEEECCCCCCEEEEe
Confidence            699999999987  2    489999999987643

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4

Probab=92.63  E-value=0.072  Score=32.06  Aligned_cols=28  Identities=25%  Similarity=0.631  Sum_probs=20.6

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      .+||.|++++...  .+  ...+.|+.|++..
T Consensus        26 ~wCP~C~~~~~~~--~~--~~~v~C~~C~~~F   53 (86)
T 2ct7_A           26 LWCAQCSFGFIYE--RE--QLEATCPQCHQTF   53 (86)
T ss_dssp             ECCSSSCCCEECC--CS--CSCEECTTTCCEE
T ss_pred             eECcCCCchheec--CC--CCceEeCCCCCcc
Confidence            3799999988665  22  3468999998754

>1vk6_A NADH pyrophosphatase; 1790429, structural genomics, JCSG, PS protein structure initiative, joint center for structural G hydrolase; HET: MSE; 2.20A {Escherichia coli} SCOP: d.113.1.4 d.113.1.4 g.41.14.1 PDB: 2gb5_A

Probab=92.54  E-value=0.072  Score=38.56  Aligned_cols=32  Identities=16%  Similarity=0.384  Sum_probs=25.7

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      ++|||.||.-+...    .......|+.|+......
T Consensus       107 ~~fC~~CG~~~~~~----~~~~~~~C~~C~~~~yp~  138 (269)
T 1vk6_A          107 HKYCGYCGHEMYPS----KTEWAMLCSHCRERYYPQ  138 (269)
T ss_dssp             TSBCTTTCCBEEEC----SSSSCEEESSSSCEECCC
T ss_pred             CCccccCCCcCccC----CCceeeeCCCCCCEecCC
Confidence            57999999998776    235689999999977643

>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1

Probab=92.16  E-value=0.12  Score=30.22  Aligned_cols=32  Identities=13%  Similarity=0.259  Sum_probs=26.5

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      .-||.|+.-|...  .+  ...+.|+.|+..+++.+
T Consensus         9 L~CP~ck~~L~~~--~~--~~~LiC~~cg~~YPI~d   40 (69)
T 2pk7_A            9 LACPICKGPLKLS--AD--KTELISKGAGLAYPIRD   40 (69)
T ss_dssp             CCCTTTCCCCEEC--TT--SSEEEETTTTEEEEEET
T ss_pred             eeCCCCCCcCeEe--CC--CCEEEcCCCCcEecCcC
Confidence            4699999999887  32  35899999999999877

>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1

Probab=92.04  E-value=0.11  Score=30.16  Aligned_cols=32  Identities=16%  Similarity=0.437  Sum_probs=26.4

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      .-||.|+.-|...  ..  ...+.|+.|+..+++.+
T Consensus         9 L~CP~ck~~L~~~--~~--~~~LiC~~cg~~YPI~d   40 (68)
T 2hf1_A            9 LVCPLCKGPLVFD--KS--KDELICKGDRLAFPIKD   40 (68)
T ss_dssp             CBCTTTCCBCEEE--TT--TTEEEETTTTEEEEEET
T ss_pred             eECCCCCCcCeEe--CC--CCEEEcCCCCcEecCCC
Confidence            3699999999887  32  35899999999999877

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}

Probab=92.04  E-value=0.12  Score=30.09  Aligned_cols=32  Identities=13%  Similarity=0.258  Sum_probs=26.5

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      .-||.|+.-|...  ..  ...+.|+.|+..+++.+
T Consensus         9 L~CP~ck~~L~~~--~~--~~~LiC~~cg~~YPI~d   40 (68)
T 2jr6_A            9 LVCPVTKGRLEYH--QD--KQELWSRQAKLAYPIKD   40 (68)
T ss_dssp             CBCSSSCCBCEEE--TT--TTEEEETTTTEEEEEET
T ss_pred             eECCCCCCcCeEe--CC--CCEEEcCCCCcEecCCC
Confidence            4699999999887  32  35899999999999877

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=91.91  E-value=0.063  Score=32.53  Aligned_cols=29  Identities=24%  Similarity=0.559  Sum_probs=21.9

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      .||.||..+..+  ..  ...|.|+.|+++..-
T Consensus        29 ~Cp~CG~~~v~r--~a--tGiW~C~~Cg~~~ag   57 (83)
T 1vq8_Z           29 ACPNCGEDRVDR--QG--TGIWQCSYCDYKFTG   57 (83)
T ss_dssp             ECSSSCCEEEEE--EE--TTEEEETTTCCEEEC
T ss_pred             cCCCCCCcceec--cC--CCeEECCCCCCEecC
Confidence            699999866555  22  459999999997543

>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=91.91  E-value=0.086  Score=34.59  Aligned_cols=29  Identities=28%  Similarity=0.696  Sum_probs=23.5

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      .=||+|++-....  .   +..|+|+-|++++..
T Consensus        28 P~CP~C~seytYe--D---g~l~vCPeC~hEW~~   56 (138)
T 2akl_A           28 PPCPQCNSEYTYE--D---GALLVCPECAHEWSP   56 (138)
T ss_dssp             CCCTTTCCCCCEE--C---SSSEEETTTTEEECT
T ss_pred             CCCCCCCCcceEe--c---CCeEECCccccccCC
Confidence            4699999988887  1   347999999999853

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

Probab=91.88  E-value=0.16  Score=28.14  Aligned_cols=32  Identities=19%  Similarity=0.447  Sum_probs=18.6

Q ss_pred             CCcCCCCCcc------cccCCCCCCceEEcCCCCCeee
Q 033869            3 FCPTCGTMLQ------YELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         3 FCp~C~nlL~------~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      -||.||+--.      .+...+...+.|.|..||+...
T Consensus        17 ~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~   54 (57)
T 1qyp_A           17 TCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWR   54 (57)
T ss_dssp             CCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEE
T ss_pred             ECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEec
Confidence            4888886411      1111123356788888888754

>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=0.072  Score=34.95  Aligned_cols=28  Identities=29%  Similarity=0.886  Sum_probs=20.7

Q ss_pred             ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      -.||+|+.+-.|-        | |.  .|+|..  |+|-|.
T Consensus        28 P~CP~C~seytYe--------D-g~--l~vCPe--C~hEW~   55 (138)
T 2akl_A           28 PPCPQCNSEYTYE--------D-GA--LLVCPE--CAHEWS   55 (138)
T ss_dssp             CCCTTTCCCCCEE--------C-SS--SEEETT--TTEEEC
T ss_pred             CCCCCCCCcceEe--------c-CC--eEECCc--cccccC
Confidence            3799999876543        1 11  299998  999996

>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}

Probab=91.80  E-value=0.12  Score=30.33  Aligned_cols=32  Identities=19%  Similarity=0.506  Sum_probs=26.5

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      .-||.|+.-|...  ..  ...+.|+.||..+++.+
T Consensus         9 L~CP~ck~~L~~~--~~--~~~LiC~~cg~~YPI~d   40 (70)
T 2js4_A            9 LVCPVCKGRLEFQ--RA--QAELVCNADRLAFPVRD   40 (70)
T ss_dssp             CBCTTTCCBEEEE--TT--TTEEEETTTTEEEEEET
T ss_pred             eECCCCCCcCEEe--CC--CCEEEcCCCCceecCCC
Confidence            4699999998887  33  35899999999999877

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

Probab=91.56  E-value=0.17  Score=27.59  Aligned_cols=32  Identities=16%  Similarity=0.248  Sum_probs=20.2

Q ss_pred             CCcCCCCCc------ccccCCCCCCceEEcCCCCCeee
Q 033869            3 FCPTCGTML------QYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         3 FCp~C~nlL------~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      -||.||+--      ..+...+...+.|.|.+||+.+.
T Consensus        11 ~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~w~   48 (50)
T 1tfi_A           11 TCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK   48 (50)
T ss_dssp             CCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred             CCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCeEE
Confidence            589998652      22211223467799999998754

>1x0t_A Ribonuclease P protein component 4; pyrococcus horikoshii OT3, hydrolase; 1.60A {Pyrococcus horikoshii} PDB: 2zae_B

Probab=91.35  E-value=0.096  Score=33.68  Aligned_cols=34  Identities=21%  Similarity=0.562  Sum_probs=25.3

Q ss_pred             CCCcCCCCCcccccCCC----CC---CceEEcCCCCCeeee
Q 033869            2 EFCPTCGTMLQYELPHM----DR---PSRFSCPACPYVCNM   35 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~----~~---~~~~~C~~C~y~~~~   35 (110)
                      .||..||++|.|-....    .+   .+.+.|-.||++.-.
T Consensus        66 ~~Ck~C~s~LiPG~t~~vri~~~~~~~vv~tCl~Cg~~kR~  106 (120)
T 1x0t_A           66 RYCKRCHTFLIPGVNARVRLRTKRMPHVVITCLECGYIMRY  106 (120)
T ss_dssp             SBCTTTCCBCCBTTTEEEEEECSSSCEEEEEETTTCCEEEE
T ss_pred             HhccCCCCEeECCCceEEEEecCCccEEEEECCCCCCEEEE
Confidence            59999999999863221    22   478999999987543

>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=90.82  E-value=0.14  Score=31.08  Aligned_cols=31  Identities=19%  Similarity=0.494  Sum_probs=23.6

Q ss_pred             CcCCCCC--cccccCCCCCCceEEcCCCCCeee
Q 033869            4 CPTCGTM--LQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         4 Cp~C~nl--L~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ||.||+.  +..+.|+......+.|+.||-...
T Consensus        26 CPfCnh~~sV~vkidk~~~~g~l~C~~Cg~~~~   58 (85)
T 1wii_A           26 CPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQ   58 (85)
T ss_dssp             CTTTCCSSCEEEEEETTTTEEEEEESSSCCEEE
T ss_pred             CCCCCCCCeEEEEEEccCCEEEEEcccCCCeEE
Confidence            8888876  666766777778888999986554

>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIR center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A

Probab=90.48  E-value=0.14  Score=35.60  Aligned_cols=32  Identities=25%  Similarity=0.593  Sum_probs=23.5

Q ss_pred             CceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCCceEEE
Q 033869           21 PSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYH   82 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~~a~~~   82 (110)
                      ...|.|+.|||+... .                          .   .+.||-||+.+..|-
T Consensus       169 ~~~~~C~~CG~i~~g-~--------------------------~---p~~CP~C~~~k~~F~  200 (202)
T 1yuz_A          169 DKFHLCPICGYIHKG-E--------------------------D---FEKCPICFRPKDTFT  200 (202)
T ss_dssp             CCEEECSSSCCEEES-S--------------------------C---CSBCTTTCCBGGGCE
T ss_pred             CcEEEECCCCCEEcC-c--------------------------C---CCCCCCCCCChHHhe
Confidence            458999999997541 0                          0   158999999887664

>4esj_A Type-2 restriction enzyme DPNI; restriction endonuclease-DNA complex, type IIM, type IIE, RE enzyme, DPNI; HET: DNA 6MA; 2.05A {Streptococcus pneumoniae}

Probab=90.46  E-value=0.18  Score=36.31  Aligned_cols=34  Identities=29%  Similarity=0.789  Sum_probs=23.3

Q ss_pred             CCCcCCCCC-c-ccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTM-L-QYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nl-L-~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      .|||.||+. | ..+  .....--|.|.+|+-..+.++
T Consensus        35 ~yCPnCG~~~l~~f~--nN~PVaDF~C~~C~EeyELKS   70 (257)
T 4esj_A           35 SYCPNCGNNPLNHFE--NNRPVADFYCNHCSEEFELKS   70 (257)
T ss_dssp             CCCTTTCCSSCEEC------CCCEEECTTTCCEEEEEE
T ss_pred             CcCCCCCChhhhhcc--CCCcccccccCCcchhheecc
Confidence            489999994 4 444  333456799999998877655

>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1

Probab=90.24  E-value=0.22  Score=28.86  Aligned_cols=32  Identities=13%  Similarity=0.154  Sum_probs=26.1

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      .-||.|..-|...  ..  ...+.|+.|+..+++.+
T Consensus        11 L~CP~ck~~L~~~--~~--~g~LvC~~c~~~YPI~d   42 (67)
T 2jny_A           11 LACPKDKGPLRYL--ES--EQLLVNERLNLAYRIDD   42 (67)
T ss_dssp             CBCTTTCCBCEEE--TT--TTEEEETTTTEEEEEET
T ss_pred             hCCCCCCCcCeEe--CC--CCEEEcCCCCccccCCC
Confidence            3699999988887  32  34899999999999877

>2k3r_A Ribonuclease P protein component 4; PFU RPP21, RNAse P, hydrolase, tRNA processing; NMR {Pyrococcus furiosus} PDB: 2ki7_B

Probab=90.10  E-value=0.12  Score=33.39  Aligned_cols=34  Identities=15%  Similarity=0.441  Sum_probs=25.2

Q ss_pred             CCCcCCCCCcccccCCC----CC---CceEEcCCCCCeeee
Q 033869            2 EFCPTCGTMLQYELPHM----DR---PSRFSCPACPYVCNM   35 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~----~~---~~~~~C~~C~y~~~~   35 (110)
                      .||..|+++|.|-....    .+   .+.+.|-.||++.-.
T Consensus        61 ~~Ck~C~s~LIPG~t~~vri~~~~k~~vv~tCl~Cg~~kR~  101 (123)
T 2k3r_A           61 RYCKKCHAFLVPGINARVRLRQKRMPHIVVKCLECGHIMRY  101 (123)
T ss_dssp             SBCTTTCCBCCBTTTEEEEEECSSSCEEEEEETTTTEEEEE
T ss_pred             HhccCCCCEeECCCceEEEEecCCccEEEEECCCCCCEEEE
Confidence            59999999999863221    21   478999999987543

>1dl6_A Transcription factor II B (TFIIB); zinc ribbon, gene regulation; NMR {Homo sapiens} SCOP: g.41.3.1 PDB: 1rly_A 1ro4_A

Probab=90.09  E-value=0.28  Score=27.49  Aligned_cols=29  Identities=28%  Similarity=0.611  Sum_probs=19.8

Q ss_pred             CCCcCCCC-CcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGT-MLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~n-lL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ..||+|++ -|...  .  ....++|..||.+..
T Consensus        12 ~~Cp~C~~~~lv~D--~--~~ge~vC~~CGlVl~   41 (58)
T 1dl6_A           12 VTCPNHPDAILVED--Y--RAGDMICPECGLVVG   41 (58)
T ss_dssp             CSBTTBSSSCCEEC--S--SSCCEECTTTCCEEC
T ss_pred             ccCcCCCCCceeEe--C--CCCeEEeCCCCCEEe
Confidence            36999987 33333  2  245799999998643

>2con_A RUH-035 protein, NIN one binding protein; ribosome, RNA binding protein, unknown function, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.41.15.1

Probab=88.15  E-value=0.16  Score=30.47  Aligned_cols=9  Identities=44%  Similarity=1.180  Sum_probs=7.8

Q ss_pred             CCCcCCCCC
Q 033869            2 EFCPTCGTM   10 (110)
Q Consensus         2 ~FCp~C~nl   10 (110)
                      .|||.|||-
T Consensus        31 ~FCp~CGn~   39 (79)
T 2con_A           31 VFCGHCGNK   39 (79)
T ss_dssp             CSCSSSCCS
T ss_pred             ccccccCcc
Confidence            599999985

>2fnf_X Putative RAS effector NORE1; zinc, signal transduction, apoptosis, cysteine rich domain; NMR {Mus musculus}

Probab=86.35  E-value=0.55  Score=27.29  Aligned_cols=25  Identities=24%  Similarity=0.959  Sum_probs=20.1

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      .||..||++| .+       .-+.|..|+|...
T Consensus        36 t~C~~C~~~l-~~-------qG~kC~~C~~~cH   60 (72)
T 2fnf_X           36 GWCDLCGREV-LR-------QALRCANCKFTCH   60 (72)
T ss_dssp             CBCTTTSSBC-SS-------CCEECTTSSCEEC
T ss_pred             cchhhhhHHH-Hh-------CcCccCCCCCeec
Confidence            5899999999 32       3689999999754

>2kv1_A Methionine-R-sulfoxide reductase B1; MSRB1, SELR, metal-binding, nucleus, oxidoreductase, seleniu; NMR {Mus musculus}

Probab=86.04  E-value=0.91  Score=29.38  Aligned_cols=76  Identities=18%  Similarity=0.352  Sum_probs=39.1

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEec---ccCccccc-cccccccccC-CCCCcccCCCCC
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQ---PLSKKEIQ-PIFTQDAMME-GPQTEVTCPACK   75 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~---~~~~~~~~-~~~~~~~~~~-~~~~~~~CpkCg   75 (110)
                      |-||..=++-+|-...   ...+|+|..|+..-...+. ++.+-.   .+.. .+. .++....... ..++++.|.+||
T Consensus         1 ~sFC~~F~ge~y~~~~---e~G~Y~C~~Cg~pLF~S~~-KfdSg~GWPSF~~-~i~~~~v~~~~d~~~~~r~Ev~C~~Cg   75 (124)
T 2kv1_A            1 MSFCSFFGGEVFQNHF---EPGVYVCAKCSYELFSSHS-KYAHSSPWPAFTE-TIHPDSVTKCPEKNRPEALKVSCGKCG   75 (124)
T ss_dssp             CCCCCCCCSCSGGGTT---CCEEEEETTTCCBCCCTTS-CCCCCSSSCCBSC-CCCCSSCEEEECSSSTTCEEEECTTTT
T ss_pred             CccccCccCccccCCC---CCEEEEecCCCCcccccCC-cccCCCCCceeec-ccccceEEEEeccCCceEEEEEEecCC
Confidence            7888755555554421   2469999999975433321 222111   1111 111 1111111112 457899999999


Q ss_pred             C-CceEE
Q 033869           76 H-GKAVY   81 (110)
Q Consensus        76 ~-~~a~~   81 (110)
                      . -..+|
T Consensus        76 ~HLGHVF   82 (124)
T 2kv1_A           76 NGLGHEF   82 (124)
T ss_dssp             CCCEEEC
T ss_pred             CccCCcc
Confidence            5 46666

>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L 1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L* 1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L 1y77_L* ...

Probab=84.64  E-value=0.61  Score=27.18  Aligned_cols=24  Identities=21%  Similarity=0.614  Sum_probs=17.2

Q ss_pred             CcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            4 CPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         4 Cp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      |++||....+.  ..   ....|+.||+.
T Consensus        31 C~~CG~~~e~~--~~---d~irCp~CG~R   54 (70)
T 1twf_L           31 CAECSSKLSLS--RT---DAVRCKDCGHR   54 (70)
T ss_dssp             CSSSCCEECCC--TT---STTCCSSSCCC
T ss_pred             CCCCCCcceeC--CC---CCccCCCCCce
Confidence            89999885554  11   24589999994

>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=84.37  E-value=1.2  Score=28.44  Aligned_cols=34  Identities=21%  Similarity=0.425  Sum_probs=21.0

Q ss_pred             CCcCCCCC------cccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTM------LQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nl------L~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      -||.||+-      +..+...+...+.|.|.+||+.+...
T Consensus        74 ~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~~n  113 (122)
T 1twf_I           74 ECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSD  113 (122)
T ss_dssp             CCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECC
T ss_pred             CCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEeccC
Confidence            58888875      22221122346778898898876543

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

Probab=83.92  E-value=0.39  Score=31.40  Aligned_cols=33  Identities=21%  Similarity=0.429  Sum_probs=20.9

Q ss_pred             cccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869           68 EVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW  108 (110)
Q Consensus        68 ~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w  108 (110)
                      -..||+||+-      +..+...+.-.+.|.|.+  |+|.+
T Consensus        24 ~~FCPeCgNm------L~pked~~~~~l~~~Crt--CgY~~   56 (133)
T 3qt1_I           24 FRFCRDCNNM------LYPREDKENNRLLFECRT--CSYVE   56 (133)
T ss_dssp             CCBCTTTCCB------CBCCBCTTTCCBCCBCSS--SCCBC
T ss_pred             CeeCCCCCCE------eeECccCCCceeEEECCC--CCCcE
Confidence            4578888872      223333333467788888  88864

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

Probab=83.59  E-value=0.46  Score=30.02  Aligned_cols=32  Identities=19%  Similarity=0.319  Sum_probs=17.7

Q ss_pred             ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccc
Q 033869           69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW  108 (110)
Q Consensus        69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~w  108 (110)
                      ..||+||+--      ..+..++.-.+.|.|.+  |+|.+
T Consensus         5 ~FCp~Cgn~L------~~~~~~~~~~~~~~C~~--C~y~~   36 (113)
T 3h0g_I            5 QYCIECNNML------YPREDKVDRVLRLACRN--CDYSE   36 (113)
T ss_dssp             CCCSSSCCCC------EECCCTTTCCCCEECSS--SCCEE
T ss_pred             eeCcCCCCEe------eEcccCCCCeeEEECCC--CCCeE
Confidence            4688887742      12222222345677877  87764

>2zjr_Z 50S ribosomal protein L32; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: g.41.8.5 PDB: 1j5a_M* 1jzy_M* 1jzz_M* 1k01_M* 1nkw_Z 1ond_Z* 1sm1_Z* 1yl3_5 2b66_5 2b9n_5 2b9p_5 2zjp_Y* 2zjq_Z 1jzx_M 3cf5_Y* 3dll_Y* 3pio_Z* 3pip_Z* 1nwy_Z* 1nwx_Z* ...

Probab=83.54  E-value=0.23  Score=28.14  Aligned_cols=21  Identities=33%  Similarity=0.814  Sum_probs=13.8

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      .||.||.+-.|         ..+|..|||-
T Consensus        32 ~c~~cG~~~~p---------H~vc~~CG~Y   52 (60)
T 2zjr_Z           32 ECPQCHGKKLS---------HHICPNCGYY   52 (60)
T ss_dssp             ECTTTCCEECT---------TBCCTTTCBS
T ss_pred             ECCCCCCEeCC---------ceEcCCCCcC
Confidence            57788877333         4567888864

>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=82.78  E-value=0.7  Score=27.90  Aligned_cols=29  Identities=21%  Similarity=0.572  Sum_probs=21.0

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ..||.||.. ..+  + ....+|.|+.|++..-
T Consensus        36 y~CpfCGk~-~vk--R-~a~GIW~C~kCg~~~A   64 (83)
T 3j21_i           36 HTCPVCGRK-AVK--R-ISTGIWQCQKCGATFA   64 (83)
T ss_dssp             BCCSSSCSS-CEE--E-EETTEEEETTTCCEEE
T ss_pred             cCCCCCCCc-eeE--e-cCcCeEEcCCCCCEEe
Confidence            379999988 343  2 1246999999998754

>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z

Probab=82.73  E-value=0.45  Score=30.49  Aligned_cols=28  Identities=25%  Similarity=0.740  Sum_probs=19.9

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      +||.||.. ..+  +. ...+|.|+.|++..-
T Consensus        62 tCPfCGk~-~vK--R~-avGIW~C~~Cgk~fA   89 (116)
T 3cc2_Z           62 ACPNCGED-RVD--RQ-GTGIWQCSYCDYKFT   89 (116)
T ss_dssp             ECSSSCCE-EEE--EE-ETTEEEETTTCCEEE
T ss_pred             cCCCCCCc-eeE--ec-CceeEECCCCCCEEE
Confidence            79999984 332  11 145999999999854

>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}

Probab=82.67  E-value=1.1  Score=24.84  Aligned_cols=30  Identities=20%  Similarity=0.565  Sum_probs=25.3

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcC--CCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCP--ACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~--~C~y~~~~~~   37 (110)
                      .-||.|+.-|...  .    ..+.|+  .|+..+++.+
T Consensus        11 L~CP~c~~~L~~~--~----~~L~C~~~~c~~~YPI~d   42 (56)
T 2kpi_A           11 LACPACHAPLEER--D----AELICTGQDCGLAYPVRD   42 (56)
T ss_dssp             CCCSSSCSCEEEE--T----TEEEECSSSCCCEEEEET
T ss_pred             eeCCCCCCcceec--C----CEEEcCCcCCCcEEeeEC
Confidence            3699999998887  2    589999  9999998876

>1rfh_A RAS association (ralgds/AF-6) domain family 5; zinc, signal transduction, apoptosis, cysteine rich domain, metal binding protein; NMR {Mus musculus}

Probab=82.38  E-value=0.67  Score=25.77  Aligned_cols=25  Identities=24%  Similarity=0.959  Sum_probs=19.7

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      .||..||++| .+       .-+.|..|++...
T Consensus        23 t~C~~C~~~i-~k-------qg~kC~~C~~~cH   47 (59)
T 1rfh_A           23 GWCDLCGREV-LR-------QALRCANCKFTCH   47 (59)
T ss_dssp             EECTTTCSEE-CS-------CCEECTTTSCEEC
T ss_pred             eEchhcchhh-hh-------CccEeCCCCCeEe
Confidence            4899999999 32       3689999998653

>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=82.29  E-value=0.67  Score=27.25  Aligned_cols=29  Identities=17%  Similarity=0.489  Sum_probs=20.8

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ..||.||..= .+  + ....+|.|+.|++..-
T Consensus        27 y~C~fCgk~~-vk--R-~a~GIW~C~~C~~~~A   55 (72)
T 3jyw_9           27 YDCSFCGKKT-VK--R-GAAGIWTCSCCKKTVA   55 (72)
T ss_dssp             BCCSSCCSSC-BS--B-CSSSCBCCSSSCCCCC
T ss_pred             ccCCCCCCce-eE--e-cCCCeEECCCCCCEEe
Confidence            3799999773 43  2 2256999999998643

>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y*

Probab=80.85  E-value=0.82  Score=26.90  Aligned_cols=29  Identities=28%  Similarity=0.635  Sum_probs=20.1

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ..||.||.. ..+  +. ...+|.|+.|++..-
T Consensus        28 y~C~fCgk~-~vk--R~-a~GIW~C~~C~~~~A   56 (73)
T 1ffk_W           28 YKCPVCGFP-KLK--RA-STSIWVCGHCGYKIA   56 (73)
T ss_pred             ccCCCCCCc-eeE--EE-EeEEEECCCCCcEEE
Confidence            379999964 332  11 246899999999754

>1faq_A RAF-1; transferase, serine/threonine-protein kinase, proto- oncogene, zinc, ATP-binding, phorbol-ester binding; NMR {Homo sapiens} SCOP: g.49.1.1 PDB: 1far_A

Probab=80.20  E-value=0.83  Score=24.35  Aligned_cols=24  Identities=33%  Similarity=0.927  Sum_probs=19.7

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      .||..|+++|. .        -+.|..|++...
T Consensus        15 t~C~~C~~~l~-q--------G~~C~~C~~~~H   38 (52)
T 1faq_A           15 AFCDICQKFLL-N--------GFRCQTCGYKFH   38 (52)
T ss_dssp             EECTTSSSEEC-S--------EEECTTTTCCBC
T ss_pred             cCCCCcccccc-c--------CCEeCCCCCeEC
Confidence            48999999986 2        689999998654

---

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	110
d1qypa_	57	g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {A	1e-16
d1twfi2	72	g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase	2e-14
d1tfia_	50	g.41.3.1 (A:) Transcriptional factor SII, C-termin	3e-12

>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 = 66.0 bits (161), Expect = 1e-16
 Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 58  QDAMMEGPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           +  +   P T++TCP C +  A + E+QTR+ DEP +IFY C    C H W  
Sbjct: 5   EQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKC--TKCGHTWRS 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 = 60.7 bits (147), Expect = 2e-14
 Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 2/46 (4%)

Query: 65  PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE 110
           P+++  CP C   + V+ + Q R  D  M +F++C   +C H +  
Sbjct: 20  PRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVC--LSCSHIFTS 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 = 54.3 bits (131), Expect = 3e-12
 Identities = 19/44 (43%), Positives = 24/44 (54%), Gaps = 2/44 (4%)

Query: 65  PQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRW 108
                TC  CK     Y ++QTRSADEPM+ F +C    C +RW
Sbjct: 6   QTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVC--NECGNRW 47

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	110
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	99.95
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	99.95
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	99.9
d1twfi1	49	RBP9 subunit of RNA polymerase II {Baker's yeast (	99.75
d1lkoa2	44	Rubrerythrin, C-terminal domain {Desulfovibrio vul	96.97
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	96.56
d1dx8a_	70	Rubredoxin {Guillardia theta [TaxId: 55529]}	96.51
d2dsxa1	52	Rubredoxin {Desulfovibrio gigas [TaxId: 879]}	96.4
d1iroa_	53	Rubredoxin {Clostridium pasteurianum [TaxId: 1501]	96.29
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	96.13
d1s24a_	56	Two-iron rubredoxin {Pseudomonas oleovorans [TaxId	96.11
d1brfa_	53	Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2	96.05
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	96.04
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	96.02
d6rxna_	45	Rubredoxin {Desulfovibrio desulfuricans, strain 27	95.84
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	95.35
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	95.05
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	94.78
d1pvma3	36	Hypothetical protein Ta0289 C-terminal domain {Arc	94.31
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	93.44
d1k3xa3	40	Endonuclease VIII {Escherichia coli [TaxId: 562]}	92.66
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	91.89
d2cona1	66	RNA-binding protein NOB1 (Nin one binding) {Mouse	90.99
d1r2za3	46	DNA repair protein MutM (Fpg) {Bacillus stearother	90.01
d2f9yb1	263	Acetyl-coenzyme A carboxylase carboxyl transferase	89.72
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	89.68
d1neea2	37	Zinc-binding domain of translation initiation fact	89.68
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	89.63
d1ee8a3	56	DNA repair protein MutM (Fpg) {Thermus thermophilu	88.94
d1tdza3	47	DNA repair protein MutM (Fpg) {Lactococcus lactis	88.58
d1k82a3	44	DNA repair protein MutM (Fpg) {Escherichia coli [T	88.54
d1k81a_	36	Zinc-binding domain of translation initiation fact	88.23
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	87.88
d1vqoz1	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	87.3
d1wiia_	85	Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m	86.09
d1jj2y_	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	86.05
d2j0151	59	Ribosomal protein L32p {Thermus thermophilus [TaxI	85.88
d1pfva3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Esch	84.62
d1rqga3	35	Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyro	81.99
d2zjrz1	58	Ribosomal protein L32p {Deinococcus radiodurans [T	81.07

>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=8.5e-29  Score=148.03  Aligned_cols=58  Identities=24%  Similarity=0.602  Sum_probs=51.5

Q ss_pred             ccccccccccccC-CCCCcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           51 EIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        51 ~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      +...|+.+...+| ||++++.||+||+++|+||++|+||||||||+||+|++  |+|+||+
T Consensus         5 e~~~v~~d~~~DPtlp~t~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~--C~h~Wr~   63 (72)
T d1twfi2           5 ETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLS--CSHIFTS   63 (72)
T ss_dssp             SSTTCCTTGGGCTTSCCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETT--TCCEEEC
T ss_pred             cccccccccccCCCCCccCCCCCCCCCCeEEEEEeecCccCCCceEEEEcCC--CCCCccc
Confidence            3344555556678 99999999999999999999999999999999999999  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=99.95  E-value=1.4e-28  Score=141.12  Aligned_cols=45  Identities=47%  Similarity=1.056  Sum_probs=44.0

Q ss_pred             CCCCcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCccccC
Q 033869           64 GPQTEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWNE  110 (110)
Q Consensus        64 ~~~~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wre  110 (110)
                      +|++++.||+|||++|+||++|+||||||||+||+|++  |||+||+
T Consensus        11 ~pt~~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~--Cg~~wre   55 (57)
T d1qypa_          11 LPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTK--CGHTWRS   55 (57)
T ss_dssp             SCEEECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESS--SCCEEEC
T ss_pred             CCcccCCCCCCCCCceEEEEeecccccCCCeEEEEeCC--CCCccee
Confidence            89999999999999999999999999999999999999  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=99.90  E-value=1.3e-24  Score=121.08  Aligned_cols=41  Identities=46%  Similarity=0.993  Sum_probs=39.1

Q ss_pred             CcccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           67 TEVTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        67 ~~~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      ...+||+||++++.|+++|+||||||||+||.|.+  |||+||
T Consensus         8 ~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~--Cg~~Wr   48 (50)
T d1tfia_           8 DLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNE--CGNRWK   48 (50)
T ss_dssp             CCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESS--SCCEEE
T ss_pred             CCEECCCCCCCccEEEEEEccCCCCCceEEEEccc--cCCeee
Confidence            34699999999999999999999999999999999  999997

>d1twfi1 g.41.3.1 (I:1-49) 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=99.75  E-value=2.7e-19  Score=97.80  Aligned_cols=44  Identities=25%  Similarity=0.535  Sum_probs=39.9

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCCceEEEEecc
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMESRVKIKRKQP   46 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~~~~~~~~~~   46 (110)
                      |+|||+|+|||||+||++.+.|.|+||+|+|.+.+++  ..||+..
T Consensus         4 ~rFC~eCnNmLYPKEDk~~~~L~yaCR~C~y~e~A~~--~cVYrn~   47 (49)
T d1twfi1           4 FRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGS--PLVYRHE   47 (49)
T ss_dssp             CCBCSSSCCBCEEEEETTTTEEEEECSSSSCEEECSC--SEEEEEE
T ss_pred             eecChhcccccccCCccccCEEEEEccCCCceeEcCC--CeEEecc
Confidence            6899999999999999999999999999999999998  5666543

>d1lkoa2 g.41.5.1 (A:148-191) Rubrerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=96.97  E-value=0.00021  Score=37.32  Aligned_cols=34  Identities=32%  Similarity=0.743  Sum_probs=25.1

Q ss_pred             CceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCCceEEEE
Q 033869           21 PSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHE   83 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~~a~~~~   83 (110)
                      ...|.|++|||+...+.                          .   -..||.|||..++|-.
T Consensus         6 ~~~W~C~~CGyi~~g~~--------------------------a---P~~CPvC~~p~~~Fe~   39 (44)
T d1lkoa2           6 ATKWRCRNCGYVHEGTG--------------------------A---PELCPACAHPKAHFEL   39 (44)
T ss_dssp             EEEEEETTTCCEEEEEE--------------------------C---CSBCTTTCCBGGGEEE
T ss_pred             CeEEEcCCCCcEEECCC--------------------------C---CCcCCCCCCcHHHHee
Confidence            45899999999765322                          1   1379999999998844

>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=96.56  E-value=0.00078  Score=33.85  Aligned_cols=31  Identities=26%  Similarity=0.656  Sum_probs=25.6

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      .-||+|++-....     .+..|+|+.|+++.....
T Consensus         4 P~CP~C~seytYe-----dg~l~vCPeC~hEW~~~~   34 (38)
T d2akla2           4 PPCPQCNSEYTYE-----DGALLVCPECAHEWSPNE   34 (38)
T ss_dssp             CCCTTTCCCCCEE-----CSSSEEETTTTEEECTTT
T ss_pred             CcCCCCCCcceEc-----CCCEEECCcccCcCCccc
Confidence            4699999998887     245999999999987654

>d1dx8a_ g.41.5.1 (A:) Rubredoxin {Guillardia theta [TaxId: 55529]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Guillardia theta [TaxId: 55529]

Probab=96.51  E-value=0.0019  Score=36.76  Aligned_cols=55  Identities=20%  Similarity=0.476  Sum_probs=35.4

Q ss_pred             CceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEeccCC
Q 033869           21 PSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHELQTRS   88 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~Q~Rs   88 (110)
                      ...|.|+.|||+++....           +....|..+ ..+. || .++.||.||..+..|..++..+
T Consensus         5 ~~ky~C~~CgyiYDp~~G-----------D~~~gI~pG-T~F~dLP-~dW~CP~Cga~K~~F~~~~~~~   60 (70)
T d1dx8a_           5 EGKYECEACGYIYEPEKG-----------DKFAGIPPG-TPFVDLS-DSFMCPACRSPKNQFKSIKKVI   60 (70)
T ss_dssp             SSCEEETTTCCEECTTTC-----------CTTTTCCSS-CCGGGSC-TTCBCTTTCCBGGGEEECCCBC
T ss_pred             CCeEEcCCCCeEECcccC-----------CcccCCCCC-CChHHCC-CCCCCcCCCCcHHHheEccccc
Confidence            458999999998865431           011112211 1233 55 5789999999999998876543

>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio gigas [TaxId: 879]

Probab=96.40  E-value=0.0014  Score=35.23  Aligned_cols=47  Identities=21%  Similarity=0.485  Sum_probs=29.4

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEE
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYH   82 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~   82 (110)
                      .|.|+.|||+++-...           +....|..+ ..+. || .++.||.||..+..|-
T Consensus         3 ~y~C~~CgyiYdp~~G-----------d~~~gi~pG-T~F~~LP-~~w~CP~C~a~K~~F~   50 (52)
T d2dsxa1           3 IYVCTVCGYEYDPAKG-----------DPDSGIKPG-TKFEDLP-DDWACPVCGASKDAFE   50 (52)
T ss_dssp             CEEETTTCCEECTTTC-----------BGGGTBCTT-CCGGGSC-TTCBCTTTCCBGGGEE
T ss_pred             eEEeCCCCeEECcccC-----------CcccCCCCC-CCHHHCC-CCCCCcCCCCcHHHhc
Confidence            7999999998764431           111112211 1233 55 6889999999887663

>d1iroa_ g.41.5.1 (A:) Rubredoxin {Clostridium pasteurianum [TaxId: 1501]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Clostridium pasteurianum [TaxId: 1501]

Probab=96.29  E-value=0.0023  Score=34.46  Aligned_cols=48  Identities=25%  Similarity=0.606  Sum_probs=30.0

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEE
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHE   83 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~   83 (110)
                      .|.|+.|||+++....           +....|..+ ..+. || .+..||.||..+..|-.
T Consensus         3 ky~C~~CgyiYd~~~G-----------d~~~gi~pG-T~F~~LP-~dw~CP~C~a~K~~F~~   51 (53)
T d1iroa_           3 KYTCTVCGYIYNPEDG-----------DPDNGVNPG-TDFKDIP-DDWVCPLCGVGKDQFEE   51 (53)
T ss_dssp             CEEETTTCCEECTTTC-----------BGGGTBCTT-CCGGGSC-TTCBCTTTCCBGGGEEE
T ss_pred             CeEcCCCCcEECcccC-----------CcccCCCCC-CCHHHCC-CCCCCcCCCCcHHHcEE
Confidence            6999999998865431           011112211 1233 55 57899999998877754

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=96.13  E-value=0.0017  Score=32.24  Aligned_cols=14  Identities=29%  Similarity=0.776  Sum_probs=11.3

Q ss_pred             CceEEcCCCCCeee
Q 033869           21 PSRFSCPACPYVCN   34 (110)
Q Consensus        21 ~~~~~C~~C~y~~~   34 (110)
                      ...|.|+.|||+..
T Consensus         3 ~~~~vC~vCGyi~~   16 (36)
T d1yuza2           3 DKFHLCPICGYIHK   16 (36)
T ss_dssp             CCEEECSSSCCEEE
T ss_pred             CCEEECCCCCCEee
Confidence            35899999999754

>d1s24a_ g.41.5.1 (A:) Two-iron rubredoxin {Pseudomonas oleovorans [TaxId: 301]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Two-iron rubredoxin
species: Pseudomonas oleovorans [TaxId: 301]

Probab=96.11  E-value=0.0036  Score=34.04  Aligned_cols=51  Identities=20%  Similarity=0.391  Sum_probs=31.6

Q ss_pred             ceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEec
Q 033869           22 SRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHELQ   85 (110)
Q Consensus        22 ~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~Q   85 (110)
                      ..|.|+.|||+++-...           +....|..+ ..+. || .+..||.||..+..|..+.
T Consensus         3 kky~C~~CgyiYdp~~G-----------d~~~gi~pG-T~F~~LP-~dw~CP~C~a~K~~F~~~e   54 (56)
T d1s24a_           3 LKWICITCGHIYDEALG-----------DEAEGFTPG-TRFEDIP-DDWCCPDCGATKEDYVLYE   54 (56)
T ss_dssp             CEEEETTTTEEEETTSC-----------CTTTTCCSC-CCGGGCC-TTCCCSSSCCCGGGEEECS
T ss_pred             ccEECCCCCcEECcccC-----------CcccCcCCC-CChhhCC-CCCCCcCCCCcHHHceEcc
Confidence            37999999998765431           011112211 1233 55 5789999999988886553

>d1brfa_ g.41.5.1 (A:) Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.05  E-value=0.0043  Score=33.33  Aligned_cols=49  Identities=22%  Similarity=0.554  Sum_probs=30.7

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEEEEe
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVYHEL   84 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~~~~   84 (110)
                      .|.|+.|||+++-...           .....|..+ ..+. || .++.||.||..+..|..+
T Consensus         2 ky~C~~CgyiYd~~~G-----------d~~~gi~pG-T~f~dLP-~dw~CP~C~a~K~~F~~~   51 (53)
T d1brfa_           2 KWVCKICGYIYDEDAG-----------DPDNGISPG-TKFEELP-DDWVCPICGAPKSEFEKL   51 (53)
T ss_dssp             EEEETTTCCEEETTTC-----------BGGGTBCTT-CCGGGSC-TTCBCTTTCCBGGGEEES
T ss_pred             ceECCCCCcEECcccC-----------CcccCCCCC-CCHHHCC-CCCCCcCCCCcHHHceEc
Confidence            6899999998865431           111112211 1233 55 489999999988877544

>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=96.04  E-value=0.0061  Score=43.25  Aligned_cols=34  Identities=21%  Similarity=0.504  Sum_probs=19.5

Q ss_pred             CCCcCCCCCccccc----CCCCCCceEEcCCCCCeeee
Q 033869            2 EFCPTCGTMLQYEL----PHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         2 ~FCp~C~nlL~~~~----~~~~~~~~~~C~~C~y~~~~   35 (110)
                      .+||-||+.=....    ...++.-++.|..|+..+..
T Consensus       165 ~~CPvCGs~P~~s~l~~~~~~~G~R~l~C~~C~teW~~  202 (290)
T d2fiya1         165 TLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHY  202 (290)
T ss_dssp             SSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEEC
T ss_pred             CcCCCCCCcchhheeeccCCCCCceEEECCCCCCcccc
Confidence            47889988522211    11122347888888887664

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=96.02  E-value=0.003  Score=34.09  Aligned_cols=30  Identities=37%  Similarity=0.913  Sum_probs=22.7

Q ss_pred             CCCcCCCC--CcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGT--MLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~n--lL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      ++||.||.  +|---      .+++.|-.|||++....
T Consensus        19 k~CP~CG~GvFmA~H------~dR~~CGKCgyTefkk~   50 (55)
T d2k4xa1          19 RFCPRCGPGVFLAEH------ADRYSCGRCGYTEFKKA   50 (55)
T ss_dssp             CCCTTTTTTCCCEEC------SSEEECTTTCCCEECCC
T ss_pred             CcCcCCCCcEEeeec------CCCccccCCcccEEecc
Confidence            58999976  44433      46999999999986544

>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]

Probab=95.84  E-value=0.0024  Score=33.24  Aligned_cols=39  Identities=21%  Similarity=0.648  Sum_probs=26.6

Q ss_pred             eEEcCCCCCeeeeCCceEEEEecccCccccccccccccccC-CCCCcccCCCCCCCceEE
Q 033869           23 RFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMME-GPQTEVTCPACKHGKAVY   81 (110)
Q Consensus        23 ~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~CpkCg~~~a~~   81 (110)
                      .|.|+.|||+.+-...                   +...+. || .+..||.||..+..|
T Consensus         3 ~y~C~~CgyiYd~~~G-------------------dgt~Fe~LP-~dw~CP~C~a~K~~F   42 (45)
T d6rxna_           3 KYVCNVCGYEYDPAEH-------------------DNVPFDQLP-DDWCCPVCGVSKDQF   42 (45)
T ss_dssp             CEEETTTCCEECGGGG-------------------TTCCGGGSC-TTCBCTTTCCBGGGE
T ss_pred             CeEeCCCCeEECcccC-------------------CCCCHHHCC-CCCCCcCCCCcHHHc
Confidence            6999999998764321                   011223 44 478999999987766

>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.35  E-value=0.0077  Score=29.93  Aligned_cols=33  Identities=27%  Similarity=0.631  Sum_probs=23.5

Q ss_pred             CceEEcCCCCCeeeeCCceEEEEecccCccccccccccccccCCCCCcccCCCCCCCceEEEE
Q 033869           21 PSRFSCPACPYVCNMESRVKIKRKQPLSKKEIQPIFTQDAMMEGPQTEVTCPACKHGKAVYHE   83 (110)
Q Consensus        21 ~~~~~C~~C~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CpkCg~~~a~~~~   83 (110)
                      ...|.|+.|||+..-+.                              -..||-||+....|-.
T Consensus         3 ~~~~~C~vCG~i~~g~~------------------------------P~~CPvCg~~~~~F~~   35 (37)
T d1nnqa2           3 KKVYICPICGYTAVDEA------------------------------PEYCPVCGAPKEKFVV   35 (37)
T ss_dssp             SCEEECTTTCCEEESCC------------------------------CSBCTTTCCBGGGSEE
T ss_pred             CcEEECCCCCCEecCCC------------------------------CCcCCCCCCcHHHcEE
Confidence            34899999999754211                              1369999998877754

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.05  E-value=0.0064  Score=34.34  Aligned_cols=28  Identities=25%  Similarity=0.660  Sum_probs=21.7

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      ++||.|++.+...  .  +...+.|+.|++..
T Consensus        19 k~CP~C~~~~~~~--~--~~~~~~C~~C~~~f   46 (73)
T d2ct7a1          19 LWCAQCSFGFIYE--R--EQLEATCPQCHQTF   46 (73)
T ss_dssp             ECCSSSCCCEECC--C--SCSCEECTTTCCEE
T ss_pred             CCCCCCCCEeEEC--C--CCCEEEcCCCCCeE
Confidence            5899999987655  2  35689999999853

>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=94.78  E-value=0.0069  Score=30.23  Aligned_cols=27  Identities=30%  Similarity=0.920  Sum_probs=19.4

Q ss_pred             cCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcccc
Q 033869           70 TCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHRWN  109 (110)
Q Consensus        70 ~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~wr  109 (110)
                      .||+|+..-.|  +.      -   -.|+|..  |+|-|.
T Consensus         5 ~CP~C~seytY--ed------g---~l~vCPe--C~hEW~   31 (38)
T d2akla2           5 PCPQCNSEYTY--ED------G---ALLVCPE--CAHEWS   31 (38)
T ss_dssp             CCTTTCCCCCE--EC------S---SSEEETT--TTEEEC
T ss_pred             cCCCCCCcceE--cC------C---CEEECCc--ccCcCC
Confidence            69999876442  21      1   2389998  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=94.31  E-value=0.07  Score=25.29  Aligned_cols=34  Identities=21%  Similarity=0.397  Sum_probs=24.1

Q ss_pred             ccCCCCCCCceEEEEeccCCCCCCceEEEEecCCCCCcc
Q 033869           69 VTCPACKHGKAVYHELQTRSADEPMSIFYMCANKNCKHR  107 (110)
Q Consensus        69 ~~CpkCg~~~a~~~~~Q~RsaDE~~T~fY~C~~~~C~~~  107 (110)
                      ..|||||-.-.+-.-.     ..|....|.|.||.|.+.
T Consensus         2 hlcpkcgvgvl~pvy~-----~kgeikvfrcsnpacdye   35 (36)
T d1pvma3           2 HLCPKCGVGVLEPVYN-----EKGEIKVFRCSNPACDYE   35 (36)
T ss_dssp             CBCTTTSSSBEEEEEC-----TTSCEEEEEESCTTCCCB
T ss_pred             ccCCccCceEEEEeec-----CCCcEEEEEcCCCccccC
Confidence            4799999874332222     237888899999999763

>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=93.44  E-value=0.027  Score=30.55  Aligned_cols=28  Identities=29%  Similarity=0.611  Sum_probs=19.8

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      =||+||+.-... |  .....++|..||++.
T Consensus        13 ~Cp~Cgs~~ii~-D--~~~Ge~vC~~CG~Vl   40 (58)
T d1dl6a_          13 TCPNHPDAILVE-D--YRAGDMICPECGLVV   40 (58)
T ss_dssp             SBTTBSSSCCEE-C--SSSCCEECTTTCCEE
T ss_pred             CCCCCCCCCEEE-E--CCCCcEecccCCCEe
Confidence            499999874433 1  224589999999864

>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: Endonuclease VIII
species: Escherichia coli [TaxId: 562]

Probab=92.66  E-value=0.023  Score=28.55  Aligned_cols=27  Identities=22%  Similarity=0.753  Sum_probs=21.6

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPY   31 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y   31 (110)
                      -|+.||+.+.-.  ..+++..|.|+.|.+
T Consensus        14 pC~~C~~~I~~~--~~~gR~t~~Cp~CQ~   40 (40)
T d1k3xa3          14 PCERCGSIIEKT--TLSSRPFYWCPGCQH   40 (40)
T ss_dssp             BCTTTCCBCEEE--EETTEEEEECTTTCC
T ss_pred             ccCcCCCEEEEE--EECCCCCEEChhhCC
Confidence            489999988777  445678999999964

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.89  E-value=0.045  Score=28.68  Aligned_cols=28  Identities=25%  Similarity=0.636  Sum_probs=19.3

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      -||+||+--... |.  ....++|..||.+.
T Consensus         7 ~Cp~Cgs~~iv~-D~--~~Ge~vC~~CG~Vi   34 (50)
T d1pfta_           7 VCPACESAELIY-DP--ERGEIVCAKCGYVI   34 (50)
T ss_dssp             SCTTTSCCCEEE-ET--TTTEEEESSSCCBC
T ss_pred             cCcCCCCCcEEE-EC--CCCeEecccCCcEe
Confidence            599998753322 23  24599999999853

>d2cona1 g.41.15.1 (A:8-73) RNA-binding protein NOB1 (Nin one binding) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: NOB1 zinc finger-like
family: NOB1 zinc finger-like
domain: RNA-binding protein NOB1 (Nin one binding)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.99  E-value=0.034  Score=30.92  Aligned_cols=9  Identities=44%  Similarity=1.180  Sum_probs=7.6

Q ss_pred             CCCcCCCCC
Q 033869            2 EFCPTCGTM   10 (110)
Q Consensus         2 ~FCp~C~nl   10 (110)
                      .|||.|||-
T Consensus        24 ~FCpkCGn~   32 (66)
T d2cona1          24 VFCGHCGNK   32 (66)
T ss_dssp             CSCSSSCCS
T ss_pred             ccCcccCCC
Confidence            599999984

>d1r2za3 g.39.1.8 (A:229-274) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=90.01  E-value=0.06  Score=27.62  Aligned_cols=26  Identities=27%  Similarity=0.677  Sum_probs=20.7

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACP   30 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~   30 (110)
                      -|+.|++.+.-.  ....+..|.|+.|.
T Consensus        20 ~C~~C~~~I~~~--~~~gR~t~~Cp~CQ   45 (46)
T d1r2za3          20 PCKRCGTPIEKT--VVAGRGTHYCPRCQ   45 (46)
T ss_dssp             BCTTTCCBCEEE--EETTEEEEECTTTC
T ss_pred             ccCCCCCeEEEE--EECCCcCEEChhhC
Confidence            589999987766  45567899999996

>d2f9yb1 c.14.1.4 (B:23-285) Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: ClpP/crotonase
superfamily: ClpP/crotonase
family: Biotin dependent carboxylase carboxyltransferase domain
domain: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, AccD
species: Escherichia coli [TaxId: 562]

Probab=89.72  E-value=0.018  Score=40.00  Aligned_cols=30  Identities=27%  Similarity=0.516  Sum_probs=23.2

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeee
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNM   35 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~   35 (110)
                      =||.|++||+-++-+   .+.++|++|+|-...
T Consensus         4 ~C~~C~~~~~~~~l~---~~~~vC~~C~~h~~l   33 (263)
T d2f9yb1           4 KCDSCGQVLYRAELE---RNLEVCPKCDHHMRM   33 (263)
T ss_dssp             CCTTTCCCEETTHHH---HTTTBCTTTCCBCCC
T ss_pred             cCCCCcceeeHHHHH---HhCCCCcCCCCCCCc
Confidence            399999999987333   357899999996543

>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein Cgl1405/cg1592
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=89.68  E-value=0.13  Score=27.77  Aligned_cols=31  Identities=13%  Similarity=0.189  Sum_probs=25.6

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      -||.|+.-|...  +.  ...++|+.|+..+++.+
T Consensus        12 ~CP~ck~~L~~~--~~--~~~Lvc~~~~~~YPI~d   42 (59)
T d2jnya1          12 ACPKDKGPLRYL--ES--EQLLVNERLNLAYRIDD   42 (59)
T ss_dssp             BCTTTCCBCEEE--TT--TTEEEETTTTEEEEEET
T ss_pred             cCCCCCCEeEEe--CC--CCEEEcCccCccccccC
Confidence            599999999887  22  45899999999998876

>d1neea2 g.59.1.1 (A:99-135) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

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 Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=89.68  E-value=0.066  Score=26.34  Aligned_cols=33  Identities=21%  Similarity=0.414  Sum_probs=22.4

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      .|++|++.=.. ..++++...+.|..||-..++.
T Consensus         3 ~C~~C~spDT~-l~ke~R~~~l~C~aCGa~r~V~   35 (37)
T d1neea2           3 ICHECNRPDTR-IIREGRISLLKCEACGAKAPLK   35 (37)
T ss_dssp             HHTCCSSCSSC-CEEETTTTEEECSTTSCCCCSC
T ss_pred             ECCCCCCCCCE-EEEcCCEEEEEeccCCCCcccc
Confidence            48899876211 1133567899999999877654

>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Hypothetical protein CV3345
species: Chromobacterium violaceum [TaxId: 536]

Probab=89.63  E-value=0.13  Score=27.77  Aligned_cols=31  Identities=16%  Similarity=0.472  Sum_probs=25.8

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      -||.|+.-|...++    ...++|+.|+..+++.+
T Consensus         9 ~CP~ck~~L~~~~~----~~~Lvc~~~~l~YPI~d   39 (59)
T d2hf1a1           9 VCPLCKGPLVFDKS----KDELICKGDRLAFPIKD   39 (59)
T ss_dssp             BCTTTCCBCEEETT----TTEEEETTTTEEEEEET
T ss_pred             cCCCCCCeeeEeCC----CCEEecCCcCccccccC
Confidence            59999999998732    34899999999999876

>d1ee8a3 g.39.1.8 (A:211-266) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Thermus thermophilus [TaxId: 274]

Probab=88.94  E-value=0.12  Score=27.56  Aligned_cols=29  Identities=24%  Similarity=0.581  Sum_probs=22.8

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      ..|+.|++.+.-.  ..+++..|.|+.|...
T Consensus        26 ~~C~~C~~~I~~~--~~~~R~t~~Cp~CQ~~   54 (56)
T d1ee8a3          26 LPCPACGRPVERR--VVAGRGTHFCPTCQGE   54 (56)
T ss_dssp             SBCTTTCCBCEEE--ESSSCEEEECTTTTTC
T ss_pred             cccccCCceEEEE--EECCCcCEECcCccCC
Confidence            3699999987666  5566889999999854

>d1tdza3 g.39.1.8 (A:225-271) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Lactococcus lactis [TaxId: 1358]

Probab=88.58  E-value=0.08  Score=27.26  Aligned_cols=27  Identities=26%  Similarity=0.641  Sum_probs=21.4

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPY   31 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y   31 (110)
                      -|+.|++.+.-.  ..+.+..|.|++|..
T Consensus        20 ~C~~C~~~I~~~--~~~gR~t~~Cp~CQk   46 (47)
T d1tdza3          20 KCSRCGAEIQKI--KVAGRGTHFCPVCQQ   46 (47)
T ss_dssp             BCTTTCCBCEEE--EETTEEEEECTTTSC
T ss_pred             CcCCCCcEEEEE--EECCcccEECccccC
Confidence            599999977666  556688999999974

>d1k82a3 g.39.1.8 (A:225-268) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Escherichia coli [TaxId: 562]

Probab=88.54  E-value=0.084  Score=26.81  Aligned_cols=26  Identities=27%  Similarity=0.658  Sum_probs=20.2

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACP   30 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~   30 (110)
                      -|+.|++.+.-.  ...++..|.|+.|.
T Consensus        18 ~C~~C~~~I~~~--~~~~R~t~~Cp~CQ   43 (44)
T d1k82a3          18 PCRVCGTPIVAT--KHAQRATFYCRQCQ   43 (44)
T ss_dssp             BCTTTCCBCEEE--EETTEEEEECTTTC
T ss_pred             CcCCCCCEEEEE--EECCcccEEChhhc
Confidence            489999887766  44567889999986

>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=88.23  E-value=0.072  Score=26.06  Aligned_cols=33  Identities=21%  Similarity=0.453  Sum_probs=23.1

Q ss_pred             CCcCCCCCcccccCCCCCCceEEcCCCCCeeeeC
Q 033869            3 FCPTCGTMLQYELPHMDRPSRFSCPACPYVCNME   36 (110)
Q Consensus         3 FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~   36 (110)
                      .|++|++.=.. ..++++...+.|..||-..++.
T Consensus         2 ~C~~C~spDT~-l~ke~R~~~l~C~aCGa~r~V~   34 (36)
T d1k81a_           2 ICRECGKPDTK-IIKEGRVHLLKCMACGAIRPIR   34 (36)
T ss_dssp             CCSSSCSCEEE-EEEETTEEEEEEETTTEEEEEC
T ss_pred             CCCCCCCCCCE-EEEcCCEEEEEeccCCCCCccc
Confidence            58999986221 1234567789999999887764

>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein PFL1779
species: Pseudomonas fluorescens [TaxId: 294]

Probab=87.88  E-value=0.21  Score=26.86  Aligned_cols=32  Identities=13%  Similarity=0.259  Sum_probs=26.3

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeeeeCC
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCNMES   37 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~~~~   37 (110)
                      .-||.|+.-|...  ++  ...++|..|+..+++.+
T Consensus         7 L~CP~ck~~L~~~--~~--~~~Lvc~~~~laYPI~d   38 (59)
T d2pk7a1           7 LACPICKGPLKLS--AD--KTELISKGAGLAYPIRD   38 (59)
T ss_dssp             CCCTTTCCCCEEC--TT--SSEEEETTTTEEEEEET
T ss_pred             eECCCCCCcceEe--CC--CCEEecCCcCccccccC
Confidence            3599999999987  32  44899999999998876

>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=87.30  E-value=0.15  Score=28.65  Aligned_cols=29  Identities=24%  Similarity=0.629  Sum_probs=21.3

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      .+||.||..=.-+    ....+|.|+.|++..-
T Consensus        28 y~Cp~Cgk~~vkR----~a~GIW~C~kC~~~~A   56 (73)
T d1vqoz1          28 HACPNCGEDRVDR----QGTGIWQCSYCDYKFT   56 (73)
T ss_dssp             BCCSSSSCSCEEE----EETTEEEETTTCCEEE
T ss_pred             ccCCCCCCceeEE----EEEEEEECCCCCCEEe
Confidence            3799999864433    1246999999999754

>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=86.09  E-value=0.19  Score=29.05  Aligned_cols=30  Identities=20%  Similarity=0.510  Sum_probs=21.5

Q ss_pred             CcCCCC--CcccccCCCCCCceEEcCCCCCee
Q 033869            4 CPTCGT--MLQYELPHMDRPSRFSCPACPYVC   33 (110)
Q Consensus         4 Cp~C~n--lL~~~~~~~~~~~~~~C~~C~y~~   33 (110)
                      ||.||.  -...+.|+..+...+.|+.||-..
T Consensus        26 CPfCnh~~sV~vk~dkk~~~g~l~C~vCg~~~   57 (85)
T d1wiia_          26 CPFCNHEKSCDVKMDRARNTGVISCTVCLEEF   57 (85)
T ss_dssp             CTTTCCSSCEEEEEETTTTEEEEEESSSCCEE
T ss_pred             CCCCCCCCeEEEEEEecCCEEEEEEecCCCeE
Confidence            888884  556666666777788888888543

>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=86.05  E-value=0.22  Score=27.94  Aligned_cols=29  Identities=24%  Similarity=0.552  Sum_probs=21.1

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCeee
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYVCN   34 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~~~   34 (110)
                      ..||.||..=.-+    ....+|.|+.|++..-
T Consensus        28 y~Cp~Cgk~~vkR----~a~GIW~C~kC~~~~A   56 (73)
T d1jj2y_          28 HKCPVCGFKKLKR----AGTGIWMCGHCGYKIA   56 (73)
T ss_dssp             BCCSSSCCSCEEE----EETTEEEETTTCCEEE
T ss_pred             ccCCCCCCCceEE----EEEEEEECCCCCCEEe
Confidence            4799999764333    1245999999999754

>d2j0151 g.41.8.5 (5:2-60) Ribosomal protein L32p {Thermus thermophilus [TaxId: 274]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Thermus thermophilus [TaxId: 274]

Probab=85.88  E-value=0.16  Score=27.42  Aligned_cols=23  Identities=35%  Similarity=0.853  Sum_probs=17.2

Q ss_pred             CCCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            1 MEFCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         1 M~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      +..||+||..-.+-         -+|..|||-
T Consensus        29 l~~C~~CG~~~~pH---------rvC~~CG~Y   51 (59)
T d2j0151          29 LVPCPECKAMKPPH---------TVCPECGYY   51 (59)
T ss_dssp             CBCCSSSSSCBCTT---------CBCTTTCCS
T ss_pred             eeECCCCCCcccce---------eECCCCCeE
Confidence            35799999966554         369999974

>d1pfva3 g.41.1.1 (A:141-175) Methionyl-tRNA synthetase (MetRS), Zn-domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Escherichia coli [TaxId: 562]

Probab=84.62  E-value=0.21  Score=24.17  Aligned_cols=12  Identities=42%  Similarity=0.833  Sum_probs=10.0

Q ss_pred             ccCCCCCCCceE
Q 033869           69 VTCPACKHGKAV   80 (110)
Q Consensus        69 ~~CpkCg~~~a~   80 (110)
                      -.||+||+.+|+
T Consensus         3 G~CP~C~~~~a~   14 (35)
T d1pfva3           3 GTCPKCKSPDQY   14 (35)
T ss_dssp             EECTTTCCSSEE
T ss_pred             eECCCCCCcccc
Confidence            479999999883

>d1rqga3 g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Methionyl-tRNA synthetase (MetRS), Zn-domain
family: Methionyl-tRNA synthetase (MetRS), Zn-domain
domain: Methionyl-tRNA synthetase (MetRS), Zn-domain
species: Pyrococcus abyssi [TaxId: 29292]

Probab=81.99  E-value=0.22  Score=24.05  Aligned_cols=12  Identities=33%  Similarity=0.625  Sum_probs=9.2

Q ss_pred             cccCCCCCCCce
Q 033869           68 EVTCPACKHGKA   79 (110)
Q Consensus        68 ~~~CpkCg~~~a   79 (110)
                      .-.||+||.++|
T Consensus         2 ~G~CP~C~~~~a   13 (35)
T d1rqga3           2 IGTCPYCGAEDQ   13 (35)
T ss_dssp             CSBCSSSCCSCC
T ss_pred             eEECCCCCCCcc
Confidence            347999998776

>d2zjrz1 g.41.8.5 (Z:2-59) Ribosomal protein L32p {Deinococcus radiodurans [TaxId: 1299]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Deinococcus radiodurans [TaxId: 1299]

Probab=81.07  E-value=0.17  Score=27.18  Aligned_cols=22  Identities=32%  Similarity=0.772  Sum_probs=14.6

Q ss_pred             CCCcCCCCCcccccCCCCCCceEEcCCCCCe
Q 033869            2 EFCPTCGTMLQYELPHMDRPSRFSCPACPYV   32 (110)
Q Consensus         2 ~FCp~C~nlL~~~~~~~~~~~~~~C~~C~y~   32 (110)
                      ..||+||.+..+-         -+|..|||-
T Consensus        30 ~~C~~CG~~~lpH---------rvC~~CG~Y   51 (58)
T d2zjrz1          30 TECPQCHGKKLSH---------HICPNCGYY   51 (58)
T ss_dssp             EECTTTCCEECTT---------BCCTTTCBS
T ss_pred             eECCCCCCCccce---------eeCCCCCcC
Confidence            3578888765554         367788864