Citrus Sinensis ID: 035423

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30-----
Protein Sequence
MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Secondary Structure (PSIPRED)
cccccccccEEEEcccccEEEEEccccEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEccccEEEEEEccccEEEEEEcc
Coil and Loop (DISEMBL)
mentlkpgdviqcrecgyrilykkRTRRIVQYEAR
Flexible Loop (DISEMBL)
mentlkpgdviqcrecgyrilykkrtrrivqyear
Low Complexity Region (SEG)
MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Disordered region (IsUnstruct)
********DVIQCRECGYRILYKKRTRRIVQ****
Disordered Region (DISOPRED)
******P**VIQCRECGYRILYKKRTRRIVQYE**
Disordered Region (DISEMBL)
MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Disordered Region (DISPRO)
****LKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
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	35	2.2.26 [Sep-21-2011]
P48011	63	DNA-directed RNA polymera	yes	no	0.942	0.523	0.606	4e-06
Q63871	58	DNA-directed RNA polymera	no	no	0.971	0.586	0.647	5e-06
P53803	58	DNA-directed RNA polymera	yes	no	0.971	0.586	0.647	5e-06
Q3ZBC0	58	DNA-directed RNA polymera	yes	no	0.971	0.586	0.647	5e-06
P40422	70	DNA-directed RNA polymera	yes	no	0.914	0.457	0.531	0.0002
Q54R66	46	DNA-directed RNA polymera	yes	no	0.971	0.739	0.470	0.0002

>sp|P48011|RPAB4_SCHPO DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc10 PE=1 SV=2

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 30/33 (90%)

Query: 3  NTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          NT++  +VI+CRECG+R++YK RT+R+VQ+EAR
Sbjct: 31 NTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR 63

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q63871|RPAB4_MOUSE DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Mus musculus GN=Polr2k PE=2 SV=2

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/34 (64%), Positives = 29/34 (85%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct: 25 ENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

Factor that activates expression from a metal response element of the mouse metallothionein-I gene.

Mus musculus (taxid: 10090)

>sp|P53803|RPAB4_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Homo sapiens GN=POLR2K PE=2 SV=1

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/34 (64%), Positives = 29/34 (85%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct: 25 ENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively.

Homo sapiens (taxid: 9606)

>sp|Q3ZBC0|RPAB4_BOVIN DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Bos taurus GN=POLR2K PE=3 SV=1

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/34 (64%), Positives = 29/34 (85%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct: 25 ENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively.

Bos taurus (taxid: 9913)

>sp|P40422|RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPC10 PE=1 SV=1

 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 26/32 (81%)

Query: 4  TLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 39 SLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 70

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center.

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

>sp|Q54R66|RPAB4_DICDI DNA-directed RNA polymerases I, II, and III subunit rpabc4 OS=Dictyostelium discoideum GN=polr2k PE=3 SV=1

 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 16/34 (47%), Positives = 29/34 (85%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          E+ +KP + ++C++C +RI+YKKRT +++Q+EAR
Sbjct: 13 EHEIKPKEPVKCKDCTHRIMYKKRTDKMIQFEAR 46


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.327    0.142    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,254,501
Number of Sequences: 539616
Number of extensions: 217699
Number of successful extensions: 923
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 917
Number of HSP's gapped (non-prelim): 6
length of query: 35
length of database: 191,569,459
effective HSP length: 9
effective length of query: 26
effective length of database: 186,712,915
effective search space: 4854535790
effective search space used: 4854535790
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.8 bits)

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively.

Dictyostelium discoideum (taxid: 44689)

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	35
224117642	51	predicted protein [Populus trichocarpa]	1.0	0.686	1.0	2e-11
414884443	100	TPA: DNA-directed RNA polymerase I, II,	0.971	0.34	1.0	4e-11
226498516	52	LOC100285004 [Zea mays] gi|297720059|ref	0.971	0.653	1.0	9e-11
225466239	51	PREDICTED: DNA-directed RNA polymerases	0.971	0.666	1.0	9e-11
297805550	52	predicted protein [Arabidopsis lyrata su	0.971	0.653	0.970	1e-10
116782140	53	unknown [Picea sitchensis] gi|116790944|	0.971	0.641	0.970	1e-10
116779038	53	unknown [Picea sitchensis]	0.971	0.641	0.970	1e-10
168064913	56	predicted protein [Physcomitrella patens	0.971	0.607	0.941	2e-10
449439515	51	PREDICTED: DNA-directed RNA polymerases	1.0	0.686	0.971	3e-10
302783643	67	hypothetical protein SELMODRAFT_173570 [	0.971	0.507	0.941	3e-10

>gi|224117642|ref|XP_002317630.1| predicted protein [Populus trichocarpa] gi|356531072|ref|XP_003534102.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC4-like [Glycine max] gi|356560019|ref|XP_003548293.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC4 [Glycine max] gi|222860695|gb|EEE98242.1| predicted protein [Populus trichocarpa] gi|255630274|gb|ACU15492.1| unknown [Glycine max]

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/35 (100%), Positives = 35/35 (100%)

Query: 1  MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 17 MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414884443|tpg|DAA60457.1| TPA: DNA-directed RNA polymerase I, II, and III polypeptide isoform 1, partial [Zea mays] gi|414884444|tpg|DAA60458.1| TPA: DNA-directed RNA polymerase I, II, and III polypeptide isoform 2, partial [Zea mays]

 Score = 72.0 bits (175), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 34/34 (100%), Positives = 34/34 (100%)

Query: 2   ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
           ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 67  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 100

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|226498516|ref|NP_001151371.1| LOC100285004 [Zea mays] gi|297720059|ref|NP_001172391.1| Os01g0530366 [Oryza sativa Japonica Group] gi|297723715|ref|NP_001174221.1| Os05g0151800 [Oryza sativa Japonica Group] gi|242048352|ref|XP_002461922.1| hypothetical protein SORBIDRAFT_02g010660 [Sorghum bicolor] gi|242078439|ref|XP_002443988.1| hypothetical protein SORBIDRAFT_07g005435 [Sorghum bicolor] gi|195609858|gb|ACG26759.1| DNA-directed RNA polymerases I, II, and III 7.3 kDa polypeptide [Zea mays] gi|195620974|gb|ACG32317.1| DNA-directed RNA polymerases I, II, and III 7.3 kDa polypeptide [Zea mays] gi|195645780|gb|ACG42358.1| DNA-directed RNA polymerases I, II, and III 7.3 kDa polypeptide [Zea mays] gi|195646246|gb|ACG42591.1| DNA-directed RNA polymerases I, II, and III 7.3 kDa polypeptide [Zea mays] gi|218188380|gb|EEC70807.1| hypothetical protein OsI_02267 [Oryza sativa Indica Group] gi|222618595|gb|EEE54727.1| hypothetical protein OsJ_02072 [Oryza sativa Japonica Group] gi|241925299|gb|EER98443.1| hypothetical protein SORBIDRAFT_02g010660 [Sorghum bicolor] gi|241940338|gb|EES13483.1| hypothetical protein SORBIDRAFT_07g005435 [Sorghum bicolor] gi|255673311|dbj|BAH91121.1| Os01g0530366 [Oryza sativa Japonica Group] gi|255676033|dbj|BAH92949.1| Os05g0151800 [Oryza sativa Japonica Group]

 Score = 70.9 bits (172), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 34/34 (100%), Positives = 34/34 (100%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 19 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 52

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225466239|ref|XP_002267800.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC4-like [Vitis vinifera] gi|225468167|ref|XP_002272054.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC4 [Vitis vinifera] gi|297738145|emb|CBI27346.3| unnamed protein product [Vitis vinifera]

 Score = 70.9 bits (172), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 34/34 (100%), Positives = 34/34 (100%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 18 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297805550|ref|XP_002870659.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297316495|gb|EFH46918.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score = 70.5 bits (171), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/34 (97%), Positives = 34/34 (100%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          ENTLKPGDVIQCRECGYRILYKKRTRR+VQYEAR
Sbjct: 19 ENTLKPGDVIQCRECGYRILYKKRTRRVVQYEAR 52

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116782140|gb|ABK22384.1| unknown [Picea sitchensis] gi|116790944|gb|ABK25799.1| unknown [Picea sitchensis] gi|148909877|gb|ABR18025.1| unknown [Picea sitchensis] gi|224284970|gb|ACN40214.1| unknown [Picea sitchensis] gi|224286085|gb|ACN40753.1| unknown [Picea sitchensis]

 Score = 70.5 bits (171), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/34 (97%), Positives = 34/34 (100%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          EN+LKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 20 ENSLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 53

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116779038|gb|ABK21111.1| unknown [Picea sitchensis]

 Score = 70.1 bits (170), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/34 (97%), Positives = 34/34 (100%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          EN+LKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 20 ENSLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 53

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168064913|ref|XP_001784402.1| predicted protein [Physcomitrella patens subsp. patens] gi|162664073|gb|EDQ50807.1| predicted protein [Physcomitrella patens subsp. patens]

 Score = 69.7 bits (169), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/34 (94%), Positives = 34/34 (100%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          +NTLKPGDVIQCRECGYRILYKKRTRRIVQ+EAR
Sbjct: 23 DNTLKPGDVIQCRECGYRILYKKRTRRIVQFEAR 56

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439515|ref|XP_004137531.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC4-like [Cucumis sativus] gi|449516854|ref|XP_004165461.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC4-like [Cucumis sativus]

 Score = 69.3 bits (168), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 34/35 (97%), Positives = 34/35 (97%)

Query: 1  MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          MENTLK GDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 17 MENTLKQGDVIQCRECGYRILYKKRTRRIVQYEAR 51

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302783643|ref|XP_002973594.1| hypothetical protein SELMODRAFT_173570 [Selaginella moellendorffii] gi|300158632|gb|EFJ25254.1| hypothetical protein SELMODRAFT_173570 [Selaginella moellendorffii]

 Score = 69.3 bits (168), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 32/34 (94%), Positives = 34/34 (100%)

Query: 2  ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          +N+LKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 34 DNSLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 67

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	35
TAIR|locus:2163051	51	NRPB12 [Arabidopsis thaliana (	0.971	0.666	0.941	3.4e-13
WB|WBGene00009078	62	rpb-12 [Caenorhabditis elegans	0.971	0.548	0.676	4.7e-09
FB|FBgn0262954	57	Rpb12 "Rpb12" [Drosophila mela	0.971	0.596	0.647	7.6e-09
UNIPROTKB|E1BW79	58	LOC771626 "Uncharacterized pro	0.971	0.586	0.647	2.6e-08
UNIPROTKB|Q3ZBC0	58	POLR2K "DNA-directed RNA polym	0.971	0.586	0.647	2.6e-08
UNIPROTKB|P53803	58	POLR2K "DNA-directed RNA polym	0.971	0.586	0.647	2.6e-08
UNIPROTKB|I3LN51	58	POLR2K "Uncharacterized protei	0.971	0.586	0.647	2.6e-08
RGD|2319895	87	LOC100361574 "mCG145114-like"	0.971	0.390	0.647	2.6e-08
UNIPROTKB|F1LTT4	88	LOC100361574 "Protein LOC10036	0.971	0.386	0.647	2.6e-08
ZFIN|ZDB-GENE-070820-18	58	polr2k "polymerase (RNA) II (D	0.971	0.586	0.647	2.6e-08

TAIR|locus:2163051 NRPB12 [Arabidopsis thaliana (taxid:3702)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 32/34 (94%), Positives = 33/34 (97%)

Query:     2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
             ENTLK GDVIQCRECGYRILYKKRTRR+VQYEAR
Sbjct:    18 ENTLKSGDVIQCRECGYRILYKKRTRRVVQYEAR 51

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

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

GO:0005634 "nucleus" evidence=ISS

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

GO:0000418 "DNA-directed RNA polymerase IV complex" evidence=IPI

GO:0000419 "DNA-directed RNA polymerase V complex" evidence=IDA;IPI

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IPI

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

WB|WBGene00009078 rpb-12 [Caenorhabditis elegans (taxid:6239)]

 Score = 134 (52.2 bits), Expect = 4.7e-09, P = 4.7e-09
 Identities = 23/34 (67%), Positives = 29/34 (85%)

Query:     2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
             EN +KP D I+CRECGYRILYKKR R+++ Y+AR
Sbjct:    29 ENEIKPKDAIRCRECGYRILYKKRCRKLMVYDAR 62

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040017 "positive regulation of locomotion" evidence=IMP

GO:0040015 "negative regulation of multicellular organism growth" evidence=IMP

FB|FBgn0262954 Rpb12 "Rpb12" [Drosophila melanogaster (taxid:7227)]

 Score = 132 (51.5 bits), Expect = 7.6e-09, P = 7.6e-09
 Identities = 22/34 (64%), Positives = 30/34 (88%)

Query:     2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
             EN ++P D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    24 ENEMRPRDPIRCRECGYRIMYKKRTKRLVVFDAR 57

GO:0006366 "transcription from RNA polymerase II promoter" evidence=NAS

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

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=NAS

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|E1BW79 LOC771626 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 22/34 (64%), Positives = 29/34 (85%)

Query:     2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
             EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    25 ENEIKARDPIRCRECGYRIMYKKRTKRLVVFDAR 58

GO:0003677 "DNA binding" evidence=IEA

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

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

UNIPROTKB|Q3ZBC0 POLR2K "DNA-directed RNA polymerases I, II, and III subunit RPABC4" [Bos taurus (taxid:9913)]

 Score = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 22/34 (64%), Positives = 29/34 (85%)

Query:     2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
             EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    25 ENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

GO:0005634 "nucleus" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P53803 POLR2K "DNA-directed RNA polymerases I, II, and III subunit RPABC4" [Homo sapiens (taxid:9606)]

 Score = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 22/34 (64%), Positives = 29/34 (85%)

Query:     2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
             EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    25 ENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

GO:0003677 "DNA binding" evidence=IEA

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

GO:0006356 "regulation of transcription from RNA polymerase I promoter" evidence=TAS

GO:0008270 "zinc ion binding" evidence=TAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006360 "transcription from RNA polymerase I promoter" evidence=TAS

GO:0006361 "transcription initiation from RNA polymerase I promoter" evidence=TAS

GO:0006362 "transcription elongation from RNA polymerase I promoter" evidence=TAS

GO:0006363 "termination of RNA polymerase I transcription" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0006370 "7-methylguanosine mRNA capping" 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:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

UNIPROTKB|I3LN51 POLR2K "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 22/34 (64%), Positives = 29/34 (85%)

Query:     2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
             EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    25 ENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

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

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

GO:0003677 "DNA binding" evidence=IEA

RGD|2319895 LOC100361574 "mCG145114-like" [Rattus norvegicus (taxid:10116)]

 Score = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 22/34 (64%), Positives = 29/34 (85%)

Query:     2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
             EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    54 ENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 87

GO:0003677 "DNA binding" evidence=IEA

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

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

UNIPROTKB|F1LTT4 LOC100361574 "Protein LOC100361574" [Rattus norvegicus (taxid:10116)]

 Score = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 22/34 (64%), Positives = 29/34 (85%)

Query:     2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
             EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    55 ENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 88

GO:0003677 "DNA binding" evidence=IEA

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

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

ZFIN|ZDB-GENE-070820-18 polr2k "polymerase (RNA) II (DNA directed) polypeptide K" [Danio rerio (taxid:7955)]

 Score = 127 (49.8 bits), Expect = 2.6e-08, P = 2.6e-08
 Identities = 22/34 (64%), Positives = 29/34 (85%)

Query:     2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
             EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    25 ENEIKARDPIRCRECGYRIMYKKRTKRLVVFDAR 58

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

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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

Your Input:
	grail3.0014029901	hypothetical protein (52 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	estExt_Genewise1_v1.C_LG_I4990	hypothetical protein (176 aa)				•	•	•	•		0.940
	estExt_Genewise1_v1.C_LG_IX3069	SubName- Full=Putative uncharacterized protein; (117 aa)				•	•	•	•		0.939
	gw1.IX.2304.1	hypothetical protein (321 aa)				•	•	•	•		0.929
	estExt_fgenesh4_pg.C_LG_XV1089	DNA-directed RNA polymerase (143 aa)				•	•	•	•		0.907
	estExt_fgenesh4_pg.C_LG_I0458	hypothetical protein (204 aa)				•		•			0.905
	eugene3.00031452	hypothetical protein (211 aa)				•		•			0.905
	estExt_fgenesh4_pg.C_1570036	hypothetical protein (206 aa)				•	•	•	•		0.901
	gw1.XIII.2192.1	polyribonucleotide nucleotidyltransferase (EC-2.7.7.8) (853 aa)						•			0.899
	gw1.XII.1350.1	hypothetical protein (612 aa)						•			0.899
	gw1.X.1387.1	CTP synthase (EC-6.3.4.2) (589 aa)						•			0.899

---

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	35
smart00659	44	smart00659, RPOLCX, RNA polymerase subunit CX	5e-11
pfam03604	32	pfam03604, DNA_RNApol_7kD, DNA directed RNA polyme	1e-07
COG1996	49	COG1996, RPC10, DNA-directed RNA polymerase, subun	8e-04

>gnl|CDD|128906 smart00659, RPOLCX, RNA polymerase subunit CX

 Score = 49.7 bits (119), Expect = 5e-11
 Identities = 23/35 (65%), Positives = 30/35 (85%)

Query: 1  MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
           EN +K  DV++CRECGYRILYKKRT+R+V+ +AR
Sbjct: 10 RENEIKSKDVVRCRECGYRILYKKRTKRLVEVKAR 44

present in RNA polymerase I, II and III. Length = 44

>gnl|CDD|202700 pfam03604, DNA_RNApol_7kD, DNA directed RNA polymerase, 7 kDa subunit

 Score = 41.1 bits (97), Expect = 1e-07
 Identities = 18/25 (72%), Positives = 21/25 (84%)

Query: 1  MENTLKPGDVIQCRECGYRILYKKR 25
           E  LKPGD I+C+ECG+RILYKKR
Sbjct: 8  AEVELKPGDPIRCKECGHRILYKKR 32

Length = 32

>gnl|CDD|224907 COG1996, RPC10, DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

 Score = 31.6 bits (72), Expect = 8e-04
 Identities = 11/31 (35%), Positives = 17/31 (54%)

Query: 5  LKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
           +    I+C  CG RIL K+R +   + +AR
Sbjct: 19 DQETRGIRCPYCGSRILVKERPKVPKRVKAR 49

Length = 49

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	35
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	99.81
KOG3507	62	consensus DNA-directed RNA polymerase, subunit RPB	99.77
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	99.61
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	99.59
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	98.92
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	96.13
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	93.44
PF13408	58	Zn_ribbon_recom: Recombinase zinc beta ribbon doma	92.19
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	91.89
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	91.7
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	90.89
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	90.45
PF01215	136	COX5B: Cytochrome c oxidase subunit Vb This family	90.37
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	90.3
cd00924	97	Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb.	89.97
PF11672	102	DUF3268: Protein of unknown function (DUF3268); In	89.59
PF10276	40	zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Z	89.37
PF13248	26	zf-ribbon_3: zinc-ribbon domain	89.27
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	89.02
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	88.86
COG4391	62	Uncharacterized protein conserved in bacteria [Fun	88.63
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	88.24
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	88.16
PF04606	47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	87.87
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	87.74
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	87.19
COG4311	97	SoxD Sarcosine oxidase delta subunit [Amino acid t	87.14
PF02591	56	DUF164: Putative zinc ribbon domain; InterPro: IPR	87.03
PF03884	57	DUF329: Domain of unknown function (DUF329); Inter	86.87
KOG3352	153	consensus Cytochrome c oxidase, subunit Vb/COX4 [E	86.68
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	86.6
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	86.02
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	85.9
PF14690	47	zf-ISL3: zinc-finger of transposase IS204/IS1001/I	85.61
PF14205	55	Cys_rich_KTR: Cysteine-rich KTR	85.46
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	85.44
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	85.07
TIGR00244	147	transcriptional regulator NrdR. Members of this al	84.96
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	84.77
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	84.72
PF06107	57	DUF951: Bacterial protein of unknown function (DUF	84.68
PLN02294	174	cytochrome c oxidase subunit Vb	84.09
smart00531	147	TFIIE Transcription initiation factor IIE.	83.37
cd00246	103	RabGEF Nucleotide exchange factor for Rab-like sma	83.22
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	83.21
COG4481	60	Uncharacterized protein conserved in bacteria [Fun	82.98
PF14353	128	CpXC: CpXC protein	82.46
COG1439	177	Predicted nucleic acid-binding protein, consists o	82.31
PF09986	214	DUF2225: Uncharacterized protein conserved in bact	81.91
PF06054	375	CoiA: Competence protein CoiA-like family; InterPr	81.9
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	81.87
PRK09710	64	lar restriction alleviation and modification prote	81.76
TIGR03831	46	YgiT_finger YgiT-type zinc finger domain. This dom	80.92
TIGR01374	84	soxD sarcosine oxidase, delta subunit family, hete	80.66
smart00709	160	Zpr1 Duplicated domain in the epidermal growth fac	80.6
smart00238	71	BIR Baculoviral inhibition of apoptosis protein re	80.17
KOG2691	113	consensus RNA polymerase II subunit 9 [Transcripti	80.14
PF05605	54	zf-Di19: Drought induced 19 protein (Di19), zinc-b	80.02

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=99.81  E-value=3.6e-20  Score=90.92  Aligned_cols=34  Identities=68%  Similarity=1.249  Sum_probs=32.5

Q ss_pred             ccccCCCCceecCCCCCeEEEeecCCceEEEEeC
Q 035423            2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR   35 (35)
Q Consensus         2 ~~~lk~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   35 (35)
                      +++++.+++|+||+||||||||+||+++++|+||
T Consensus        11 ~~~~~~~~~irC~~CG~rIlyK~R~~~~~~~~Ar   44 (44)
T smart00659       11 ENEIKSKDVVRCRECGYRILYKKRTKRLVEVKAR   44 (44)
T ss_pred             EeecCCCCceECCCCCceEEEEeCCCceEEEEcC
Confidence            6788999999999999999999999999999997

present in RNA polymerase I, II and III

>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7

Probab=99.77  E-value=1.1e-20  Score=99.03  Aligned_cols=35  Identities=83%  Similarity=1.401  Sum_probs=33.7

Q ss_pred             CccccCCCCceecCCCCCeEEEeecCCceEEEEeC
Q 035423            1 MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR   35 (35)
Q Consensus         1 ~~~~lk~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   35 (35)
                      .+|+|+.+|+|||++||||||||+|+++++||+||
T Consensus        28 ~en~lk~~D~irCReCG~RIlyKkRtkrlvqfear   62 (62)
T KOG3507|consen   28 QENTLKRGDVIRCRECGYRILYKKRTKRLVQFEAR   62 (62)
T ss_pred             ccccccCCCcEehhhcchHHHHHHHHhhhheeecC
Confidence            47999999999999999999999999999999997

0 [Transcription]

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=99.61  E-value=6.5e-16  Score=77.89  Aligned_cols=31  Identities=35%  Similarity=0.515  Sum_probs=29.7

Q ss_pred             cCCCCceecCCCCCeEEEeecCCceEEEEeC
Q 035423            5 LKPGDVIQCRECGYRILYKKRTRRIVQYEAR   35 (35)
Q Consensus         5 lk~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   35 (35)
                      ++.++.||||+||||||||.||+.+++|+|+
T Consensus        19 ~~~~~~irCp~Cg~rIl~K~R~~~~krvkA~   49 (49)
T COG1996          19 DQETRGIRCPYCGSRILVKERPKVPKRVKAR   49 (49)
T ss_pred             hhccCceeCCCCCcEEEEeccCCccEEEecC
Confidence            6789999999999999999999999999997

>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=99.59  E-value=3.6e-16  Score=72.93  Aligned_cols=25  Identities=72%  Similarity=1.226  Sum_probs=19.8

Q ss_pred             CccccCCCCceecCCCCCeEEEeec
Q 035423            1 MENTLKPGDVIQCRECGYRILYKKR   25 (35)
Q Consensus         1 ~~~~lk~~~~irC~~CG~RIlyK~R   25 (35)
                      ++|+|+.+|+|||++||||||||+|
T Consensus         8 ~~~~~~~~~~irC~~CG~RIlyK~R   32 (32)
T PF03604_consen    8 AEVELKPGDPIRCPECGHRILYKKR   32 (32)
T ss_dssp             SSE-BSTSSTSSBSSSS-SEEBE--
T ss_pred             CeeEcCCCCcEECCcCCCeEEEecC
Confidence            3688999999999999999999998

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 ....

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

Probab=98.92  E-value=1.7e-09  Score=52.15  Aligned_cols=26  Identities=42%  Similarity=0.888  Sum_probs=25.0

Q ss_pred             ceecCCCCCeEEEeecCCceEEEEeC
Q 035423           10 VIQCRECGYRILYKKRTRRIVQYEAR   35 (35)
Q Consensus        10 ~irC~~CG~RIlyK~R~~~~~~~~Ar   35 (35)
                      .++||+||++++||.|++.++.++|+
T Consensus        21 ~~~Cp~CG~~~~~~~~~~~v~~~~~~   46 (46)
T PRK00398         21 GVRCPYCGYRILFKERPPVVKRVKAR   46 (46)
T ss_pred             ceECCCCCCeEEEccCCCcceEeecC
Confidence            89999999999999999999999986

>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]

Probab=96.13  E-value=0.0013  Score=41.26  Aligned_cols=18  Identities=44%  Similarity=0.997  Sum_probs=14.5

Q ss_pred             CCCCceecCCCCCeEEEee
Q 035423            6 KPGDVIQCRECGYRILYKK   24 (35)
Q Consensus         6 k~~~~irC~~CG~RIlyK~   24 (35)
                      +..+.|.||+|| ||||..
T Consensus       217 ~~d~iv~CP~Cg-RILy~~  234 (239)
T COG1579         217 KKDEIVFCPYCG-RILYYD  234 (239)
T ss_pred             cCCCCccCCccc-hHHHhh
Confidence            467889999999 678754

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=93.44  E-value=0.037  Score=27.77  Aligned_cols=12  Identities=50%  Similarity=0.822  Sum_probs=9.8

Q ss_pred             eecCCCCCeEEE
Q 035423           11 IQCRECGYRILY   22 (35)
Q Consensus        11 irC~~CG~RIly   22 (35)
                      |.||+||+.|-.
T Consensus         1 i~CPyCge~~~~   12 (52)
T PF14255_consen    1 IQCPYCGEPIEI   12 (52)
T ss_pred             CCCCCCCCeeEE
Confidence            579999998754

>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain

Probab=92.19  E-value=0.29  Score=23.04  Aligned_cols=21  Identities=24%  Similarity=0.765  Sum_probs=16.4

Q ss_pred             CCceecCCCCCeEEEeecCCc
Q 035423            8 GDVIQCRECGYRILYKKRTRR   28 (35)
Q Consensus         8 ~~~irC~~CG~RIlyK~R~~~   28 (35)
                      ...++|.+||++...+.++..
T Consensus         3 ~g~l~C~~CG~~m~~~~~~~~   23 (58)
T PF13408_consen    3 SGLLRCGHCGSKMTRRKRKGK   23 (58)
T ss_pred             CCcEEcccCCcEeEEEECCCC
Confidence            356899999999888776643

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=91.89  E-value=0.19  Score=22.65  Aligned_cols=14  Identities=29%  Similarity=0.795  Sum_probs=10.9

Q ss_pred             CCceecCCCCCeEE
Q 035423            8 GDVIQCRECGYRIL   21 (35)
Q Consensus         8 ~~~irC~~CG~RIl   21 (35)
                      +..++|++||+.+.
T Consensus        23 ~~~v~C~~C~~~~~   36 (38)
T TIGR02098        23 GGKVRCGKCGHVWY   36 (38)
T ss_pred             CCEEECCCCCCEEE
Confidence            34699999999753

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.

>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=91.70  E-value=0.071  Score=23.41  Aligned_cols=12  Identities=33%  Similarity=0.880  Sum_probs=9.5

Q ss_pred             CCceecCCCCCe
Q 035423            8 GDVIQCRECGYR   19 (35)
Q Consensus         8 ~~~irC~~CG~R   19 (35)
                      .....||+|||-
T Consensus        12 ~~~~~Cp~CG~~   23 (26)
T PF10571_consen   12 ESAKFCPHCGYD   23 (26)
T ss_pred             hhcCcCCCCCCC
Confidence            456789999985

Several members are annotated as putative helicases.

>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=90.89  E-value=0.13  Score=28.81  Aligned_cols=14  Identities=43%  Similarity=0.904  Sum_probs=11.2

Q ss_pred             cCCCCceecCCCCCe
Q 035423            5 LKPGDVIQCRECGYR   19 (35)
Q Consensus         5 lk~~~~irC~~CG~R   19 (35)
                      |+. ++|.||+||.-
T Consensus        22 Lnk-~PivCP~CG~~   35 (108)
T PF09538_consen   22 LNK-DPIVCPKCGTE   35 (108)
T ss_pred             CCC-CCccCCCCCCc
Confidence            455 78999999974

The function of members of this family is unknown.

>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=90.45  E-value=0.48  Score=22.41  Aligned_cols=22  Identities=27%  Similarity=0.552  Sum_probs=16.9

Q ss_pred             cCCCCceecCCCCCeEEEeecC
Q 035423            5 LKPGDVIQCRECGYRILYKKRT   26 (35)
Q Consensus         5 lk~~~~irC~~CG~RIlyK~R~   26 (35)
                      +.=.+++.||.||+.-.|..++
T Consensus        13 ~RW~~g~~CP~Cg~~~~~~~~~   34 (46)
T PF12760_consen   13 IRWPDGFVCPHCGSTKHYRLKT   34 (46)
T ss_pred             hcCCCCCCCCCCCCeeeEEeCC
Confidence            3445668899999987887776

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

>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1

Probab=90.37  E-value=0.13  Score=30.06  Aligned_cols=15  Identities=40%  Similarity=0.833  Sum_probs=12.6

Q ss_pred             cCCCCceecCCCCCe
Q 035423            5 LKPGDVIQCRECGYR   19 (35)
Q Consensus         5 lk~~~~irC~~CG~R   19 (35)
                      |..+.+-||++||+=
T Consensus       107 l~~g~~~RCpeCG~~  121 (136)
T PF01215_consen  107 LHKGKPQRCPECGQV  121 (136)
T ss_dssp             EETTSEEEETTTEEE
T ss_pred             EeCCCccCCCCCCeE
Confidence            567889999999983

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=90.30  E-value=0.26  Score=22.64  Aligned_cols=15  Identities=27%  Similarity=0.753  Sum_probs=11.8

Q ss_pred             CCCCceecCCCCCeE
Q 035423            6 KPGDVIQCRECGYRI   20 (35)
Q Consensus         6 k~~~~irC~~CG~RI   20 (35)
                      ..+..+||+.||+..
T Consensus        21 ~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen   21 AGGRKVRCPKCGHVF   35 (37)
T ss_pred             cCCcEEECCCCCcEe
Confidence            346689999999864

>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb

Probab=89.97  E-value=0.18  Score=27.91  Aligned_cols=19  Identities=32%  Similarity=0.607  Sum_probs=14.6

Q ss_pred             cCCCCceecCCCCCeEEEe
Q 035423            5 LKPGDVIQCRECGYRILYK   23 (35)
Q Consensus         5 lk~~~~irC~~CG~RIlyK   23 (35)
                      |..+.+-||++||+=...+
T Consensus        74 l~~g~~~rC~eCG~~fkL~   92 (97)
T cd00924          74 LEKGKPKRCPECGHVFKLV   92 (97)
T ss_pred             EeCCCceeCCCCCcEEEEE
Confidence            5677899999999954433

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.

>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150

Probab=89.59  E-value=0.23  Score=27.79  Aligned_cols=13  Identities=31%  Similarity=0.457  Sum_probs=11.5

Q ss_pred             ceecCCCCCeEEE
Q 035423           10 VIQCRECGYRILY   22 (35)
Q Consensus        10 ~irC~~CG~RIly   22 (35)
                      +++||+||-.+.+
T Consensus         2 p~~CpYCg~~~~l   14 (102)
T PF11672_consen    2 PIICPYCGGPAEL   14 (102)
T ss_pred             CcccCCCCCeeEE
Confidence            6899999998876

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.37  E-value=0.24  Score=23.68  Aligned_cols=11  Identities=36%  Similarity=0.869  Sum_probs=9.3

Q ss_pred             CceecCCCCCe
Q 035423            9 DVIQCRECGYR   19 (35)
Q Consensus         9 ~~irC~~CG~R   19 (35)
                      ..+.|||||-+
T Consensus        28 ~~~~CpYCg~~   38 (40)
T PF10276_consen   28 GPVVCPYCGTR   38 (40)
T ss_dssp             CEEEETTTTEE
T ss_pred             CeEECCCCCCE
Confidence            46999999976

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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=89.27  E-value=0.15  Score=21.87  Aligned_cols=10  Identities=30%  Similarity=0.860  Sum_probs=7.0

Q ss_pred             ceecCCCCCe
Q 035423           10 VIQCRECGYR   19 (35)
Q Consensus        10 ~irC~~CG~R   19 (35)
                      .+.||+||..
T Consensus         2 ~~~Cp~Cg~~   11 (26)
T PF13248_consen    2 EMFCPNCGAE   11 (26)
T ss_pred             cCCCcccCCc
Confidence            4678888874

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=89.02  E-value=0.35  Score=22.22  Aligned_cols=14  Identities=29%  Similarity=0.857  Sum_probs=11.0

Q ss_pred             CCCceecCCCCCeE
Q 035423            7 PGDVIQCRECGYRI   20 (35)
Q Consensus         7 ~~~~irC~~CG~RI   20 (35)
                      .+..++|+.||+.+
T Consensus        22 ~g~~v~C~~C~~~f   35 (36)
T PF13717_consen   22 KGRKVRCSKCGHVF   35 (36)
T ss_pred             CCcEEECCCCCCEe
Confidence            45679999999864

>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=88.86  E-value=0.34  Score=25.13  Aligned_cols=27  Identities=30%  Similarity=0.634  Sum_probs=21.5

Q ss_pred             ccccCCCCceecCCCCCeEEEeecCCc
Q 035423            2 ENTLKPGDVIQCRECGYRILYKKRTRR   28 (35)
Q Consensus         2 ~~~lk~~~~irC~~CG~RIlyK~R~~~   28 (35)
                      +++.+....+-|++|||-=||+.-+..
T Consensus        28 dvq~~~f~~v~C~~CGYTE~Y~~~~~~   54 (64)
T PF09855_consen   28 DVQNKKFTTVSCTNCGYTEFYKAKTSN   54 (64)
T ss_pred             EecCcEEEEEECCCCCCEEEEeecCcc
Confidence            445566778999999999999976654

>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.63  E-value=0.46  Score=24.95  Aligned_cols=16  Identities=19%  Similarity=0.472  Sum_probs=13.1

Q ss_pred             ccCCCCceecCCCCCe
Q 035423            4 TLKPGDVIQCRECGYR   19 (35)
Q Consensus         4 ~lk~~~~irC~~CG~R   19 (35)
                      ++.....+.|||||-+
T Consensus        42 ~mg~~gev~CPYC~t~   57 (62)
T COG4391          42 DMGDEGEVVCPYCSTR   57 (62)
T ss_pred             EcCCCCcEecCccccE
Confidence            4567778999999986

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=88.24  E-value=0.17  Score=21.52  Aligned_cols=12  Identities=33%  Similarity=0.825  Sum_probs=8.2

Q ss_pred             CceecCCCCCeE
Q 035423            9 DVIQCRECGYRI   20 (35)
Q Consensus         9 ~~irC~~CG~RI   20 (35)
                      +..-|++||+.|
T Consensus        12 ~~~fC~~CG~~l   23 (23)
T PF13240_consen   12 DAKFCPNCGTPL   23 (23)
T ss_pred             cCcchhhhCCcC
Confidence            455688888764

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=88.16  E-value=0.26  Score=22.09  Aligned_cols=12  Identities=33%  Similarity=0.789  Sum_probs=10.1

Q ss_pred             CCceecCCCCCe
Q 035423            8 GDVIQCRECGYR   19 (35)
Q Consensus         8 ~~~irC~~CG~R   19 (35)
                      .+.+.||+||..
T Consensus        24 ~~~~~CP~Cg~~   35 (41)
T smart00834       24 DPLATCPECGGD   35 (41)
T ss_pred             CCCCCCCCCCCc
Confidence            678899999984

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.

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

Probab=87.87  E-value=0.47  Score=22.67  Aligned_cols=13  Identities=23%  Similarity=0.782  Sum_probs=9.8

Q ss_pred             ecCCCCCeEEEee
Q 035423           12 QCRECGYRILYKK   24 (35)
Q Consensus        12 rC~~CG~RIlyK~   24 (35)
                      +||+||.+-....
T Consensus         1 ~CP~Cg~~a~ir~   13 (47)
T PF04606_consen    1 RCPHCGSKARIRT   13 (47)
T ss_pred             CcCCCCCeeEEEE
Confidence            5999999865544

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

>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=87.74  E-value=0.39  Score=22.53  Aligned_cols=12  Identities=42%  Similarity=0.994  Sum_probs=9.6

Q ss_pred             CCCceecCCCCC
Q 035423            7 PGDVIQCRECGY   18 (35)
Q Consensus         7 ~~~~irC~~CG~   18 (35)
                      ..+.+.||.||.
T Consensus        23 ~~~~~~CP~Cg~   34 (42)
T PF09723_consen   23 EDDPVPCPECGS   34 (42)
T ss_pred             CCCCCcCCCCCC
Confidence            356888999998

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.

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

Probab=87.19  E-value=0.36  Score=21.89  Aligned_cols=17  Identities=35%  Similarity=0.864  Sum_probs=11.7

Q ss_pred             ccCCCCceecCCCCCeE
Q 035423            4 TLKPGDVIQCRECGYRI   20 (35)
Q Consensus         4 ~lk~~~~irC~~CG~RI   20 (35)
                      .+..+...-||+|||-|
T Consensus        13 ~y~D~~~~vCp~C~~ew   29 (30)
T PF08274_consen   13 TYEDGELLVCPECGHEW   29 (30)
T ss_dssp             -EE-SSSEEETTTTEEE
T ss_pred             eeccCCEEeCCcccccC
Confidence            34567778899999864

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.

>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]

Probab=87.14  E-value=0.28  Score=27.67  Aligned_cols=11  Identities=45%  Similarity=0.896  Sum_probs=9.1

Q ss_pred             CceecCCCCCe
Q 035423            9 DVIQCRECGYR   19 (35)
Q Consensus         9 ~~irC~~CG~R   19 (35)
                      ..|.||+||-|
T Consensus         2 lLI~CP~Cg~R   12 (97)
T COG4311           2 LLIPCPYCGER   12 (97)
T ss_pred             ceecCCCCCCC
Confidence            35899999976

>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function

Probab=87.03  E-value=0.26  Score=24.06  Aligned_cols=13  Identities=31%  Similarity=1.214  Sum_probs=9.8

Q ss_pred             cCCC-CceecCCCC
Q 035423            5 LKPG-DVIQCRECG   17 (35)
Q Consensus         5 lk~~-~~irC~~CG   17 (35)
                      ++.. ..+.||+||
T Consensus        40 i~~~~~i~~Cp~Cg   53 (56)
T PF02591_consen   40 IRKGDEIVFCPNCG   53 (56)
T ss_pred             HHcCCCeEECcCCC
Confidence            4344 679999998

>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc

Probab=86.87  E-value=0.43  Score=24.39  Aligned_cols=13  Identities=23%  Similarity=0.820  Sum_probs=8.1

Q ss_pred             ceecCCCCCeEEE
Q 035423           10 VIQCRECGYRILY   22 (35)
Q Consensus        10 ~irC~~CG~RIly   22 (35)
                      .++||.||..+.+
T Consensus         2 ~v~CP~C~k~~~~   14 (57)
T PF03884_consen    2 TVKCPICGKPVEW   14 (57)
T ss_dssp             EEE-TTT--EEE-
T ss_pred             cccCCCCCCeecc
Confidence            5899999999988

YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.

>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]

Probab=86.68  E-value=0.3  Score=29.39  Aligned_cols=18  Identities=39%  Similarity=0.888  Sum_probs=14.3

Q ss_pred             cCCCCceecCCCCCeEEEee
Q 035423            5 LKPGDVIQCRECGYRILYKK   24 (35)
Q Consensus         5 lk~~~~irC~~CG~RIlyK~   24 (35)
                      |..++.-||++|||-  ||.
T Consensus       128 l~Kge~~rc~eCG~~--fkL  145 (153)
T KOG3352|consen  128 LEKGETQRCPECGHY--FKL  145 (153)
T ss_pred             EEcCCcccCCcccce--EEe
Confidence            567888999999995  553

>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=86.60  E-value=0.61  Score=21.70  Aligned_cols=14  Identities=21%  Similarity=0.804  Sum_probs=10.2

Q ss_pred             eecCCCCCeEEEee
Q 035423           11 IQCRECGYRILYKK   24 (35)
Q Consensus        11 irC~~CG~RIlyK~   24 (35)
                      ..||.||..++.|.
T Consensus         2 ~~CP~Cg~~lv~r~   15 (39)
T PF01396_consen    2 EKCPKCGGPLVLRR   15 (39)
T ss_pred             cCCCCCCceeEEEE
Confidence            57999997755544

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

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=86.02  E-value=0.32  Score=28.68  Aligned_cols=8  Identities=38%  Similarity=1.107  Sum_probs=6.1

Q ss_pred             eecCCCCC
Q 035423           11 IQCRECGY   18 (35)
Q Consensus        11 irC~~CG~   18 (35)
                      .+||+||+
T Consensus         1 m~cp~c~~    8 (154)
T PRK00464          1 MRCPFCGH    8 (154)
T ss_pred             CcCCCCCC
Confidence            37888886

>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=85.90  E-value=0.48  Score=22.01  Aligned_cols=12  Identities=33%  Similarity=0.791  Sum_probs=6.4

Q ss_pred             eecCCCCCeEEE
Q 035423           11 IQCRECGYRILY   22 (35)
Q Consensus        11 irC~~CG~RIly   22 (35)
                      |.||.||++-.+
T Consensus         1 ~~Cp~Cg~~~a~   12 (39)
T PF01096_consen    1 IKCPKCGHNEAV   12 (39)
T ss_dssp             S--SSS-SSEEE
T ss_pred             CCCcCCCCCeEE
Confidence            579999987543

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 ....

>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165

Probab=85.61  E-value=0.47  Score=21.85  Aligned_cols=14  Identities=21%  Similarity=0.570  Sum_probs=11.1

Q ss_pred             ceecCCCCCeEEEe
Q 035423           10 VIQCRECGYRILYK   23 (35)
Q Consensus        10 ~irC~~CG~RIlyK   23 (35)
                      +..||.||..-+++
T Consensus         2 ~~~Cp~Cg~~~~~~   15 (47)
T PF14690_consen    2 PPRCPHCGSPSVHR   15 (47)
T ss_pred             CccCCCcCCCceEC
Confidence            56899999887554

>PF14205 Cys_rich_KTR: Cysteine-rich KTR

Probab=85.46  E-value=0.87  Score=23.41  Aligned_cols=20  Identities=30%  Similarity=0.544  Sum_probs=16.6

Q ss_pred             ceecCCCCCeEEEeecCCce
Q 035423           10 VIQCRECGYRILYKKRTRRI   29 (35)
Q Consensus        10 ~irC~~CG~RIlyK~R~~~~   29 (35)
                      =+.||.||.+-..|.|.+.+
T Consensus         4 Wi~CP~CgnKTR~kir~DT~   23 (55)
T PF14205_consen    4 WILCPICGNKTRLKIREDTV   23 (55)
T ss_pred             EEECCCCCCccceeeecCce
Confidence            47899999998888888754

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

Probab=85.44  E-value=0.92  Score=20.71  Aligned_cols=18  Identities=22%  Similarity=0.586  Sum_probs=13.8

Q ss_pred             CceecCCCCCeEEE-eecC
Q 035423            9 DVIQCRECGYRILY-KKRT   26 (35)
Q Consensus         9 ~~irC~~CG~RIly-K~R~   26 (35)
                      +..+|..||+..++ ++..
T Consensus         2 ~~~~C~~C~~~~i~~~~~~   20 (33)
T PF08792_consen    2 NLKKCSKCGGNGIVNKEDD   20 (33)
T ss_pred             CceEcCCCCCCeEEEecCC
Confidence            45789999999888 6544

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

Probab=85.07  E-value=0.53  Score=24.67  Aligned_cols=13  Identities=31%  Similarity=1.048  Sum_probs=9.1

Q ss_pred             CCCceecCCCCCe
Q 035423            7 PGDVIQCRECGYR   19 (35)
Q Consensus         7 ~~~~irC~~CG~R   19 (35)
                      .+.+.+||+||+.
T Consensus        47 ~g~~Y~Cp~CGF~   59 (61)
T COG2888          47 LGNPYRCPKCGFE   59 (61)
T ss_pred             cCCceECCCcCcc
Confidence            4566778888863

>TIGR00244 transcriptional regulator NrdR

Probab=84.96  E-value=0.37  Score=28.65  Aligned_cols=8  Identities=25%  Similarity=0.779  Sum_probs=5.9

Q ss_pred             eecCCCCC
Q 035423           11 IQCRECGY   18 (35)
Q Consensus        11 irC~~CG~   18 (35)
                      ++||+|||
T Consensus         1 M~CP~C~~    8 (147)
T TIGR00244         1 MHCPFCQH    8 (147)
T ss_pred             CCCCCCCC
Confidence            36888877

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.

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=84.77  E-value=0.82  Score=21.59  Aligned_cols=11  Identities=36%  Similarity=0.869  Sum_probs=9.2

Q ss_pred             CCceecCCCCC
Q 035423            8 GDVIQCRECGY   18 (35)
Q Consensus         8 ~~~irC~~CG~   18 (35)
                      .+.+.||.||.
T Consensus        24 ~~~~~CP~Cg~   34 (52)
T TIGR02605        24 DPLATCPECGG   34 (52)
T ss_pred             CCCCCCCCCCC
Confidence            45788999998

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

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

Probab=84.72  E-value=0.68  Score=20.16  Aligned_cols=12  Identities=25%  Similarity=0.863  Sum_probs=9.3

Q ss_pred             CCCceecCCCCC
Q 035423            7 PGDVIQCRECGY   18 (35)
Q Consensus         7 ~~~~irC~~CG~   18 (35)
                      .+-...||+||.
T Consensus        13 ~~v~f~CPnCG~   24 (24)
T PF07754_consen   13 QAVPFPCPNCGF   24 (24)
T ss_pred             cCceEeCCCCCC
Confidence            355788999995

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

>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function

Probab=84.68  E-value=0.84  Score=23.52  Aligned_cols=15  Identities=33%  Similarity=0.722  Sum_probs=12.5

Q ss_pred             CceecCCCCCeEEEe
Q 035423            9 DVIQCRECGYRILYK   23 (35)
Q Consensus         9 ~~irC~~CG~RIlyK   23 (35)
                      -.++|..||+.||.-
T Consensus        30 ikikC~gCg~~imlp   44 (57)
T PF06107_consen   30 IKIKCLGCGRQIMLP   44 (57)
T ss_pred             EEEEECCCCCEEEEe
Confidence            358999999998864

>PLN02294 cytochrome c oxidase subunit Vb

Probab=84.09  E-value=1.2  Score=27.26  Aligned_cols=19  Identities=21%  Similarity=0.499  Sum_probs=15.3

Q ss_pred             cCCCCceecCCCCCeEEEe
Q 035423            5 LKPGDVIQCRECGYRILYK   23 (35)
Q Consensus         5 lk~~~~irC~~CG~RIlyK   23 (35)
                      |..+.+.||++||+-...|
T Consensus       136 L~kGkp~RCpeCG~~fkL~  154 (174)
T PLN02294        136 LEKGKSFECPVCTQYFELE  154 (174)
T ss_pred             ecCCCceeCCCCCCEEEEE
Confidence            5678899999999965544

>smart00531 TFIIE Transcription initiation factor IIE

Probab=83.37  E-value=0.57  Score=26.65  Aligned_cols=20  Identities=15%  Similarity=0.459  Sum_probs=15.4

Q ss_pred             CceecCCCCCeEEEeecCCc
Q 035423            9 DVIQCRECGYRILYKKRTRR   28 (35)
Q Consensus         9 ~~irC~~CG~RIlyK~R~~~   28 (35)
                      ....||+||..+.+...+..
T Consensus       122 ~~f~Cp~Cg~~l~~~dn~~~  141 (147)
T smart00531      122 GTFTCPRCGEELEEDDNSEP  141 (147)
T ss_pred             CcEECCCCCCEEEEcCchhh
Confidence            34899999999888766554

>cd00246 RabGEF Nucleotide exchange factor for Rab-like small GTPases (RabGEF), Mss4 type; RabGEF positely regulates the function of Rab GTPase by promoting exchange of GDP for GTP; members of the Rab subfamily of Ras GTPases are important in vesicular transport;

Probab=83.22  E-value=0.85  Score=25.84  Aligned_cols=13  Identities=38%  Similarity=1.053  Sum_probs=11.4

Q ss_pred             ceecCCCCCeEEE
Q 035423           10 VIQCRECGYRILY   22 (35)
Q Consensus        10 ~irC~~CG~RIly   22 (35)
                      .|+|+.||..||=
T Consensus         2 ~v~C~~C~S~VL~   14 (103)
T cd00246           2 AVLCQRCGSRVLT   14 (103)
T ss_pred             ceECCCCCCEEEe
Confidence            4899999999983

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

Probab=83.21  E-value=0.75  Score=23.86  Aligned_cols=12  Identities=25%  Similarity=0.969  Sum_probs=7.5

Q ss_pred             CCCceecCCCCC
Q 035423            7 PGDVIQCRECGY   18 (35)
Q Consensus         7 ~~~~irC~~CG~   18 (35)
                      .+.+.+||+||+
T Consensus        45 ~~~~Y~CP~CGF   56 (59)
T PRK14890         45 QSNPYTCPKCGF   56 (59)
T ss_pred             cCCceECCCCCC
Confidence            345567777775

>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=82.98  E-value=0.98  Score=23.58  Aligned_cols=13  Identities=31%  Similarity=0.973  Sum_probs=11.4

Q ss_pred             ceecCCCCCeEEE
Q 035423           10 VIQCRECGYRILY   22 (35)
Q Consensus        10 ~irC~~CG~RIly   22 (35)
                      .|+|.+|||-||.
T Consensus        34 kikC~nC~h~vm~   46 (60)
T COG4481          34 KIKCENCGHSVMM   46 (60)
T ss_pred             EEEecCCCcEEEe
Confidence            5789999999886

>PF14353 CpXC: CpXC protein

Probab=82.46  E-value=0.86  Score=24.97  Aligned_cols=11  Identities=27%  Similarity=0.921  Sum_probs=8.8

Q ss_pred             ceecCCCCCeE
Q 035423           10 VIQCRECGYRI   20 (35)
Q Consensus        10 ~irC~~CG~RI   20 (35)
                      ...||+||+..
T Consensus        38 ~~~CP~Cg~~~   48 (128)
T PF14353_consen   38 SFTCPSCGHKF   48 (128)
T ss_pred             EEECCCCCCce
Confidence            57899999764

>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]

Probab=82.31  E-value=0.97  Score=27.57  Aligned_cols=17  Identities=24%  Similarity=0.362  Sum_probs=12.5

Q ss_pred             CCceecCCCCCeEEEee
Q 035423            8 GDVIQCRECGYRILYKK   24 (35)
Q Consensus         8 ~~~irC~~CG~RIlyK~   24 (35)
                      .+.-.||.||++++-|.
T Consensus       151 ~~~~~Cp~CG~~~~~~~  167 (177)
T COG1439         151 EPKDFCPICGSPLKRKR  167 (177)
T ss_pred             CCCCcCCCCCCceEEee
Confidence            45567999999955543

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

Probab=81.91  E-value=0.66  Score=28.00  Aligned_cols=15  Identities=33%  Similarity=0.722  Sum_probs=11.7

Q ss_pred             CCCceecCCCCCeEE
Q 035423            7 PGDVIQCRECGYRIL   21 (35)
Q Consensus         7 ~~~~irC~~CG~RIl   21 (35)
                      .++.+-||+|||--+
T Consensus        45 ~Y~V~vCP~CgyA~~   59 (214)
T PF09986_consen   45 FYEVWVCPHCGYAAF   59 (214)
T ss_pred             eeeEEECCCCCCccc
Confidence            467889999998643

>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation

Probab=81.90  E-value=2  Score=27.88  Aligned_cols=25  Identities=24%  Similarity=0.582  Sum_probs=21.3

Q ss_pred             CCceecCCCCCeEEEeecCCceEEE
Q 035423            8 GDVIQCRECGYRILYKKRTRRIVQY   32 (35)
Q Consensus         8 ~~~irC~~CG~RIlyK~R~~~~~~~   32 (35)
                      .....||.||..++.|.-..+.-.|
T Consensus        28 ~~~~~CP~C~~~v~lk~G~~k~~HF   52 (375)
T PF06054_consen   28 KGKYFCPGCGEPVILKKGKKKIPHF   52 (375)
T ss_pred             CCcEECCCCCCeeEEEEcCccccee
Confidence            7789999999999999877766655

It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.

>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=81.87  E-value=1  Score=19.80  Aligned_cols=11  Identities=27%  Similarity=0.920  Sum_probs=6.3

Q ss_pred             ecCCCCCeEEE
Q 035423           12 QCRECGYRILY   22 (35)
Q Consensus        12 rC~~CG~RIly   22 (35)
                      .||.||..++.
T Consensus         1 ~CP~C~s~l~~   11 (28)
T PF03119_consen    1 TCPVCGSKLVR   11 (28)
T ss_dssp             B-TTT--BEEE
T ss_pred             CcCCCCCEeEc
Confidence            49999999773

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.

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=81.76  E-value=2.5  Score=22.21  Aligned_cols=21  Identities=19%  Similarity=0.286  Sum_probs=15.6

Q ss_pred             ecCCCCCeEEEeecCCceEEE
Q 035423           12 QCRECGYRILYKKRTRRIVQY   32 (35)
Q Consensus        12 rC~~CG~RIlyK~R~~~~~~~   32 (35)
                      -||.||+.++.-+.+...-++
T Consensus         8 PCPFCG~~~~~v~~~~g~~~v   28 (64)
T PRK09710          8 PCPFCGCPSVTVKAISGYYRA   28 (64)
T ss_pred             CCCCCCCceeEEEecCceEEE
Confidence            399999999887776554443

>TIGR03831 YgiT_finger YgiT-type zinc finger domain

Probab=80.92  E-value=1.1  Score=20.15  Aligned_cols=17  Identities=24%  Similarity=0.626  Sum_probs=12.8

Q ss_pred             cCCCCceecCCCCCeEE
Q 035423            5 LKPGDVIQCRECGYRIL   21 (35)
Q Consensus         5 lk~~~~irC~~CG~RIl   21 (35)
                      ++..+...|+.||-.++
T Consensus        27 i~~vp~~~C~~CGE~~~   43 (46)
T TIGR03831        27 IENVPALVCPQCGEEYL   43 (46)
T ss_pred             EeCCCccccccCCCEee
Confidence            45566778999998764

This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.

>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form

Probab=80.66  E-value=0.73  Score=25.18  Aligned_cols=9  Identities=56%  Similarity=1.161  Sum_probs=7.8

Q ss_pred             eecCCCCCe
Q 035423           11 IQCRECGYR   19 (35)
Q Consensus        11 irC~~CG~R   19 (35)
                      |.||.||-|
T Consensus         2 I~CP~CG~R   10 (84)
T TIGR01374         2 IPCPYCGPR   10 (84)
T ss_pred             ccCCCCCCc
Confidence            789999976

Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form

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

Probab=80.60  E-value=0.89  Score=26.77  Aligned_cols=10  Identities=50%  Similarity=1.484  Sum_probs=8.7

Q ss_pred             ceecCCCCCe
Q 035423           10 VIQCRECGYR   19 (35)
Q Consensus        10 ~irC~~CG~R   19 (35)
                      ...|++||||
T Consensus        29 sf~C~~CGyk   38 (160)
T smart00709       29 SFECEHCGYR   38 (160)
T ss_pred             EEECCCCCCc
Confidence            5689999998

Also present in archaeal proteins.

>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat

Probab=80.17  E-value=1.1  Score=22.09  Aligned_cols=13  Identities=38%  Similarity=0.915  Sum_probs=11.4

Q ss_pred             CCceecCCCCCeE
Q 035423            8 GDVIQCRECGYRI   20 (35)
Q Consensus         8 ~~~irC~~CG~RI   20 (35)
                      +|.++|.+||..+
T Consensus        34 ~d~v~C~~C~~~l   46 (71)
T smart00238       34 GDEVKCFFCGGEL   46 (71)
T ss_pred             CCEEEeCCCCCCc
Confidence            6789999999875

Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.

>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]

Probab=80.14  E-value=0.99  Score=26.08  Aligned_cols=26  Identities=31%  Similarity=0.703  Sum_probs=18.8

Q ss_pred             ccccCCCCceecCCCCCe--EEEeecCC
Q 035423            2 ENTLKPGDVIQCRECGYR--ILYKKRTR   27 (35)
Q Consensus         2 ~~~lk~~~~irC~~CG~R--IlyK~R~~   27 (35)
                      |+.|+......||.||++  ++|-.++.
T Consensus        65 DPTLPrts~~~C~~C~~~eavffQ~~~~   92 (113)
T KOG2691|consen   65 DPTLPRTSDKHCPKCGHREAVFFQAQTR   92 (113)
T ss_pred             CCCcCccccccCCccCCcceEEEecccc
Confidence            455677678899999997  55655544

>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins

Probab=80.02  E-value=0.84  Score=21.99  Aligned_cols=9  Identities=33%  Similarity=0.885  Sum_probs=6.0

Q ss_pred             ceecCCCCC
Q 035423           10 VIQCRECGY   18 (35)
Q Consensus        10 ~irC~~CG~   18 (35)
                      ...||+||.
T Consensus         2 ~f~CP~C~~   10 (54)
T PF05605_consen    2 SFTCPYCGK   10 (54)
T ss_pred             CcCCCCCCC
Confidence            456777775

Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	35
3h0g_L	63	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		3e-07
1i3q_L	70	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		1e-05
3j0k_L	46	Orientation Of Rna Polymerase Ii Within The Human V		2e-05

>pdb|3H0G|L Chain L, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 63

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 20/33 (60%), Positives = 30/33 (90%)
Query: 3  NTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          NT++  +VI+CRECG+R++YK RT+R+VQ+EAR
Sbjct: 31 NTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR 63

>pdb|1I3Q|L Chain L, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 70

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 26/32 (81%)
Query: 4  TLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 39 SLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 70

>pdb|3J0K|L Chain L, Orientation Of Rna Polymerase Ii Within The Human Vp16-Mediator-Pol Ii-Tfiif Assembly Length = 46

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 17/32 (53%), Positives = 26/32 (81%)
Query: 4  TLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
          +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 15 SLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 46

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	35
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	8e-16
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	2e-15

>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* ... Length = 70

 Score = 62.2 bits (151), Expect = 8e-16
 Identities = 17/35 (48%), Positives = 27/35 (77%)

Query: 1  MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
           + +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 36 SKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 70

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 63

 Score = 61.1 bits (148), Expect = 2e-15
 Identities = 20/35 (57%), Positives = 30/35 (85%)

Query: 1  MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
            NT++  +VI+CRECG+R++YK RT+R+VQ+EAR
Sbjct: 29 ARNTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	35
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	99.8
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	99.73
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	99.49
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	95.99
2odx_A	80	Cytochrome C oxidase polypeptide IV; all beta-prot	93.73
1v54_F	98	VI, cytochrome C oxidase polypeptide VB; oxidoredu	92.91
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	91.84
2jvm_A	80	Uncharacterized protein; alpha+beta, structural ge	91.72
2y69_F	129	Cytochrome C oxidase subunit 5B; electron transpor	91.13
2jrr_A	67	Uncharacterized protein; solution structure, SIR90	90.58
2jz8_A	87	Uncharacterized protein BH09830; zinc binding, str	90.53
2i5o_A	39	DNA polymerase ETA; zinc finger, DNA polymerase,PO	88.48
1hxr_A	115	Guanine nucleotide exchange factor MSS4; RAB GTPas	87.04
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	86.48
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	84.34
1tfi_A	50	Transcriptional elongation factor SII; transcripti	82.81

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.80  E-value=8.8e-21  Score=98.48  Aligned_cols=35  Identities=57%  Similarity=1.103  Sum_probs=33.2

Q ss_pred             CccccCCCCceecCCCCCeEEEeecCCceEEEEeC
Q 035423            1 MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR   35 (35)
Q Consensus         1 ~~~~lk~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   35 (35)
                      .+++|+.+++||||+||||||||+||++++||+||
T Consensus        29 ~~~~l~~~~~iRC~~CG~RILyK~Rt~r~~~~~Ar   63 (63)
T 3h0g_L           29 ARNTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR   63 (63)
T ss_dssp             CBCCCCSSSCCCCSSSCCCCCBCCCCCCCEEECCC
T ss_pred             CeeecCCCCceECCCCCcEEEEEecCCceEEEECC
Confidence            36889999999999999999999999999999998

>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=99.73  E-value=3.9e-19  Score=93.22  Aligned_cols=34  Identities=50%  Similarity=0.968  Sum_probs=32.3

Q ss_pred             ccccCCCCceecCCCCCeEEEeecCCceEEEEeC
Q 035423            2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR   35 (35)
Q Consensus         2 ~~~lk~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   35 (35)
                      +++++..|+|+||+||||||||+||++++||+||
T Consensus        37 ~~e~~~~d~irCp~CG~RILyK~R~~r~v~~~ar   70 (70)
T 1twf_L           37 KLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR   70 (70)
T ss_dssp             EECCCTTSTTCCSSSCCCCCBCCCCSSCEEECCC
T ss_pred             cceeCCCCCccCCCCCceEeEecCCCccEEEecC
Confidence            5778899999999999999999999999999998

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=99.49  E-value=1.4e-14  Score=72.24  Aligned_cols=33  Identities=30%  Similarity=0.577  Sum_probs=31.0

Q ss_pred             ccccCCCCceecCCCCCeEEEeecCCceEEEEe
Q 035423            2 ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEA   34 (35)
Q Consensus         2 ~~~lk~~~~irC~~CG~RIlyK~R~~~~~~~~A   34 (35)
                      +.+|+..+.|+||+|||||+||.|++.++.++|
T Consensus        15 ~~el~~lP~IrCpyCGyrii~KvR~p~vK~vkA   47 (48)
T 4ayb_P           15 DEQLKVLPGVRCPYCGYKIIFMVRKPTIKIVKA   47 (48)
T ss_dssp             CCCSCCCSSSCCTTTCCSCEECCCCCSCEEEEC
T ss_pred             HHHHhhCCCcccCccCcEEEEEecCCcceeeec
Confidence            467899999999999999999999999999988

>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon, coiled post-transcriptional, gene regulation, chaperone; HET: EPE; 2.20A {Helicobacter pylori}

Probab=95.99  E-value=0.0034  Score=37.23  Aligned_cols=19  Identities=53%  Similarity=1.125  Sum_probs=14.9

Q ss_pred             CCCceecCCCCCeEEEeecC
Q 035423            7 PGDVIQCRECGYRILYKKRT   26 (35)
Q Consensus         7 ~~~~irC~~CG~RIlyK~R~   26 (35)
                      ..+.+.||+|| ||||....
T Consensus       219 ~~~Iv~Cp~Cg-RIL~~~~~  237 (256)
T 3na7_A          219 SGDMITCPYCG-RILYAEGA  237 (256)
T ss_dssp             SSSCEECTTTC-CEEECSCC
T ss_pred             CCCEEECCCCC-eeEEeCcc
Confidence            34679999998 89997644

>2odx_A Cytochrome C oxidase polypeptide IV; all beta-protein, metallo-protein, oxidoreductase; NMR {Saccharomyces cerevisiae}

Probab=93.73  E-value=0.047  Score=28.59  Aligned_cols=15  Identities=33%  Similarity=0.687  Sum_probs=12.9

Q ss_pred             cCCCCceecCCCCCe
Q 035423            5 LKPGDVIQCRECGYR   19 (35)
Q Consensus         5 lk~~~~irC~~CG~R   19 (35)
                      |..+.+-||++||+-
T Consensus        51 l~~g~~~RC~eCG~~   65 (80)
T 2odx_A           51 PTVNEVARCWECGSV   65 (80)
T ss_dssp             CCTTCEEECSSSCCE
T ss_pred             ecCCCCeECCCCCeE
Confidence            677888999999994

>1v54_F VI, cytochrome C oxidase polypeptide VB; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: g.41.5.3 PDB: 1oco_F* 1occ_F* 1ocz_F* 1ocr_F* 1v55_F* 2dyr_F* 2dys_F* 2eij_F* 2eik_F* 2eil_F* 2eim_F* 2ein_F* 2occ_F* 2ybb_Q* 2zxw_F* 3abk_F* 3abl_F* 3abm_F* 3ag1_F* 3ag2_F* ...

Probab=92.91  E-value=0.055  Score=29.24  Aligned_cols=17  Identities=41%  Similarity=0.962  Sum_probs=13.4

Q ss_pred             cCCCCceecCCCCCeEEEe
Q 035423            5 LKPGDVIQCRECGYRILYK   23 (35)
Q Consensus         5 lk~~~~irC~~CG~RIlyK   23 (35)
                      |..+.+-||++||+  .||
T Consensus        74 l~~g~~~RC~eCG~--~fk   90 (98)
T 1v54_F           74 LHKGEAQRCPSCGT--HYK   90 (98)
T ss_dssp             EESSSCEECTTTCC--EEE
T ss_pred             EeCCCceECCCCCe--EEE
Confidence            56677899999998  454

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

Probab=91.84  E-value=0.077  Score=29.34  Aligned_cols=17  Identities=24%  Similarity=0.495  Sum_probs=12.3

Q ss_pred             CceecCCCCCeEEEeec
Q 035423            9 DVIQCRECGYRILYKKR   25 (35)
Q Consensus         9 ~~irC~~CG~RIlyK~R   25 (35)
                      +...||.||+.+-.+.|
T Consensus       147 ~~~~Cp~CG~~~~~~~~  163 (165)
T 2lcq_A          147 PGGVCPDCGSKVKLIPR  163 (165)
T ss_dssp             GGGBCTTTCCBEEECCC
T ss_pred             CCCcCCCCCCcceeCCc
Confidence            34699999999654444

>2jvm_A Uncharacterized protein; alpha+beta, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Rhodobacter sphaeroides 2}

Probab=91.72  E-value=0.11  Score=27.56  Aligned_cols=17  Identities=18%  Similarity=0.526  Sum_probs=13.8

Q ss_pred             CCCceecCCCCCeEEEe
Q 035423            7 PGDVIQCRECGYRILYK   23 (35)
Q Consensus         7 ~~~~irC~~CG~RIlyK   23 (35)
                      ....+.|||||-+-.+|
T Consensus        50 ~~g~~~CpYCg~~f~l~   66 (80)
T 2jvm_A           50 ETGFVECGYCDRRYIHE   66 (80)
T ss_dssp             TTCEEECSSSSCEEEEH
T ss_pred             CCCeEECCCCCCEEEec
Confidence            46789999999986655

>2y69_F Cytochrome C oxidase subunit 5B; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=91.13  E-value=0.11  Score=29.37  Aligned_cols=15  Identities=33%  Similarity=0.902  Sum_probs=12.3

Q ss_pred             cCCCCceecCCCCCe
Q 035423            5 LKPGDVIQCRECGYR   19 (35)
Q Consensus         5 lk~~~~irC~~CG~R   19 (35)
                      |..+.+-||++||+-
T Consensus       105 L~kg~p~RCpeCG~~  119 (129)
T 2y69_F          105 LHKGEAQRCPSCGTH  119 (129)
T ss_dssp             EESSSCEECTTTCCE
T ss_pred             EeCCCceeCCCCCeE
Confidence            566778999999983

>2jrr_A Uncharacterized protein; solution structure, SIR90, structural genomics, PSI-2, protein structure initiative; NMR {Silicibacter pomeroyi}

Probab=90.58  E-value=0.13  Score=26.31  Aligned_cols=17  Identities=18%  Similarity=0.520  Sum_probs=13.6

Q ss_pred             CCCceecCCCCCeEEEe
Q 035423            7 PGDVIQCRECGYRILYK   23 (35)
Q Consensus         7 ~~~~irC~~CG~RIlyK   23 (35)
                      ....+.|||||-+-.+|
T Consensus        37 ~~g~~~CpYCg~~f~l~   53 (67)
T 2jrr_A           37 DTGWVECPYCDCKYVLK   53 (67)
T ss_dssp             TTSEEEETTTTEEEEET
T ss_pred             CCCeEECCCCCCEEEEC
Confidence            45789999999886655

>2jz8_A Uncharacterized protein BH09830; zinc binding, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Bartonella henselae str}

Probab=90.53  E-value=0.13  Score=27.64  Aligned_cols=20  Identities=20%  Similarity=0.340  Sum_probs=15.4

Q ss_pred             cCCCCceecCCCCCeEEEee
Q 035423            5 LKPGDVIQCRECGYRILYKK   24 (35)
Q Consensus         5 lk~~~~irC~~CG~RIlyK~   24 (35)
                      |.....+.|||||-+-.++.
T Consensus        43 i~~~g~~~CpYCg~~y~~~~   62 (87)
T 2jz8_A           43 MGSTDEKICPYCSTLYRYDP   62 (87)
T ss_dssp             CTTCCEECCTTTCCEEECCT
T ss_pred             cCCCCeEECCCCCCEeEcCC
Confidence            45567899999999866553

>2i5o_A DNA polymerase ETA; zinc finger, DNA polymerase,POL ETA, UBZ, ubiquitin-binding zinc finger, translesion synthesis, ubiquitin-binding domain; HET: DNA; NMR {Homo sapiens}

Probab=88.48  E-value=0.29  Score=22.55  Aligned_cols=20  Identities=20%  Similarity=0.517  Sum_probs=14.3

Q ss_pred             ccCCCCceecCCCCCeEEEe
Q 035423            4 TLKPGDVIQCRECGYRILYK   23 (35)
Q Consensus         4 ~lk~~~~irC~~CG~RIlyK   23 (35)
                      .+...+...|+.||-.|--+
T Consensus         3 ~~~~~~~~~C~~C~~~i~~~   22 (39)
T 2i5o_A            3 HMAAEDQVPCEKCGSLVPVW   22 (39)
T ss_dssp             ---CCCEEECTTTCCEEEGG
T ss_pred             CCCcCCCcccccccCcCCcc
Confidence            46778899999999987643

>1hxr_A Guanine nucleotide exchange factor MSS4; RAB GTPase, membrane trafficking, Zn binding site, metal binding protein; 1.65A {Rattus norvegicus} SCOP: b.88.1.1 PDB: 1fwq_A 2fu5_A

Probab=87.04  E-value=0.35  Score=26.50  Aligned_cols=19  Identities=26%  Similarity=0.718  Sum_probs=14.9

Q ss_pred             CCCCceecCCCCCeEEEee
Q 035423            6 KPGDVIQCRECGYRILYKK   24 (35)
Q Consensus         6 k~~~~irC~~CG~RIlyK~   24 (35)
                      +....++|+.|+.+||-+.
T Consensus         8 ~N~~~i~C~~C~s~il~~~   26 (115)
T 1hxr_A            8 RNRKAVLCQRCGSRVLQPG   26 (115)
T ss_dssp             BBSSCEEETTTCCEEECTT
T ss_pred             cccCeEECCCCCCEEeccC
Confidence            3456899999999998543

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

Probab=86.48  E-value=0.31  Score=23.11  Aligned_cols=13  Identities=38%  Similarity=0.935  Sum_probs=10.9

Q ss_pred             ceecCCCCCeEEE
Q 035423           10 VIQCRECGYRILY   22 (35)
Q Consensus        10 ~irC~~CG~RIly   22 (35)
                      .+.||.||++-++
T Consensus        15 ~~~Cp~Cg~~~~~   27 (57)
T 1qyp_A           15 KITCPKCGNDTAY   27 (57)
T ss_dssp             ECCCTTTCCSEEE
T ss_pred             EeECCCCCCCEEE
Confidence            5789999998765

>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=84.34  E-value=0.27  Score=25.15  Aligned_cols=18  Identities=28%  Similarity=0.556  Sum_probs=13.1

Q ss_pred             CceecCCCCCeEEEeecCC
Q 035423            9 DVIQCRECGYRILYKKRTR   27 (35)
Q Consensus         9 ~~irC~~CG~RIlyK~R~~   27 (35)
                      ....|| ||.+|=+++++-
T Consensus        20 kT~~C~-CG~~~~~~k~ri   37 (71)
T 1gh9_A           20 KTRKCV-CGRTVNVKDRRI   37 (71)
T ss_dssp             SEEEET-TTEEEECCSSSC
T ss_pred             cEEECC-CCCeeeeceEEE
Confidence            456788 888887777653

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

Probab=82.81  E-value=0.45  Score=22.62  Aligned_cols=14  Identities=21%  Similarity=0.591  Sum_probs=10.4

Q ss_pred             CCceecCCCCCeEE
Q 035423            8 GDVIQCRECGYRIL   21 (35)
Q Consensus         8 ~~~irC~~CG~RIl   21 (35)
                      ...+.||.||++=.
T Consensus         7 t~~~~Cp~Cg~~~a   20 (50)
T 1tfi_A            7 TDLFTCGKCKKKNC   20 (50)
T ss_dssp             CCCSCCSSSCSSCE
T ss_pred             eCccCCCCCCCCEE
Confidence            45678999998643

---

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	35
d1twfl_	46	g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {	4e-15

>d1twfl_ g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 46

class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RBP12 subunit of RNA polymerase II
domain: RBP12 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 58.6 bits (142), Expect = 4e-15
 Identities = 17/35 (48%), Positives = 27/35 (77%)

Query: 1  MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 35
           + +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 12 SKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 46

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	35
d1twfl_	46	RBP12 subunit of RNA polymerase II {Baker's yeast	99.86
d1hxra_	115	RabGEF Mss4 {Rat (Rattus norvegicus) [TaxId: 10116	92.12
d1v54f_	98	Cytochrome c oxidase Subunit F {Cow (Bos taurus) [	91.09
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	87.47
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	86.9
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	84.47
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	83.2
d1x5wa1	28	Zinc finger protein 64, ZFP68 {Human (Homo sapiens	82.57
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	82.5
d1lv3a_	65	Hypothetical zinc finger protein YacG {Escherichia	82.12

>d1twfl_ g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RBP12 subunit of RNA polymerase II
domain: RBP12 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=1.1e-23  Score=103.41  Aligned_cols=35  Identities=49%  Similarity=0.927  Sum_probs=33.7

Q ss_pred             CccccCCCCceecCCCCCeEEEeecCCceEEEEeC
Q 035423            1 MENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR   35 (35)
Q Consensus         1 ~~~~lk~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   35 (35)
                      ++|+|+++|+|||.+||||||||+||++++||+||
T Consensus        12 ~~~~l~~~d~irCreCG~RIlYK~RTkr~vqfeAR   46 (46)
T d1twfl_          12 SKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR   46 (46)
T ss_dssp             CEECCCTTSTTCCSSSCCCCCBCCCCSSCEEECCC
T ss_pred             CceEeCCCCcEEeccCCcEEEEeecccceeeEecC
Confidence            47899999999999999999999999999999998

>d1hxra_ b.88.1.1 (A:) RabGEF Mss4 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All beta proteins
fold: Mss4-like
superfamily: Mss4-like
family: RabGEF Mss4
domain: RabGEF Mss4
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.12  E-value=0.037  Score=29.49  Aligned_cols=16  Identities=31%  Similarity=0.922  Sum_probs=13.6

Q ss_pred             CCCCceecCCCCCeEE
Q 035423            6 KPGDVIQCRECGYRIL   21 (35)
Q Consensus         6 k~~~~irC~~CG~RIl   21 (35)
                      +....|+|+.|+.+||
T Consensus         8 kN~~~v~C~~C~S~il   23 (115)
T d1hxra_           8 RNRKAVLCQRCGSRVL   23 (115)
T ss_dssp             BBSSCEEETTTCCEEE
T ss_pred             cCcceEECCCCCCEee
Confidence            4566899999999996

>d1v54f_ g.41.5.3 (F:) Cytochrome c oxidase Subunit F {Cow (Bos taurus) [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Cytochrome c oxidase Subunit F
domain: Cytochrome c oxidase Subunit F
species: Cow (Bos taurus) [TaxId: 9913]

Probab=91.09  E-value=0.038  Score=28.73  Aligned_cols=15  Identities=33%  Similarity=0.902  Sum_probs=12.7

Q ss_pred             cCCCCceecCCCCCe
Q 035423            5 LKPGDVIQCRECGYR   19 (35)
Q Consensus         5 lk~~~~irC~~CG~R   19 (35)
                      |..+.+-||++||+=
T Consensus        74 l~~g~p~RC~eCG~~   88 (98)
T d1v54f_          74 LHKGEAQRCPSCGTH   88 (98)
T ss_dssp             EESSSCEECTTTCCE
T ss_pred             EeCCCCcccCCCCcE
Confidence            567788999999994

>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=87.47  E-value=0.077  Score=25.01  Aligned_cols=18  Identities=17%  Similarity=0.200  Sum_probs=14.0

Q ss_pred             cccCCCCceecCCCCCeE
Q 035423            3 NTLKPGDVIQCRECGYRI   20 (35)
Q Consensus         3 ~~lk~~~~irC~~CG~RI   20 (35)
                      +.+.....++||+||..-
T Consensus         4 ~~~~~~~~~~Cp~Cgs~~   21 (58)
T d1dl6a_           4 SRLDALPRVTCPNHPDAI   21 (58)
T ss_dssp             CSCCCCSCCSBTTBSSSC
T ss_pred             cccccccccCCCCCCCCC
Confidence            346677889999999873

>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=86.90  E-value=0.1  Score=23.28  Aligned_cols=14  Identities=29%  Similarity=0.816  Sum_probs=11.3

Q ss_pred             CCCCceecCCCCCe
Q 035423            6 KPGDVIQCRECGYR   19 (35)
Q Consensus         6 k~~~~irC~~CG~R   19 (35)
                      ..++...||+|||-
T Consensus        16 edg~l~vCPeC~hE   29 (38)
T d2akla2          16 EDGALLVCPECAHE   29 (38)
T ss_dssp             ECSSSEEETTTTEE
T ss_pred             cCCCEEECCcccCc
Confidence            45778899999984

>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=84.47  E-value=0.14  Score=23.66  Aligned_cols=15  Identities=20%  Similarity=0.547  Sum_probs=11.5

Q ss_pred             CCCceecCCCCCeEE
Q 035423            7 PGDVIQCRECGYRIL   21 (35)
Q Consensus         7 ~~~~irC~~CG~RIl   21 (35)
                      +.+.++||.||++=.
T Consensus         6 ~T~~~~C~kC~~~~~   20 (50)
T d1tfia_           6 QTDLFTCGKCKKKNC   20 (50)
T ss_dssp             ECCCSCCSSSCSSCE
T ss_pred             ccCCEECCCCCCCcc
Confidence            457789999998743

>d1x4la2 g.39.1.3 (A:37-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.20  E-value=0.023  Score=24.33  Aligned_cols=16  Identities=44%  Similarity=0.829  Sum_probs=12.3

Q ss_pred             cCCCCceecCCCCCeE
Q 035423            5 LKPGDVIQCRECGYRI   20 (35)
Q Consensus         5 lk~~~~irC~~CG~RI   20 (35)
                      |...|.|-||+||.-|
T Consensus        15 lterddilc~dcgkdi   30 (30)
T d1x4la2          15 LTERDDILCPDCGKDI   30 (30)
T ss_dssp             EECSSSEECHHHHHTC
T ss_pred             cccccceeccccCcCC
Confidence            4567889999999643

>d1x5wa1 g.37.1.1 (A:8-35) Zinc finger protein 64, ZFP68 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein 64, ZFP68
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.57  E-value=0.25  Score=20.65  Aligned_cols=10  Identities=40%  Similarity=1.046  Sum_probs=8.5

Q ss_pred             ceecCCCCCe
Q 035423           10 VIQCRECGYR   19 (35)
Q Consensus        10 ~irC~~CG~R   19 (35)
                      +.+|++|.|-
T Consensus         2 pekc~ecsys   11 (28)
T d1x5wa1           2 PEKCSECSYS   11 (28)
T ss_dssp             SEECSSSSCE
T ss_pred             CccCcccccc
Confidence            6899999984

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.50  E-value=0.17  Score=21.98  Aligned_cols=15  Identities=33%  Similarity=0.749  Sum_probs=12.2

Q ss_pred             cCCCCceecCCCCCe
Q 035423            5 LKPGDVIQCRECGYR   19 (35)
Q Consensus         5 lk~~~~irC~~CG~R   19 (35)
                      |...+.|-|++||.-
T Consensus        15 ltq~~~i~c~~cgsg   29 (34)
T d1x68a2          15 LTQNKEIFCQKCGSG   29 (34)
T ss_dssp             EEETTEEEETTTTCC
T ss_pred             eeccCcEEehhcCCC
Confidence            556789999999963

>d1lv3a_ g.39.1.9 (A:) Hypothetical zinc finger protein YacG {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Hypothetical zinc finger protein YacG
domain: Hypothetical zinc finger protein YacG
species: Escherichia coli [TaxId: 562]

Probab=82.12  E-value=0.42  Score=22.92  Aligned_cols=16  Identities=19%  Similarity=0.690  Sum_probs=12.9

Q ss_pred             CCceecCCCCCeEEEe
Q 035423            8 GDVIQCRECGYRILYK   23 (35)
Q Consensus         8 ~~~irC~~CG~RIlyK   23 (35)
                      ...|+||.||..+.+.
T Consensus         4 ~~~v~CP~C~k~~~w~   19 (65)
T d1lv3a_           4 TITVNCPTCGKTVVWG   19 (65)
T ss_dssp             CCEEECTTTCCEEECS
T ss_pred             CceeeCCCCCCccccC
Confidence            3469999999988764