Citrus Sinensis ID: 035461

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50-
Protein Sequence
MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Secondary Structure (PSIPRED)
cccccccEEEEcccccccEEcccccEEEccccccEEEEEEccccEEEEEEc
Secondary Structure Prediction (SSPRO)
cccccccEEEEEccccccccccccccEEccccccEEEEEEcccEEEEEEcc
Coil and Loop (DISEMBL)
mdpqpepvsyicgdcgmentlkpgdviqcrecgyrilykkRTRRIVQYEAR
Flexible Loop (DISEMBL)
MDPQPEPVSYICGDCGMEntlkpgdviqcrecgyrilykkrtrrivqyear
Low Complexity Region (SEG)
MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Disordered region (IsUnstruct)
********SYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQ****
Disordered Region (DISOPRED)
****PEP*SYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEA*
Disordered Region (DISEMBL)
MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Disordered Region (DISPRO)
****PEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
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	51	2.2.26 [Sep-21-2011]
P48011	63	DNA-directed RNA polymera	yes	no	0.960	0.777	0.551	9e-12
Q63871	58	DNA-directed RNA polymera	no	no	0.960	0.844	0.591	3e-11
P53803	58	DNA-directed RNA polymera	yes	no	0.960	0.844	0.591	3e-11
Q3ZBC0	58	DNA-directed RNA polymera	yes	no	0.960	0.844	0.591	3e-11
Q54R66	46	DNA-directed RNA polymera	yes	no	0.882	0.978	0.511	5e-09
P40422	70	DNA-directed RNA polymera	yes	no	0.960	0.7	0.428	7e-08

>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 = 68.9 bits (167), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 27/49 (55%), Positives = 40/49 (81%)

Query: 3  PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          P+P  + Y+C DCG  NT++  +VI+CRECG+R++YK RT+R+VQ+EAR
Sbjct: 15 PRPATMIYLCADCGARNTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR 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 = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query: 3  PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct: 10 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 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 = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query: 3  PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct: 10 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 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 = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query: 3  PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct: 10 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 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|Q54R66|RPAB4_DICDI DNA-directed RNA polymerases I, II, and III subunit rpabc4 OS=Dictyostelium discoideum GN=polr2k PE=3 SV=1

 Score = 59.7 bits (143), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 37/45 (82%)

Query: 7  PVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          P  YICG+CG E+ +KP + ++C++C +RI+YKKRT +++Q+EAR
Sbjct: 2  PCLYICGECGAEHEIKPKEPVKCKDCTHRIMYKKRTDKMIQFEAR 46

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)

>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 = 55.8 bits (133), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 34/49 (69%)

Query: 3  PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
           +   + YIC +C  + +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 22 ARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 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)

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	51
224117642	51	predicted protein [Populus trichocarpa]	1.0	1.0	1.0	1e-21
225466239	51	PREDICTED: DNA-directed RNA polymerases	1.0	1.0	0.980	7e-21
449439515	51	PREDICTED: DNA-directed RNA polymerases	1.0	1.0	0.980	9e-21
414884443	100	TPA: DNA-directed RNA polymerase I, II,	1.0	0.51	0.942	5e-20
226498516	52	LOC100285004 [Zea mays] gi|297720059|ref	1.0	0.980	0.942	2e-19
15237533	51	DNA-directed RNA Polymerase II subunit K	1.0	1.0	0.882	4e-19
388506340	51	unknown [Medicago truncatula]	1.0	1.0	0.901	4e-19
357451245	121	DNA-directed RNA polymerases I, II, and	1.0	0.421	0.901	5e-19
298204818	82	unnamed protein product [Vitis vinifera]	0.921	0.573	0.978	6e-19
357122946	52	PREDICTED: DNA-directed RNA polymerases	1.0	0.980	0.923	9e-19

>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 =  106 bits (265), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 51/51 (100%), Positives = 51/51 (100%)

Query: 1  MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 1  MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  104 bits (259), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 50/51 (98%), Positives = 50/51 (98%)

Query: 1  MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          MDPQPEPVSYICGDCG ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 1  MDPQPEPVSYICGDCGQENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  104 bits (259), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 50/51 (98%), Positives = 50/51 (98%)

Query: 1  MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          MDPQPEPVSYICGDCGMENTLK GDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 1  MDPQPEPVSYICGDCGMENTLKQGDVIQCRECGYRILYKKRTRRIVQYEAR 51

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  101 bits (252), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 49/52 (94%), Positives = 50/52 (96%), Gaps = 1/52 (1%)

Query: 1   MDPQ-PEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
           MDPQ PEPVSY+CGDCG ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 49  MDPQQPEPVSYLCGDCGAENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 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 = 99.8 bits (247), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 49/52 (94%), Positives = 50/52 (96%), Gaps = 1/52 (1%)

Query: 1  MDPQ-PEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          MDPQ PEPVSY+CGDCG ENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 1  MDPQQPEPVSYLCGDCGAENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 52

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15237533|ref|NP_198917.1| DNA-directed RNA Polymerase II subunit K [Arabidopsis thaliana] gi|9759147|dbj|BAB09703.1| unnamed protein product [Arabidopsis thaliana] gi|15028303|gb|AAK76628.1| unknown protein [Arabidopsis thaliana] gi|19310615|gb|AAL85038.1| unknown protein [Arabidopsis thaliana] gi|21618239|gb|AAM67289.1| DNA directed RNA polymerase II polypeptide K [Arabidopsis thaliana] gi|332007242|gb|AED94625.1| DNA-directed RNA Polymerase II subunit K [Arabidopsis thaliana]

 Score = 98.6 bits (244), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 45/51 (88%), Positives = 48/51 (94%)

Query: 1  MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          MDP PEPV+Y+CGDCG ENTLK GDVIQCRECGYRILYKKRTRR+VQYEAR
Sbjct: 1  MDPAPEPVTYVCGDCGQENTLKSGDVIQCRECGYRILYKKRTRRVVQYEAR 51

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388506340|gb|AFK41236.1| unknown [Medicago truncatula]

 Score = 98.6 bits (244), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 46/51 (90%), Positives = 49/51 (96%)

Query: 1  MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          MDP PEPVSY+CGDCG+ENTLK GDVIQCR+CGYRILYKKRTRRIVQYEAR
Sbjct: 1  MDPLPEPVSYLCGDCGVENTLKSGDVIQCRDCGYRILYKKRTRRIVQYEAR 51

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357451245|ref|XP_003595899.1| DNA-directed RNA polymerases I, II, and III subunit RPABC4 [Medicago truncatula] gi|355484947|gb|AES66150.1| DNA-directed RNA polymerases I, II, and III subunit RPABC4 [Medicago truncatula]

 Score = 98.2 bits (243), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 46/51 (90%), Positives = 49/51 (96%)

Query: 1  MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          MDP PEPVSY+CGDCG+ENTLK GDVIQCR+CGYRILYKKRTRRIVQYEAR
Sbjct: 14 MDPLPEPVSYLCGDCGVENTLKSGDVIQCRDCGYRILYKKRTRRIVQYEAR 64

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298204818|emb|CBI25651.3| unnamed protein product [Vitis vinifera]

 Score = 98.2 bits (243), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 46/47 (97%), Positives = 46/47 (97%)

Query: 1  MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQ 47
          MDPQPEPVSYICGDCG ENTLKPGDVIQCRECGYRILYKKRTRRIVQ
Sbjct: 1  MDPQPEPVSYICGDCGQENTLKPGDVIQCRECGYRILYKKRTRRIVQ 47

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357122946|ref|XP_003563174.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC4-like [Brachypodium distachyon] gi|357145250|ref|XP_003573577.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit RPABC4-like [Brachypodium distachyon]

 Score = 97.4 bits (241), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 48/52 (92%), Positives = 49/52 (94%), Gaps = 1/52 (1%)

Query: 1  MDPQ-PEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          MDPQ PEPVSY+CGDCG ENTLK GDVIQCRECGYRILYKKRTRRIVQYEAR
Sbjct: 1  MDPQQPEPVSYLCGDCGAENTLKSGDVIQCRECGYRILYKKRTRRIVQYEAR 52

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	51
TAIR|locus:2163051	51	NRPB12 [Arabidopsis thaliana (	1.0	1.0	0.882	2.1e-22
UNIPROTKB|E1BW79	58	LOC771626 "Uncharacterized pro	0.960	0.844	0.591	1.6e-13
UNIPROTKB|Q3ZBC0	58	POLR2K "DNA-directed RNA polym	0.960	0.844	0.591	1.6e-13
UNIPROTKB|P53803	58	POLR2K "DNA-directed RNA polym	0.960	0.844	0.591	1.6e-13
UNIPROTKB|I3LN51	58	POLR2K "Uncharacterized protei	0.960	0.844	0.591	1.6e-13
RGD|2319895	87	LOC100361574 "mCG145114-like"	0.960	0.563	0.591	1.6e-13
UNIPROTKB|F1LTT4	88	LOC100361574 "Protein LOC10036	0.960	0.556	0.591	1.6e-13
ZFIN|ZDB-GENE-070820-18	58	polr2k "polymerase (RNA) II (D	0.960	0.844	0.591	1.6e-13
POMBASE|SPBC19C2.03	63	rpc10 "DNA-directed RNA polyme	0.960	0.777	0.551	3.4e-13
UNIPROTKB|J9NXU3	58	POLR2K "Uncharacterized protei	0.960	0.844	0.551	7.1e-13

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

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 45/51 (88%), Positives = 48/51 (94%)

Query:     1 MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             MDP PEPV+Y+CGDCG ENTLK GDVIQCRECGYRILYKKRTRR+VQYEAR
Sbjct:     1 MDPAPEPVTYVCGDCGQENTLKSGDVIQCRECGYRILYKKRTRRVVQYEAR 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

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

 Score = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query:     3 PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    10 PKQQPMIYICGECHTENEIKARDPIRCRECGYRIMYKKRTKRLVVFDAR 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 = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query:     3 PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    10 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 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 = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query:     3 PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    10 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 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 = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query:     3 PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    10 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 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 = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query:     3 PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    39 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 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 = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query:     3 PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    40 PKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 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 = 176 (67.0 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 29/49 (59%), Positives = 40/49 (81%)

Query:     3 PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             P+ +P+ YICG+C  EN +K  D I+CRECGYRI+YKKRT+R+V ++AR
Sbjct:    10 PKQQPMIYICGECHTENEIKARDPIRCRECGYRIMYKKRTKRLVVFDAR 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

POMBASE|SPBC19C2.03 rpc10 "DNA-directed RNA polymerase I, II and III subunit Rpc10" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 27/49 (55%), Positives = 40/49 (81%)

Query:     3 PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             P+P  + Y+C DCG  NT++  +VI+CRECG+R++YK RT+R+VQ+EAR
Sbjct:    15 PRPATMIYLCADCGARNTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR 63

GO:0003677 "DNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0005730 "nucleolus" evidence=IDA

GO:0005736 "DNA-directed RNA polymerase I complex" evidence=IGI

GO:0005829 "cytosol" evidence=IDA

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

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

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

GO:0046872 "metal ion binding" evidence=IEA

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

UNIPROTKB|J9NXU3 POLR2K "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 170 (64.9 bits), Expect = 7.1e-13, P = 7.1e-13
 Identities = 27/49 (55%), Positives = 40/49 (81%)

Query:     3 PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             P+ +P+ YICG+C  EN +K  D I+CRECGY+I+YKKRT+R++ ++AR
Sbjct:    10 PKQQPMIYICGECHTENEIKSRDPIRCRECGYKIMYKKRTKRLLVFDAR 58

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

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

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q3ZBC0	RPAB4_BOVIN	No assigned EC number	0.5918	0.9607	0.8448	yes	no
P48011	RPAB4_SCHPO	No assigned EC number	0.5510	0.9607	0.7777	yes	no
P53803	RPAB4_HUMAN	No assigned EC number	0.5918	0.9607	0.8448	yes	no
Q54R66	RPAB4_DICDI	No assigned EC number	0.5111	0.8823	0.9782	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.7	LOW CONFIDENCE prediction!
4th Layer	2.7.7.6	LOW CONFIDENCE prediction!

---

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	51
smart00659	44	smart00659, RPOLCX, RNA polymerase subunit CX	1e-17
pfam03604	32	pfam03604, DNA_RNApol_7kD, DNA directed RNA polyme	1e-13
COG1996	49	COG1996, RPC10, DNA-directed RNA polymerase, subun	3e-08

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

 Score = 67.4 bits (165), Expect = 1e-17
 Identities = 29/44 (65%), Positives = 38/44 (86%)

Query: 8  VSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          + YICG+CG EN +K  DV++CRECGYRILYKKRT+R+V+ +AR
Sbjct: 1  MIYICGECGRENEIKSKDVVRCRECGYRILYKKRTKRLVEVKAR 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 = 56.9 bits (138), Expect = 1e-13
 Identities = 24/32 (75%), Positives = 28/32 (87%)

Query: 10 YICGDCGMENTLKPGDVIQCRECGYRILYKKR 41
          YICG+CG E  LKPGD I+C+ECG+RILYKKR
Sbjct: 1  YICGECGAEVELKPGDPIRCKECGHRILYKKR 32

Length = 32

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

 Score = 43.9 bits (104), Expect = 3e-08
 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 4  QPEPVSYICGDCGMENTL-KPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          +   + Y C  CG E  L +    I+C  CG RIL K+R +   + +AR
Sbjct: 1  REAMMEYKCARCGREVELDQETRGIRCPYCGSRILVKERPKVPKRVKAR 49

Length = 49

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	51
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	99.93
KOG3507	62	consensus DNA-directed RNA polymerase, subunit RPB	99.91
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	99.85
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	99.81
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	99.56
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	98.06
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	97.98
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	97.88
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	97.78
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	97.38
smart00531	147	TFIIE Transcription initiation factor IIE.	97.36
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	97.32
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	97.26
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	97.18
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	97.16
PF13248	26	zf-ribbon_3: zinc-ribbon domain	97.09
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	97.01
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	97.0
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	96.92
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	96.83
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	96.81
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	96.79
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	96.78
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	96.77
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	96.73
PRK06266	178	transcription initiation factor E subunit alpha; V	96.67
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	96.61
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	96.55
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	96.52
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	96.46
PF07295	146	DUF1451: Protein of unknown function (DUF1451); In	96.4
COG1439	177	Predicted nucleic acid-binding protein, consists o	96.37
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	96.27
PF08274	30	PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR01	96.26
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	96.19
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	96.0
PRK12496	164	hypothetical protein; Provisional	95.93
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	95.85
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.61
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	95.61
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	95.46
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	95.43
PF09845	131	DUF2072: Zn-ribbon containing protein (DUF2072); I	95.12
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	95.04
PF12773	50	DZR: Double zinc ribbon	94.85
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	94.76
smart00661	52	RPOL9 RNA polymerase subunit 9.	94.71
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	94.55
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	94.53
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	94.49
PRK00420	112	hypothetical protein; Validated	94.45
PF13451	49	zf-trcl: Probable zinc-binding domain	94.44
COG1592	166	Rubrerythrin [Energy production and conversion]	94.43
PF02318	118	FYVE_2: FYVE-type zinc finger; InterPro: IPR003315	94.34
PF14369	35	zf-RING_3: zinc-finger	94.34
PF10263	157	SprT-like: SprT-like family; InterPro: IPR006640 T	94.17
PF09082	68	DUF1922: Domain of unknown function (DUF1922); Int	94.1
TIGR00686	109	phnA alkylphosphonate utilization operon protein P	94.1
PRK00432	50	30S ribosomal protein S27ae; Validated	94.05
PRK06450	338	threonine synthase; Validated	94.0
PF06397	36	Desulfoferrod_N: Desulfoferrodoxin, N-terminal dom	93.98
PRK07591	421	threonine synthase; Validated	93.91
COG1571	421	Predicted DNA-binding protein containing a Zn-ribb	93.76
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	93.75
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	93.68
PHA02768	55	hypothetical protein; Provisional	93.65
PF14353	128	CpXC: CpXC protein	93.54
COG3364	112	Zn-ribbon containing protein [General function pre	93.52
PRK11032	160	hypothetical protein; Provisional	93.45
PRK10220	111	hypothetical protein; Provisional	93.41
cd00730	50	rubredoxin Rubredoxin; nonheme iron binding domain	93.02
COG3357	97	Predicted transcriptional regulator containing an	92.83
PF05207	55	zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc	92.79
COG2331	82	Uncharacterized protein conserved in bacteria [Fun	92.78
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	92.69
PRK06260	397	threonine synthase; Validated	92.65
PF12172	37	DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35	92.56
PHA00626	59	hypothetical protein	92.53
COG2816	279	NPY1 NTP pyrophosphohydrolases containing a Zn-fin	92.35
PF02591	56	DUF164: Putative zinc ribbon domain; InterPro: IPR	92.24
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	92.21
PF00301	47	Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubred	92.03
smart00731	146	SprT SprT homologues. Predicted to have roles in t	91.97
PRK04351	149	hypothetical protein; Provisional	91.94
PRK04136	48	rpl40e 50S ribosomal protein L40e; Provisional	91.91
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	91.86
COG1326	201	Uncharacterized archaeal Zn-finger protein [Genera	91.85
PRK14714	1337	DNA polymerase II large subunit; Provisional	91.68
PRK11823	446	DNA repair protein RadA; Provisional	91.63
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	91.49
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	91.42
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	91.23
COG1379	403	PHP family phosphoesterase with a Zn ribbon [Gener	91.22
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	90.99
PF11781	36	RRN7: RNA polymerase I-specific transcription init	90.97
COG5216	67	Uncharacterized conserved protein [Function unknow	90.64
PF13408	58	Zn_ribbon_recom: Recombinase zinc beta ribbon doma	90.34
PF10058	54	DUF2296: Predicted integral membrane metal-binding	90.24
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	90.21
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	90.12
COG1545	140	Predicted nucleic-acid-binding protein containing	89.82
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	89.82
PHA02942	383	putative transposase; Provisional	89.73
TIGR03844	398	cysteate_syn cysteate synthase. Members of this fa	89.73
PF14311	55	DUF4379: Domain of unknown function (DUF4379)	89.63
PF08996	188	zf-DNA_Pol: DNA Polymerase alpha zinc finger; Inte	89.13
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	89.01
COG0675	364	Transposase and inactivated derivatives [DNA repli	88.63
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	88.26
PF14599	61	zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.	88.02
TIGR01053	31	LSD1 zinc finger domain, LSD1 subclass. This model	88.0
PF02146	178	SIR2: Sir2 family; InterPro: IPR003000 These seque	87.97
PF08772	73	NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon lik	87.97
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	87.87
PRK08351	61	DNA-directed RNA polymerase subunit E''; Validated	87.86
TIGR00155	403	pqiA_fam integral membrane protein, PqiA family. T	87.76
PRK06393	64	rpoE DNA-directed RNA polymerase subunit E''; Vali	87.61
PRK15103	419	paraquat-inducible membrane protein A; Provisional	87.53
PRK08197	394	threonine synthase; Validated	87.03
smart00709	160	Zpr1 Duplicated domain in the epidermal growth fac	86.76
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	86.75
smart00647	64	IBR In Between Ring fingers. the domains occurs be	86.73
PF15616	131	TerY-C: TerY-C metal binding domain	86.69
TIGR00375	374	conserved hypothetical protein TIGR00375. The memb	86.57
PRK08329	347	threonine synthase; Validated	86.56
COG1552	50	RPL40A Ribosomal protein L40E [Translation, riboso	86.51
PRK04860	160	hypothetical protein; Provisional	86.5
PF14205	55	Cys_rich_KTR: Cysteine-rich KTR	86.5
PF09986	214	DUF2225: Uncharacterized protein conserved in bact	86.44
TIGR00354	1095	polC DNA polymerase, archaeal type II, large subun	86.38
COG4530	129	Uncharacterized protein conserved in bacteria [Fun	86.19
COG0846	250	SIR2 NAD-dependent protein deacetylases, SIR2 fami	86.19
PRK14714	1337	DNA polymerase II large subunit; Provisional	85.98
PF06943	25	zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zin	85.98
PF00130	53	C1_1: Phorbol esters/diacylglycerol binding domain	85.8
PF03367	161	zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004	85.76
PRK00241	256	nudC NADH pyrophosphatase; Reviewed	85.57
PRK14892	99	putative transcription elongation factor Elf1; Pro	85.44
COG2995	418	PqiA Uncharacterized paraquat-inducible protein A	85.28
PF04161	208	Arv1: Arv1-like family ; InterPro: IPR007290 Arv1	85.14
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	85.02
PRK04023	1121	DNA polymerase II large subunit; Validated	84.99
PF05495	71	zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc	84.94
cd01675	555	RNR_III Class III ribonucleotide reductase. Ribonu	84.93
PF06221	57	zf-C2HC5: Putative zinc finger motif, C2HC5-type;	84.88
TIGR00310	192	ZPR1_znf ZPR1 zinc finger domain.	84.76
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	84.66
PF14319	111	Zn_Tnp_IS91: Transposase zinc-binding domain	84.64
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	84.52
PRK05638	442	threonine synthase; Validated	84.52
PRK11788	389	tetratricopeptide repeat protein; Provisional	84.51
COG1656	165	Uncharacterized conserved protein [Function unknow	84.39
TIGR00340	163	zpr1_rel ZPR1-related zinc finger protein. A model	84.36
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	84.21
COG3091	156	SprT Zn-dependent metalloprotease, SprT family [Ge	84.19
KOG2923	67	consensus Uncharacterized conserved protein [Funct	84.06
COG1773	55	Rubredoxin [Energy production and conversion]	84.05
TIGR03831	46	YgiT_finger YgiT-type zinc finger domain. This dom	83.99
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	83.71
PRK14559	645	putative protein serine/threonine phosphatase; Pro	83.29
COG1675	176	TFA1 Transcription initiation factor IIE, alpha su	83.28
COG4391	62	Uncharacterized protein conserved in bacteria [Fun	83.23
PF00096	23	zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR0070	83.16
TIGR00155	403	pqiA_fam integral membrane protein, PqiA family. T	83.08
PRK12495	226	hypothetical protein; Provisional	82.87
PRK13130	56	H/ACA RNA-protein complex component Nop10p; Review	82.78
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	82.48
PF13597	546	NRDD: Anaerobic ribonucleoside-triphosphate reduct	82.36
PF11672	102	DUF3268: Protein of unknown function (DUF3268); In	82.3
COG4031	227	Predicted metal-binding protein [General function	82.28
PF13397	105	DUF4109: Domain of unknown function (DUF4109)	82.07
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	81.81
PF10276	40	zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Z	81.57
PF04606	47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	81.54
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	81.52
cd01413	222	SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group	81.51
cd01407	218	SIR2-fam SIR2 family of proteins includes silent i	81.26
PRK00481	242	NAD-dependent deacetylase; Provisional	81.22
COG2824	112	PhnA Uncharacterized Zn-ribbon-containing protein	80.8
PRK14715	1627	DNA polymerase II large subunit; Provisional	80.46
PF01927	147	Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T	80.42
PRK05452	479	anaerobic nitric oxide reductase flavorubredoxin;	80.4
cd00924	97	Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb.	80.01

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=99.93  E-value=4.9e-26  Score=120.02  Aligned_cols=44  Identities=66%  Similarity=1.334  Sum_probs=42.8

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEecCceEEEEcC
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR   51 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   51 (51)
                      |.|+|++||.+|+++..++|+||+||||||||+||+++++|+||
T Consensus         1 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~R~~~~~~~~Ar   44 (44)
T smart00659        1 MIYICGECGRENEIKSKDVVRCRECGYRILYKKRTKRLVEVKAR   44 (44)
T ss_pred             CEEECCCCCCEeecCCCCceECCCCCceEEEEeCCCceEEEEcC
Confidence            68999999999999999999999999999999999999999997

present in RNA polymerase I, II and III

>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7

Probab=99.91  E-value=1.7e-26  Score=129.28  Aligned_cols=47  Identities=77%  Similarity=1.416  Sum_probs=45.5

Q ss_pred             CCceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEecCceEEEEcC
Q 035461            5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR   51 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   51 (51)
                      +++|.|+|++||.+++++.+|.|||++||||||||+|+++++||+||
T Consensus        16 ~~~miYiCgdC~~en~lk~~D~irCReCG~RIlyKkRtkrlvqfear   62 (62)
T KOG3507|consen   16 TATMIYICGDCGQENTLKRGDVIRCRECGYRILYKKRTKRLVQFEAR   62 (62)
T ss_pred             cccEEEEeccccccccccCCCcEehhhcchHHHHHHHHhhhheeecC
Confidence            37799999999999999999999999999999999999999999998

0 [Transcription]

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

Probab=99.85  E-value=1.8e-21  Score=105.10  Aligned_cols=46  Identities=37%  Similarity=0.647  Sum_probs=42.6

Q ss_pred             CceEEEcCCCCCeeecC-CCCeeEcCCCCCcEEEEEecCceEEEEcC
Q 035461            6 EPVSYICGDCGMENTLK-PGDVIQCRECGYRILYKKRTRRIVQYEAR   51 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   51 (51)
                      ..+.|+|++||+++++. ..+.||||+||||||+|.|++.+++|+||
T Consensus         3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~R~~~~krvkA~   49 (49)
T COG1996           3 AMMEYKCARCGREVELDQETRGIRCPYCGSRILVKERPKVPKRVKAR   49 (49)
T ss_pred             ceEEEEhhhcCCeeehhhccCceeCCCCCcEEEEeccCCccEEEecC
Confidence            45899999999999954 67899999999999999999999999997

>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=99.81  E-value=8e-21  Score=94.85  Aligned_cols=32  Identities=75%  Similarity=1.485  Sum_probs=27.7

Q ss_pred             EEcCCCCCeeecCCCCeeEcCCCCCcEEEEEe
Q 035461           10 YICGDCGMENTLKPGDVIQCRECGYRILYKKR   41 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R   41 (51)
                      |+|++||++++++.+++|||++||||||||+|
T Consensus         1 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R   32 (32)
T PF03604_consen    1 YICGECGAEVELKPGDPIRCPECGHRILYKKR   32 (32)
T ss_dssp             EBESSSSSSE-BSTSSTSSBSSSS-SEEBE--
T ss_pred             CCCCcCCCeeEcCCCCcEECCcCCCeEEEecC
Confidence            89999999999999999999999999999998

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=99.56  E-value=9.7e-15  Score=76.17  Aligned_cols=44  Identities=39%  Similarity=0.794  Sum_probs=40.8

Q ss_pred             eEEEcCCCCCeeecCCCC-eeEcCCCCCcEEEEEecCceEEEEcC
Q 035461            8 VSYICGDCGMENTLKPGD-VIQCRECGYRILYKKRTRRIVQYEAR   51 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~-~irC~~CG~RIlyK~R~~~~~~~~Ar   51 (51)
                      +.|+|.+||++++++... .++||+||++++||.|++.+..++|+
T Consensus         2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~~~v~~~~~~   46 (46)
T PRK00398          2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFKERPPVVKRVKAR   46 (46)
T ss_pred             CEEECCCCCCEEEECCCCCceECCCCCCeEEEccCCCcceEeecC
Confidence            579999999999998654 89999999999999999999999986

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=98.06  E-value=3.5e-06  Score=41.78  Aligned_cols=28  Identities=32%  Similarity=0.730  Sum_probs=23.6

Q ss_pred             eEEEcCCCCCeeecCC----CCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLKP----GDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~----~~~irC~~CG~R   35 (51)
                      ..|+|.+||..+++..    .+.+.||+||..
T Consensus         4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~   35 (41)
T smart00834        4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGD   35 (41)
T ss_pred             EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence            6899999999998642    567999999984

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.

>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=97.98  E-value=7e-06  Score=42.15  Aligned_cols=28  Identities=36%  Similarity=0.838  Sum_probs=23.6

Q ss_pred             eEEEcCCCCCeeecC----CCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLK----PGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~----~~~~irC~~CG~R   35 (51)
                      ..|+|.+||..|+..    ..+.+.||.||..
T Consensus         4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~   35 (42)
T PF09723_consen    4 YEYRCEECGHEFEVLQSISEDDPVPCPECGST   35 (42)
T ss_pred             EEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCC
Confidence            579999999999964    3468999999993

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.

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=97.88  E-value=2.8e-05  Score=40.56  Aligned_cols=28  Identities=29%  Similarity=0.681  Sum_probs=23.1

Q ss_pred             eEEEcCCCCCeeecCC----CCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLKP----GDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~----~~~irC~~CG~R   35 (51)
                      .+|+|.+||.+|++..    .+.+.||.||..
T Consensus         4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~   35 (52)
T TIGR02605         4 YEYRCTACGHRFEVLQKMSDDPLATCPECGGE   35 (52)
T ss_pred             EEEEeCCCCCEeEEEEecCCCCCCCCCCCCCC
Confidence            6899999999999752    256889999984

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.

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=97.78  E-value=5.7e-05  Score=37.32  Aligned_cols=30  Identities=20%  Similarity=0.561  Sum_probs=24.5

Q ss_pred             eEEEcCCCCCeeecCC------CCeeEcCCCCCcEE
Q 035461            8 VSYICGDCGMENTLKP------GDVIQCRECGYRIL   37 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~------~~~irC~~CG~RIl   37 (51)
                      |.+.|.+||+.+.+..      +..++||+||+.+.
T Consensus         1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence            5689999999999862      34599999998764

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.

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=97.38  E-value=0.00017  Score=44.67  Aligned_cols=32  Identities=34%  Similarity=0.708  Sum_probs=25.9

Q ss_pred             CCceEEEcCCCCCeeecCC--------------------CCeeEcCCCCCcE
Q 035461            5 PEPVSYICGDCGMENTLKP--------------------GDVIQCRECGYRI   36 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~--------------------~~~irC~~CG~RI   36 (51)
                      ..|..|.|.+||..+++..                    ....+||.||+.-
T Consensus        66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~  117 (135)
T PRK03824         66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD  117 (135)
T ss_pred             ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence            4678999999999998862                    3457899999863

>smart00531 TFIIE Transcription initiation factor IIE

Probab=97.36  E-value=0.00033  Score=43.45  Aligned_cols=41  Identities=17%  Similarity=0.442  Sum_probs=31.7

Q ss_pred             CCCceEEEcCCCCCeeecC-------CCCeeEcCCCCCcEEEEEecCc
Q 035461            4 QPEPVSYICGDCGMENTLK-------PGDVIQCRECGYRILYKKRTRR   44 (51)
Q Consensus         4 ~~~~~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~RIlyK~R~~~   44 (51)
                      ......|+|..||..++..       ..+...||+||..+.....+..
T Consensus        94 e~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~~~  141 (147)
T smart00531       94 ETNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDNSEP  141 (147)
T ss_pred             ccCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCchhh
Confidence            3456899999999999863       2123999999999998766543

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=97.32  E-value=0.00042  Score=34.67  Aligned_cols=29  Identities=21%  Similarity=0.683  Sum_probs=23.9

Q ss_pred             eEEEcCCCCCeeecC------CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~------~~~~irC~~CG~RI   36 (51)
                      |.-.|.+|++.+++.      .+..++|+.||+.+
T Consensus         1 M~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    1 MIITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             CEEECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence            456899999999986      34679999999864

>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=97.26  E-value=0.00016  Score=43.90  Aligned_cols=36  Identities=25%  Similarity=0.433  Sum_probs=29.1

Q ss_pred             CCCCCCceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            1 MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         1 ~~~~~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      |-.+....+-+|.+||+.|---..++|.||+||.-.
T Consensus         1 MakpelGtKR~Cp~CG~kFYDLnk~PivCP~CG~~~   36 (108)
T PF09538_consen    1 MAKPELGTKRTCPSCGAKFYDLNKDPIVCPKCGTEF   36 (108)
T ss_pred             CCccccCCcccCCCCcchhccCCCCCccCCCCCCcc
Confidence            555667788999999999975555999999999643

The function of members of this family is unknown.

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=97.18  E-value=0.00078  Score=33.69  Aligned_cols=29  Identities=21%  Similarity=0.611  Sum_probs=23.9

Q ss_pred             eEEEcCCCCCeeecC------CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~------~~~~irC~~CG~RI   36 (51)
                      |.-.|-+|++.+.+.      .+..+||+.||+.+
T Consensus         1 M~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    1 MIITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             CEEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            456899999999986      24679999999865

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=97.16  E-value=0.00025  Score=43.03  Aligned_cols=33  Identities=24%  Similarity=0.395  Sum_probs=27.0

Q ss_pred             CCceEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461            5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      ..|....|.+||..+++......+||.||+.-+
T Consensus        67 ~vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~   99 (117)
T PRK00564         67 DEKVELECKDCSHVFKPNALDYGVCEKCHSKNV   99 (117)
T ss_pred             ecCCEEEhhhCCCccccCCccCCcCcCCCCCce
Confidence            457889999999999887666678999998643

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=97.09  E-value=0.00012  Score=34.26  Aligned_cols=25  Identities=32%  Similarity=0.826  Sum_probs=19.2

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      .-.|.+||++++.   +.--||+||.++
T Consensus         2 ~~~Cp~Cg~~~~~---~~~fC~~CG~~L   26 (26)
T PF13248_consen    2 EMFCPNCGAEIDP---DAKFCPNCGAKL   26 (26)
T ss_pred             cCCCcccCCcCCc---ccccChhhCCCC
Confidence            4579999996533   458899999874

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=97.01  E-value=0.00059  Score=41.21  Aligned_cols=32  Identities=22%  Similarity=0.421  Sum_probs=26.4

Q ss_pred             CCceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      ..|....|.+||..+.+......+||.||+.-
T Consensus        66 ~~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~   97 (114)
T PRK03681         66 EQEAECWCETCQQYVTLLTQRVRRCPQCHGDM   97 (114)
T ss_pred             eeCcEEEcccCCCeeecCCccCCcCcCcCCCC
Confidence            45788999999999988765557899999764

>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation

Probab=97.00  E-value=0.00023  Score=42.78  Aligned_cols=32  Identities=31%  Similarity=0.580  Sum_probs=22.8

Q ss_pred             CCceEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461            5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      ..|....|.+||.++++.... ..||.||+.-+
T Consensus        66 ~~p~~~~C~~Cg~~~~~~~~~-~~CP~Cgs~~~   97 (113)
T PF01155_consen   66 EVPARARCRDCGHEFEPDEFD-FSCPRCGSPDV   97 (113)
T ss_dssp             EE--EEEETTTS-EEECHHCC-HH-SSSSSS-E
T ss_pred             ecCCcEECCCCCCEEecCCCC-CCCcCCcCCCc
Confidence            356889999999999998655 78999998743

The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.

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

Probab=96.92  E-value=0.00039  Score=32.93  Aligned_cols=22  Identities=36%  Similarity=0.912  Sum_probs=18.1

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|-+|++++.+.   ...||+|||.
T Consensus         2 ~CP~C~~~V~~~---~~~Cp~CG~~   23 (26)
T PF10571_consen    2 TCPECGAEVPES---AKFCPHCGYD   23 (26)
T ss_pred             cCCCCcCCchhh---cCcCCCCCCC
Confidence            488999998654   4899999985

Several members are annotated as putative helicases.

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

Probab=96.83  E-value=0.0013  Score=32.52  Aligned_cols=27  Identities=22%  Similarity=0.540  Sum_probs=21.3

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      +.|+|..||...+.+. .+-.||.||..
T Consensus         1 ~~~~C~~CG~i~~g~~-~p~~CP~Cg~~   27 (34)
T cd00729           1 KVWVCPVCGYIHEGEE-APEKCPICGAP   27 (34)
T ss_pred             CeEECCCCCCEeECCc-CCCcCcCCCCc
Confidence            3699999999877543 45699999973

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

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

Probab=96.81  E-value=0.0012  Score=31.86  Aligned_cols=25  Identities=36%  Similarity=0.876  Sum_probs=16.4

Q ss_pred             cCCCCCeeecCC-CCeeEcCCCCCcE
Q 035461           12 CGDCGMENTLKP-GDVIQCRECGYRI   36 (51)
Q Consensus        12 C~~Cg~~~~~~~-~~~irC~~CG~RI   36 (51)
                      |+.||.+..+.. +-..+||.||+..
T Consensus         6 C~~CG~~t~~~~~g~~r~C~~Cg~~~   31 (32)
T PF09297_consen    6 CGRCGAPTKPAPGGWARRCPSCGHEH   31 (32)
T ss_dssp             -TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred             cCcCCccccCCCCcCEeECCCCcCEe
Confidence            899999999875 4789999999864

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

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=96.79  E-value=0.0015  Score=35.57  Aligned_cols=33  Identities=33%  Similarity=0.827  Sum_probs=26.2

Q ss_pred             eEEEcCCCCCeeecCC---CCeeEcCCCCCcEEEEE
Q 035461            8 VSYICGDCGMENTLKP---GDVIQCRECGYRILYKK   40 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~---~~~irC~~CG~RIlyK~   40 (51)
                      |.+.|..||.++++..   +..+.||.||..+=.-.
T Consensus         1 ~~~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv~   36 (54)
T TIGR01206         1 MQFECPDCGAEIELENPELGELVICDECGAELEVVS   36 (54)
T ss_pred             CccCCCCCCCEEecCCCccCCEEeCCCCCCEEEEEe
Confidence            3578999999999863   57899999997765433

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

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=96.78  E-value=0.00046  Score=31.73  Aligned_cols=23  Identities=35%  Similarity=0.800  Sum_probs=18.1

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      .|.+||++++.   +..-|++||..|
T Consensus         1 ~Cp~CG~~~~~---~~~fC~~CG~~l   23 (23)
T PF13240_consen    1 YCPNCGAEIED---DAKFCPNCGTPL   23 (23)
T ss_pred             CCcccCCCCCC---cCcchhhhCCcC
Confidence            38899999754   457799999875

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

Probab=96.77  E-value=0.0014  Score=32.01  Aligned_cols=25  Identities=28%  Similarity=0.631  Sum_probs=20.9

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGY   34 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~   34 (51)
                      .|+|..||...+... ++-+||.||.
T Consensus         1 ~~~C~~CGy~y~~~~-~~~~CP~Cg~   25 (33)
T cd00350           1 KYVCPVCGYIYDGEE-APWVCPVCGA   25 (33)
T ss_pred             CEECCCCCCEECCCc-CCCcCcCCCC
Confidence            489999999987553 6779999997

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

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=96.73  E-value=0.0015  Score=39.39  Aligned_cols=30  Identities=27%  Similarity=0.521  Sum_probs=24.0

Q ss_pred             CCceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            5 PEPVSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      ..|....|.+||.++++.... ..||.||+.
T Consensus        66 ~vp~~~~C~~Cg~~~~~~~~~-~~CP~Cgs~   95 (113)
T PRK12380         66 YKPAQAWCWDCSQVVEIHQHD-AQCPHCHGE   95 (113)
T ss_pred             eeCcEEEcccCCCEEecCCcC-ccCcCCCCC
Confidence            356889999999999987533 459999975

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=96.67  E-value=0.0012  Score=42.49  Aligned_cols=37  Identities=16%  Similarity=0.424  Sum_probs=29.7

Q ss_pred             CCCCceEEEcCCCCCeeecC--CCCeeEcCCCCCcEEEE
Q 035461            3 PQPEPVSYICGDCGMENTLK--PGDVIQCRECGYRILYK   39 (51)
Q Consensus         3 ~~~~~~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RIlyK   39 (51)
                      .......|+|..||..++..  ....-.||.||.-..+-
T Consensus       111 ~e~~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~  149 (178)
T PRK06266        111 EEENNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEY  149 (178)
T ss_pred             hccCCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCeec
Confidence            34566899999999999976  34579999999987764

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

Probab=96.61  E-value=0.0005  Score=46.67  Aligned_cols=30  Identities=37%  Similarity=0.914  Sum_probs=23.1

Q ss_pred             EEcCCCCCeeecC-------CCCeeEcCCCCCcEEEEE
Q 035461           10 YICGDCGMENTLK-------PGDVIQCRECGYRILYKK   40 (51)
Q Consensus        10 Y~C~~Cg~~~~~~-------~~~~irC~~CG~RIlyK~   40 (51)
                      -.|+.|+-.+...       .++.+.||+|| ||||..
T Consensus       198 ~~C~GC~m~l~~~~~~~V~~~d~iv~CP~Cg-RILy~~  234 (239)
T COG1579         198 RVCGGCHMKLPSQTLSKVRKKDEIVFCPYCG-RILYYD  234 (239)
T ss_pred             CcccCCeeeecHHHHHHHhcCCCCccCCccc-hHHHhh
Confidence            4799998887642       56789999998 677753

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=96.55  E-value=0.0014  Score=41.28  Aligned_cols=36  Identities=14%  Similarity=0.034  Sum_probs=29.0

Q ss_pred             CCCCCCceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            1 MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         1 ~~~~~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      |-.+....+.+|-+||+.|---..++|.||+||.-.
T Consensus         1 m~k~elGtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~   36 (129)
T TIGR02300         1 MAKPDLGTKRICPNTGSKFYDLNRRPAVSPYTGEQF   36 (129)
T ss_pred             CCchhhCccccCCCcCccccccCCCCccCCCcCCcc
Confidence            444556688999999999976666999999999764

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. The function of members of this family is unknown.

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=96.52  E-value=0.0016  Score=41.10  Aligned_cols=37  Identities=19%  Similarity=0.367  Sum_probs=29.3

Q ss_pred             CCCCceEEEcCCCCCeeecC--CCCeeEcCCCCCcEEEE
Q 035461            3 PQPEPVSYICGDCGMENTLK--PGDVIQCRECGYRILYK   39 (51)
Q Consensus         3 ~~~~~~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RIlyK   39 (51)
                      ....+..|.|..||..++..  ....-.||.||....+-
T Consensus       103 ~e~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~~  141 (158)
T TIGR00373       103 FETNNMFFICPNMCVRFTFNEAMELNFTCPRCGAMLDYL  141 (158)
T ss_pred             hccCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCEeeec
Confidence            34567899999999999876  23568999999986653

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=96.46  E-value=0.0028  Score=38.22  Aligned_cols=31  Identities=29%  Similarity=0.604  Sum_probs=25.1

Q ss_pred             CCceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      ..|....|.+||.++++... ...||.||+.-
T Consensus        66 ~~p~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~~   96 (115)
T TIGR00100        66 DEPVECECEDCSEEVSPEID-LYRCPKCHGIM   96 (115)
T ss_pred             eeCcEEEcccCCCEEecCCc-CccCcCCcCCC
Confidence            45788999999999988753 47799999753

In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.

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

Probab=96.40  E-value=0.004  Score=39.45  Aligned_cols=34  Identities=26%  Similarity=0.619  Sum_probs=27.9

Q ss_pred             CCceEEEcCCCCCeeecCC-CCeeEcCCCCCcEEE
Q 035461            5 PEPVSYICGDCGMENTLKP-GDVIQCRECGYRILY   38 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~-~~~irC~~CG~RIly   38 (51)
                      +.+-.|+|.+||..+.+.. ..-..||.||+.-+.
T Consensus       108 ~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~  142 (146)
T PF07295_consen  108 VGPGTLVCENCGHEVELTHPERLPPCPKCGHTEFT  142 (146)
T ss_pred             ecCceEecccCCCEEEecCCCcCCCCCCCCCCeee
Confidence            4567899999999999974 455789999997664

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

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

Probab=96.37  E-value=0.0034  Score=41.24  Aligned_cols=32  Identities=19%  Similarity=0.257  Sum_probs=26.1

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEec
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYKKRT   42 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~   42 (51)
                      -.|+|-.|++.|.   .+.-.||.||++++-|...
T Consensus       138 w~~rC~GC~~~f~---~~~~~Cp~CG~~~~~~~~~  169 (177)
T COG1439         138 WRLRCHGCKRIFP---EPKDFCPICGSPLKRKRVK  169 (177)
T ss_pred             eeEEEecCceecC---CCCCcCCCCCCceEEeeec
Confidence            6799999999998   4556899999997666544

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

Probab=96.27  E-value=0.0039  Score=29.24  Aligned_cols=23  Identities=26%  Similarity=0.808  Sum_probs=17.7

Q ss_pred             cCCCCCeeecCC-CCeeEcCCCCC
Q 035461           12 CGDCGMENTLKP-GDVIQCRECGY   34 (51)
Q Consensus        12 C~~Cg~~~~~~~-~~~irC~~CG~   34 (51)
                      |..||..+.... ...-.||+||.
T Consensus         1 C~sC~~~i~~r~~~v~f~CPnCG~   24 (24)
T PF07754_consen    1 CTSCGRPIAPREQAVPFPCPNCGF   24 (24)
T ss_pred             CccCCCcccCcccCceEeCCCCCC
Confidence            678888877654 56788999984

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

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

Probab=96.26  E-value=0.0022  Score=31.36  Aligned_cols=26  Identities=38%  Similarity=0.856  Sum_probs=16.3

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      .|-.||.+.....+...-||.|||-+
T Consensus         4 ~Cp~C~se~~y~D~~~~vCp~C~~ew   29 (30)
T PF08274_consen    4 KCPLCGSEYTYEDGELLVCPECGHEW   29 (30)
T ss_dssp             --TTT-----EE-SSSEEETTTTEEE
T ss_pred             CCCCCCCcceeccCCEEeCCcccccC
Confidence            68899999999999999999999864

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.

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=96.19  E-value=0.0036  Score=38.27  Aligned_cols=31  Identities=35%  Similarity=0.840  Sum_probs=22.9

Q ss_pred             CCceEEEcCCCCCeeecCCCC------eeEcCCCCCcE
Q 035461            5 PEPVSYICGDCGMENTLKPGD------VIQCRECGYRI   36 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~------~irC~~CG~RI   36 (51)
                      ..|....| +||.++++...+      ...||.||..-
T Consensus        66 ~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~  102 (124)
T PRK00762         66 MIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKR  102 (124)
T ss_pred             ecCeeEEe-eCcCcccccccchhccccCCcCcCCCCCC
Confidence            45788999 999998876321      26799999643

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

Probab=96.00  E-value=0.0098  Score=33.43  Aligned_cols=27  Identities=30%  Similarity=0.935  Sum_probs=13.6

Q ss_pred             eEEEcCCCCCeeecC------CCCeeEcCCCCC
Q 035461            8 VSYICGDCGMENTLK------PGDVIQCRECGY   34 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~------~~~~irC~~CG~   34 (51)
                      +.|.|-+||.+.-..      .+.+-+||+||+
T Consensus        26 v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF   58 (61)
T COG2888          26 VKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF   58 (61)
T ss_pred             eEeeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence            555555555433221      345556666654

>PRK12496 hypothetical protein; Provisional

Probab=95.93  E-value=0.004  Score=39.64  Aligned_cols=31  Identities=19%  Similarity=0.326  Sum_probs=23.5

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      -.|+|..||+.++... ..-.||.||+.+--|
T Consensus       126 w~~~C~gC~~~~~~~~-~~~~C~~CG~~~~r~  156 (164)
T PRK12496        126 WRKVCKGCKKKYPEDY-PDDVCEICGSPVKRK  156 (164)
T ss_pred             eeEECCCCCccccCCC-CCCcCCCCCChhhhc
Confidence            3599999999997654 225899999987433

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

Probab=95.85  E-value=0.017  Score=32.27  Aligned_cols=28  Identities=29%  Similarity=0.650  Sum_probs=13.4

Q ss_pred             EEcCCCCCeeecCC-CCeeEcCCCCCcEE
Q 035461           10 YICGDCGMENTLKP-GDVIQCRECGYRIL   37 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~-~~~irC~~CG~RIl   37 (51)
                      ..|..||.++.... ...-.||+||.-++
T Consensus         8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I   36 (59)
T PRK14890          8 PKCTSCGIEIAPREKAVKFLCPNCGEVII   36 (59)
T ss_pred             ccccCCCCcccCCCccCEeeCCCCCCeeE
Confidence            34555555554332 34455555555433

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.61  E-value=0.0082  Score=32.90  Aligned_cols=26  Identities=31%  Similarity=0.671  Sum_probs=21.1

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGY   34 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~   34 (51)
                      ...+|..||..|..+ .|.+.||.||-
T Consensus         4 ~~~~C~~Cg~~~~~~-dDiVvCp~Cga   29 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDG-DDIVVCPECGA   29 (54)
T ss_pred             cCccChhhCCcccCC-CCEEECCCCCC
Confidence            346899999998655 48899999994

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

Probab=95.61  E-value=0.016  Score=38.53  Aligned_cols=31  Identities=23%  Similarity=0.550  Sum_probs=26.2

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      +.=+|++|+.+... .+..++||+||+.-.-|
T Consensus       148 I~A~CsrC~~~L~~-~~~~l~Cp~Cg~tEkRK  178 (188)
T COG1096         148 IYARCSRCRAPLVK-KGNMLKCPNCGNTEKRK  178 (188)
T ss_pred             EEEEccCCCcceEE-cCcEEECCCCCCEEeee
Confidence            55689999999988 67999999999876544

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

Probab=95.46  E-value=0.019  Score=32.07  Aligned_cols=29  Identities=28%  Similarity=0.840  Sum_probs=23.1

Q ss_pred             ceEEEcCCCCCeeec------CCCCeeEcCCCCCc
Q 035461            7 PVSYICGDCGMENTL------KPGDVIQCRECGYR   35 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~------~~~~~irC~~CG~R   35 (51)
                      .+.|.|-+||.++-.      +...+.+||+||+.
T Consensus        23 ~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF~   57 (59)
T PRK14890         23 AVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFE   57 (59)
T ss_pred             cCEeeCCCCCCeeEeechhHHhcCCceECCCCCCc
Confidence            589999999998433      25678999999974

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

Probab=95.43  E-value=0.015  Score=29.43  Aligned_cols=27  Identities=22%  Similarity=0.727  Sum_probs=18.9

Q ss_pred             EEcCCCCCeee-cC-CCCeeEcCCCCCcE
Q 035461           10 YICGDCGMENT-LK-PGDVIQCRECGYRI   36 (51)
Q Consensus        10 Y~C~~Cg~~~~-~~-~~~~irC~~CG~RI   36 (51)
                      |+|..||...- .+ ....+.|++||.=|
T Consensus         1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl   29 (43)
T PF08271_consen    1 MKCPNCGSKEIVFDPERGELVCPNCGLVL   29 (43)
T ss_dssp             ESBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred             CCCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence            78999998752 22 45778999998643

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

>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function

Probab=95.12  E-value=0.0069  Score=38.25  Aligned_cols=31  Identities=23%  Similarity=0.399  Sum_probs=22.0

Q ss_pred             EEcCCCCCeeecCCCC-eeEcCCCCCcEEEEE
Q 035461           10 YICGDCGMENTLKPGD-VIQCRECGYRILYKK   40 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~~~-~irC~~CG~RIlyK~   40 (51)
                      .+|.+||+.|+-.... --=||+||.+-+-=.
T Consensus         2 H~Ct~Cg~~f~dgs~eil~GCP~CGg~kF~yv   33 (131)
T PF09845_consen    2 HQCTKCGRVFEDGSKEILSGCPECGGNKFQYV   33 (131)
T ss_pred             cccCcCCCCcCCCcHHHHccCcccCCcceEEc
Confidence            4799999999865432 245999997655433

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

Probab=95.04  E-value=0.03  Score=27.60  Aligned_cols=26  Identities=31%  Similarity=0.600  Sum_probs=22.0

Q ss_pred             EEEcCCCCCeeec-CCCCeeEcCCCCC
Q 035461            9 SYICGDCGMENTL-KPGDVIQCRECGY   34 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~-~~~~~irC~~CG~   34 (51)
                      .++|..||.+..+ +..+-..|++||.
T Consensus         3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~   29 (33)
T PF08792_consen    3 LKKCSKCGGNGIVNKEDDYEVCIFCGS   29 (33)
T ss_pred             ceEcCCCCCCeEEEecCCeEEcccCCc
Confidence            3689999999888 6778899999996

>PF12773 DZR: Double zinc ribbon

Probab=94.85  E-value=0.01  Score=30.36  Aligned_cols=25  Identities=24%  Similarity=0.579  Sum_probs=16.2

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|..||..+.......+.|+.||..
T Consensus        14 fC~~CG~~l~~~~~~~~~C~~Cg~~   38 (50)
T PF12773_consen   14 FCPHCGTPLPPPDQSKKICPNCGAE   38 (50)
T ss_pred             CChhhcCChhhccCCCCCCcCCcCC
Confidence            4666777766444456777777765

>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]

Probab=94.76  E-value=0.027  Score=34.78  Aligned_cols=30  Identities=40%  Similarity=0.733  Sum_probs=25.2

Q ss_pred             CCceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            5 PEPVSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .+|....|.+|+.++++...+.. ||.||+.
T Consensus        66 ~~p~~~~C~~C~~~~~~e~~~~~-CP~C~s~   95 (115)
T COG0375          66 EEPAECWCLDCGQEVELEELDYR-CPKCGSI   95 (115)
T ss_pred             EeccEEEeccCCCeecchhheeE-CCCCCCC
Confidence            35788999999999999876655 9999964

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=94.71  E-value=0.031  Score=28.55  Aligned_cols=24  Identities=42%  Similarity=0.952  Sum_probs=18.5

Q ss_pred             cCCCCCeeecCCC---CeeEcCCCCCc
Q 035461           12 CGDCGMENTLKPG---DVIQCRECGYR   35 (51)
Q Consensus        12 C~~Cg~~~~~~~~---~~irC~~CG~R   35 (51)
                      |.+||..+..+..   .-..||.|||.
T Consensus         3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~   29 (52)
T smart00661        3 CPKCGNMLIPKEGKEKRRFVCRKCGYE   29 (52)
T ss_pred             CCCCCCccccccCCCCCEEECCcCCCe
Confidence            8899998877643   36889999974

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

Probab=94.55  E-value=0.033  Score=30.02  Aligned_cols=25  Identities=36%  Similarity=1.024  Sum_probs=18.8

Q ss_pred             EcCCCCCeeec-CCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTL-KPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~-~~~~~irC~~CG~R   35 (51)
                      .|..||..... .......||.||+.
T Consensus        30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~   55 (69)
T PF07282_consen   30 TCPRCGHRNKKRRSGRVFTCPNCGFE   55 (69)
T ss_pred             CccCcccccccccccceEEcCCCCCE
Confidence            48888888776 35577888888875

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

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

Probab=94.53  E-value=0.048  Score=34.40  Aligned_cols=31  Identities=26%  Similarity=0.558  Sum_probs=24.5

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~   40 (51)
                      .+-|..||.+..- ..+.|-||.||++....+
T Consensus        28 ~~hCp~Cg~PLF~-KdG~v~CPvC~~~~~~v~   58 (131)
T COG1645          28 AKHCPKCGTPLFR-KDGEVFCPVCGYREVVVE   58 (131)
T ss_pred             HhhCcccCCccee-eCCeEECCCCCceEEEee
Confidence            4679999999855 557799999999765543

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

Probab=94.49  E-value=0.045  Score=30.76  Aligned_cols=29  Identities=28%  Similarity=0.698  Sum_probs=23.5

Q ss_pred             EcCCCCCeeecC-CCCeeEcCCCCCcEEEE
Q 035461           11 ICGDCGMENTLK-PGDVIQCRECGYRILYK   39 (51)
Q Consensus        11 ~C~~Cg~~~~~~-~~~~irC~~CG~RIlyK   39 (51)
                      .|..||.++.+. ....--||+||.-++|.
T Consensus        11 ~CtSCg~~i~p~e~~v~F~CPnCGe~~I~R   40 (61)
T COG2888          11 VCTSCGREIAPGETAVKFPCPNCGEVEIYR   40 (61)
T ss_pred             eeccCCCEeccCCceeEeeCCCCCceeeeh
Confidence            799999999655 45678999999877763

>PRK00420 hypothetical protein; Validated

Probab=94.45  E-value=0.043  Score=33.66  Aligned_cols=31  Identities=19%  Similarity=0.286  Sum_probs=24.4

Q ss_pred             EEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461           10 YICGDCGMENTLKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~   40 (51)
                      -.|..||.++.-.....+.||.||.-+..+.
T Consensus        24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~   54 (112)
T PRK00420         24 KHCPVCGLPLFELKDGEVVCPVHGKVYIVKS   54 (112)
T ss_pred             CCCCCCCCcceecCCCceECCCCCCeeeecc
Confidence            4699999988654567899999999776543

>PF13451 zf-trcl: Probable zinc-binding domain

Probab=94.44  E-value=0.017  Score=31.04  Aligned_cols=26  Identities=27%  Similarity=0.713  Sum_probs=21.1

Q ss_pred             eEEEcCCCCCeeecC------------CCCeeEcCCCC
Q 035461            8 VSYICGDCGMENTLK------------PGDVIQCRECG   33 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~------------~~~~irC~~CG   33 (51)
                      ..+.|-+||++|.+.            .+.+.||+.|-
T Consensus         3 k~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR   40 (49)
T PF13451_consen    3 KTLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCR   40 (49)
T ss_pred             eeEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHH
Confidence            468999999999874            24689999885

>COG1592 Rubrerythrin [Energy production and conversion]

Probab=94.43  E-value=0.031  Score=36.28  Aligned_cols=25  Identities=24%  Similarity=0.581  Sum_probs=21.9

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|+|..||..+.-  ..+-+||.||..
T Consensus       134 ~~vC~vCGy~~~g--e~P~~CPiCga~  158 (166)
T COG1592         134 VWVCPVCGYTHEG--EAPEVCPICGAP  158 (166)
T ss_pred             EEEcCCCCCcccC--CCCCcCCCCCCh
Confidence            8999999999876  577899999964

>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A

Probab=94.34  E-value=0.029  Score=33.64  Aligned_cols=29  Identities=21%  Similarity=0.390  Sum_probs=23.6

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      ....|+.|+.+|.+-.+.+..|.+|+++|
T Consensus        53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~V   81 (118)
T PF02318_consen   53 GERHCARCGKPFGFLFNRGRVCVDCKHRV   81 (118)
T ss_dssp             CCSB-TTTS-BCSCTSTTCEEETTTTEEE
T ss_pred             CCcchhhhCCcccccCCCCCcCCcCCccc
Confidence            45689999999988888889999999887

The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.

>PF14369 zf-RING_3: zinc-finger

Probab=94.34  E-value=0.065  Score=26.60  Aligned_cols=29  Identities=21%  Similarity=0.578  Sum_probs=23.1

Q ss_pred             EEEcCCCCCeeecCC--CCeeEcCCCCCcEE
Q 035461            9 SYICGDCGMENTLKP--GDVIQCRECGYRIL   37 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~--~~~irC~~CG~RIl   37 (51)
                      .|=|-.|.+.+.+..  .+.+.||+|+.-.|
T Consensus         2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFv   32 (35)
T PF14369_consen    2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGFV   32 (35)
T ss_pred             CEeCccCCCEeEeCcCCCCCcCCcCCCCcEe
Confidence            488999999999853  34456999998776

>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT)

Probab=94.17  E-value=0.071  Score=32.19  Aligned_cols=34  Identities=24%  Similarity=0.531  Sum_probs=25.6

Q ss_pred             CceEEEcCCCCCeeecCCC---CeeEcCCCCCcEEEE
Q 035461            6 EPVSYICGDCGMENTLKPG---DVIQCRECGYRILYK   39 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~---~~irC~~CG~RIlyK   39 (51)
                      ....|.|..||.++.....   ...+|+.||..+...
T Consensus       120 ~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~~  156 (157)
T PF10263_consen  120 KKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQV  156 (157)
T ss_pred             cceEEEcCCCCCEeeeecccchhhEECCCCCCEEEEc
Confidence            3478999999998876532   457899999776543

SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.

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

Probab=94.10  E-value=0.059  Score=30.77  Aligned_cols=33  Identities=30%  Similarity=0.642  Sum_probs=22.8

Q ss_pred             eEEEcCCCCCeeecCC-CCeeEcCCCCCcEEEEEec
Q 035461            8 VSYICGDCGMENTLKP-GDVIQCRECGYRILYKKRT   42 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~-~~~irC~~CG~RIlyK~R~   42 (51)
                      +.|+| +||+..-.+. ...-+| .||++|=.|+|.
T Consensus         2 lifrC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~r   35 (68)
T PF09082_consen    2 LIFRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERR   35 (68)
T ss_dssp             EEEEE-TTS--EEEETT-SEEEE-TTTEEEE--SSS
T ss_pred             EEEEe-cCCCEEEecCCcceeEe-cCCCeeeeeeEE
Confidence            47899 7999887664 467899 999999887764

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

>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA

Probab=94.10  E-value=0.038  Score=34.08  Aligned_cols=25  Identities=32%  Similarity=0.733  Sum_probs=22.0

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|..|+.++.-+.++..-||+|||-
T Consensus         4 ~CP~C~seytY~dg~~~iCpeC~~E   28 (109)
T TIGR00686         4 PCPKCNSEYTYHDGTQLICPSCLYE   28 (109)
T ss_pred             cCCcCCCcceEecCCeeECcccccc
Confidence            4889999999888889999999985

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

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=94.05  E-value=0.049  Score=28.93  Aligned_cols=27  Identities=30%  Similarity=0.693  Sum_probs=20.8

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      -|.+||.++.....+...|..||+...
T Consensus        22 fCP~Cg~~~m~~~~~r~~C~~Cgyt~~   48 (50)
T PRK00432         22 FCPRCGSGFMAEHLDRWHCGKCGYTEF   48 (50)
T ss_pred             cCcCCCcchheccCCcEECCCcCCEEe
Confidence            688999875455567899999998654

>PRK06450 threonine synthase; Validated

Probab=94.00  E-value=0.046  Score=37.78  Aligned_cols=29  Identities=31%  Similarity=0.612  Sum_probs=22.3

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILY   38 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIly   38 (51)
                      +.|+|.+||++...  ....+||.||..+..
T Consensus         2 ~~~~C~~Cg~~~~~--~~~~~C~~cg~~l~~   30 (338)
T PRK06450          2 VKEVCMKCGKERES--IYEIRCKKCGGPFEI   30 (338)
T ss_pred             ceeEECCcCCcCCC--cccccCCcCCCEeEE
Confidence            56899999999754  234799999976544

>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein

Probab=93.98  E-value=0.061  Score=27.23  Aligned_cols=25  Identities=32%  Similarity=0.728  Sum_probs=15.1

Q ss_pred             eEEEcCCCCCeeecC--CCCeeEcCCCCC
Q 035461            8 VSYICGDCGMENTLK--PGDVIQCRECGY   34 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~   34 (51)
                      -.|+|..||..+++-  .+.++-|  ||-
T Consensus         5 ~~YkC~~CGniVev~~~g~g~lvC--CGe   31 (36)
T PF06397_consen    5 EFYKCEHCGNIVEVVHDGGGPLVC--CGE   31 (36)
T ss_dssp             EEEE-TTT--EEEEEE--SS-EEE--TTE
T ss_pred             cEEEccCCCCEEEEEECCCCCEEe--CCc
Confidence            579999999999874  2356777  553

It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....

>PRK07591 threonine synthase; Validated

Probab=93.91  E-value=0.063  Score=38.00  Aligned_cols=30  Identities=33%  Similarity=0.597  Sum_probs=23.7

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      ..++|.+||+++.+.. . .+||.||.-+-..
T Consensus        17 ~~l~C~~Cg~~~~~~~-~-~~C~~cg~~l~~~   46 (421)
T PRK07591         17 VALKCRECGAEYPLGP-I-HVCEECFGPLEVA   46 (421)
T ss_pred             eEEEeCCCCCcCCCCC-C-ccCCCCCCeEEEE
Confidence            4599999999998764 3 9999999755443

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

Probab=93.76  E-value=0.029  Score=40.94  Aligned_cols=32  Identities=22%  Similarity=0.503  Sum_probs=25.3

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcEEEEEec
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRILYKKRT   42 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~   42 (51)
                      +|..||...+..-....||+.||+|+=...+.
T Consensus       352 ~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~  383 (421)
T COG1571         352 VCPRCGGRMKSAGRNGFRCKKCGTRARETLIK  383 (421)
T ss_pred             CCCccCCchhhcCCCCcccccccccCCccccc
Confidence            79999999987743499999999987554443

>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=93.75  E-value=0.068  Score=29.88  Aligned_cols=21  Identities=33%  Similarity=0.823  Sum_probs=17.6

Q ss_pred             CeeEcCCCCCcEEEEEecCce
Q 035461           25 DVIQCRECGYRILYKKRTRRI   45 (51)
Q Consensus        25 ~~irC~~CG~RIlyK~R~~~~   45 (51)
                      ..+-|++|||-=||+..+...
T Consensus        35 ~~v~C~~CGYTE~Y~~~~~~~   55 (64)
T PF09855_consen   35 TTVSCTNCGYTEFYKAKTSNG   55 (64)
T ss_pred             EEEECCCCCCEEEEeecCccc
Confidence            468999999999999877643

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

Probab=93.68  E-value=0.034  Score=30.24  Aligned_cols=29  Identities=21%  Similarity=0.299  Sum_probs=20.6

Q ss_pred             EEEcCCCCCeeec-CCC--CeeEcCCCCCcEE
Q 035461            9 SYICGDCGMENTL-KPG--DVIQCRECGYRIL   37 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~-~~~--~~irC~~CG~RIl   37 (51)
                      +++|+.|++..-. ...  -.|+||.||.--.
T Consensus         4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~   35 (51)
T PF10122_consen    4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINH   35 (51)
T ss_pred             ceeccchhHHHhhhcCccEEEEECCCCCccce
Confidence            5789999887654 222  4799999986433

>PHA02768 hypothetical protein; Provisional

Probab=93.65  E-value=0.045  Score=29.99  Aligned_cols=40  Identities=23%  Similarity=0.423  Sum_probs=29.4

Q ss_pred             eEEEcCCCCCeeecCCC---------CeeEcCCCCCcEEEEEecCceEEEEc
Q 035461            8 VSYICGDCGMENTLKPG---------DVIQCRECGYRILYKKRTRRIVQYEA   50 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~---------~~irC~~CG~RIlyK~R~~~~~~~~A   50 (51)
                      .-|.|..||+.|...+.         .+-+|.+||- +..  |+...+.++|
T Consensus         4 ~~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k-~f~--~~s~l~~~~~   52 (55)
T PHA02768          4 LGYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKR-ISL--RTGEYIEIKA   52 (55)
T ss_pred             cccCcchhCCeeccHHHHHHHHHhcCCcccCCcccc-eec--ccceeEEEec
Confidence            35899999999986421         4789999997 333  6666777665

>PF14353 CpXC: CpXC protein

Probab=93.54  E-value=0.09  Score=31.39  Aligned_cols=26  Identities=27%  Similarity=0.667  Sum_probs=19.5

Q ss_pred             EcCCCCCeeecC--------------------CCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLK--------------------PGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~--------------------~~~~irC~~CG~RI   36 (51)
                      .|..||..++.+                    .--...||+||+.+
T Consensus         3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~   48 (128)
T PF14353_consen    3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKF   48 (128)
T ss_pred             CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCce
Confidence            589999998864                    11368999999754

>COG3364 Zn-ribbon containing protein [General function prediction only]

Probab=93.52  E-value=0.014  Score=36.01  Aligned_cols=32  Identities=25%  Similarity=0.485  Sum_probs=22.2

Q ss_pred             eEEEcCCCCCeeecCC-CCeeEcCCCCCcE-EEE
Q 035461            8 VSYICGDCGMENTLKP-GDVIQCRECGYRI-LYK   39 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~-~~~irC~~CG~RI-lyK   39 (51)
                      |..+|.+||..|+--+ .-.-=||+||.+- +|-
T Consensus         1 MpH~CtrCG~vf~~g~~~il~GCp~CG~nkF~yv   34 (112)
T COG3364           1 MPHQCTRCGEVFDDGSEEILSGCPKCGCNKFLYV   34 (112)
T ss_pred             CCceecccccccccccHHHHccCccccchheEec
Confidence            4578999999987632 1224599999764 443

>PRK11032 hypothetical protein; Provisional

Probab=93.45  E-value=0.07  Score=34.41  Aligned_cols=33  Identities=18%  Similarity=0.433  Sum_probs=26.7

Q ss_pred             CceEEEcCCCCCeeecC-CCCeeEcCCCCCcEEE
Q 035461            6 EPVSYICGDCGMENTLK-PGDVIQCRECGYRILY   38 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RIly   38 (51)
                      .+-...|-+||....+. +..-..||+||+.-+-
T Consensus       121 g~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~F~  154 (160)
T PRK11032        121 GLGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQ  154 (160)
T ss_pred             ecceEEecCCCCEEEecCCCcCCCCCCCCCCeee
Confidence            44678999999999997 4566789999997653

>PRK10220 hypothetical protein; Provisional

Probab=93.41  E-value=0.074  Score=32.89  Aligned_cols=25  Identities=28%  Similarity=0.638  Sum_probs=21.4

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|..|+.++.-+.++..-||+|||.
T Consensus         5 ~CP~C~seytY~d~~~~vCpeC~hE   29 (111)
T PRK10220          5 HCPKCNSEYTYEDNGMYICPECAHE   29 (111)
T ss_pred             cCCCCCCcceEcCCCeEECCcccCc
Confidence            4888999988888888999999984

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

Probab=93.02  E-value=0.069  Score=28.50  Aligned_cols=26  Identities=35%  Similarity=0.670  Sum_probs=20.1

Q ss_pred             EEEcCCCCCeeecCCC----------------CeeEcCCCCC
Q 035461            9 SYICGDCGMENTLKPG----------------DVIQCRECGY   34 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~   34 (51)
                      .|+|..||-..+.+.+                +.-+||.||.
T Consensus         1 ~y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a   42 (50)
T cd00730           1 KYECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA   42 (50)
T ss_pred             CcCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence            4899999999886533                3359999995

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

>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]

Probab=92.83  E-value=0.049  Score=32.99  Aligned_cols=25  Identities=24%  Similarity=0.539  Sum_probs=20.6

Q ss_pred             EcCCCCCeeecC-CCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLK-PGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~-~~~~irC~~CG~R   35 (51)
                      .|-+||.+|..+ .+-+-|||.|-+-
T Consensus        60 ~CkkCGfef~~~~ik~pSRCP~CKSE   85 (97)
T COG3357          60 RCKKCGFEFRDDKIKKPSRCPKCKSE   85 (97)
T ss_pred             hhcccCccccccccCCcccCCcchhh
Confidence            699999999874 4568999999764

>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=92.79  E-value=0.25  Score=26.47  Aligned_cols=35  Identities=29%  Similarity=0.578  Sum_probs=25.9

Q ss_pred             CCCCceEEEcCCCCCeeecCC------CCeeEcCCCCCcEEE
Q 035461            3 PQPEPVSYICGDCGMENTLKP------GDVIQCRECGYRILY   38 (51)
Q Consensus         3 ~~~~~~~Y~C~~Cg~~~~~~~------~~~irC~~CG~RIly   38 (51)
                      ...+...|-| +||..+.+..      ...+-|+.|.-.|-.
T Consensus        12 ~~~~~~~y~C-RCG~~f~i~e~~l~~~~~iv~C~sCSL~I~V   52 (55)
T PF05207_consen   12 EEEGVYSYPC-RCGGEFEISEEDLEEGEVIVQCDSCSLWIRV   52 (55)
T ss_dssp             TTTTEEEEEE-TTSSEEEEEHHHHHCT--EEEETTTTEEEEE
T ss_pred             CCCCEEEEcC-CCCCEEEEcchhccCcCEEEECCCCccEEEE
Confidence            3445689999 9999999852      245999999977653

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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.

>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.78  E-value=0.027  Score=33.22  Aligned_cols=28  Identities=36%  Similarity=0.816  Sum_probs=23.2

Q ss_pred             eEEEcCCCCCeeecC----CCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLK----PGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~----~~~~irC~~CG~R   35 (51)
                      ..|.|.+||..+++-    .....-|++||.+
T Consensus        11 Y~Y~c~~cg~~~dvvq~~~ddplt~ce~c~a~   42 (82)
T COG2331          11 YSYECTECGNRFDVVQAMTDDPLTTCEECGAR   42 (82)
T ss_pred             eEEeecccchHHHHHHhcccCccccChhhChH
Confidence            689999999999874    3355899999985

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=92.69  E-value=0.091  Score=30.41  Aligned_cols=25  Identities=40%  Similarity=0.842  Sum_probs=19.9

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      -|.+||..+... .+.+.|+.||+..
T Consensus         2 fC~~Cg~~l~~~-~~~~~C~~C~~~~   26 (104)
T TIGR01384         2 FCPKCGSLMTPK-NGVYVCPSCGYEK   26 (104)
T ss_pred             CCcccCcccccC-CCeEECcCCCCcc
Confidence            388999998654 4679999999763

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

>PRK06260 threonine synthase; Validated

Probab=92.65  E-value=0.13  Score=35.98  Aligned_cols=29  Identities=28%  Similarity=0.512  Sum_probs=22.6

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRILY   38 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIly   38 (51)
                      .++|.+||++..+.. ...+||.||..+..
T Consensus         3 ~~~C~~cg~~~~~~~-~~~~Cp~cg~~l~~   31 (397)
T PRK06260          3 WLKCIECGKEYDPDE-IIYTCPECGGLLEV   31 (397)
T ss_pred             EEEECCCCCCCCCCC-ccccCCCCCCeEEE
Confidence            589999999987664 34789999976443

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

Probab=92.56  E-value=0.15  Score=24.83  Aligned_cols=26  Identities=27%  Similarity=0.552  Sum_probs=15.6

Q ss_pred             ceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            7 PVSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      -+.-+|.+||..+-...   ..||.||..
T Consensus         9 l~~~rC~~Cg~~~~pPr---~~Cp~C~s~   34 (37)
T PF12172_consen    9 LLGQRCRDCGRVQFPPR---PVCPHCGSD   34 (37)
T ss_dssp             EEEEE-TTT--EEES-----SEETTTT--
T ss_pred             EEEEEcCCCCCEecCCC---cCCCCcCcc
Confidence            37789999999865443   789999864

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

>PHA00626 hypothetical protein

Probab=92.53  E-value=0.14  Score=28.63  Aligned_cols=26  Identities=38%  Similarity=0.758  Sum_probs=17.3

Q ss_pred             EcCCCCCeeecC------CCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLK------PGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~------~~~~irC~~CG~RI   36 (51)
                      .|.+||...-++      +...-.|+.|||+.
T Consensus         2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f   33 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND   33 (59)
T ss_pred             CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence            477888743332      24668899999874

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

Probab=92.35  E-value=0.089  Score=36.64  Aligned_cols=27  Identities=30%  Similarity=0.759  Sum_probs=22.6

Q ss_pred             EcCCCCCeeecCC-CCeeEcCCCCCcEE
Q 035461           11 ICGDCGMENTLKP-GDVIQCRECGYRIL   37 (51)
Q Consensus        11 ~C~~Cg~~~~~~~-~~~irC~~CG~RIl   37 (51)
                      -|+.||.+..... +....|+.||+...
T Consensus       113 FCg~CG~~~~~~~~g~~~~C~~cg~~~f  140 (279)
T COG2816         113 FCGRCGTKTYPREGGWARVCPKCGHEHF  140 (279)
T ss_pred             CCCCCCCcCccccCceeeeCCCCCCccC
Confidence            3999999999875 46799999999753

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

Probab=92.24  E-value=0.09  Score=27.77  Aligned_cols=23  Identities=30%  Similarity=0.885  Sum_probs=18.4

Q ss_pred             EcCCCCCeeecC------C-CCeeEcCCCC
Q 035461           11 ICGDCGMENTLK------P-GDVIQCRECG   33 (51)
Q Consensus        11 ~C~~Cg~~~~~~------~-~~~irC~~CG   33 (51)
                      .|+.|+..+...      . ...+.||+||
T Consensus        24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~Cg   53 (56)
T PF02591_consen   24 TCSGCHMELPPQELNEIRKGDEIVFCPNCG   53 (56)
T ss_pred             ccCCCCEEcCHHHHHHHHcCCCeEECcCCC
Confidence            799999888753      3 3679999998

>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2

Probab=92.21  E-value=0.096  Score=26.17  Aligned_cols=28  Identities=25%  Similarity=0.526  Sum_probs=22.7

Q ss_pred             EEcCCCCCeeecCC---CCeeEcCCCCCcEE
Q 035461           10 YICGDCGMENTLKP---GDVIQCRECGYRIL   37 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~---~~~irC~~CG~RIl   37 (51)
                      .+|..||+...+..   ...-.|..||..++
T Consensus         2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~   32 (36)
T PF05191_consen    2 RICPKCGRIYHIEFNPPKVEGVCDNCGGELV   32 (36)
T ss_dssp             EEETTTTEEEETTTB--SSTTBCTTTTEBEB
T ss_pred             cCcCCCCCccccccCCCCCCCccCCCCCeeE
Confidence            58999999999874   35689999999553

7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....

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

Probab=92.03  E-value=0.16  Score=26.83  Aligned_cols=27  Identities=33%  Similarity=0.676  Sum_probs=19.4

Q ss_pred             EEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPG----------------DVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R   35 (51)
                      .|+|..||...+...+                +.-+||.||..
T Consensus         1 ky~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~   43 (47)
T PF00301_consen    1 KYQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP   43 (47)
T ss_dssp             EEEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred             CcCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence            5999999988886543                35699999863

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

>smart00731 SprT SprT homologues

Probab=91.97  E-value=0.24  Score=30.31  Aligned_cols=32  Identities=22%  Similarity=0.622  Sum_probs=24.5

Q ss_pred             ceEEEcCCCCCeeecC--C-C-CeeEcCCCCCcEEE
Q 035461            7 PVSYICGDCGMENTLK--P-G-DVIQCRECGYRILY   38 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~--~-~-~~irC~~CG~RIly   38 (51)
                      ...|.|..||....-.  . + ...+|..||.++..
T Consensus       110 ~~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l~~  145 (146)
T smart00731      110 KYPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKLIL  145 (146)
T ss_pred             eEEEECCCCCCCCceEccccCcceEEcCCCCCEEEe
Confidence            5799999999876422  1 2 55999999999875

Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.

>PRK04351 hypothetical protein; Provisional

Probab=91.94  E-value=0.37  Score=30.42  Aligned_cols=34  Identities=21%  Similarity=0.463  Sum_probs=25.7

Q ss_pred             CceEEEcCCCCCeeecC---CCCeeEcCCCCCcEEEE
Q 035461            6 EPVSYICGDCGMENTLK---PGDVIQCRECGYRILYK   39 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~---~~~~irC~~CG~RIlyK   39 (51)
                      ....|.|.+||...--.   ....-+|..||.++..+
T Consensus       109 ~~y~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L~~~  145 (149)
T PRK04351        109 KNYLYECQSCGQQYLRKRRINTKRYRCGKCRGKLKLI  145 (149)
T ss_pred             ceEEEECCCCCCEeeeeeecCCCcEEeCCCCcEeeec
Confidence            34889999999866432   12558999999998876

>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional

Probab=91.91  E-value=0.069  Score=28.75  Aligned_cols=27  Identities=37%  Similarity=0.906  Sum_probs=21.7

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      ...+|-.|++.+...+   .+|..|||.-|
T Consensus        13 ~k~ICrkC~ARnp~~A---~~CRKCg~~~L   39 (48)
T PRK04136         13 NKKICMRCNARNPWRA---TKCRKCGYKNL   39 (48)
T ss_pred             cccchhcccCCCCccc---cccccCCCCCc
Confidence            4579999999987664   88999999643

>TIGR00416 sms DNA repair protein RadA

Probab=91.86  E-value=0.14  Score=36.93  Aligned_cols=31  Identities=16%  Similarity=0.434  Sum_probs=23.6

Q ss_pred             ceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461            7 PVSYICGDCGMENTLKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~   40 (51)
                      ...|.|.+||.+..-   -.-+||.||.+==+++
T Consensus         5 ~~~y~C~~Cg~~~~~---~~g~Cp~C~~w~t~~~   35 (454)
T TIGR00416         5 KSKFVCQHCGADSPK---WQGKCPACHAWNTITE   35 (454)
T ss_pred             CCeEECCcCCCCCcc---ccEECcCCCCccccch
Confidence            357999999998533   3479999998766555

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

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

Probab=91.85  E-value=0.2  Score=33.72  Aligned_cols=31  Identities=35%  Similarity=0.861  Sum_probs=21.0

Q ss_pred             CCceEEEcCCCCCeee----cCC-C--CeeEcCCCCCc
Q 035461            5 PEPVSYICGDCGMENT----LKP-G--DVIQCRECGYR   35 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~----~~~-~--~~irC~~CG~R   35 (51)
                      .+...+.|..||.+-.    ++. +  ..+||.+||+=
T Consensus         2 ~~~iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V   39 (201)
T COG1326           2 TEEIYIECPSCGSEEVSHEVIKERGREPLVRCEECGTV   39 (201)
T ss_pred             cceEEEECCCCCcchhhHHHHHhcCCceEEEccCCCcE
Confidence            3567899999992221    122 2  47999999963

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=91.68  E-value=0.1  Score=42.69  Aligned_cols=29  Identities=28%  Similarity=0.779  Sum_probs=18.0

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      .|.|.+||.++.........||+||....
T Consensus       692 vy~CPsCGaev~~des~a~~CP~CGtplv  720 (1337)
T PRK14714        692 VYVCPDCGAEVPPDESGRVECPRCDVELT  720 (1337)
T ss_pred             ceeCccCCCccCCCccccccCCCCCCccc
Confidence            45677777766554333667777776554

>PRK11823 DNA repair protein RadA; Provisional

Probab=91.63  E-value=0.15  Score=36.48  Aligned_cols=32  Identities=28%  Similarity=0.650  Sum_probs=24.8

Q ss_pred             ceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEe
Q 035461            7 PVSYICGDCGMENTLKPGDVIQCRECGYRILYKKR   41 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R   41 (51)
                      ...|+|.+||.+..-   -.-+||.||.+==+++.
T Consensus         5 ~~~y~C~~Cg~~~~~---~~g~Cp~C~~w~t~~e~   36 (446)
T PRK11823          5 KTAYVCQECGAESPK---WLGRCPECGAWNTLVEE   36 (446)
T ss_pred             CCeEECCcCCCCCcc---cCeeCcCCCCccceeee
Confidence            467999999998643   23799999988777663

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

Probab=91.49  E-value=0.44  Score=27.18  Aligned_cols=31  Identities=29%  Similarity=0.650  Sum_probs=24.5

Q ss_pred             eEEEcCCCCCeeecC--CCCeeEcCCCCCcEEE
Q 035461            8 VSYICGDCGMENTLK--PGDVIQCRECGYRILY   38 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RIly   38 (51)
                      +.-+|.+||.+.-+-  +...++|..||--+..
T Consensus        18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l~~   50 (67)
T COG2051          18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTLAE   50 (67)
T ss_pred             EEEECCCCCCEEEEeccCceEEEecccccEEEe
Confidence            667899999987764  5578999999976553

>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=91.42  E-value=0.24  Score=25.29  Aligned_cols=22  Identities=27%  Similarity=0.552  Sum_probs=14.5

Q ss_pred             cCCCCeeEcCCCCCcEEEEEec
Q 035461           21 LKPGDVIQCRECGYRILYKKRT   42 (51)
Q Consensus        21 ~~~~~~irC~~CG~RIlyK~R~   42 (51)
                      +...+++.||.||+.-.|..++
T Consensus        13 ~RW~~g~~CP~Cg~~~~~~~~~   34 (46)
T PF12760_consen   13 IRWPDGFVCPHCGSTKHYRLKT   34 (46)
T ss_pred             hcCCCCCCCCCCCCeeeEEeCC
Confidence            3445566788888776666665

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

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=91.23  E-value=0.36  Score=26.84  Aligned_cols=29  Identities=31%  Similarity=0.767  Sum_probs=24.1

Q ss_pred             eEEEcCCCCCeeecC--CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK--PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RI   36 (51)
                      +.=+|.+|+.+.-+-  +...+.|..||.-+
T Consensus        10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L   40 (59)
T PRK00415         10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTL   40 (59)
T ss_pred             EEEECCCCCCeEEEEecCCcEEECcccCCCc
Confidence            777999999998764  56789999999754

>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]

Probab=91.22  E-value=0.044  Score=39.73  Aligned_cols=26  Identities=27%  Similarity=0.638  Sum_probs=21.1

Q ss_pred             EcCCCCCeeecCCC--CeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPG--DVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~--~~irC~~CG~RI   36 (51)
                      -|.+|.+.++++..  ...|||.||.+|
T Consensus       248 AC~rC~t~y~le~A~~~~wrCpkCGg~i  275 (403)
T COG1379         248 ACSRCYTRYSLEEAKSLRWRCPKCGGKI  275 (403)
T ss_pred             HHHHhhhccCcchhhhhcccCcccccch
Confidence            49999999998853  448999999954

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=90.99  E-value=0.36  Score=30.76  Aligned_cols=30  Identities=20%  Similarity=0.496  Sum_probs=24.4

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      +.=+|..||..........+.||+||.+-.
T Consensus       148 v~a~~~~~g~~~~~~~~~~~~c~~~~~~e~  177 (189)
T PRK09521        148 IYAMCSRCRTPLVKKGENELKCPNCGNIET  177 (189)
T ss_pred             EEEEccccCCceEECCCCEEECCCCCCEEe
Confidence            445699999999776668899999997654

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

Probab=90.97  E-value=0.23  Score=24.75  Aligned_cols=25  Identities=24%  Similarity=0.561  Sum_probs=20.0

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|+.||..+-........|..||+-
T Consensus        10 ~C~~C~~~~~~~~dG~~yC~~cG~~   34 (36)
T PF11781_consen   10 PCPVCGSRWFYSDDGFYYCDRCGHQ   34 (36)
T ss_pred             cCCCCCCeEeEccCCEEEhhhCceE
Confidence            4999999966666677889999874

>COG5216 Uncharacterized conserved protein [Function unknown]

Probab=90.64  E-value=0.36  Score=27.41  Aligned_cols=31  Identities=26%  Similarity=0.664  Sum_probs=23.8

Q ss_pred             CCCCceEEEcCCCCCeeecCC-----C-CeeEcCCCCC
Q 035461            3 PQPEPVSYICGDCGMENTLKP-----G-DVIQCRECGY   34 (51)
Q Consensus         3 ~~~~~~~Y~C~~Cg~~~~~~~-----~-~~irC~~CG~   34 (51)
                      +..+...|-|. ||..|++..     + ...|||.|.-
T Consensus        16 ~e~~~ftyPCP-CGDRFeIsLeDl~~GE~VArCPSCSL   52 (67)
T COG5216          16 REEKTFTYPCP-CGDRFEISLEDLRNGEVVARCPSCSL   52 (67)
T ss_pred             CCCceEEecCC-CCCEeEEEHHHhhCCceEEEcCCceE
Confidence            44566889998 999999862     2 5689999973

>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain

Probab=90.34  E-value=0.46  Score=24.20  Aligned_cols=20  Identities=25%  Similarity=0.796  Sum_probs=15.8

Q ss_pred             CeeEcCCCCCcEEEEEecCc
Q 035461           25 DVIQCRECGYRILYKKRTRR   44 (51)
Q Consensus        25 ~~irC~~CG~RIlyK~R~~~   44 (51)
                      +.|+|.+||++...+.++.+
T Consensus         4 g~l~C~~CG~~m~~~~~~~~   23 (58)
T PF13408_consen    4 GLLRCGHCGSKMTRRKRKGK   23 (58)
T ss_pred             CcEEcccCCcEeEEEECCCC
Confidence            56899999999888777643

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

Probab=90.24  E-value=0.43  Score=25.66  Aligned_cols=31  Identities=26%  Similarity=0.476  Sum_probs=22.5

Q ss_pred             CCceEEEcCCCCCeeecC-----CCCeeEcCCCCCc
Q 035461            5 PEPVSYICGDCGMENTLK-----PGDVIQCRECGYR   35 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~-----~~~~irC~~CG~R   35 (51)
                      .....-||.+|...+.+-     ..-.-+|++||+-
T Consensus        18 ~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~   53 (54)
T PF10058_consen   18 SNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGAL   53 (54)
T ss_pred             cCceeEECcccchhhcccccccCCceEEEcCCCCCc
Confidence            455778999998777654     1235899999973

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=90.21  E-value=0.15  Score=35.93  Aligned_cols=29  Identities=28%  Similarity=0.665  Sum_probs=22.7

Q ss_pred             EEcCCCCCeeecCCCCeeEcCCCCCcEEEEEe
Q 035461           10 YICGDCGMENTLKPGDVIQCRECGYRILYKKR   41 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R   41 (51)
                      |.|.+||.+..-   -.-+||.||.+==+++.
T Consensus         1 ~~c~~cg~~~~~---~~g~cp~c~~w~~~~e~   29 (372)
T cd01121           1 YVCSECGYVSPK---WLGKCPECGEWNTLVEE   29 (372)
T ss_pred             CCCCCCCCCCCC---ccEECcCCCCceeeeeh
Confidence            899999998532   34799999988777764

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

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

Probab=90.12  E-value=0.19  Score=24.90  Aligned_cols=23  Identities=26%  Similarity=0.820  Sum_probs=13.4

Q ss_pred             cCCCCCeeecC--C---CCeeEcCCCCC
Q 035461           12 CGDCGMENTLK--P---GDVIQCRECGY   34 (51)
Q Consensus        12 C~~Cg~~~~~~--~---~~~irC~~CG~   34 (51)
                      |..||..++..  .   ..-..|+.||+
T Consensus         3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~   30 (34)
T PF14803_consen    3 CPQCGGPLERRIPEGDDRERLVCPACGF   30 (34)
T ss_dssp             -TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred             cccccChhhhhcCCCCCccceECCCCCC
Confidence            88999998874  2   23488999985

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

Probab=89.82  E-value=0.7  Score=28.67  Aligned_cols=30  Identities=23%  Similarity=0.396  Sum_probs=22.9

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCc-EEEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYR-ILYKK   40 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R-IlyK~   40 (51)
                      +-=+|.+||+.+-...   ..||+||.+ .|...
T Consensus        28 ~g~kC~~CG~v~~PPr---~~Cp~C~~~~~~E~v   58 (140)
T COG1545          28 LGTKCKKCGRVYFPPR---AYCPKCGSETELEWV   58 (140)
T ss_pred             EEEEcCCCCeEEcCCc---ccCCCCCCCCceEEE
Confidence            5568999999986654   789999999 44433

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=89.82  E-value=0.35  Score=27.68  Aligned_cols=25  Identities=24%  Similarity=0.671  Sum_probs=14.6

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      ..|.|..|+.++...    ..||+||..+
T Consensus        16 ~~~~C~~C~~~~~~~----a~CPdC~~~L   40 (70)
T PF07191_consen   16 GHYHCEACQKDYKKE----AFCPDCGQPL   40 (70)
T ss_dssp             TEEEETTT--EEEEE----EE-TTT-SB-
T ss_pred             CEEECccccccceec----ccCCCcccHH
Confidence            468888888887765    5788887653

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

>PHA02942 putative transposase; Provisional

Probab=89.73  E-value=0.31  Score=34.50  Aligned_cols=25  Identities=28%  Similarity=0.751  Sum_probs=17.0

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|..||............|++||+.
T Consensus       327 ~Cs~CG~~~~~l~~r~f~C~~CG~~  351 (383)
T PHA02942        327 SCPKCGHKMVEIAHRYFHCPSCGYE  351 (383)
T ss_pred             cCCCCCCccCcCCCCEEECCCCCCE
Confidence            5888887654223456788888874

>TIGR03844 cysteate_syn cysteate synthase

Probab=89.73  E-value=0.26  Score=34.92  Aligned_cols=26  Identities=15%  Similarity=0.248  Sum_probs=20.4

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      .++|.+||+++. .. ...+||.||..+
T Consensus         2 ~l~C~~Cg~~~~-~~-~~~~C~~c~g~l   27 (398)
T TIGR03844         2 TLRCPGCGEVLP-DH-YTLSCPLDCGLL   27 (398)
T ss_pred             EEEeCCCCCccC-Cc-cccCCCCCCCce
Confidence            589999999986 33 468999998543

Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.

>PF14311 DUF4379: Domain of unknown function (DUF4379)

Probab=89.63  E-value=0.54  Score=24.57  Aligned_cols=28  Identities=25%  Similarity=0.452  Sum_probs=21.0

Q ss_pred             CCceEEEcCCCCCeeecCC----CCeeEcCCC
Q 035461            5 PEPVSYICGDCGMENTLKP----GDVIQCREC   32 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~----~~~irC~~C   32 (51)
                      ...+-.+|..||.+.....    ...-.||+|
T Consensus        24 ~~~v~W~C~~Cgh~w~~~v~~R~~~~~~CP~C   55 (55)
T PF14311_consen   24 NKKVWWKCPKCGHEWKASVNDRTRRGKGCPYC   55 (55)
T ss_pred             CCEEEEECCCCCCeeEccHhhhccCCCCCCCC
Confidence            3457789999999988652    356788887

>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.13  E-value=0.45  Score=30.50  Aligned_cols=30  Identities=30%  Similarity=0.668  Sum_probs=17.8

Q ss_pred             CCceEEEcCCCCCeeecCC----------CCeeEcCCCCC
Q 035461            5 PEPVSYICGDCGMENTLKP----------GDVIQCRECGY   34 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~----------~~~irC~~CG~   34 (51)
                      -+|....|..||.++.+..          ...+.||+|+.
T Consensus        14 c~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~   53 (188)
T PF08996_consen   14 CEPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST   53 (188)
T ss_dssp             ---EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred             CCceEeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence            3679999999999998741          24799999998

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. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.

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

Probab=89.01  E-value=0.38  Score=23.69  Aligned_cols=24  Identities=38%  Similarity=0.904  Sum_probs=15.6

Q ss_pred             cCCCCCeeecCCC--CeeEcCCCCCc
Q 035461           12 CGDCGMENTLKPG--DVIQCRECGYR   35 (51)
Q Consensus        12 C~~Cg~~~~~~~~--~~irC~~CG~R   35 (51)
                      |.+||.-...+.+  ..+.|+.|||-
T Consensus         4 Cp~C~nlL~p~~~~~~~~~C~~C~Y~   29 (35)
T PF02150_consen    4 CPECGNLLYPKEDKEKRVACRTCGYE   29 (35)
T ss_dssp             ETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred             CCCCCccceEcCCCccCcCCCCCCCc
Confidence            7788888776522  22379999874

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

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

Probab=88.63  E-value=0.37  Score=30.97  Aligned_cols=22  Identities=32%  Similarity=0.937  Sum_probs=15.5

Q ss_pred             EEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           10 YICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      =.|..||.    .......||.||+.
T Consensus       310 ~~C~~cg~----~~~r~~~C~~cg~~  331 (364)
T COG0675         310 KTCPCCGH----LSGRLFKCPRCGFV  331 (364)
T ss_pred             ccccccCC----ccceeEECCCCCCe
Confidence            35888888    33466888888873

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=88.26  E-value=0.21  Score=26.90  Aligned_cols=14  Identities=43%  Similarity=0.605  Sum_probs=10.7

Q ss_pred             eEcCCCCCcEEEEE
Q 035461           27 IQCRECGYRILYKK   40 (51)
Q Consensus        27 irC~~CG~RIlyK~   40 (51)
                      |.||+||..|-.-.
T Consensus         1 i~CPyCge~~~~~i   14 (52)
T PF14255_consen    1 IQCPYCGEPIEILI   14 (52)
T ss_pred             CCCCCCCCeeEEEE
Confidence            57999999886543

>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A

Probab=88.02  E-value=0.51  Score=26.13  Aligned_cols=27  Identities=26%  Similarity=0.545  Sum_probs=15.5

Q ss_pred             eEEEcCCCCCeeecCC-CCeeEcCCCCC
Q 035461            8 VSYICGDCGMENTLKP-GDVIQCRECGY   34 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~-~~~irC~~CG~   34 (51)
                      +.-.|.+|++..+... --+.+|.+||+
T Consensus        29 v~IlCNDC~~~s~v~fH~lg~KC~~C~S   56 (61)
T PF14599_consen   29 VWILCNDCNAKSEVPFHFLGHKCSHCGS   56 (61)
T ss_dssp             EEEEESSS--EEEEE--TT----TTTS-
T ss_pred             EEEECCCCCCccceeeeHhhhcCCCCCC
Confidence            6667999999888764 35799999996

>TIGR01053 LSD1 zinc finger domain, LSD1 subclass

Probab=88.00  E-value=0.74  Score=22.37  Aligned_cols=24  Identities=25%  Similarity=0.704  Sum_probs=19.6

Q ss_pred             EcCCCCCeeecCCC-CeeEcCCCCC
Q 035461           11 ICGDCGMENTLKPG-DVIQCRECGY   34 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~-~~irC~~CG~   34 (51)
                      .|+.|+.......+ ..+||.-|..
T Consensus         3 ~C~~C~t~L~yP~gA~~vrCs~C~~   27 (31)
T TIGR01053         3 VCGGCRTLLMYPRGASSVRCALCQT   27 (31)
T ss_pred             CcCCCCcEeecCCCCCeEECCCCCe
Confidence            58999999988765 6699999963

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

>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases

Probab=87.97  E-value=0.58  Score=29.14  Aligned_cols=29  Identities=24%  Similarity=0.607  Sum_probs=22.1

Q ss_pred             eEEEcCCCCCeeecC-------CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK-------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~RI   36 (51)
                      ....|..|+.++...       ....-+||.||..+
T Consensus       104 ~~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~l  139 (178)
T PF02146_consen  104 FRLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGLL  139 (178)
T ss_dssp             EEEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCBE
T ss_pred             ceeeecCCCccccchhhcccccccccccccccCccC
Confidence            457899999988754       24556999999953

This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....

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

Probab=87.97  E-value=0.61  Score=26.64  Aligned_cols=33  Identities=18%  Similarity=0.281  Sum_probs=15.7

Q ss_pred             CceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461            6 EPVSYICGDCGMENTLKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~   40 (51)
                      ....++|..|-+...  ..+-.-||.||+.-|.|.
T Consensus         6 k~~vlrC~aCf~~t~--~~~k~FCp~CGn~TL~rv   38 (73)
T PF08772_consen    6 KTWVLRCHACFKITK--DMTKQFCPKCGNATLKRV   38 (73)
T ss_dssp             --EEEE-SSS--EES---SS--S-SSS--S--EEE
T ss_pred             heeeEEccccccCcC--CCCceeCcccCCCcceEE
Confidence            446789999987764  336689999999988775

; PDB: 2CON_A.

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

Probab=87.87  E-value=0.65  Score=23.87  Aligned_cols=23  Identities=35%  Similarity=0.755  Sum_probs=15.1

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCC
Q 035461           11 ICGDCGMENTLKPGDVIQCRECG   33 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG   33 (51)
                      .|..||.+.--..+..+.|+.|+
T Consensus        19 ~Cp~C~~PL~~~k~g~~~Cv~C~   41 (41)
T PF06677_consen   19 HCPDCGTPLMRDKDGKIYCVSCG   41 (41)
T ss_pred             ccCCCCCeeEEecCCCEECCCCC
Confidence            47777776655445567777775

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

>PRK08351 DNA-directed RNA polymerase subunit E''; Validated

Probab=87.86  E-value=0.25  Score=27.57  Aligned_cols=22  Identities=36%  Similarity=0.747  Sum_probs=16.8

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      -|-+|+..++-+     +||+||+.-|
T Consensus         5 AC~~C~~i~~~~-----~CP~Cgs~~~   26 (61)
T PRK08351          5 ACRHCHYITTED-----RCPVCGSRDL   26 (61)
T ss_pred             hhhhCCcccCCC-----cCCCCcCCcc
Confidence            588999988422     6999998653

>TIGR00155 pqiA_fam integral membrane protein, PqiA family

Probab=87.76  E-value=0.47  Score=33.89  Aligned_cols=26  Identities=31%  Similarity=0.839  Sum_probs=22.0

Q ss_pred             EcCCCCCeeecC---CCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLK---PGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~---~~~~irC~~CG~RI   36 (51)
                      .|-+|+..++..   .++..+||.||+.+
T Consensus        15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L   43 (403)
T TIGR00155        15 LCSQCDMLVALPRIESGQKAACPRCGTTL   43 (403)
T ss_pred             eCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence            599999888754   57789999999986

This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.

>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated

Probab=87.61  E-value=0.26  Score=27.79  Aligned_cols=21  Identities=19%  Similarity=0.338  Sum_probs=16.0

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      -|-+|+..++-     -.||.||+.-
T Consensus         7 AC~~C~~i~~~-----~~Cp~Cgs~~   27 (64)
T PRK06393          7 ACKKCKRLTPE-----KTCPVHGDEK   27 (64)
T ss_pred             hHhhCCcccCC-----CcCCCCCCCc
Confidence            48899988842     2899999853

>PRK15103 paraquat-inducible membrane protein A; Provisional

Probab=87.53  E-value=0.54  Score=33.79  Aligned_cols=27  Identities=30%  Similarity=0.757  Sum_probs=22.6

Q ss_pred             EEcCCCCCeeecC---CCCeeEcCCCCCcE
Q 035461           10 YICGDCGMENTLK---PGDVIQCRECGYRI   36 (51)
Q Consensus        10 Y~C~~Cg~~~~~~---~~~~irC~~CG~RI   36 (51)
                      -.|-+||..++..   .+..-+||.||+.+
T Consensus        11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L   40 (419)
T PRK15103         11 ILCPQCDMLVALPRLEHGQKAACPRCGTTL   40 (419)
T ss_pred             ccCCCCCceeecCCCCCCCeeECCCCCCCC
Confidence            4599999998765   46778999999987

>PRK08197 threonine synthase; Validated

Probab=87.03  E-value=0.72  Score=32.20  Aligned_cols=29  Identities=24%  Similarity=0.572  Sum_probs=22.2

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      .|+|.+||++..++.. ..+| .||.....-
T Consensus         7 ~~~C~~Cg~~~~~~~~-~~~C-~cg~~l~~~   35 (394)
T PRK08197          7 HLECSKCGETYDADQV-HNLC-KCGKPLLVR   35 (394)
T ss_pred             EEEECCCCCCCCCCCc-ceec-CCCCeeEEE
Confidence            5999999999876643 4789 899875543

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

Probab=86.76  E-value=0.3  Score=31.16  Aligned_cols=11  Identities=45%  Similarity=1.259  Sum_probs=8.1

Q ss_pred             CeeEcCCCCCc
Q 035461           25 DVIQCRECGYR   35 (51)
Q Consensus        25 ~~irC~~CG~R   35 (51)
                      ....|++||||
T Consensus        28 ~sf~C~~CGyk   38 (160)
T smart00709       28 MSFECEHCGYR   38 (160)
T ss_pred             EEEECCCCCCc
Confidence            35678888876

Also present in archaeal proteins.

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=86.75  E-value=0.44  Score=30.39  Aligned_cols=29  Identities=31%  Similarity=0.729  Sum_probs=18.0

Q ss_pred             EEcCCCCCee-e---cC---CCCee----EcCCCCCcEEE
Q 035461           10 YICGDCGMEN-T---LK---PGDVI----QCRECGYRILY   38 (51)
Q Consensus        10 Y~C~~Cg~~~-~---~~---~~~~i----rC~~CG~RIly   38 (51)
                      ++|..||.+. .   ..   .+..|    +|++||++.--
T Consensus         1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~   40 (154)
T PRK00464          1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT   40 (154)
T ss_pred             CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence            4799999654 2   12   22234    49999988543

>smart00647 IBR In Between Ring fingers

Probab=86.73  E-value=1.1  Score=23.05  Aligned_cols=28  Identities=21%  Similarity=0.787  Sum_probs=21.6

Q ss_pred             cC--CCCCeeecC---CCCeeEcCCCCCcEEEE
Q 035461           12 CG--DCGMENTLK---PGDVIQCRECGYRILYK   39 (51)
Q Consensus        12 C~--~Cg~~~~~~---~~~~irC~~CG~RIlyK   39 (51)
                      |.  .|+..+...   ....+.|+.||+..-++
T Consensus        21 CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~   53 (64)
T smart00647       21 CPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFR   53 (64)
T ss_pred             CCCCCCcceEEecCCCCCCeeECCCCCCeECCC
Confidence            77  898888876   34679999999876543

the domains occurs between pairs og RING fingers

>PF15616 TerY-C: TerY-C metal binding domain

Probab=86.69  E-value=1  Score=28.28  Aligned_cols=29  Identities=17%  Similarity=0.353  Sum_probs=24.0

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      .+-.||+.+=+...+.+.||-||..+.|-
T Consensus        90 a~C~CGkl~Ci~g~~~~~CPwCg~~g~~~  118 (131)
T PF15616_consen   90 AVCGCGKLFCIDGEGEVTCPWCGNEGSFG  118 (131)
T ss_pred             EEecCCCEEEeCCCCCEECCCCCCeeeec
Confidence            33379999999888899999999988764

>TIGR00375 conserved hypothetical protein TIGR00375

Probab=86.57  E-value=0.24  Score=35.42  Aligned_cols=25  Identities=32%  Similarity=0.757  Sum_probs=19.4

Q ss_pred             EcCCCCCeeecCCC--CeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPG--DVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~--~~irC~~CG~RI   36 (51)
                      -|.+|+..++....  ...+|| ||++|
T Consensus       242 ~c~~C~~~~~~~~~~~~~~~Cp-CG~~i  268 (374)
T TIGR00375       242 ACEACGEPAVSEDAETACANCP-CGGRI  268 (374)
T ss_pred             hhcccCCcCCchhhhhcCCCCC-CCCcc
Confidence            58999998887631  358899 99994

The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.

>PRK08329 threonine synthase; Validated

Probab=86.56  E-value=0.58  Score=32.19  Aligned_cols=27  Identities=30%  Similarity=0.701  Sum_probs=21.0

Q ss_pred             EEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461           10 YICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      ++|.+||++....  ...+| .||..+...
T Consensus         2 l~C~~Cg~~~~~~--~~~~C-~c~~~l~~~   28 (347)
T PRK08329          2 LRCTKCGRTYEEK--FKLRC-DCGGTLLVE   28 (347)
T ss_pred             cCcCCCCCCcCCC--Cceec-CCCCcEEEE
Confidence            7899999999743  33899 799876554

>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]

Probab=86.51  E-value=0.064  Score=29.11  Aligned_cols=27  Identities=37%  Similarity=0.865  Sum_probs=21.7

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRILY   38 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIly   38 (51)
                      ..||-+|++.+.+.   +.+|..|||+-|-
T Consensus        14 kkIC~rC~Arnp~~---A~kCRkC~~k~LR   40 (50)
T COG1552          14 KKICRRCYARNPPR---ATKCRKCGYKNLR   40 (50)
T ss_pred             HHHHHHhcCCCCcc---hhHHhhccCCCcc
Confidence            46899999987654   4899999998774

>PRK04860 hypothetical protein; Provisional

Probab=86.50  E-value=1.3  Score=28.35  Aligned_cols=33  Identities=27%  Similarity=0.682  Sum_probs=23.8

Q ss_pred             ceEEEcCCCCCeeecC-------C-CCeeEcCCCCCcEEEEE
Q 035461            7 PVSYICGDCGMENTLK-------P-GDVIQCRECGYRILYKK   40 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~-------~-~~~irC~~CG~RIlyK~   40 (51)
                      ...|.|. |+......       . ....+|..|+..+.++.
T Consensus       117 ~~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~  157 (160)
T PRK04860        117 TFPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFKG  157 (160)
T ss_pred             EEEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence            4789998 98733211       2 24599999999998864

>PF14205 Cys_rich_KTR: Cysteine-rich KTR

Probab=86.50  E-value=0.73  Score=25.41  Aligned_cols=19  Identities=32%  Similarity=0.618  Sum_probs=11.6

Q ss_pred             eEcCCCCCcEEEEEecCce
Q 035461           27 IQCRECGYRILYKKRTRRI   45 (51)
Q Consensus        27 irC~~CG~RIlyK~R~~~~   45 (51)
                      +.||-||++-..|.|....
T Consensus         5 i~CP~CgnKTR~kir~DT~   23 (55)
T PF14205_consen    5 ILCPICGNKTRLKIREDTV   23 (55)
T ss_pred             EECCCCCCccceeeecCce
Confidence            5666666666666665543

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

Probab=86.44  E-value=0.59  Score=30.62  Aligned_cols=29  Identities=34%  Similarity=0.661  Sum_probs=21.9

Q ss_pred             EEEcCCCCCeeecC--------------------------CCCeeEcCCCCCcEE
Q 035461            9 SYICGDCGMENTLK--------------------------PGDVIQCRECGYRIL   37 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~--------------------------~~~~irC~~CG~RIl   37 (51)
                      .+.|.-|+.+|..+                          ..+.+-||+||+--+
T Consensus         5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~   59 (214)
T PF09986_consen    5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAF   59 (214)
T ss_pred             ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccc
Confidence            57899999988752                          115789999998655

>TIGR00354 polC DNA polymerase, archaeal type II, large subunit

Probab=86.38  E-value=0.54  Score=37.94  Aligned_cols=31  Identities=23%  Similarity=0.489  Sum_probs=24.2

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      -.++|..||+...--+. .-+||.||++|+--
T Consensus      1011 Q~fRC~kC~~kYRR~PL-~G~C~kCGg~lilT 1041 (1095)
T TIGR00354      1011 QEVRCTKCNTKYRRIPL-VGKCLKCGNNLTLT 1041 (1095)
T ss_pred             cceeecccCCccccCCC-CCcccccCCeEEEE
Confidence            46899999999865443 35899999998754

This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.

>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=86.19  E-value=0.49  Score=29.77  Aligned_cols=28  Identities=18%  Similarity=-0.012  Sum_probs=23.8

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .+-+|.+||+.|---..++|.||+||..
T Consensus         8 tKridPetg~KFYDLNrdPiVsPytG~s   35 (129)
T COG4530           8 TKRIDPETGKKFYDLNRDPIVSPYTGKS   35 (129)
T ss_pred             ccccCccccchhhccCCCccccCccccc
Confidence            5668999999997667799999999964

>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]

Probab=86.19  E-value=0.54  Score=31.95  Aligned_cols=28  Identities=25%  Similarity=0.565  Sum_probs=20.8

Q ss_pred             eEEEcCCCCCeeecC-------CCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLK-------PGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~R   35 (51)
                      -...|..||..+...       ....-+||.||..
T Consensus       121 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~  155 (250)
T COG0846         121 KRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP  155 (250)
T ss_pred             eeeEeCCCcCccchhhhhhhcccCCCCcCccCCCc
Confidence            457899999887632       2245789999996

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=85.98  E-value=0.58  Score=38.49  Aligned_cols=31  Identities=32%  Similarity=0.709  Sum_probs=24.2

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      -.++|..||+...--+. .-+||.||++|+--
T Consensus      1252 Q~~RC~kC~~kyRR~PL-~G~C~kCGg~iilT 1282 (1337)
T PRK14714       1252 QEFRCLKCGTKYRRMPL-AGKCRKCGGRIILT 1282 (1337)
T ss_pred             cceeecccCcccccCCC-CCcccccCCeEEEE
Confidence            46899999999865443 25899999999753

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

Probab=85.98  E-value=1.2  Score=20.87  Aligned_cols=23  Identities=26%  Similarity=0.664  Sum_probs=18.5

Q ss_pred             cCCCCCeeecCCC-CeeEcCCCCC
Q 035461           12 CGDCGMENTLKPG-DVIQCRECGY   34 (51)
Q Consensus        12 C~~Cg~~~~~~~~-~~irC~~CG~   34 (51)
                      |+.|...+....+ ..+||.-|..
T Consensus         1 C~~Cr~~L~yp~GA~sVrCa~C~~   24 (25)
T PF06943_consen    1 CGGCRTLLMYPRGAPSVRCACCHT   24 (25)
T ss_pred             CCCCCceEEcCCCCCCeECCccCc
Confidence            7889998887765 5699998864

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].

>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger

Probab=85.80  E-value=1.2  Score=22.60  Aligned_cols=27  Identities=22%  Similarity=0.295  Sum_probs=19.4

Q ss_pred             EEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           10 YICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      -.|..|+..+......+++|..|+..+
T Consensus        12 ~~C~~C~~~i~g~~~~g~~C~~C~~~~   38 (53)
T PF00130_consen   12 TYCDVCGKFIWGLGKQGYRCSWCGLVC   38 (53)
T ss_dssp             EB-TTSSSBECSSSSCEEEETTTT-EE
T ss_pred             CCCcccCcccCCCCCCeEEECCCCChH
Confidence            368899998855566889999998754

Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....

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

Probab=85.76  E-value=0.32  Score=30.89  Aligned_cols=26  Identities=35%  Similarity=0.975  Sum_probs=14.6

Q ss_pred             EcCCCCCeeecC------C------CCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLK------P------GDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~------~------~~~irC~~CG~RI   36 (51)
                      .|..||......      +      -....|++||||-
T Consensus         3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~   40 (161)
T PF03367_consen    3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKN   40 (161)
T ss_dssp             E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EE
T ss_pred             cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEe
Confidence            688898875432      1      1467999999974

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

>PRK00241 nudC NADH pyrophosphatase; Reviewed

Probab=85.57  E-value=0.84  Score=30.66  Aligned_cols=27  Identities=26%  Similarity=0.566  Sum_probs=20.3

Q ss_pred             EcCCCCCeeecC-CCCeeEcCCCCCcEE
Q 035461           11 ICGDCGMENTLK-PGDVIQCRECGYRIL   37 (51)
Q Consensus        11 ~C~~Cg~~~~~~-~~~~irC~~CG~RIl   37 (51)
                      -|+.||..+... .+-...|+.||....
T Consensus       101 fC~~CG~~~~~~~~~~~~~C~~c~~~~y  128 (256)
T PRK00241        101 FCGYCGHPMHPSKTEWAMLCPHCRERYY  128 (256)
T ss_pred             cccccCCCCeecCCceeEECCCCCCEEC
Confidence            399999988765 345688999996543

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=85.44  E-value=1.2  Score=26.68  Aligned_cols=28  Identities=29%  Similarity=0.763  Sum_probs=20.2

Q ss_pred             ceEEEcCCCCCeeecC-----CCCeeEcCCCCCc
Q 035461            7 PVSYICGDCGMENTLK-----PGDVIQCRECGYR   35 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~-----~~~~irC~~CG~R   35 (51)
                      +..+.|..||. ..+.     ...-+.|+.||+.
T Consensus        19 pt~f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y   51 (99)
T PRK14892         19 PKIFECPRCGK-VSISVKIKKNIAIITCGNCGLY   51 (99)
T ss_pred             CcEeECCCCCC-eEeeeecCCCcceEECCCCCCc
Confidence            46899999993 3332     2256999999975

>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]

Probab=85.28  E-value=0.87  Score=33.49  Aligned_cols=31  Identities=26%  Similarity=0.618  Sum_probs=25.4

Q ss_pred             ceEEEcCCCCCeeecC---CCCeeEcCCCCCcEE
Q 035461            7 PVSYICGDCGMENTLK---PGDVIQCRECGYRIL   37 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~---~~~~irC~~CG~RIl   37 (51)
                      .-.=.|.+|+..+++.   .+..-.||.||+.+-
T Consensus        16 ~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~   49 (418)
T COG2995          16 GHLILCPECDMLVSLPRLDSGQSAYCPRCGHTLT   49 (418)
T ss_pred             cceecCCCCCceeccccCCCCCcccCCCCCCccc
Confidence            3556899999999865   567899999999874

>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis

Probab=85.14  E-value=0.44  Score=30.99  Aligned_cols=25  Identities=36%  Similarity=0.901  Sum_probs=17.9

Q ss_pred             EEcCCCCCeeecC-----CC--CeeEcCCCCC
Q 035461           10 YICGDCGMENTLK-----PG--DVIQCRECGY   34 (51)
Q Consensus        10 Y~C~~Cg~~~~~~-----~~--~~irC~~CG~   34 (51)
                      ++|-+||.+++--     ++  .--+|++||.
T Consensus         1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~   32 (208)
T PF04161_consen    1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGK   32 (208)
T ss_pred             CEeccCCCcchhhhhccCCCcEEEeeccccCC
Confidence            5899999997631     11  3378999994

Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=85.02  E-value=0.62  Score=34.56  Aligned_cols=25  Identities=28%  Similarity=0.816  Sum_probs=19.3

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      ..|.|.+||.... +  -.-+||+||.+
T Consensus         6 t~f~C~~CG~~s~-K--W~GkCp~Cg~W   30 (456)
T COG1066           6 TAFVCQECGYVSP-K--WLGKCPACGAW   30 (456)
T ss_pred             cEEEcccCCCCCc-c--ccccCCCCCCc
Confidence            7799999999853 2  33589999943

>PRK04023 DNA polymerase II large subunit; Validated

Probab=84.99  E-value=0.68  Score=37.49  Aligned_cols=31  Identities=23%  Similarity=0.620  Sum_probs=24.2

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      -.++|..||+...--+. .-+||.||++|+.-
T Consensus      1036 Q~fRC~kC~~kYRR~PL-~G~C~kCGg~lilT 1066 (1121)
T PRK04023       1036 QEFRCTKCGAKYRRPPL-SGKCPKCGGNLILT 1066 (1121)
T ss_pred             cceeecccCcccccCCC-CCcCccCCCeEEEE
Confidence            36899999999865443 35899999999753

>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=84.94  E-value=0.63  Score=25.87  Aligned_cols=26  Identities=31%  Similarity=0.691  Sum_probs=18.1

Q ss_pred             EEEcCCCCCeeecCCC---CeeEcCCCCC
Q 035461            9 SYICGDCGMENTLKPG---DVIQCRECGY   34 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~---~~irC~~CG~   34 (51)
                      .=+|+.|+.+..+...   ....||.|+.
T Consensus        41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~   69 (71)
T PF05495_consen   41 RVICGKCRTEQPIDEYSCGADYFCPICGL   69 (71)
T ss_dssp             EEEETTT--EEES-SBTT--SEEETTTTE
T ss_pred             CeECCCCCCccChhhhhcCCCccCcCcCC
Confidence            6789999999998754   3479999985

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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.

>cd01675 RNR_III Class III ribonucleotide reductase

Probab=84.93  E-value=0.46  Score=35.09  Aligned_cols=22  Identities=41%  Similarity=1.105  Sum_probs=17.6

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      +|.+||...+   +..-.||.||++
T Consensus       520 ~C~~CG~~~~---~~~~~CP~CGs~  541 (555)
T cd01675         520 ICNDCGYIGE---GEGFKCPKCGSE  541 (555)
T ss_pred             cCCCCCCCCc---CCCCCCcCCCCc
Confidence            9999998653   344789999977

Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w

>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=84.88  E-value=0.45  Score=26.11  Aligned_cols=31  Identities=26%  Similarity=0.468  Sum_probs=24.4

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      .=.|..||+.+=...+..--|+.||..++-+
T Consensus        18 ~~NCl~CGkIiC~~Eg~~~pC~fCg~~l~~~   48 (57)
T PF06221_consen   18 APNCLNCGKIICEQEGPLGPCPFCGTPLLSS   48 (57)
T ss_pred             cccccccChhhcccccCcCcCCCCCCcccCH
Confidence            5579999999877765467899999877643

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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>TIGR00310 ZPR1_znf ZPR1 zinc finger domain

Probab=84.76  E-value=0.58  Score=30.72  Aligned_cols=10  Identities=50%  Similarity=1.311  Sum_probs=7.2

Q ss_pred             eeEcCCCCCc
Q 035461           26 VIQCRECGYR   35 (51)
Q Consensus        26 ~irC~~CG~R   35 (51)
                      ...|++||||
T Consensus        30 sf~C~~CGyr   39 (192)
T TIGR00310        30 STICEHCGYR   39 (192)
T ss_pred             EEECCCCCCc
Confidence            5677777776

>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins

Probab=84.66  E-value=0.64  Score=28.86  Aligned_cols=32  Identities=22%  Similarity=0.513  Sum_probs=23.0

Q ss_pred             CCceEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461            5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      ...+..+|.+||+....-- ..-+|.+|+....
T Consensus        65 tkav~V~CP~C~K~TKmLG-r~D~CM~C~~pLT   96 (114)
T PF11023_consen   65 TKAVQVECPNCGKQTKMLG-RVDACMHCKEPLT   96 (114)
T ss_pred             ccceeeECCCCCChHhhhc-hhhccCcCCCcCc
Confidence            3457788999999976442 3349999997543

; GO: 0005887 integral to plasma membrane

>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain

Probab=84.64  E-value=1.4  Score=26.34  Aligned_cols=30  Identities=27%  Similarity=0.586  Sum_probs=22.0

Q ss_pred             CceEEEcCCCCCeeecCCC-CeeEcCCCCCc
Q 035461            6 EPVSYICGDCGMENTLKPG-DVIQCRECGYR   35 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~-~~irC~~CG~R   35 (51)
                      ....|.|.+||.+.-+-.. ..=-||.||.+
T Consensus        39 G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~   69 (111)
T PF14319_consen   39 GFHRYRCEDCGHEKIVYNSCKNRHCPSCQAK   69 (111)
T ss_pred             CcceeecCCCCceEEecCcccCcCCCCCCCh
Confidence            4588999999998866421 22379999975

>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate

Probab=84.52  E-value=1.2  Score=30.95  Aligned_cols=34  Identities=21%  Similarity=0.509  Sum_probs=25.6

Q ss_pred             CCceEEEcCCCCCeeecCC---CCeeEcCCCCCcEEE
Q 035461            5 PEPVSYICGDCGMENTLKP---GDVIQCRECGYRILY   38 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~---~~~irC~~CG~RIly   38 (51)
                      +.....+|+.|...|-...   +...|||+|....-.
T Consensus       153 p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSV  189 (256)
T PF09788_consen  153 PGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSV  189 (256)
T ss_pred             CCceeEECCCCCCcEeccCCCCCccccCCCCceeccc
Confidence            3458899999999998763   455799999855443

>PRK05638 threonine synthase; Validated

Probab=84.52  E-value=0.71  Score=32.74  Aligned_cols=27  Identities=26%  Similarity=0.416  Sum_probs=20.3

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRILY   38 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RIly   38 (51)
                      +++|.+||++....  ...+| .||..+-.
T Consensus         1 ~l~C~~Cg~~~~~~--~~~~C-~c~~~l~~   27 (442)
T PRK05638          1 KMKCPKCGREYNSY--IPPFC-ICGELLEI   27 (442)
T ss_pred             CeEeCCCCCCCCCC--Cceec-CCCCcEEE
Confidence            37899999998743  34899 89976544

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=84.51  E-value=0.76  Score=30.26  Aligned_cols=29  Identities=24%  Similarity=0.496  Sum_probs=20.8

Q ss_pred             EEcCCCCCeeecCCCCeeEcCCCCCcEEEEEe
Q 035461           10 YICGDCGMENTLKPGDVIQCRECGYRILYKKR   41 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R   41 (51)
                      |.|.+||...+.   -.-.||.||..==++.|
T Consensus       355 ~~c~~cg~~~~~---~~~~c~~c~~~~~~~~~  383 (389)
T PRK11788        355 YRCRNCGFTART---LYWHCPSCKAWETIKPI  383 (389)
T ss_pred             EECCCCCCCCcc---ceeECcCCCCccCcCCc
Confidence            899999987543   34799999975444443

>COG1656 Uncharacterized conserved protein [Function unknown]

Probab=84.39  E-value=0.41  Score=31.27  Aligned_cols=29  Identities=24%  Similarity=0.474  Sum_probs=19.9

Q ss_pred             CceEEEcCCCCCeeecCCCCe----------------eEcCCCCC
Q 035461            6 EPVSYICGDCGMENTLKPGDV----------------IQCRECGY   34 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~~~----------------irC~~CG~   34 (51)
                      ++..=+|..|+.++..-+.+.                -+||.||.
T Consensus        94 ~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgk  138 (165)
T COG1656          94 FPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGK  138 (165)
T ss_pred             ccccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcc
Confidence            344568999998887544333                45999984

>TIGR00340 zpr1_rel ZPR1-related zinc finger protein

Probab=84.36  E-value=0.66  Score=29.81  Aligned_cols=11  Identities=45%  Similarity=1.259  Sum_probs=8.2

Q ss_pred             CeeEcCCCCCc
Q 035461           25 DVIQCRECGYR   35 (51)
Q Consensus        25 ~~irC~~CG~R   35 (51)
                      ....|++||||
T Consensus        27 ~sf~C~~CGyr   37 (163)
T TIGR00340        27 STYICEKCGYR   37 (163)
T ss_pred             EEEECCCCCCc
Confidence            45778888886

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

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

Probab=84.21  E-value=0.81  Score=28.10  Aligned_cols=22  Identities=36%  Similarity=0.892  Sum_probs=13.3

Q ss_pred             cCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           12 CGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        12 C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      |..||.+..+..   ++|++||-.|
T Consensus         1 CPvCg~~l~vt~---l~C~~C~t~i   22 (113)
T PF09862_consen    1 CPVCGGELVVTR---LKCPSCGTEI   22 (113)
T ss_pred             CCCCCCceEEEE---EEcCCCCCEE
Confidence            556666665543   6677776544

>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]

Probab=84.19  E-value=1.2  Score=28.94  Aligned_cols=34  Identities=26%  Similarity=0.696  Sum_probs=25.3

Q ss_pred             CceEEEcCCCCCeeecC-------CCCeeEcCCCCCcEEEEE
Q 035461            6 EPVSYICGDCGMENTLK-------PGDVIQCRECGYRILYKK   40 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~RIlyK~   40 (51)
                      ....|.|. |+.-..-.       .+...||..||.+++++.
T Consensus       114 ~~~~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gkL~~~~  154 (156)
T COG3091         114 TTYPYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGKLVFKG  154 (156)
T ss_pred             cceeEEee-cCCccchhhhcccccccceEEeccCCceEEecc
Confidence            34789999 98875432       334588999999998863

>KOG2923 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.06  E-value=1.3  Score=25.23  Aligned_cols=31  Identities=26%  Similarity=0.638  Sum_probs=23.2

Q ss_pred             CCCCceEEEcCCCCCeeecC-----C-CCeeEcCCCCC
Q 035461            3 PQPEPVSYICGDCGMENTLK-----P-GDVIQCRECGY   34 (51)
Q Consensus         3 ~~~~~~~Y~C~~Cg~~~~~~-----~-~~~irC~~CG~   34 (51)
                      ...+...|-|. ||..|++.     . .+..+||.|.-
T Consensus        16 ~e~~~y~yPCp-CGDrf~It~edL~~ge~Va~CpsCSL   52 (67)
T KOG2923|consen   16 EENQTYYYPCP-CGDRFQITLEDLENGEDVARCPSCSL   52 (67)
T ss_pred             cCCCeEEcCCC-CCCeeeecHHHHhCCCeeecCCCceE
Confidence            44556778886 99999985     2 26789999973

>COG1773 Rubredoxin [Energy production and conversion]

Probab=84.05  E-value=0.88  Score=24.96  Aligned_cols=25  Identities=36%  Similarity=0.810  Sum_probs=19.7

Q ss_pred             EEEcCCCCCeeecCCC----------------CeeEcCCCC
Q 035461            9 SYICGDCGMENTLKPG----------------DVIQCRECG   33 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG   33 (51)
                      .|+|.-||-..+.+.+                +.-.||.||
T Consensus         3 ~~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg   43 (55)
T COG1773           3 RWRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECG   43 (55)
T ss_pred             ceEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCC
Confidence            6999999998886532                456899999

>TIGR03831 YgiT_finger YgiT-type zinc finger domain

Probab=83.99  E-value=0.9  Score=22.15  Aligned_cols=17  Identities=24%  Similarity=0.626  Sum_probs=12.5

Q ss_pred             cCCCCeeEcCCCCCcEE
Q 035461           21 LKPGDVIQCRECGYRIL   37 (51)
Q Consensus        21 ~~~~~~irC~~CG~RIl   37 (51)
                      ++..+...|+.||-.++
T Consensus        27 i~~vp~~~C~~CGE~~~   43 (46)
T TIGR03831        27 IENVPALVCPQCGEEYL   43 (46)
T ss_pred             EeCCCccccccCCCEee
Confidence            34446778999998775

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.

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

Probab=83.71  E-value=2  Score=23.43  Aligned_cols=29  Identities=24%  Similarity=0.519  Sum_probs=19.3

Q ss_pred             eEEEcCCCCCeeecC--CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK--PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RI   36 (51)
                      |.=+|.+|+.+..+-  +...|.|..||.-+
T Consensus         6 m~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L   36 (55)
T PF01667_consen    6 MDVKCPGCYNIQTVFSHAQTVVKCVVCGTVL   36 (55)
T ss_dssp             EEEE-TTT-SEEEEETT-SS-EE-SSSTSEE
T ss_pred             EEEECCCCCCeeEEEecCCeEEEcccCCCEe
Confidence            667899999998764  45789999999754

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

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=83.29  E-value=0.56  Score=35.65  Aligned_cols=21  Identities=38%  Similarity=0.993  Sum_probs=11.2

Q ss_pred             cCCCCCeeecCCCCeeEcCCCCCc
Q 035461           12 CGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        12 C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      |.+||+++..   +.--|++||.+
T Consensus        30 Cp~CG~~~~~---~~~fC~~CG~~   50 (645)
T PRK14559         30 CPQCGTEVPV---DEAHCPNCGAE   50 (645)
T ss_pred             CCCCCCCCCc---ccccccccCCc
Confidence            5555555433   23466667665

>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]

Probab=83.28  E-value=0.42  Score=31.23  Aligned_cols=34  Identities=21%  Similarity=0.528  Sum_probs=26.6

Q ss_pred             CCceEEEcCCCCCeeecCC--CCeeEcCCCCCcEEE
Q 035461            5 PEPVSYICGDCGMENTLKP--GDVIQCRECGYRILY   38 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~--~~~irC~~CG~RIly   38 (51)
                      .+.+.|.|..|+-.+++..  ...-.||.||.-+-|
T Consensus       109 ~~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~  144 (176)
T COG1675         109 TENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDLEE  144 (176)
T ss_pred             ccCCceeCCCCCCcccHHHHHHhCCCCCCCCchhhh
Confidence            4668999999999998862  345899999986543

>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.23  E-value=1.3  Score=24.87  Aligned_cols=16  Identities=19%  Similarity=0.353  Sum_probs=12.2

Q ss_pred             CCCCeeEcCCCCCcEE
Q 035461           22 KPGDVIQCRECGYRIL   37 (51)
Q Consensus        22 ~~~~~irC~~CG~RIl   37 (51)
                      .....+.|||||-+.-
T Consensus        44 g~~gev~CPYC~t~y~   59 (62)
T COG4391          44 GDEGEVVCPYCSTRYR   59 (62)
T ss_pred             CCCCcEecCccccEEE
Confidence            3557899999997643

>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.16  E-value=0.68  Score=19.76  Aligned_cols=12  Identities=33%  Similarity=0.695  Sum_probs=9.2

Q ss_pred             EEcCCCCCeeec
Q 035461           10 YICGDCGMENTL   21 (51)
Q Consensus        10 Y~C~~Cg~~~~~   21 (51)
                      |.|..||+.|..
T Consensus         1 y~C~~C~~~f~~   12 (23)
T PF00096_consen    1 YKCPICGKSFSS   12 (23)
T ss_dssp             EEETTTTEEESS
T ss_pred             CCCCCCCCccCC
Confidence            788888887753

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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....

>TIGR00155 pqiA_fam integral membrane protein, PqiA family

Probab=83.08  E-value=0.78  Score=32.79  Aligned_cols=26  Identities=19%  Similarity=0.466  Sum_probs=20.7

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      .-.|.+|+..+  ..+...+||.||+.+
T Consensus       215 ~~~C~~Cd~~~--~~~~~a~CpRC~~~L  240 (403)
T TIGR00155       215 LRSCSACHTTI--LPAQEPVCPRCSTPL  240 (403)
T ss_pred             CCcCCCCCCcc--CCCCCcCCcCCCCcc
Confidence            34599999965  446778999999987

This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.

>PRK12495 hypothetical protein; Provisional

Probab=82.87  E-value=0.85  Score=31.15  Aligned_cols=29  Identities=17%  Similarity=0.398  Sum_probs=22.9

Q ss_pred             ceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            7 PVSYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      ...+.|..||..+. .....++|+.|+..+
T Consensus        40 msa~hC~~CG~PIp-a~pG~~~Cp~CQ~~~   68 (226)
T PRK12495         40 MTNAHCDECGDPIF-RHDGQEFCPTCQQPV   68 (226)
T ss_pred             cchhhcccccCccc-CCCCeeECCCCCCcc
Confidence            35688999999987 345779999999654

>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed

Probab=82.78  E-value=1  Score=24.60  Aligned_cols=22  Identities=27%  Similarity=0.608  Sum_probs=16.6

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .-.|.+||.-.-     ...||.||..
T Consensus         5 mr~C~~CgvYTL-----k~~CP~CG~~   26 (56)
T PRK13130          5 IRKCPKCGVYTL-----KEICPVCGGK   26 (56)
T ss_pred             ceECCCCCCEEc-----cccCcCCCCC
Confidence            357999998764     4679999964

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

Probab=82.48  E-value=1  Score=26.97  Aligned_cols=30  Identities=23%  Similarity=0.690  Sum_probs=22.3

Q ss_pred             ceEEEcCCCCCeeecC-CCCeeEcCCCCCcE
Q 035461            7 PVSYICGDCGMENTLK-PGDVIQCRECGYRI   36 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RI   36 (51)
                      .-.|.|..||+..-.. ...--.|..||+..
T Consensus        33 ~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f   63 (89)
T COG1997          33 RAKHVCPFCGRTTVKRIATGIWKCRKCGAKF   63 (89)
T ss_pred             hcCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence            3579999999984333 34567999999864

>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A

Probab=82.36  E-value=1.2  Score=32.87  Aligned_cols=29  Identities=34%  Similarity=0.590  Sum_probs=13.9

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCc-EEEEEe
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYR-ILYKKR   41 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~R-IlyK~R   41 (51)
                      .=+|.+||.....    .-.||.||.. |-+-.|
T Consensus       491 ~~~C~~CG~~~~~----~~~CP~CGs~~~~~~~R  520 (546)
T PF13597_consen  491 IDICPDCGYIGGE----GDKCPKCGSENIEVYSR  520 (546)
T ss_dssp             EEEETTT---S------EEE-CCC----EEEEB-
T ss_pred             cccccCCCcCCCC----CCCCCCCCCcccceEEE
Confidence            4589999986542    6789999998 554444

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

Probab=82.30  E-value=0.83  Score=27.59  Aligned_cols=13  Identities=31%  Similarity=0.457  Sum_probs=11.3

Q ss_pred             eeEcCCCCCcEEE
Q 035461           26 VIQCRECGYRILY   38 (51)
Q Consensus        26 ~irC~~CG~RIly   38 (51)
                      +++||+||..+.+
T Consensus         2 p~~CpYCg~~~~l   14 (102)
T PF11672_consen    2 PIICPYCGGPAEL   14 (102)
T ss_pred             CcccCCCCCeeEE
Confidence            5899999998876

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

>COG4031 Predicted metal-binding protein [General function prediction only]

Probab=82.28  E-value=0.62  Score=31.67  Aligned_cols=20  Identities=45%  Similarity=0.996  Sum_probs=16.4

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      +| +||.++++.    ..|++||-+
T Consensus         2 ~C-rCG~~l~~p----~~Cl~Cg~~   21 (227)
T COG4031           2 IC-RCGAELSSP----AFCLNCGRR   21 (227)
T ss_pred             cc-ccCCccccc----chhcccCCc
Confidence            58 999997654    789999976

>PF13397 DUF4109: Domain of unknown function (DUF4109)

Probab=82.07  E-value=2.2  Score=26.04  Aligned_cols=30  Identities=30%  Similarity=0.628  Sum_probs=23.5

Q ss_pred             CCceEEEcCCCCCeeecCC------CCeeEcCCCCCc
Q 035461            5 PEPVSYICGDCGMENTLKP------GDVIQCRECGYR   35 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~------~~~irC~~CG~R   35 (51)
                      -+.+.|.|.+ |.+|.+..      -+..-|+.||.-
T Consensus        24 R~~v~Y~C~~-Gh~~~v~Fa~eAevP~~WeC~~cG~~   59 (105)
T PF13397_consen   24 RQRVSYWCPN-GHETEVPFAAEAEVPATWECPRCGLP   59 (105)
T ss_pred             ceEEEEECCC-CCEEeccccccCCCCCceeCCCCCCc
Confidence            3569999999 99988752      256899999964

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

Probab=81.81  E-value=1  Score=23.00  Aligned_cols=26  Identities=23%  Similarity=0.670  Sum_probs=15.0

Q ss_pred             EcCC--CCCeeecCCC-Ce--eEcCCCCCcE
Q 035461           11 ICGD--CGMENTLKPG-DV--IQCRECGYRI   36 (51)
Q Consensus        11 ~C~~--Cg~~~~~~~~-~~--irC~~CG~RI   36 (51)
                      -|..  |+..+..... ..  +.|+.||+.+
T Consensus        20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f   50 (64)
T PF01485_consen   20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF   50 (64)
T ss_dssp             --TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred             CCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence            6755  9999888754 33  8999999865

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.

>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=81.57  E-value=1.6  Score=22.33  Aligned_cols=12  Identities=33%  Similarity=0.778  Sum_probs=9.6

Q ss_pred             CeeEcCCCCCcE
Q 035461           25 DVIQCRECGYRI   36 (51)
Q Consensus        25 ~~irC~~CG~RI   36 (51)
                      ..+.|||||-+.
T Consensus        28 ~~~~CpYCg~~y   39 (40)
T PF10276_consen   28 GPVVCPYCGTRY   39 (40)
T ss_dssp             CEEEETTTTEEE
T ss_pred             CeEECCCCCCEE
Confidence            469999999653

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.

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

Probab=81.54  E-value=1.2  Score=22.87  Aligned_cols=13  Identities=23%  Similarity=0.782  Sum_probs=7.8

Q ss_pred             EcCCCCCcEEEEE
Q 035461           28 QCRECGYRILYKK   40 (51)
Q Consensus        28 rC~~CG~RIlyK~   40 (51)
                      +||+||.+.....
T Consensus         1 ~CP~Cg~~a~ir~   13 (47)
T PF04606_consen    1 RCPHCGSKARIRT   13 (47)
T ss_pred             CcCCCCCeeEEEE
Confidence            4777777664443

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

>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=81.52  E-value=1.5  Score=21.88  Aligned_cols=14  Identities=21%  Similarity=0.804  Sum_probs=8.4

Q ss_pred             eEcCCCCCcEEEEE
Q 035461           27 IQCRECGYRILYKK   40 (51)
Q Consensus        27 irC~~CG~RIlyK~   40 (51)
                      ..||.||+.++.|.
T Consensus         2 ~~CP~Cg~~lv~r~   15 (39)
T PF01396_consen    2 EKCPKCGGPLVLRR   15 (39)
T ss_pred             cCCCCCCceeEEEE
Confidence            46888885544443

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

>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation

Probab=81.51  E-value=0.96  Score=29.47  Aligned_cols=28  Identities=29%  Similarity=0.663  Sum_probs=20.3

Q ss_pred             eEEEcCCCCCeeecC------CCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLK------PGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~------~~~~irC~~CG~R   35 (51)
                      ....|..|+......      ....-+||.||..
T Consensus       112 ~~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~  145 (222)
T cd01413         112 QTAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGI  145 (222)
T ss_pred             CcceECCCCCCcchhHHHHhccCCCCcCCCCCCc
Confidence            456799999887654      1234689999975

Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.

>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose

Probab=81.26  E-value=0.99  Score=29.10  Aligned_cols=28  Identities=29%  Similarity=0.615  Sum_probs=20.4

Q ss_pred             eEEEcCCCCCeeecC-------CCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLK-------PGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~R   35 (51)
                      ....|..|+..+...       ....-+||.||..
T Consensus       108 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~  142 (218)
T cd01407         108 FRVRCTKCGKEYPRDELQADIDREEVPRCPKCGGL  142 (218)
T ss_pred             CcceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCc
Confidence            356799999887643       2345689999976

Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.

>PRK00481 NAD-dependent deacetylase; Provisional

Probab=81.22  E-value=0.96  Score=29.66  Aligned_cols=28  Identities=25%  Similarity=0.585  Sum_probs=19.6

Q ss_pred             eEEEcCCCCCeeecC---CCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLK---PGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~---~~~~irC~~CG~R   35 (51)
                      ....|..|+......   ..+..+||.||+.
T Consensus       121 ~~~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~  151 (242)
T PRK00481        121 LRARCTKCGQTYDLDEYLKPEPPRCPKCGGI  151 (242)
T ss_pred             CceeeCCCCCCcChhhhccCCCCCCCCCCCc
Confidence            456799998876543   2234569999975

>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]

Probab=80.80  E-value=1.3  Score=27.42  Aligned_cols=24  Identities=33%  Similarity=0.786  Sum_probs=18.1

Q ss_pred             cCCCCCeeecCCCCeeEcCCCCCc
Q 035461           12 CGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        12 C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      |..|+.+..-+.+...-||+|+|.
T Consensus         6 cp~c~sEytYed~~~~~cpec~~e   29 (112)
T COG2824           6 CPKCNSEYTYEDGGQLICPECAHE   29 (112)
T ss_pred             CCccCCceEEecCceEeCchhccc
Confidence            677777777777777888888764

>PRK14715 DNA polymerase II large subunit; Provisional

Probab=80.46  E-value=1.3  Score=37.11  Aligned_cols=30  Identities=23%  Similarity=0.682  Sum_probs=23.0

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYK   39 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK   39 (51)
                      -.++| .||+...--+. .-+||.||++|+.-
T Consensus      1541 Q~~RC-kC~~kyRR~PL-~G~C~kCGg~~ilT 1570 (1627)
T PRK14715       1541 QEFRC-KCGAKYRRVPL-KGKCPKCGSKLILT 1570 (1627)
T ss_pred             cceee-cCCCccccCCC-CCcCcccCCeEEEE
Confidence            46899 99998865443 35899999998753

>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function

Probab=80.42  E-value=1.2  Score=27.37  Aligned_cols=17  Identities=18%  Similarity=0.331  Sum_probs=11.5

Q ss_pred             CCceEEEcCCCCCeeec
Q 035461            5 PEPVSYICGDCGMENTL   21 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~   21 (51)
                      ..+..-+|..|+..+..
T Consensus        87 ~~~~~sRC~~CN~~L~~  103 (147)
T PF01927_consen   87 LDPIFSRCPKCNGPLRP  103 (147)
T ss_pred             cCCCCCccCCCCcEeee
Confidence            34556788888877653

The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.

>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional

Probab=80.40  E-value=1.9  Score=31.25  Aligned_cols=31  Identities=23%  Similarity=0.383  Sum_probs=23.8

Q ss_pred             CCceEEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461            5 PEPVSYICGDCGMENTLKPG----------------DVIQCRECGYR   35 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R   35 (51)
                      .....|+|..||..-+...+                +.-+||.||..
T Consensus       421 ~~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~  467 (479)
T PRK05452        421 DLGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG  467 (479)
T ss_pred             CCCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence            35578999999998887533                35699999954

>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb

Probab=80.01  E-value=2.4  Score=25.28  Aligned_cols=21  Identities=29%  Similarity=0.502  Sum_probs=15.8

Q ss_pred             ecCCCCeeEcCCCCCcEEEEE
Q 035461           20 TLKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus        20 ~~~~~~~irC~~CG~RIlyK~   40 (51)
                      .+..+.+-||++||+-...+.
T Consensus        73 ~l~~g~~~rC~eCG~~fkL~~   93 (97)
T cd00924          73 WLEKGKPKRCPECGHVFKLVD   93 (97)
T ss_pred             EEeCCCceeCCCCCcEEEEEE
Confidence            355678999999998766553

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	51
3h0g_L	63	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		7e-13
1i3q_L	70	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		6e-09
3j0k_L	46	Orientation Of Rna Polymerase Ii Within The Human V		9e-09

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 27/49 (55%), Positives = 40/49 (81%)
Query: 3  PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
          P+P  + Y+C DCG  NT++  +VI+CRECG+R++YK RT+R+VQ+EAR
Sbjct: 15 PRPATMIYLCADCGARNTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR 63

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

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 34/49 (69%)
Query: 3  PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
           +   + YIC +C  + +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 22 ARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 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 = 55.1 bits (131), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 21/45 (46%), Positives = 33/45 (73%)
Query: 7  PVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
           + YIC +C  + +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 2  TLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 46

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	51
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	7e-25
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	3e-24

>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 = 85.7 bits (212), Expect = 7e-25
 Identities = 21/51 (41%), Positives = 34/51 (66%)

Query: 1  MDPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
             +   + YIC +C  + +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 20 SQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 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 = 83.8 bits (207), Expect = 3e-24
 Identities = 27/50 (54%), Positives = 40/50 (80%)

Query: 2  DPQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
           P+P  + Y+C DCG  NT++  +VI+CRECG+R++YK RT+R+VQ+EAR
Sbjct: 14 PPRPATMIYLCADCGARNTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	51
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	99.93
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	99.9
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	99.69
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	97.93
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	97.72
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	97.08
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	97.07
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	96.58
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	95.95
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	95.92
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	95.77
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	95.31
1lko_A	191	Rubrerythrin all-iron(II) form; reduced form, DIIR	95.19
1dxg_A	36	Desulforedoxin; non-heme iron protein, rubredoxin	94.98
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	94.6
1yuz_A	202	Nigerythrin; rubrythrin, rubredoxin, hemerythrin,	94.44
2v3b_B	55	Rubredoxin 2, rubredoxin; alkane degradation, iron	93.9
1yk4_A	52	Rubredoxin, RD; electron transport; 0.69A {Pyrococ	93.7
1vd4_A	62	Transcription initiation factor IIE, alpha subunit	93.24
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	93.19
4gzn_C	60	ZFP-57, zinc finger protein 57; transcription-DNA	92.97
2k2d_A	79	Ring finger and CHY zinc finger domain- containing	92.95
2kn9_A	81	Rubredoxin; metalloprotein, ssgcid, structural gen	92.85
1e8j_A	52	Rubredoxin; iron-sulfur-protein, zinc-substitution	92.83
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	92.75
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	92.71
2zet_C	153	Melanophilin; complex, GTP-binding protein, GTPase	92.7
1s24_A	87	Rubredoxin 2; electron transport; NMR {Pseudomonas	92.62
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	92.58
2akl_A	138	PHNA-like protein PA0128; two domains, Zn binding	92.34
3uk3_C	57	Zinc finger protein 217; transcription factor, DNA	92.22
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	92.15
2epq_A	45	POZ-, at HOOK-, and zinc finger-containing protein	92.11
1zbd_B	134	Rabphilin-3A; G protein, effector, RABCDR, synapti	91.99
1ltl_A	279	DNA replication initiator (CDC21/CDC54); HET: DNA;	91.97
2ayj_A	56	50S ribosomal protein L40E; Zn-binding, beta-stran	91.7
1bbo_A	57	Human enhancer-binding protein MBP-1; DNA-binding	91.58
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	91.42
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	91.42
1x5w_A	70	Zinc finger protein 64, isoforms 1; ZNF338, nuclea	91.26
2adr_A	60	ADR1; transcription regulation, zinc finger,; NMR	91.11
1x6e_A	72	Zinc finger protein 24; ZNF24, KOX17, ZNF191, zsca	91.08
2lv2_A	85	Insulinoma-associated protein 1; structural genomi	90.22
2yt9_A	95	Zinc finger-containing protein 1; C2H2, structural	89.75
2lce_A	74	B-cell lymphoma 6 protein; structural genomics, no	89.51
2eod_A	66	TNF receptor-associated factor 4; zinc binding, NF	89.4
1llm_C	88	Chimera of ZIF23-GCN4; dimerization, DNA recogniti	89.11
2csz_A	76	Synaptotagmin-like protein 4; exophilin 2, granuph	89.09
2d9k_A	75	FLN29 gene product; zinc finger, ZF-TRAF, structur	89.02
2kmk_A	82	Zinc finger protein GFI-1; tandem repeat zinc fing	88.95
2epr_A	48	POZ-, at HOOK-, and zinc finger-containing protein	88.88
3flo_B	206	DNA polymerase alpha catalytic subunit A; protein-	88.82
2drp_A	66	Protein (tramtrack DNA-binding domain); protein-DN	88.63
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	88.62
2jvm_A	80	Uncharacterized protein; alpha+beta, structural ge	88.5
2con_A	79	RUH-035 protein, NIN one binding protein; ribosome	88.42
2vl6_A	268	SSO MCM N-TER, minichromosome maintenance protein	88.21
1a1h_A	90	QGSR zinc finger peptide; complex (zinc finger/DNA	88.06
4a17_Y	103	RPL37A, 60S ribosomal protein L32; eukaryotic ribo	87.56
1vzi_A	126	Desulfoferrodoxin; ferrocyanide, microspectrophoto	87.44
2ct1_A	77	Transcriptional repressor CTCF; CCCTC-BINDING fact	87.27
2lt7_A	133	Transcriptional regulator kaiso; zinc finger, doub	87.03
2jz8_A	87	Uncharacterized protein BH09830; zinc binding, str	86.98
2csh_A	110	Zinc finger protein 297B; ZF-C2H2 domain, zinc fin	86.61
2d9h_A	78	Zinc finger protein 692; ZF-C2H2 domain, structura	86.48
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	86.47
2jrr_A	67	Uncharacterized protein; solution structure, SIR90	86.4
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	86.32
1yc5_A	246	NAD-dependent deacetylase; SIR2, sirtuin, SIR2TM,	85.86
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	85.61
2dmd_A	96	Zinc finger protein 64, isoforms 1 and 2; ZNF338,	85.57
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	85.49
1y07_A	128	Desulfoferrodoxin (RBO); beta-sheet, iron binding,	85.36
2dlq_A	124	GLI-kruppel family member HKR3; ZF-C2H2 domain, st	85.16
3iz5_m	92	60S ribosomal protein L43 (L37AE); eukaryotic ribo	85.15
1ffk_W	73	Ribosomal protein L37AE; ribosome assembly, RNA-RN	84.81
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	84.78
1rfh_A	59	RAS association (ralgds/AF-6) domain family 5; zin	84.75
2eps_A	54	POZ-, at HOOK-, and zinc finger-containing protein	84.72
3irb_A	145	Uncharacterized protein from DUF35 family; 1381535	84.67
3lpe_B	59	DNA-directed RNA polymerase subunit E''; transcrip	84.59
2ytg_A	46	ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, s	84.55
3izc_m	92	60S ribosomal protein RPL43 (L37AE); eukaryotic ri	84.52
2cot_A	77	Zinc finger protein 435; ADK_LID domain, zinc fing	84.17
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	84.13
2fnf_X	72	Putative RAS effector NORE1; zinc, signal transduc	84.09
3p8b_A	81	DNA-directed RNA polymerase, subunit E''; transcri	83.81
2epw_A	46	Zinc finger protein 268; C2H2, zinc finger domain,	83.81
2jr7_A	89	DPH3 homolog; DESR1, CSL zinc finger, metal bindin	83.8
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	83.78
1q1a_A	289	HST2 protein; ternary complex, histone deacetylase	83.59
2m0d_A	30	Zinc finger and BTB domain-containing protein 17;	83.56
2yu8_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	83.49
2l6l_A	155	DNAJ homolog subfamily C member 24; DPH4, Zn-CSL,	83.48
2kvh_A	27	Zinc finger and BTB domain-containing protein 32;	83.41
1m2k_A	249	Silent information regulator 2; protein-ligand com	83.4
2odx_A	80	Cytochrome C oxidase polypeptide IV; all beta-prot	83.37
2eme_A	46	Zinc finger protein 473; ZF-C2H2, structural genom	82.99
1f2i_G	73	Fusion of N-terminal 17-MER peptide extension to Z	82.8
2kvf_A	28	Zinc finger and BTB domain-containing protein 32;	82.73
3p2a_A	148	Thioredoxin 2, putative thioredoxin-like protein;	82.67
2m0f_A	29	Zinc finger and BTB domain-containing protein 17;	82.28
2yso_A	46	ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, s	82.16
1x6h_A	86	Transcriptional repressor CTCF; zinc finger protei	82.03
2gnr_A	145	Conserved hypothetical protein; 13815350, structur	81.97
2em5_A	46	ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, s	81.87
2ene_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	81.69
1rik_A	29	E6APC1 peptide; E6-binding domain, zinc finger, hu	81.6
1ptq_A	50	Protein kinase C delta type; phosphotransferase; 1	81.46
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	81.36
2em8_A	46	Zinc finger protein 224; ZF-C2H2, structural genom	81.27
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	81.2
2eml_A	46	Zinc finger protein 28 homolog; ZF-C2H2, structura	81.07
2kvg_A	27	Zinc finger and BTB domain-containing protein 32;	81.06
2wbt_A	129	B-129; zinc finger; 2.70A {Sulfolobus virus 1}	80.93
2i13_A	190	AART; DNA binding, zinc finger, DNA binding protei	80.85
2eoo_A	46	ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, s	80.8
2emm_A	46	ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, s	80.76
2elm_A	37	Zinc finger protein 406; ZFAT zinc finger 1, struc	80.74
2em9_A	46	Zinc finger protein 224; ZF-C2H2, structural genom	80.62
2emp_A	46	Zinc finger protein 347; ZF-C2H2, structural genom	80.61
1ma3_A	253	SIR2-AF2, transcriptional regulatory protein, SIR2	80.57
2em7_A	46	Zinc finger protein 224; ZF-C2H2, structural genom	80.35
1v54_F	98	VI, cytochrome C oxidase polypeptide VB; oxidoredu	80.35
2ysp_A	46	Zinc finger protein 224; ZF-C2H2, structural genom	80.34
1wge_A	83	Hypothetical protein 2610018L09RIK; diphthamide,CS	80.19
2emy_A	46	Zinc finger protein 268; ZF-C2H2, structural genom	80.05
2lvu_A	26	Zinc finger and BTB domain-containing protein 17;	81.17

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

Probab=99.93  E-value=1.3e-27  Score=133.61  Aligned_cols=49  Identities=55%  Similarity=1.209  Sum_probs=44.3

Q ss_pred             CCCCceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEecCceEEEEcC
Q 035461            3 PQPEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR   51 (51)
Q Consensus         3 ~~~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   51 (51)
                      +++++|.|+|++||.+++++.+++||||+||||||||+|+++++||+||
T Consensus        15 ~~~~~v~Y~C~~Cg~~~~l~~~~~iRC~~CG~RILyK~Rt~r~~~~~Ar   63 (63)
T 3h0g_L           15 PRPATMIYLCADCGARNTIQAKEVIRCRECGHRVMYKMRTKRMVQFEAR   63 (63)
T ss_dssp             ----CCCCBCSSSCCBCCCCSSSCCCCSSSCCCCCBCCCCCCCEEECCC
T ss_pred             CCCCCeEEECCCCCCeeecCCCCceECCCCCcEEEEEecCCceEEEECC
Confidence            4556799999999999999999999999999999999999999999998

>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=99.90  E-value=6e-25  Score=124.34  Aligned_cols=47  Identities=45%  Similarity=0.977  Sum_probs=44.7

Q ss_pred             CCceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEecCceEEEEcC
Q 035461            5 PEPVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR   51 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   51 (51)
                      +.++.|+|++||.+|++...++|+||+||+|||||+|+++++||+||
T Consensus        24 ~~~v~Y~C~~CG~~~e~~~~d~irCp~CG~RILyK~R~~r~v~~~ar   70 (70)
T 1twf_L           24 TATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR   70 (70)
T ss_dssp             -CCCCEECSSSCCEECCCTTSTTCCSSSCCCCCBCCCCSSCEEECCC
T ss_pred             CceEEEECCCCCCcceeCCCCCccCCCCCceEeEecCCCccEEEecC
Confidence            36799999999999999999999999999999999999999999998

>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=99.69  E-value=9.1e-18  Score=89.60  Aligned_cols=42  Identities=31%  Similarity=0.571  Sum_probs=37.1

Q ss_pred             EEEcCCCCCeeecC---CCCeeEcCCCCCcEEEEEecCceEEEEc
Q 035461            9 SYICGDCGMENTLK---PGDVIQCRECGYRILYKKRTRRIVQYEA   50 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~---~~~~irC~~CG~RIlyK~R~~~~~~~~A   50 (51)
                      .|+|++||++|+.+   ..++||||+||+||+||.|++.++.++|
T Consensus         3 iY~C~rCg~~fs~~el~~lP~IrCpyCGyrii~KvR~p~vK~vkA   47 (48)
T 4ayb_P            3 VYRCGKCWKTFTDEQLKVLPGVRCPYCGYKIIFMVRKPTIKIVKA   47 (48)
T ss_dssp             --CCCCTTTTCCCCCSCCCSSSCCTTTCCSCEECCCCCSCEEEEC
T ss_pred             EEEeeccCCCccHHHHhhCCCcccCccCcEEEEEecCCcceeeec
Confidence            69999999999875   3588999999999999999999999988

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

Probab=97.93  E-value=5.1e-06  Score=50.68  Aligned_cols=35  Identities=23%  Similarity=0.486  Sum_probs=27.3

Q ss_pred             ceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEec
Q 035461            7 PVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRT   42 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~   42 (51)
                      ...|+|..||+.++.. .....||.||+.+-.+.|.
T Consensus       130 ~~~y~C~~Cg~~~~~~-~~~~~Cp~CG~~~~~~~~~  164 (165)
T 2lcq_A          130 KWRYVCIGCGRKFSTL-PPGGVCPDCGSKVKLIPRK  164 (165)
T ss_dssp             CCCEEESSSCCEESSC-CGGGBCTTTCCBEEECCCC
T ss_pred             cEEEECCCCCCcccCC-CCCCcCCCCCCcceeCCcC
Confidence            4679999999999864 3446999999997555553

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

Probab=97.72  E-value=1.4e-05  Score=47.12  Aligned_cols=34  Identities=21%  Similarity=0.330  Sum_probs=27.7

Q ss_pred             CCceEEEcCCCCCeeecCCCCee-EcCCCCCcEEEE
Q 035461            5 PEPVSYICGDCGMENTLKPGDVI-QCRECGYRILYK   39 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~i-rC~~CG~RIlyK   39 (51)
                      ..|..|+|.+||.++++... .. .||.||+..++-
T Consensus        69 ~~p~~~~C~~CG~~~e~~~~-~~~~CP~Cgs~~~~i  103 (119)
T 2kdx_A           69 DEKVELECKDCSHVFKPNAL-DYGVCEKCHSKNVII  103 (119)
T ss_dssp             EECCEEECSSSSCEECSCCS-TTCCCSSSSSCCCEE
T ss_pred             eccceEEcCCCCCEEeCCCC-CCCcCccccCCCcEE
Confidence            35789999999999998653 45 899999986553

>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82

Probab=97.08  E-value=8.6e-05  Score=44.44  Aligned_cols=33  Identities=15%  Similarity=0.324  Sum_probs=26.1

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~   40 (51)
                      ..|+|.+||.+|....+.+.+||.|++.-+-.+
T Consensus        66 ~p~~C~~CG~~F~~~~~kPsrCP~CkSe~Ie~P   98 (105)
T 2gmg_A           66 KPAQCRKCGFVFKAEINIPSRCPKCKSEWIEEP   98 (105)
T ss_dssp             CCCBBTTTCCBCCCCSSCCSSCSSSCCCCBCCC
T ss_pred             ECcChhhCcCeecccCCCCCCCcCCCCCccCCc
Confidence            569999999999445567899999998755433

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

Probab=97.07  E-value=0.00025  Score=43.13  Aligned_cols=35  Identities=26%  Similarity=0.546  Sum_probs=28.2

Q ss_pred             CCceEEEcCCCCCeeecCC-----------CC---------eeEcCCCCCcEEEE
Q 035461            5 PEPVSYICGDCGMENTLKP-----------GD---------VIQCRECGYRILYK   39 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~-----------~~---------~irC~~CG~RIlyK   39 (51)
                      ..|..++|.+||.+++++.           ..         ..+||.||+.=++-
T Consensus        66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~h~~p~~~~~~~~CP~Cgs~~~~i  120 (139)
T 3a43_A           66 EEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEV  120 (139)
T ss_dssp             EECCEEEETTTCCEEEGGGCTTCCSCCCGGGCCCCGGGCGGGCSCSSSSCCCEEE
T ss_pred             ecCCcEECCCCCCEEecccccccccccccccccccccccccCCcCccccCCccEE
Confidence            3568899999999999865           21         68999999987663

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

Probab=96.58  E-value=0.001  Score=43.10  Aligned_cols=31  Identities=45%  Similarity=0.940  Sum_probs=24.2

Q ss_pred             EcCCCCCeeecC-------CCCeeEcCCCCCcEEEEEec
Q 035461           11 ICGDCGMENTLK-------PGDVIQCRECGYRILYKKRT   42 (51)
Q Consensus        11 ~C~~Cg~~~~~~-------~~~~irC~~CG~RIlyK~R~   42 (51)
                      .|+.|+..+...       ....++||+|| ||||....
T Consensus       200 ~C~GC~~~lppq~~~~i~~~~~Iv~Cp~Cg-RIL~~~~~  237 (256)
T 3na7_A          200 ACGGCFIRLNDKIYTEVLTSGDMITCPYCG-RILYAEGA  237 (256)
T ss_dssp             BCTTTCCBCCHHHHHHHHHSSSCEECTTTC-CEEECSCC
T ss_pred             ccCCCCeeeCHHHHHHHHCCCCEEECCCCC-eeEEeCcc
Confidence            699999988742       34679999998 89987654

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

Probab=95.95  E-value=0.0035  Score=32.33  Aligned_cols=27  Identities=33%  Similarity=0.723  Sum_probs=21.1

Q ss_pred             EEEcCCCCCeeecCCCC---------eeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPGD---------VIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~---------~irC~~CG~R   35 (51)
                      .|+|..||...+...++         .-+||.||..
T Consensus         4 ~y~C~vCGyvyd~~~Gd~t~f~~lP~dw~CP~Cg~~   39 (46)
T 6rxn_A            4 KYVCNVCGYEYDPAEHDNVPFDQLPDDWCCPVCGVS   39 (46)
T ss_dssp             CEEETTTCCEECGGGGTTCCGGGSCTTCBCTTTCCB
T ss_pred             EEECCCCCeEEeCCcCCCcchhhCCCCCcCcCCCCc
Confidence            59999999998864333         3599999974

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

Probab=95.92  E-value=0.0034  Score=35.75  Aligned_cols=31  Identities=23%  Similarity=0.614  Sum_probs=24.6

Q ss_pred             CceEEEcCCCCCeeecCC-CCeeEcCCCCCcE
Q 035461            6 EPVSYICGDCGMENTLKP-GDVIQCRECGYRI   36 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~-~~~irC~~CG~RI   36 (51)
                      +...|.|..||++..... .....|++||+.+
T Consensus        24 q~~~y~Cp~CG~~~v~r~atGiW~C~~Cg~~~   55 (83)
T 1vq8_Z           24 MNEDHACPNCGEDRVDRQGTGIWQCSYCDYKF   55 (83)
T ss_dssp             HHSCEECSSSCCEEEEEEETTEEEETTTCCEE
T ss_pred             ccccCcCCCCCCcceeccCCCeEECCCCCCEe
Confidence            346899999999776653 4679999999864

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

Probab=95.77  E-value=0.0072  Score=37.63  Aligned_cols=27  Identities=30%  Similarity=0.552  Sum_probs=21.7

Q ss_pred             CceEEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461            6 EPVSYICGDCGMENTLKPGDVIQCRECGY   34 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~   34 (51)
                      .+..|+|..||...+.+  .+-.||-||+
T Consensus       135 ~~~~~~C~~CG~i~~~~--~p~~CP~Cg~  161 (170)
T 3pwf_A          135 IKKVYICPICGYTAVDE--APEYCPVCGA  161 (170)
T ss_dssp             CSCEEECTTTCCEEESC--CCSBCTTTCC
T ss_pred             CCCeeEeCCCCCeeCCC--CCCCCCCCCC
Confidence            34789999999998833  3459999996

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

Probab=95.31  E-value=0.0068  Score=31.98  Aligned_cols=28  Identities=39%  Similarity=0.936  Sum_probs=22.5

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILY   38 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIly   38 (51)
                      ..++|..||+.+.   .....|..|||..|-
T Consensus        13 ~k~iCpkC~a~~~---~gaw~CrKCG~~~lr   40 (51)
T 3j21_g           13 KKYVCLRCGATNP---WGAKKCRKCGYKRLR   40 (51)
T ss_dssp             SEEECTTTCCEEC---TTCSSCSSSSSCCCE
T ss_pred             CCccCCCCCCcCC---CCceecCCCCCcccc
Confidence            6799999999943   356899999998553

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

Probab=95.19  E-value=0.011  Score=36.97  Aligned_cols=27  Identities=19%  Similarity=0.480  Sum_probs=20.9

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      ..|+|..||...+-+. .+-.||.||+.
T Consensus       154 ~~~~C~~CG~~~~g~~-~p~~CP~C~~~  180 (191)
T 1lko_A          154 TKWRCRNCGYVHEGTG-APELCPACAHP  180 (191)
T ss_dssp             EEEEETTTCCEEEEEE-CCSBCTTTCCB
T ss_pred             ceEEECCCCCEeeCCC-CCCCCCCCcCC
Confidence            5899999999987432 22399999984

>1dxg_A Desulforedoxin; non-heme iron protein, rubredoxin type metal center, electron transport; 1.80A {Desulfovibrio gigas} SCOP: g.41.5.2 PDB: 1dcd_A 1dhg_A 1cfw_A 2lk5_A 2lk6_A

Probab=94.98  E-value=0.03  Score=27.01  Aligned_cols=26  Identities=31%  Similarity=0.722  Sum_probs=20.2

Q ss_pred             ceEEEcCCCCCeeec--CCCCeeEcCCCCC
Q 035461            7 PVSYICGDCGMENTL--KPGDVIQCRECGY   34 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~--~~~~~irC~~CG~   34 (51)
                      .-.|+|..||..++.  ..+.++.|  ||-
T Consensus         4 ~~fY~C~~CGnivev~~~g~~~l~C--CG~   31 (36)
T 1dxg_A            4 GDVYKCELCGQVVKVLEEGGGTLVC--CGE   31 (36)
T ss_dssp             TCEEECTTTCCEEEEEECCSSCEEE--TTE
T ss_pred             ccEEEcCCCCcEEEEEeCCCcCEEe--CCc
Confidence            357999999999997  45567777  664

>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=94.60  E-value=0.021  Score=31.71  Aligned_cols=34  Identities=26%  Similarity=0.626  Sum_probs=27.1

Q ss_pred             eEEEcCCCCCeeecCCC-CeeEcCCCCCcEEEEEecC
Q 035461            8 VSYICGDCGMENTLKPG-DVIQCRECGYRILYKKRTR   43 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~-~~irC~~CG~RIlyK~R~~   43 (51)
                      ..+.|. ||.-.-.+.+ ....|| ||.+|=++++..
T Consensus         3 ~vv~C~-C~~~~~~~~~~kT~~C~-CG~~~~~~k~ri   37 (71)
T 1gh9_A            3 IIFRCD-CGRALYSREGAKTRKCV-CGRTVNVKDRRI   37 (71)
T ss_dssp             EEEEET-TSCCEEEETTCSEEEET-TTEEEECCSSSC
T ss_pred             EEEECC-CCCEEEEcCCCcEEECC-CCCeeeeceEEE
Confidence            357899 9998877754 679999 999998877653

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

Probab=94.44  E-value=0.031  Score=35.48  Aligned_cols=28  Identities=21%  Similarity=0.365  Sum_probs=22.8

Q ss_pred             CceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            6 EPVSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      ....|+|..||...+-  ..+-.||.||+.
T Consensus       168 ~~~~~~C~~CG~i~~g--~~p~~CP~C~~~  195 (202)
T 1yuz_A          168 DDKFHLCPICGYIHKG--EDFEKCPICFRP  195 (202)
T ss_dssp             SCCEEECSSSCCEEES--SCCSBCTTTCCB
T ss_pred             CCcEEEECCCCCEEcC--cCCCCCCCCCCC
Confidence            3468999999999874  456899999974

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

Probab=93.90  E-value=0.04  Score=29.04  Aligned_cols=27  Identities=26%  Similarity=0.582  Sum_probs=21.0

Q ss_pred             EEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPG----------------DVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R   35 (51)
                      .|+|..||...+...+                +.-+||.||..
T Consensus         3 ~y~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cga~   45 (55)
T 2v3b_B            3 KWQCVVCGFIYDEALGLPEEGIPAGTRWEDIPADWVCPDCGVG   45 (55)
T ss_dssp             EEEETTTCCEEETTTCBTTTTBCTTCCGGGSCTTCCCTTTCCC
T ss_pred             cEEeCCCCeEECCCcCCcccCcCCCCChhHCCCCCcCCCCCCC
Confidence            6999999999886432                33489999963

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

Probab=93.70  E-value=0.056  Score=28.15  Aligned_cols=27  Identities=30%  Similarity=0.542  Sum_probs=21.0

Q ss_pred             EEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPG----------------DVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R   35 (51)
                      .|+|..||...+...+                +.-+||.||..
T Consensus         2 ~~~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cg~~   44 (52)
T 1yk4_A            2 KLSCKICGYIYDEDEGDPDNGISPGTKFEDLPDDWVCPLCGAP   44 (52)
T ss_dssp             EEEESSSSCEEETTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             cEEeCCCCeEECCCcCCcccCcCCCCCHhHCCCCCcCCCCCCC
Confidence            6999999999886432                33589999964

>1vd4_A Transcription initiation factor IIE, alpha subunit; zinc finger; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=93.24  E-value=0.15  Score=25.38  Aligned_cols=32  Identities=19%  Similarity=0.291  Sum_probs=24.3

Q ss_pred             ceEEEcCCCCCeeecC--------CCCeeEcCCCCCcEEE
Q 035461            7 PVSYICGDCGMENTLK--------PGDVIQCRECGYRILY   38 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~--------~~~~irC~~CG~RIly   38 (51)
                      ...|.|..||+.|...        ...+..|+.||.....
T Consensus        12 ~k~~~C~~C~k~F~~~~~l~~~H~~~k~~~C~~C~k~f~~   51 (62)
T 1vd4_A           12 RASFKCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVEE   51 (62)
T ss_dssp             SSEEECSSSCCEEEHHHHHHHEETTTTEEBCSSSCCBCEE
T ss_pred             CCCccCCCCCchhccHHHhHhhcCCCCCEECCCCCCcccc
Confidence            4569999999988642        1357899999987644

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

Probab=93.19  E-value=0.042  Score=27.58  Aligned_cols=27  Identities=30%  Similarity=0.689  Sum_probs=20.5

Q ss_pred             EEEcCCCCC-eeecC-CCCeeEcCCCCCc
Q 035461            9 SYICGDCGM-ENTLK-PGDVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~-~~~~~-~~~~irC~~CG~R   35 (51)
                      .+.|..||. .+... ....+.|++||.-
T Consensus         5 ~~~CP~C~~~~l~~d~~~gelvC~~CG~v   33 (50)
T 1pft_A            5 QKVCPACESAELIYDPERGEIVCAKCGYV   33 (50)
T ss_dssp             CCSCTTTSCCCEEEETTTTEEEESSSCCB
T ss_pred             cEeCcCCCCcceEEcCCCCeEECcccCCc
Confidence            367999988 66554 3477999999973

>4gzn_C ZFP-57, zinc finger protein 57; transcription-DNA complex; HET: DNA 5CM; 0.99A {Mus musculus}

Probab=92.97  E-value=0.093  Score=26.99  Aligned_cols=28  Identities=25%  Similarity=0.520  Sum_probs=22.1

Q ss_pred             EEEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            9 SYICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      .|.|..||+.|...           ...+-.|+.||...
T Consensus         4 py~C~~C~k~F~~~~~L~~H~~~Ht~ekp~~C~~C~k~F   42 (60)
T 4gzn_C            4 PFFCNFCGKTYRDASGLSRHRRAHLGYRPRSCPECGKCF   42 (60)
T ss_dssp             CEECTTTCCEESSHHHHHHHHHHHHTCCCEECTTTCCEE
T ss_pred             CccCCCCCCEeCCHHHHHHHHHHhCCCcCeECCCCCCCc
Confidence            49999999999753           23578999999754

>2k2d_A Ring finger and CHY zinc finger domain- containing protein 1; zinc-binding protein, cytoplasm, metal-binding, nucleus, metal binding protein; NMR {Homo sapiens}

Probab=92.95  E-value=0.094  Score=29.29  Aligned_cols=30  Identities=23%  Similarity=0.514  Sum_probs=23.7

Q ss_pred             CceEEEcCCCCCeeecCCC-CeeEcCCCCCc
Q 035461            6 EPVSYICGDCGMENTLKPG-DVIQCRECGYR   35 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~-~~irC~~CG~R   35 (51)
                      +++.-.|.+|+..++.... -..+|+.||+-
T Consensus        34 ~~v~I~CnDC~~~s~v~~h~lg~kC~~C~Sy   64 (79)
T 2k2d_A           34 MTVDILCNDCNGRSTVQFHILGMKCKICESY   64 (79)
T ss_dssp             CEEEEEESSSCCEEEEECCTTCCCCTTTSCC
T ss_pred             CEeEEECCCCCCCccCCceeecccCcCCCCc
Confidence            3467899999999998753 34699999964

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

Probab=92.85  E-value=0.063  Score=30.52  Aligned_cols=27  Identities=33%  Similarity=0.731  Sum_probs=21.2

Q ss_pred             eEEEcCCCCCeeecCCC----------------CeeEcCCCCC
Q 035461            8 VSYICGDCGMENTLKPG----------------DVIQCRECGY   34 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~   34 (51)
                      ..|+|..||...+...+                +.-+||.||.
T Consensus        26 ~~y~C~vCGyvYD~~~Gdp~~gI~pGT~fedlPddW~CPvCga   68 (81)
T 2kn9_A           26 KLFRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGA   68 (81)
T ss_dssp             CEEEETTTCCEEETTTCBTTTTBCTTCCTTTSCTTCCCTTTCC
T ss_pred             ceEEeCCCCEEEcCCcCCcccCcCCCCChhHCCCCCcCCCCCC
Confidence            58999999999886432                3358999996

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

Probab=92.83  E-value=0.061  Score=28.01  Aligned_cols=27  Identities=37%  Similarity=0.792  Sum_probs=20.6

Q ss_pred             EEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPG----------------DVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R   35 (51)
                      .|+|..||...+...+                +.-+||.||..
T Consensus         3 ~y~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cg~~   45 (52)
T 1e8j_A            3 IYVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGAS   45 (52)
T ss_dssp             CEECSSSCCCCCTTTCCTTTTCCSSCCTTSSCTTCCCSSSCCC
T ss_pred             cEEeCCCCeEEcCCcCCcccCcCCCCchHHCCCCCcCCCCCCc
Confidence            5999999999875543                23489999963

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

Probab=92.75  E-value=0.053  Score=28.51  Aligned_cols=34  Identities=29%  Similarity=0.623  Sum_probs=25.8

Q ss_pred             eEEEcCCCCCeeec-CCCCeeEcCCCCCcEEEEEe
Q 035461            8 VSYICGDCGMENTL-KPGDVIQCRECGYRILYKKR   41 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~-~~~~~irC~~CG~RIlyK~R   41 (51)
                      ....|.+||..+-+ ...+-..|..||+..++|..
T Consensus        17 ~~~fCPkCG~~~~ma~~~dr~~C~kCgyt~~~~~~   51 (55)
T 2k4x_A           17 KHRFCPRCGPGVFLAEHADRYSCGRCGYTEFKKAK   51 (55)
T ss_dssp             SSCCCTTTTTTCCCEECSSEEECTTTCCCEECCCC
T ss_pred             ccccCcCCCCceeEeccCCEEECCCCCCEEEeCcc
Confidence            45789999985543 33578999999999877654

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

Probab=92.71  E-value=0.072  Score=29.28  Aligned_cols=28  Identities=29%  Similarity=0.630  Sum_probs=21.2

Q ss_pred             eEEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLKPG----------------DVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R   35 (51)
                      ..|+|..||...+...+                +.-+||.||..
T Consensus         6 ~~y~C~vCGyiYd~~~Gdp~~gi~pGT~f~~lPddw~CP~Cga~   49 (70)
T 1dx8_A            6 GKYECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSP   49 (70)
T ss_dssp             SCEEETTTCCEECTTTCCTTTTCCSSCCGGGSCTTCBCTTTCCB
T ss_pred             ceEEeCCCCEEEcCCCCCcccCcCCCCchhhCCCCCcCCCCCCC
Confidence            36999999999885432                33489999963

>2zet_C Melanophilin; complex, GTP-binding protein, GTPase, G-protein, RAB, RAB27B, effector, SLP homology domain, acetylation, lipoprotein, membrane; HET: GTP; 3.00A {Mus musculus}

Probab=92.70  E-value=0.074  Score=32.84  Aligned_cols=28  Identities=25%  Similarity=0.421  Sum_probs=25.1

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      .=.|+.|+.+|.+-.+....|.+|.++|
T Consensus        68 ~~~C~~C~~~fg~l~~~g~~C~~C~~~V   95 (153)
T 2zet_C           68 ETHCARCLQPYRLLLNSRRQCLECSLFV   95 (153)
T ss_dssp             GTBCTTTCCBGGGCSSCCEECTTTCCEE
T ss_pred             CccchhhcCccccccCCCCcCCCCCchh
Confidence            3469999999999988999999999987

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

Probab=92.62  E-value=0.066  Score=30.79  Aligned_cols=27  Identities=33%  Similarity=0.711  Sum_probs=20.8

Q ss_pred             eEEEcCCCCCeeecCCC----------------CeeEcCCCCC
Q 035461            8 VSYICGDCGMENTLKPG----------------DVIQCRECGY   34 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~   34 (51)
                      ..|+|..||...+...+                +.-+||.||.
T Consensus        34 ~~y~C~vCGyvYD~~~Gdp~~gI~pGT~fedlPddW~CPvCga   76 (87)
T 1s24_A           34 LKWICITCGHIYDEALGDEAEGFTPGTRFEDIPDDWCCPDCGA   76 (87)
T ss_dssp             CEEEETTTTEEEETTSCCTTTTCCSCCCGGGCCTTCCCSSSCC
T ss_pred             ceEECCCCCeEecCCcCCcccCcCCCCChhHCCCCCCCCCCCC
Confidence            47999999998886422                3358999996

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

Probab=92.58  E-value=0.067  Score=33.08  Aligned_cols=31  Identities=26%  Similarity=0.625  Sum_probs=24.5

Q ss_pred             CceEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461            6 EPVSYICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      ..+.=.|.+||....... ..++||+||..-.
T Consensus       137 Gvv~a~~~~~g~~m~~~~-~~~~cp~~g~~e~  167 (179)
T 3m7n_A          137 GVLRALCSNCKTEMVREG-DILKCPECGRVEK  167 (179)
T ss_dssp             EEEECBCTTTCCBCEECS-SSEECSSSCCEEC
T ss_pred             CEEEecccccCCceEECC-CEEECCCCCCEEE
Confidence            345667889999987666 8899999998644

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

Probab=92.34  E-value=0.048  Score=33.92  Aligned_cols=26  Identities=31%  Similarity=0.700  Sum_probs=22.7

Q ss_pred             EEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           10 YICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      -.|..|+.+..-+.++..-||+|||-
T Consensus        28 P~CP~C~seytYeDg~l~vCPeC~hE   53 (138)
T 2akl_A           28 PPCPQCNSEYTYEDGALLVCPECAHE   53 (138)
T ss_dssp             CCCTTTCCCCCEECSSSEEETTTTEE
T ss_pred             CCCCCCCCcceEecCCeEECCccccc
Confidence            35899999999888889999999985

>3uk3_C Zinc finger protein 217; transcription factor, DNA binding, DNA-metal BI protein complex; 2.10A {Homo sapiens}

Probab=92.22  E-value=0.065  Score=25.45  Aligned_cols=29  Identities=24%  Similarity=0.417  Sum_probs=21.0

Q ss_pred             eEEEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      ..|.|..||+.|...           ...+..|+.||...
T Consensus         3 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f   42 (57)
T 3uk3_C            3 SSRECSYCGKFFRSNYYLNIHLRTHTGEKPYKCEFCEYAA   42 (57)
T ss_dssp             --CBCTTTCCBCSCHHHHHHHHHHHHCCCCEECSSSSCEE
T ss_pred             CCccCCCCcchhCChHHHHHHHHHcCCCCCcCCCCCcchh
Confidence            358999999998743           23568999999753

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

Probab=92.15  E-value=0.099  Score=27.57  Aligned_cols=27  Identities=33%  Similarity=0.688  Sum_probs=20.7

Q ss_pred             EEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPG----------------DVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R   35 (51)
                      .|+|..||...+...+                +.-+||.||..
T Consensus         3 ~y~C~vCGyvYd~~~Gdp~~gi~pGt~fe~lP~dw~CP~Cg~~   45 (54)
T 4rxn_A            3 KYTCTVCGYIYDPEDGDPDDGVNPGTDFKDIPDDWVCPLCGVG   45 (54)
T ss_dssp             CEEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             ceECCCCCeEECCCcCCcccCcCCCCChhHCCCCCcCcCCCCc
Confidence            5999999998876433                23499999964

>2epq_A POZ-, at HOOK-, and zinc finger-containing protein 1; C2H2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1

Probab=92.11  E-value=0.034  Score=25.61  Aligned_cols=26  Identities=23%  Similarity=0.331  Sum_probs=19.6

Q ss_pred             eEEEcCCCCCeeecC-----------CCCeeEcCCCC
Q 035461            8 VSYICGDCGMENTLK-----------PGDVIQCRECG   33 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-----------~~~~irC~~CG   33 (51)
                      ..|.|..||+.|...           ...+..|+.||
T Consensus         9 k~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~cg   45 (45)
T 2epq_A            9 KPYSCPVCGLRFKRKDRMSYHVRSHDGSVGKSGPSSG   45 (45)
T ss_dssp             CSSEETTTTEECSCHHHHHHHHHHHSCCCCCCCCCCC
T ss_pred             CCCcCCCCCcccCCHHHHHHHHHHccCCCCCCCcCCC
Confidence            458999999998642           23568899987

>1zbd_B Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: g.50.1.1

Probab=91.99  E-value=0.12  Score=31.25  Aligned_cols=27  Identities=19%  Similarity=0.482  Sum_probs=23.6

Q ss_pred             EEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           10 YICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      -.|+.|+.++.+-.+....|.+|.++|
T Consensus        56 ~~C~~C~~~~g~l~~~g~~C~~C~~~V   82 (134)
T 1zbd_B           56 NRCILCGEQLGMLGSASVVCEDCKKNV   82 (134)
T ss_dssp             SBCSSSCCBCSTTSCCEEECTTTCCEE
T ss_pred             ccccccCCCcccccCCCCCCCCCCccc
Confidence            469999999987777889999999887

>1ltl_A DNA replication initiator (CDC21/CDC54); HET: DNA; 3.00A {Methanothermobacterthermautotrophicus} SCOP: b.40.4.11

Probab=91.97  E-value=0.1  Score=33.94  Aligned_cols=30  Identities=23%  Similarity=0.556  Sum_probs=23.4

Q ss_pred             ceEEEcCCCCCeeecCC-----CCeeEcCCCCCcE
Q 035461            7 PVSYICGDCGMENTLKP-----GDVIQCRECGYRI   36 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~-----~~~irC~~CG~RI   36 (51)
                      ...|.|..||.++.+..     ..+..||.|+.+=
T Consensus       132 ~~~f~C~~C~~~~~v~~~~~~~~~P~~Cp~C~~~~  166 (279)
T 1ltl_A          132 KAVFECRGCMRHHAVTQSTNMITEPSLCSECGGRS  166 (279)
T ss_dssp             EEEEEETTTCCEEEEECSSSSCCCCSCCTTTCCCC
T ss_pred             EEEEEcCCCCCEEEEEecCCcccCCCcCCCCCCCC
Confidence            37899999998876542     2467899999874

>2ayj_A 50S ribosomal protein L40E; Zn-binding, beta-strand protein, structural genomics, PSI, protein structure initiative; NMR {Sulfolobus solfataricus} SCOP: g.41.8.7

Probab=91.70  E-value=0.11  Score=27.94  Aligned_cols=27  Identities=30%  Similarity=0.801  Sum_probs=23.0

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      ...+|-.|++.+.+.+   .+|..|||.-|
T Consensus        18 ~k~ICrkC~ARnp~~A---~~CRKCg~~~L   44 (56)
T 2ayj_A           18 LKKVCRKCGALNPIRA---TKCRRCHSTNL   44 (56)
T ss_dssp             CCEEETTTCCEECTTC---SSCTTTCCCCE
T ss_pred             chhhhccccCcCCccc---ccccCCCCCCC
Confidence            5689999999988765   88999999855

>1bbo_A Human enhancer-binding protein MBP-1; DNA-binding protein; HET: ABA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1 PDB: 3znf_A 4znf_A

Probab=91.58  E-value=0.082  Score=25.08  Aligned_cols=27  Identities=26%  Similarity=0.791  Sum_probs=20.2

Q ss_pred             EEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461           10 YICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus        10 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      |.|..||..|...           ...+..|+.||...
T Consensus         2 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f   39 (57)
T 1bbo_A            2 YICEECGIRXKKPSMLKKHIRTHTDVRPYHCTYCNFSF   39 (57)
T ss_dssp             CBCTTTCCBCSSHHHHHHHHHHTSSCCCEECSSSSCEE
T ss_pred             CcCCCCcCcCCCHHHHHHHHHhcCCCCCccCCCCCchh
Confidence            7899999988642           23568999999754

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=91.42  E-value=0.11  Score=29.53  Aligned_cols=25  Identities=20%  Similarity=0.598  Sum_probs=18.1

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      ..|.|..|++++...+    .||+||..+
T Consensus        17 ~~~~C~~C~~~~~~~a----fCPeCgq~L   41 (81)
T 2jrp_A           17 DTAHCETCAKDFSLQA----LCPDCRQPL   41 (81)
T ss_dssp             SEEECTTTCCEEEEEE----ECSSSCSCC
T ss_pred             CceECccccccCCCcc----cCcchhhHH
Confidence            4677999998876652    788777654

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

Probab=91.42  E-value=0.2  Score=25.77  Aligned_cols=26  Identities=35%  Similarity=0.837  Sum_probs=18.2

Q ss_pred             EcCCCCCeeec-CCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTL-KPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~-~~~~~irC~~CG~RI   36 (51)
                      -|.+||..+.. ...+-.+|+.||+-.
T Consensus        21 ~CP~CG~~~fm~~~~~R~~C~kCG~t~   47 (50)
T 3j20_Y           21 FCPRCGPGVFMADHGDRWACGKCGYTE   47 (50)
T ss_dssp             ECSSSCSSCEEEECSSEEECSSSCCEE
T ss_pred             cCCCCCCceEEecCCCeEECCCCCCEE
Confidence            48889874433 345778999999754

>1x5w_A Zinc finger protein 64, isoforms 1; ZNF338, nuclear protein, DNA binding, transcription, C2H2 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=91.26  E-value=0.18  Score=25.07  Aligned_cols=29  Identities=17%  Similarity=0.537  Sum_probs=22.3

Q ss_pred             eEEEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      ..|.|..||+.|...           ...+..|+.||...
T Consensus         8 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~~~f   47 (70)
T 1x5w_A            8 HPEKCSECSYSCSSKAALRIHERIHCTDRPFKCNYCSFDT   47 (70)
T ss_dssp             CSEECSSSSCEESSHHHHHHHHGGGCCSCSEECSSSSCEE
T ss_pred             CCeECCCCCcccCCHHHHHHHHHHcCCCCCEeCCCCCCcc
Confidence            459999999998742           23568999999764

>2adr_A ADR1; transcription regulation, zinc finger,; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1 g.37.1.1

Probab=91.11  E-value=0.1  Score=25.05  Aligned_cols=27  Identities=15%  Similarity=0.443  Sum_probs=20.4

Q ss_pred             EEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461           10 YICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus        10 Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      |.|..||+.|...           ...+..|+.||...
T Consensus         3 ~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f   40 (60)
T 2adr_A            3 FVCEVCTRAFARQEHLKRHYRSHTNEKPYPCGLCNRAF   40 (60)
T ss_dssp             BCCTTTCCCBSCHHHHHHHHHTTTSSCSEECTTTCCEE
T ss_pred             CcCCCCccccCCHHHHHHHHHHhCCCCCccCCCCCCcc
Confidence            8899999988642           22468999999754

>1x6e_A Zinc finger protein 24; ZNF24, KOX17, ZNF191, zscan3, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=91.08  E-value=0.2  Score=25.03  Aligned_cols=30  Identities=27%  Similarity=0.576  Sum_probs=23.0

Q ss_pred             ceEEEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            7 PVSYICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      ...|.|..|++.|...           ...+..|+.||...
T Consensus        12 ~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~C~~C~~~f   52 (72)
T 1x6e_A           12 EKPYGCVECGKAFSRSSILVQHQRVHTGEKPYKCLECGKAF   52 (72)
T ss_dssp             CCCEECSSSCCEESSHHHHHHHHHGGGCSCCEECSSSCCEE
T ss_pred             CCCccCCCCCCccCCHHHHHHHHHhcCCCCCeECCCCCccc
Confidence            3569999999998642           23578999999754

>2lv2_A Insulinoma-associated protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=90.22  E-value=0.21  Score=27.23  Aligned_cols=29  Identities=24%  Similarity=0.536  Sum_probs=22.7

Q ss_pred             eEEEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      -.|+|..||+.|...           ...+..|+.||...
T Consensus        27 ~~h~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~k~F   66 (85)
T 2lv2_A           27 ECHLCPVCGESFASKGAQERHLRLLHAAQVFPCKYCPATF   66 (85)
T ss_dssp             TTEECTTSCCEESSHHHHHHHHHTTSCSSSEECTTSSCEE
T ss_pred             CCEECCCCCCCcCcHHHHhhhhhhccCCCccCCCCCCCEe
Confidence            349999999999853           23578999999764

>2yt9_A Zinc finger-containing protein 1; C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1 g.37.1.1

Probab=89.75  E-value=0.41  Score=24.63  Aligned_cols=13  Identities=23%  Similarity=0.388  Sum_probs=8.0

Q ss_pred             eEEEcCCCCCeee
Q 035461            8 VSYICGDCGMENT   20 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~   20 (51)
                      ..|.|..|+..|.
T Consensus         6 ~~~~C~~C~~~f~   18 (95)
T 2yt9_A            6 SGVACEICGKIFR   18 (95)
T ss_dssp             SCEECSSSCCEES
T ss_pred             CCeECCCCCCccC
Confidence            3466666666664

>2lce_A B-cell lymphoma 6 protein; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=89.51  E-value=0.16  Score=25.44  Aligned_cols=31  Identities=23%  Similarity=0.535  Sum_probs=23.3

Q ss_pred             CceEEEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            6 EPVSYICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      ....|.|..||+.|...           ...+..|+.||...
T Consensus        14 ~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~f   55 (74)
T 2lce_A           14 SDKPYKCDRCQASFRYKGNLASHKTVHTGEKPYRCNICGAQF   55 (74)
T ss_dssp             CCCSBCCTTSSCCBSCHHHHHHHHHHHCCCCSEECTTTCCEE
T ss_pred             CCCCeECCCCCceeCCHHHHHHHHHHcCCCCCEECCCCCchh
Confidence            34569999999998742           23568999999754

>2eod_A TNF receptor-associated factor 4; zinc binding, NF-KB, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.40  E-value=0.45  Score=23.43  Aligned_cols=30  Identities=23%  Similarity=0.445  Sum_probs=23.3

Q ss_pred             eEEEcCCCCCeeecC----------CCCeeEcC-CCCCcEEE
Q 035461            8 VSYICGDCGMENTLK----------PGDVIQCR-ECGYRILY   38 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~----------~~~~irC~-~CG~RIly   38 (51)
                      -.|.|..||+.|. .          ...+..|+ .||.....
T Consensus         9 ~~~~C~~C~k~f~-~~~L~~H~~~~~~~p~~C~~~C~k~f~~   49 (66)
T 2eod_A            9 RTQPCTYCTKEFV-FDTIQSHQYQCPRLPVACPNQCGVGTVA   49 (66)
T ss_dssp             CEEECSSSCCEEE-HHHHHHHHHHCSSSEEECTTCCSCCEEE
T ss_pred             CCeeccccCCccC-HHHHHHHHHHcCCcCccCCcccCccccc
Confidence            5699999999986 3          23578999 99987554

>1llm_C Chimera of ZIF23-GCN4; dimerization, DNA recognition, leucine zipper, X-RAY crystallography, structure-based design, zinc fingers; 1.50A {Mus musculus} SCOP: g.37.1.1 g.37.1.1 PDB: 1xf7_A

Probab=89.11  E-value=0.38  Score=24.80  Aligned_cols=28  Identities=18%  Similarity=0.470  Sum_probs=21.1

Q ss_pred             EEEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            9 SYICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      .|.|..||+.|...           ...+..|+.||...
T Consensus         3 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~~~~C~~C~k~f   41 (88)
T 1llm_C            3 PFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKF   41 (88)
T ss_dssp             CEECTTTCCEESCHHHHHHHHHHHHCCCCEECTTTCCEE
T ss_pred             CCcCCCCCCccCCHHHHHHHHHHcCCCCCccCCCCCCcc
Confidence            38999999998742           23568999999653

>2csz_A Synaptotagmin-like protein 4; exophilin 2, granuphilin, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=89.09  E-value=0.13  Score=28.94  Aligned_cols=30  Identities=17%  Similarity=0.318  Sum_probs=26.1

Q ss_pred             ceEEEcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461            7 PVSYICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      ...=.|+.|+..+.+-.+....|+.|-++|
T Consensus        23 ~~~r~CarC~~~LG~l~~~g~~C~~Ck~rV   52 (76)
T 2csz_A           23 YSDRTCARCQESLGRLSPKTNTCRGCNHLV   52 (76)
T ss_dssp             CCCCBCSSSCCBCSSSCTTTSEETTTTEEC
T ss_pred             CCccchhhhCccccccccCCCcCcccChhh
Confidence            345679999999999888999999999886

>2d9k_A FLN29 gene product; zinc finger, ZF-TRAF, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.02  E-value=0.19  Score=26.30  Aligned_cols=30  Identities=23%  Similarity=0.604  Sum_probs=23.4

Q ss_pred             eEEEcCCCCCeeecC---------CCCeeEcCCCCCcEE
Q 035461            8 VSYICGDCGMENTLK---------PGDVIQCRECGYRIL   37 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~---------~~~~irC~~CG~RIl   37 (51)
                      -.|.|..|+..|...         ...++.|++||..+.
T Consensus        16 r~~~C~~C~~~~~~~~L~~H~~~c~~~~~~C~~C~~~~~   54 (75)
T 2d9k_A           16 RLAVCQHCDLELSILKLKEHEDYCGARTELCGNCGRNVL   54 (75)
T ss_dssp             CCEECSSSCCEECHHHHHHHHHHHHHCEEECSSSCCEEE
T ss_pred             cccCCcccChHhhHHHHHHHHhHcCCCceEcccCCCcCc
Confidence            468999999999653         236899999998643

>2kmk_A Zinc finger protein GFI-1; tandem repeat zinc finger domain, protein-DNA complex, DNA-B metal-binding, nucleus; HET: DNA; NMR {Rattus norvegicus}

Probab=88.95  E-value=0.39  Score=23.89  Aligned_cols=27  Identities=30%  Similarity=0.626  Sum_probs=16.7

Q ss_pred             EEEcCCCCCeeecC-----------CCCeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLK-----------PGDVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~R   35 (51)
                      .|.|..|+..+...           ...+..|+.||..
T Consensus        29 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~   66 (82)
T 2kmk_A           29 PYPCQYCGKRFHQKSDMKKHTFIHTGEKPHKCQVCGKA   66 (82)
T ss_dssp             CEECSSSCCEESSHHHHHHHHHHHHTCCCEECTTTSCE
T ss_pred             CeeCCcCChhhCCHHHHHHHHHHhcCCCCCcCCCcchh
Confidence            47777777776532           2245777777754

>2epr_A POZ-, at HOOK-, and zinc finger-containing protein 1; C2H2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1

Probab=88.88  E-value=0.18  Score=23.46  Aligned_cols=28  Identities=11%  Similarity=-0.015  Sum_probs=20.5

Q ss_pred             ceEEEcCCCCCeeecC-----------CCCeeEcCCCCC
Q 035461            7 PVSYICGDCGMENTLK-----------PGDVIQCRECGY   34 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~   34 (51)
                      ...|.|..||+.|...           ...+..|+.||.
T Consensus        10 ~k~~~C~~C~k~f~~~~~L~~H~~~H~~~k~~~C~~C~k   48 (48)
T 2epr_A           10 RKQVACEICGKIFRDVYHLNRHKLSHSGEKPYSSGPSSG   48 (48)
T ss_dssp             CCSEEETTTTEEESSHHHHHHHGGGSCSCCCCCSCCCCC
T ss_pred             CcCeeCCCCCcccCCHHHHHHHHHhcCCCCCccCCCCCC
Confidence            3569999999998642           224578999983

>3flo_B DNA polymerase alpha catalytic subunit A; protein-protein complex, phosphoesterase fold, OB fold, zinc motif, DNA replication, nucleus; HET: DNA; 2.50A {Saccharomyces cerevisiae}

Probab=88.82  E-value=0.45  Score=30.57  Aligned_cols=32  Identities=16%  Similarity=0.449  Sum_probs=25.1

Q ss_pred             CCceEEEcCCCCCeeecCC----C------CeeEcCCCCCcE
Q 035461            5 PEPVSYICGDCGMENTLKP----G------DVIQCRECGYRI   36 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~----~------~~irC~~CG~RI   36 (51)
                      -++....|..||.++....    .      ..+.||.|+..+
T Consensus        18 c~~l~l~Cp~C~~~~~F~gv~~~~~~~~~~sg~~C~~C~~~~   59 (206)
T 3flo_B           18 TVTLELSCPSCDKRFPFGGIVSSNYYRVSYNGLQCKHCEQLF   59 (206)
T ss_dssp             CCCEEEECTTTCCEEEECSSSCCSSEEEETTEEEETTTCCBC
T ss_pred             CceeEEECCCCCCccCCCCcccCCCcccccccccCCCCCCcC
Confidence            4678999999999888651    1      368899999864

>2drp_A Protein (tramtrack DNA-binding domain); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 2.80A {Drosophila melanogaster} SCOP: g.37.1.1 g.37.1.1

Probab=88.63  E-value=0.52  Score=22.83  Aligned_cols=29  Identities=24%  Similarity=0.333  Sum_probs=22.1

Q ss_pred             eEEEcCCCCCeeecC-------------CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK-------------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-------------~~~~irC~~CG~RI   36 (51)
                      ..|.|..||+.|...             ...+..|+.||...
T Consensus         9 k~~~C~~C~k~f~~~~~l~~H~~~~H~~~~~~~~C~~C~k~f   50 (66)
T 2drp_A            9 HTYRCKVCSRVYTHISNFCRHYVTSHKRNVKVYPCPFCFKEF   50 (66)
T ss_dssp             TEEECTTTCCEESSHHHHHHHHHHHSSSSCCCEECTTTCCEE
T ss_pred             cceECCCCcchhCCHHHHHHHHHHHcCCCCcCeECCCCCCcc
Confidence            569999999998631             22568999999754

>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=88.62  E-value=0.15  Score=28.45  Aligned_cols=30  Identities=23%  Similarity=0.534  Sum_probs=21.5

Q ss_pred             ceEEEcCCCCCeeecCCCCee-EcCCCCCcE
Q 035461            7 PVSYICGDCGMENTLKPGDVI-QCRECGYRI   36 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~i-rC~~CG~RI   36 (51)
                      ...|.|..||++--......| .|..||..+
T Consensus        24 ~~ky~C~fCgk~~vkR~a~GIW~C~~C~~~~   54 (72)
T 3jyw_9           24 HARYDCSFCGKKTVKRGAAGIWTCSCCKKTV   54 (72)
T ss_dssp             HSCBCCSSCCSSCBSBCSSSCBCCSSSCCCC
T ss_pred             ccCccCCCCCCceeEecCCCeEECCCCCCEE
Confidence            357999999988433344444 999999754

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

Probab=88.50  E-value=0.3  Score=27.72  Aligned_cols=18  Identities=17%  Similarity=0.499  Sum_probs=14.4

Q ss_pred             CCCeeEcCCCCCcEEEEE
Q 035461           23 PGDVIQCRECGYRILYKK   40 (51)
Q Consensus        23 ~~~~irC~~CG~RIlyK~   40 (51)
                      ....+.|||||-+..+|.
T Consensus        50 ~~g~~~CpYCg~~f~l~~   67 (80)
T 2jvm_A           50 ETGFVECGYCDRRYIHES   67 (80)
T ss_dssp             TTCEEECSSSSCEEEEHH
T ss_pred             CCCeEECCCCCCEEEecC
Confidence            357899999999887763

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

Probab=88.42  E-value=0.61  Score=26.20  Aligned_cols=33  Identities=21%  Similarity=0.412  Sum_probs=25.8

Q ss_pred             CceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461            6 EPVSYICGDCGMENTLKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~   40 (51)
                      ....++|-.|-+..  +...-.-||.||+.-|.|.
T Consensus        12 k~~iLrC~aCf~~t--~~~~k~FCp~CGn~TL~Rv   44 (79)
T 2con_A           12 RSYILRCHGCFKTT--SDMNRVFCGHCGNKTLKKV   44 (79)
T ss_dssp             CCEEEECSSSCCEE--SCSSCCSCSSSCCSCCEEE
T ss_pred             eeeeeEecccceEC--CCcccccccccCcccceEE
Confidence            45789999998875  3335688999999988774

>2vl6_A SSO MCM N-TER, minichromosome maintenance protein MCM; helicase, hydrolase, zinc-finger, ATP-binding, DNA-BIND ssDNA binding; 2.8A {Sulfolobus solfataricus}

Probab=88.21  E-value=0.4  Score=30.79  Aligned_cols=29  Identities=24%  Similarity=0.379  Sum_probs=23.0

Q ss_pred             ceEEEc--CCCCCeeecC---C-----CCeeEcCCCCCc
Q 035461            7 PVSYIC--GDCGMENTLK---P-----GDVIQCRECGYR   35 (51)
Q Consensus         7 ~~~Y~C--~~Cg~~~~~~---~-----~~~irC~~CG~R   35 (51)
                      ...|.|  ..||.++...   .     ..+..||.|+.+
T Consensus       139 ~~~f~C~~~~C~~~~~~~~~~~~~~~~~~P~~Cp~C~~~  177 (268)
T 2vl6_A          139 KATYKHIHPDCMQEFEWPEDEEMPEVLEMPTICPKCGKP  177 (268)
T ss_dssp             ECEEEEECTTCCCEEESSTTSCCCTTCCCCSBCTTTCCB
T ss_pred             EEEEECCCCCCCCEEeeeecccCCCcccCCccCCCCCCC
Confidence            367999  9999988766   2     246789999986

>1a1h_A QGSR zinc finger peptide; complex (zinc finger/DNA), DNA-binding protein, transcription/DNA complex; HET: DNA; 1.60A {Mus musculus} SCOP: g.37.1.1 g.37.1.1 g.37.1.1 PDB: 1jk2_A 1jk1_A 1a1g_A* 1a1f_A* 1a1i_A* 1a1j_A* 1a1k_A* 1aay_A* 1a1l_A* 1p47_A 1zaa_C* 1g2f_C 1g2d_C

Probab=88.06  E-value=0.5  Score=23.96  Aligned_cols=27  Identities=19%  Similarity=0.475  Sum_probs=15.2

Q ss_pred             EEEcCCCCCeeecC-----------CCCeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLK-----------PGDVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~R   35 (51)
                      .|.|..||..|...           ...+..|+.||..
T Consensus        34 ~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~   71 (90)
T 1a1h_A           34 PFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRK   71 (90)
T ss_dssp             CEECTTTCCEESCHHHHHHHHHHHHCCCCEECTTTCCE
T ss_pred             CccCCCCCcccCCHHHHHHHHHHcCCCCCccCCCCCch
Confidence            36666666666532           1234667666654

>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_Y 4a1c_Y 4a1e_Y

Probab=87.56  E-value=0.24  Score=29.34  Aligned_cols=30  Identities=23%  Similarity=0.454  Sum_probs=21.5

Q ss_pred             ceEEEcCCCCCeeecCCCCe-eEcCCCCCcE
Q 035461            7 PVSYICGDCGMENTLKPGDV-IQCRECGYRI   36 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~-irC~~CG~RI   36 (51)
                      ...|.|..||+.---....+ -.|..||..+
T Consensus        34 ~aky~CpfCgk~~vKR~a~GIW~C~kCg~~~   64 (103)
T 4a17_Y           34 HAKYGCPFCGKVAVKRAAVGIWKCKPCKKII   64 (103)
T ss_dssp             HSCEECTTTCCEEEEEEETTEEEETTTTEEE
T ss_pred             hcCCCCCCCCCceeeecCcceEEcCCCCCEE
Confidence            35799999998854333344 4999999754

>1vzi_A Desulfoferrodoxin; ferrocyanide, microspectrophotometry, redox states, photoreduction, dinuclear iron cluster, oxidoreductase; 1.15A {Desulfovibrio baarsii} SCOP: b.1.13.1 g.41.5.2 PDB: 1vzh_A* 1vzg_A 2ji1_A 2ji2_A 2ji3_A 1dfx_A

Probab=87.44  E-value=0.56  Score=27.86  Aligned_cols=26  Identities=23%  Similarity=0.442  Sum_probs=19.5

Q ss_pred             ceEEEcCCCCCeeecC--CCCeeEcCCCCC
Q 035461            7 PVSYICGDCGMENTLK--PGDVIQCRECGY   34 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~--~~~~irC~~CG~   34 (51)
                      ...|+|..||..++.-  .+..+.|  ||-
T Consensus         5 ~~fYkC~~CGnivev~~~g~~~l~C--CG~   32 (126)
T 1vzi_A            5 LQVYKCEVCGNIVEVLNGGIGELVC--CNQ   32 (126)
T ss_dssp             TCEEECTTTCCEEEEEECCSSCEEE--TTE
T ss_pred             CcEEEcCCCCeEEEEEcCCCcceec--CCc
Confidence            4689999999999853  4456777  664

>2ct1_A Transcriptional repressor CTCF; CCCTC-BINDING factor, zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=87.27  E-value=0.5  Score=23.75  Aligned_cols=29  Identities=24%  Similarity=0.431  Sum_probs=22.0

Q ss_pred             eEEEcCCCCCeeecC-----------CC--CeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK-----------PG--DVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-----------~~--~~irC~~CG~RI   36 (51)
                      ..|.|..|++.|...           ..  .+..|+.||...
T Consensus        14 k~~~C~~C~k~f~~~~~L~~H~~~~h~~~~~~~~C~~C~~~f   55 (77)
T 2ct1_A           14 KPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVI   55 (77)
T ss_dssp             CSEECTTTCCEESCHHHHHHHHHHHSSSSCSSEECSSSSCEE
T ss_pred             CCeECCCcCchhCCHHHHHHHHHHhcCCCCCccCCCCCCCcc
Confidence            459999999998742           22  468999999754

>2lt7_A Transcriptional regulator kaiso; zinc finger, double helix, metal binding protein-DNA complex; HET: DNA; NMR {Homo sapiens} PDB: 4f6m_A* 4f6n_A*

Probab=87.03  E-value=0.65  Score=26.70  Aligned_cols=29  Identities=28%  Similarity=0.376  Sum_probs=19.0

Q ss_pred             ceEEEcCCCCCeeecC-----------CCCeeEcCCCCCc
Q 035461            7 PVSYICGDCGMENTLK-----------PGDVIQCRECGYR   35 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~R   35 (51)
                      ...|.|..||+.|...           ...+-.|+.||..
T Consensus        20 ek~y~C~~C~k~F~~~~~L~~H~~~H~~~k~~~C~~C~k~   59 (133)
T 2lt7_A           20 RVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKV   59 (133)
T ss_dssp             EEEEEETTTCCEESCHHHHHHHHHHHHCCSCEECSSSSCE
T ss_pred             CcCeECCCCCCCcCCHHHHHHHHHHcCCCCCeeCCccCee
Confidence            3568888888877642           1235678888754

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

Probab=86.98  E-value=0.33  Score=27.98  Aligned_cols=20  Identities=20%  Similarity=0.340  Sum_probs=15.4

Q ss_pred             cCCCCeeEcCCCCCcEEEEE
Q 035461           21 LKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus        21 ~~~~~~irC~~CG~RIlyK~   40 (51)
                      +...+.+.|||||-+..+|.
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            34457899999999887764

>2csh_A Zinc finger protein 297B; ZF-C2H2 domain, zinc finger and BTB domain containing protein 22B, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=86.61  E-value=0.84  Score=24.16  Aligned_cols=11  Identities=45%  Similarity=1.011  Sum_probs=5.3

Q ss_pred             EEcCCCCCeee
Q 035461           10 YICGDCGMENT   20 (51)
Q Consensus        10 Y~C~~Cg~~~~   20 (51)
                      |.|..|+..|.
T Consensus        38 ~~C~~C~~~f~   48 (110)
T 2csh_A           38 YGCGVCGKKFK   48 (110)
T ss_dssp             EECTTTSCEES
T ss_pred             ccCCCCCcccC
Confidence            44555554443

>2d9h_A Zinc finger protein 692; ZF-C2H2 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=86.48  E-value=0.46  Score=23.86  Aligned_cols=30  Identities=27%  Similarity=0.549  Sum_probs=22.7

Q ss_pred             ceEEEcCCCCCeeecC--------------CCCeeEcCCCCCcE
Q 035461            7 PVSYICGDCGMENTLK--------------PGDVIQCRECGYRI   36 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~--------------~~~~irC~~CG~RI   36 (51)
                      ...|.|..||+.|...              ...+..|+.||...
T Consensus         5 ~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~C~~C~k~f   48 (78)
T 2d9h_A            5 SSGLQCEICGFTCRQKASLNWHQRKHAETVAALRFPCEFCGKRF   48 (78)
T ss_dssp             CCCEECSSSCCEESSHHHHHHHHHHHHHHTTTCCEECTTTCCEE
T ss_pred             CcCeECCCCCCeeCCHHHHHHHHHHhhccCCCcccCCCCCCchh
Confidence            3569999999998642              13568999999764

>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z

Probab=86.47  E-value=0.58  Score=28.16  Aligned_cols=31  Identities=23%  Similarity=0.599  Sum_probs=22.5

Q ss_pred             CceEEEcCCCCCeeecC-CCCeeEcCCCCCcE
Q 035461            6 EPVSYICGDCGMENTLK-PGDVIQCRECGYRI   36 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RI   36 (51)
                      +...|.|..||++.-.. ....-.|+.||+.+
T Consensus        57 q~akytCPfCGk~~vKR~avGIW~C~~Cgk~f   88 (116)
T 3cc2_Z           57 MNEDHACPNCGEDRVDRQGTGIWQCSYCDYKF   88 (116)
T ss_dssp             HHSCEECSSSCCEEEEEEETTEEEETTTCCEE
T ss_pred             hccCCcCCCCCCceeEecCceeEECCCCCCEE
Confidence            34679999999853222 44678999999864

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

Probab=86.40  E-value=0.38  Score=26.40  Aligned_cols=18  Identities=17%  Similarity=0.471  Sum_probs=14.1

Q ss_pred             CCCeeEcCCCCCcEEEEE
Q 035461           23 PGDVIQCRECGYRILYKK   40 (51)
Q Consensus        23 ~~~~irC~~CG~RIlyK~   40 (51)
                      ....+.|||||-+...|.
T Consensus        37 ~~g~~~CpYCg~~f~l~~   54 (67)
T 2jrr_A           37 DTGWVECPYCDCKYVLKG   54 (67)
T ss_dssp             TTSEEEETTTTEEEEETT
T ss_pred             CCCeEECCCCCCEEEECC
Confidence            347899999998877664

>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=86.32  E-value=0.21  Score=28.49  Aligned_cols=29  Identities=24%  Similarity=0.615  Sum_probs=20.8

Q ss_pred             eEEEcCCCCCeeecCCC-CeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLKPG-DVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~-~~irC~~CG~RI   36 (51)
                      ..|.|..||+.---... .--.|..||..+
T Consensus        34 ~ky~CpfCGk~~vkR~a~GIW~C~kCg~~~   63 (83)
T 3j21_i           34 QKHTCPVCGRKAVKRISTGIWQCQKCGATF   63 (83)
T ss_dssp             SCBCCSSSCSSCEEEEETTEEEETTTCCEE
T ss_pred             cccCCCCCCCceeEecCcCeEEcCCCCCEE
Confidence            57999999988433333 445999999865

>1yc5_A NAD-dependent deacetylase; SIR2, sirtuin, SIR2TM, SIRT1, nicotinamide, hydrolase; HET: ALY; 1.40A {Thermotoga maritima} SCOP: c.31.1.5 PDB: 2h2d_A* 2h2f_A 2h2g_A* 2h2h_A* 2h2i_A* 2h4f_A* 2h4j_A* 3d4b_A* 3d81_A* 3pdh_A* 2h4h_A* 3jr3_A* 2h59_A*

Probab=85.86  E-value=0.71  Score=29.47  Aligned_cols=29  Identities=31%  Similarity=0.670  Sum_probs=20.8

Q ss_pred             eEEEcCCCCCeeecC-------CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK-------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~RI   36 (51)
                      ....|..|+...+.+       ....-+||.||..+
T Consensus       120 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~l  155 (246)
T 1yc5_A          120 EEYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLI  155 (246)
T ss_dssp             EEEEETTTCCEEEHHHHHHHTTTCSSCBCTTTCCBE
T ss_pred             ceeEcCCCCCCCcHHHHHHHhccCCCCCCCCCCCcc
Confidence            456799999987642       22356999999853

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

Probab=85.61  E-value=1.7  Score=23.61  Aligned_cols=29  Identities=31%  Similarity=0.739  Sum_probs=24.0

Q ss_pred             eEEEcCCCCCeeecC--CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK--PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RI   36 (51)
                      |.=+|.+|+.+..+-  +...+.|..||.-+
T Consensus        14 m~VkCp~C~~~q~VFSha~t~V~C~~Cgt~L   44 (63)
T 3j20_W           14 LRVKCIDCGNEQIVFSHPATKVRCLICGATL   44 (63)
T ss_dssp             EEEECSSSCCEEEEESSCSSCEECSSSCCEE
T ss_pred             EEEECCCCCCeeEEEecCCeEEEccCcCCEE
Confidence            888999999988764  55789999999644

>2dmd_A Zinc finger protein 64, isoforms 1 and 2; ZNF338, nuclear protein, DNA- binding, transcription, C2H2-type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1 g.37.1.1

Probab=85.57  E-value=0.75  Score=23.61  Aligned_cols=11  Identities=27%  Similarity=0.842  Sum_probs=6.2

Q ss_pred             EEcCCCCCeee
Q 035461           10 YICGDCGMENT   20 (51)
Q Consensus        10 Y~C~~Cg~~~~   20 (51)
                      |.|..|+..|.
T Consensus        37 ~~C~~C~~~f~   47 (96)
T 2dmd_A           37 YKCKTCDYAAA   47 (96)
T ss_dssp             EECSSSCCEES
T ss_pred             EeCCCCCCccC
Confidence            55666655554

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

Probab=85.49  E-value=0.49  Score=24.70  Aligned_cols=25  Identities=20%  Similarity=0.339  Sum_probs=17.4

Q ss_pred             EcCCCCC-eeecC-CCCeeEcCCCCCc
Q 035461           11 ICGDCGM-ENTLK-PGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~-~~~~~-~~~~irC~~CG~R   35 (51)
                      .|.+||. .+... ....+.|..||.=
T Consensus        13 ~Cp~C~~~~lv~D~~~ge~vC~~CGlV   39 (58)
T 1dl6_A           13 TCPNHPDAILVEDYRAGDMICPECGLV   39 (58)
T ss_dssp             SBTTBSSSCCEECSSSCCEECTTTCCE
T ss_pred             cCcCCCCCceeEeCCCCeEEeCCCCCE
Confidence            6999987 33333 3467999999853

>1y07_A Desulfoferrodoxin (RBO); beta-sheet, iron binding, oxidoreductase; 1.55A {Treponema pallidum subsp}

Probab=85.36  E-value=0.7  Score=27.53  Aligned_cols=27  Identities=15%  Similarity=0.298  Sum_probs=16.8

Q ss_pred             CceEEEcCC-CCCeeec--CCCCeeEcCCCCC
Q 035461            6 EPVSYICGD-CGMENTL--KPGDVIQCRECGY   34 (51)
Q Consensus         6 ~~~~Y~C~~-Cg~~~~~--~~~~~irC~~CG~   34 (51)
                      +...|+|.. ||..++.  ..+..+.|  ||-
T Consensus         4 ~~~fYkC~~~CGnivev~~~g~~~l~C--CG~   33 (128)
T 1y07_A            4 ELSFFLQKESAGFFLGMDAPAGSSVAC--GSE   33 (128)
T ss_dssp             CEEEECC-----CEEEESCCTTCEEEE--TTE
T ss_pred             cCcEEECCCCCCCEEEEEcCCCcceee--cCc
Confidence            456899999 9999987  34466777  664

>2dlq_A GLI-kruppel family member HKR3; ZF-C2H2 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: g.37.1.1 g.37.1.1 g.37.1.1 g.37.1.1

Probab=85.16  E-value=0.74  Score=24.52  Aligned_cols=29  Identities=14%  Similarity=0.397  Sum_probs=19.1

Q ss_pred             eEEEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      ..|.|..||..|...           ...+..|+.||...
T Consensus        65 ~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f  104 (124)
T 2dlq_A           65 QVFTCSVCQETFRRRMELRLHMVSHTGEMPYKCSSCSQQF  104 (124)
T ss_dssp             CCEECSSSCCEESSHHHHHHHHHHHSSSCSEECSSSCCEE
T ss_pred             CCeECCCCCCccCCHHHHHHHHHHcCCCCCccCCCccchh
Confidence            457888888877642           22457888887653

>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y*

Probab=84.81  E-value=0.43  Score=26.51  Aligned_cols=32  Identities=28%  Similarity=0.757  Sum_probs=23.2

Q ss_pred             CCceEEEcCCCCCeeecC-CCCeeEcCCCCCcE
Q 035461            5 PEPVSYICGDCGMENTLK-PGDVIQCRECGYRI   36 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~-~~~~irC~~CG~RI   36 (51)
                      .+...|.|..||++--.. ....-.|..||..+
T Consensus        23 ~q~~ky~C~fCgk~~vkR~a~GIW~C~~C~~~~   55 (73)
T 1ffk_W           23 KHKKKYKCPVCGFPKLKRASTSIWVCGHCGYKI   55 (73)
T ss_pred             hcccCccCCCCCCceeEEEEeEEEECCCCCcEE
Confidence            356789999999853332 34568899999764

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

Probab=84.78  E-value=1.4  Score=24.24  Aligned_cols=29  Identities=31%  Similarity=0.797  Sum_probs=23.5

Q ss_pred             eEEEcCCCCCeeecC--CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK--PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RI   36 (51)
                      |.=+|.+|+.+..+-  +...+.|..||.-+
T Consensus         6 m~VKCp~C~niq~VFShA~tvV~C~~Cg~~L   36 (66)
T 1qxf_A            6 VKVKCPDCEHEQVIFDHPSTIVKCIICGRTV   36 (66)
T ss_dssp             EEEECTTTCCEEEEESSCSSCEECSSSCCEE
T ss_pred             EEEECCCCCCceEEEecCceEEEcccCCCEE
Confidence            667899999988764  56789999999644

>1rfh_A RAS association (ralgds/AF-6) domain family 5; zinc, signal transduction, apoptosis, cysteine rich domain, metal binding protein; NMR {Mus musculus}

Probab=84.75  E-value=0.95  Score=23.31  Aligned_cols=23  Identities=26%  Similarity=0.748  Sum_probs=17.9

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      -|..||..+   ...+++|..||+.+
T Consensus        24 ~C~~C~~~i---~kqg~kC~~C~~~c   46 (59)
T 1rfh_A           24 WCDLCGREV---LRQALRCANCKFTC   46 (59)
T ss_dssp             ECTTTCSEE---CSCCEECTTTSCEE
T ss_pred             Echhcchhh---hhCccEeCCCCCeE
Confidence            488898887   45678999998754

>2eps_A POZ-, at HOOK-, and zinc finger-containing protein 1; C2H2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1

Probab=84.72  E-value=0.67  Score=22.01  Aligned_cols=30  Identities=20%  Similarity=0.337  Sum_probs=21.7

Q ss_pred             CceEEEcCCCCCeeecC------------CCCeeEcCCCCCc
Q 035461            6 EPVSYICGDCGMENTLK------------PGDVIQCRECGYR   35 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~------------~~~~irC~~CG~R   35 (51)
                      ....|.|..||+.|...            ...+..|+.||..
T Consensus         9 ~~k~~~C~~C~k~f~~~~~L~~H~~~~H~~~k~~~C~~C~k~   50 (54)
T 2eps_A            9 VGKPYICQSCGKGFSRPDHLNGHIKQVHTSERPHKCQVWVSG   50 (54)
T ss_dssp             SSCCEECSSSCCEESSHHHHHHHHHHTSCCCCCCCSSSSCCS
T ss_pred             CCCCeECCCCCcccCCHHHHHHHHHHhcCCCCCccCCCCCCC
Confidence            34569999999998632            1245789999965

>3irb_A Uncharacterized protein from DUF35 family; 13815350, protein with unknown function from DUF35 family, S genomics; 1.80A {Sulfolobus solfataricus}

Probab=84.67  E-value=0.7  Score=27.72  Aligned_cols=30  Identities=20%  Similarity=0.352  Sum_probs=23.6

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~   40 (51)
                      +.-+|.+||+.+-...   ..||.||..-+--.
T Consensus        46 ~~~rC~~CG~~~~PPr---~~Cp~C~s~~~~~v   75 (145)
T 3irb_A           46 IGSKCSKCGRIFVPAR---SYCEHCFVKIENYV   75 (145)
T ss_dssp             EEEECTTTCCEEESCC---SEETTTTEECCEEE
T ss_pred             EEEEeCCCCcEEcCch---hhCcCCCCCceeee
Confidence            6789999999986653   56999999876543

>3lpe_B DNA-directed RNA polymerase subunit E''; transcription regulation, SPT4, SPT5, NUSG, archaea, evoluti directed RNA polymerase; 1.90A {Methanocaldococcus jannaschii} SCOP: g.41.9.0

Probab=84.59  E-value=0.47  Score=25.33  Aligned_cols=20  Identities=20%  Similarity=0.429  Sum_probs=15.5

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      -|..|+...+.+     .||+||+.
T Consensus         3 AC~~C~~v~~~~-----~CpnC~~~   22 (59)
T 3lpe_B            3 ACLKCKYLTNDE-----ICPICHSP   22 (59)
T ss_dssp             EETTTCBEESSS-----BCTTTCCB
T ss_pred             ccccCCcccCCC-----CCCCCCCC
Confidence            488999886544     69999983

>2ytg_A ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=84.55  E-value=0.72  Score=20.81  Aligned_cols=15  Identities=27%  Similarity=0.880  Sum_probs=12.0

Q ss_pred             eEEEcCCCCCeeecC
Q 035461            8 VSYICGDCGMENTLK   22 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~   22 (51)
                      ..|.|..||+.|...
T Consensus        11 ~~~~C~~C~k~f~~~   25 (46)
T 2ytg_A           11 KPFKCGECGKSYNQR   25 (46)
T ss_dssp             CSEECTTTCCEESSS
T ss_pred             CCeECCCCCcccCCH
Confidence            459999999998753

>2cot_A Zinc finger protein 435; ADK_LID domain, zinc finger and SCAN domain containing protein 16, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=84.17  E-value=0.4  Score=24.13  Aligned_cols=31  Identities=29%  Similarity=0.670  Sum_probs=22.8

Q ss_pred             CceEEEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            6 EPVSYICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      +...|.|..||+.|...           ...+..|+.||...
T Consensus        15 ~~~~~~C~~C~~~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f   56 (77)
T 2cot_A           15 ERRRYKCDECGKSFSHSSDLSKHRRTHTGEKPYKCDECGKAF   56 (77)
T ss_dssp             CSCSSBCSSSCCBCSCHHHHHHHHTTTCCSCSEECSSSCCEE
T ss_pred             CCCCEECCCCCcccCCHHHHHHHHHHcCCCcCeeCCCCCCcc
Confidence            34569999999998732           12468999999754

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

Probab=84.13  E-value=0.71  Score=26.72  Aligned_cols=24  Identities=25%  Similarity=0.693  Sum_probs=18.8

Q ss_pred             cCCCCCeeecCCCC-----eeEcCCCCCc
Q 035461           12 CGDCGMENTLKPGD-----VIQCRECGYR   35 (51)
Q Consensus        12 C~~Cg~~~~~~~~~-----~irC~~CG~R   35 (51)
                      |.+||..+.++...     ...|+.|||.
T Consensus         7 Cp~Cgn~L~~~~~~~~~~~~~~C~~C~y~   35 (113)
T 3h0g_I            7 CIECNNMLYPREDKVDRVLRLACRNCDYS   35 (113)
T ss_dssp             CSSSCCCCEECCCTTTCCCCEECSSSCCE
T ss_pred             CcCCCCEeeEcccCCCCeeEEECCCCCCe
Confidence            88999988776432     5899999984

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

Probab=84.09  E-value=0.79  Score=24.67  Aligned_cols=23  Identities=26%  Similarity=0.748  Sum_probs=17.6

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      -|..||..+   ...+++|..||+.+
T Consensus        37 ~C~~C~~~l---~~qG~kC~~C~~~c   59 (72)
T 2fnf_X           37 WCDLCGREV---LRQALRCANCKFTC   59 (72)
T ss_dssp             BCTTTSSBC---SSCCEECTTSSCEE
T ss_pred             chhhhhHHH---HhCcCccCCCCCee
Confidence            388888887   45678999998754

>3p8b_A DNA-directed RNA polymerase, subunit E''; transcription elongation factor, RNA polymerase, transferase transcription complex; 1.80A {Pyrococcus furiosus}

Probab=83.81  E-value=0.45  Score=27.10  Aligned_cols=21  Identities=29%  Similarity=0.703  Sum_probs=16.7

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      -|.+|+..++-+     .||+||+.-
T Consensus        25 AC~~C~~v~~~d-----~CPnCgs~~   45 (81)
T 3p8b_A           25 ACRHCHYITSED-----RCPVCGSRD   45 (81)
T ss_dssp             EETTTCBEESSS-----SCTTTCCCC
T ss_pred             HHhhCCCccCCC-----CCCCCCCCc
Confidence            599999997543     599999854

>2epw_A Zinc finger protein 268; C2H2, zinc finger domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=83.81  E-value=0.85  Score=20.48  Aligned_cols=15  Identities=27%  Similarity=0.552  Sum_probs=11.9

Q ss_pred             eEEEcCCCCCeeecC
Q 035461            8 VSYICGDCGMENTLK   22 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~   22 (51)
                      ..|.|..||+.|...
T Consensus        11 k~~~C~~C~k~F~~~   25 (46)
T 2epw_A           11 KPCKCTECGKAFCWK   25 (46)
T ss_dssp             CSEECSSSCCEESSS
T ss_pred             CCeeCCCCCCccCCH
Confidence            459999999998753

>2jr7_A DPH3 homolog; DESR1, CSL zinc finger, metal binding protein; NMR {Homo sapiens}

Probab=83.80  E-value=2.6  Score=24.11  Aligned_cols=34  Identities=29%  Similarity=0.597  Sum_probs=25.7

Q ss_pred             CCCCceEEEcCCCCCeeecC-----C-CCeeEcCCCCCcEE
Q 035461            3 PQPEPVSYICGDCGMENTLK-----P-GDVIQCRECGYRIL   37 (51)
Q Consensus         3 ~~~~~~~Y~C~~Cg~~~~~~-----~-~~~irC~~CG~RIl   37 (51)
                      ...+...|-|- ||..|.+.     . ...+.|+.|.=.|-
T Consensus        17 e~~~~y~ypCr-CGd~F~IteedLe~ge~iv~C~sCSL~Ik   56 (89)
T 2jr7_A           17 EDSETYFYPCP-CGDNFSITKEDLENGEDVATCPSCSLIIK   56 (89)
T ss_dssp             TTTTEEEEECT-TSSEEEEEHHHHHHTCCEEECTTTCCEEE
T ss_pred             CCCCEEEEcCC-CCCEEEECHHHHhCCCEEEECCCCccEEE
Confidence            34456789995 99999985     2 25799999997663

>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1

Probab=83.78  E-value=0.87  Score=26.92  Aligned_cols=23  Identities=26%  Similarity=0.579  Sum_probs=14.5

Q ss_pred             EEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|.|..|+.++...    ..||+|+..
T Consensus        48 ~~hC~~C~~~f~~~----a~CPdC~q~   70 (101)
T 2jne_A           48 HARCRSCGEFIEMK----ALCPDCHQP   70 (101)
T ss_dssp             EEEETTTCCEEEEE----EECTTTCSB
T ss_pred             EEECccccchhhcc----ccCcchhhH
Confidence            45577777666554    567777654

>1q1a_A HST2 protein; ternary complex, histone deacetylase, 2'-O-ADP ribose,, gene regulation; HET: ALY OAD; 1.50A {Saccharomyces cerevisiae} SCOP: c.31.1.5 PDB: 1szd_A* 1szc_A* 2od7_A* 2od9_A* 2qqf_A* 2qqg_A* 1q17_A* 2od2_A*

Probab=83.59  E-value=0.95  Score=29.57  Aligned_cols=29  Identities=24%  Similarity=0.556  Sum_probs=20.4

Q ss_pred             eEEEcCCCCCeeecC----------CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK----------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~----------~~~~irC~~CG~RI   36 (51)
                      ....|..|+......          ....-+||.||..+
T Consensus       135 ~~~~C~~C~~~~~~~~~~~~~~~~~~~~~P~C~~Cgg~l  173 (289)
T 1q1a_A          135 AHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELV  173 (289)
T ss_dssp             EEEEETTTCCEECHHHHHHHHTCSSCCSCCBCTTTCCBE
T ss_pred             CceEECCCCCCCcHHHHHHHHhhccCCCCccCCCCCCEE
Confidence            356799999987642          11346999999854

>2m0d_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}

Probab=83.56  E-value=0.63  Score=18.49  Aligned_cols=13  Identities=31%  Similarity=0.670  Sum_probs=10.4

Q ss_pred             EEEcCCCCCeeec
Q 035461            9 SYICGDCGMENTL   21 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~   21 (51)
                      .|.|..||+.|..
T Consensus         3 ~~~C~~C~~~f~~   15 (30)
T 2m0d_A            3 PYQCDYCGRSFSD   15 (30)
T ss_dssp             CEECTTTCCEESC
T ss_pred             CccCCCCCcccCC
Confidence            4899999998753

>2yu8_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=83.49  E-value=0.89  Score=20.49  Aligned_cols=15  Identities=33%  Similarity=0.720  Sum_probs=11.8

Q ss_pred             eEEEcCCCCCeeecC
Q 035461            8 VSYICGDCGMENTLK   22 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~   22 (51)
                      ..|.|..||+.|...
T Consensus        11 k~~~C~~C~k~f~~~   25 (46)
T 2yu8_A           11 KPYKCNECGKVFTQN   25 (46)
T ss_dssp             SSEECSSSCCEESSS
T ss_pred             CCeECCcCCchhCCH
Confidence            458999999988753

>2l6l_A DNAJ homolog subfamily C member 24; DPH4, Zn-CSL, J-domain, chaperone; NMR {Homo sapiens}

Probab=83.48  E-value=1.9  Score=25.41  Aligned_cols=31  Identities=23%  Similarity=0.574  Sum_probs=24.4

Q ss_pred             CceEEEcCCCCCeeecCCC-----CeeEcCCCCCcEE
Q 035461            6 EPVSYICGDCGMENTLKPG-----DVIQCRECGYRIL   37 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~-----~~irC~~CG~RIl   37 (51)
                      +...|.|- ||..+.+...     ..+.|+.|.-.|.
T Consensus       109 ~~f~~~Cr-CG~~f~i~~~~l~~~~~v~C~sCSl~~~  144 (155)
T 2l6l_A          109 HSFYLSCR-CGGKYSVSKDEAEEVSLISCDTCSLIIE  144 (155)
T ss_dssp             TEEEEECS-SSCEEEEETTHHHHCCEEECSSSSCEEE
T ss_pred             cEEEEcCC-CCCeEEecHHHhCCCCEEECCCCceEEE
Confidence            45789995 9999998643     5799999996654

>2kvh_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}

Probab=83.41  E-value=0.63  Score=18.53  Aligned_cols=13  Identities=15%  Similarity=0.452  Sum_probs=10.3

Q ss_pred             EEEcCCCCCeeec
Q 035461            9 SYICGDCGMENTL   21 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~   21 (51)
                      .|.|..||+.|..
T Consensus         3 ~~~C~~C~k~f~~   15 (27)
T 2kvh_A            3 PFSCSLCPQRSRD   15 (27)
T ss_dssp             CEECSSSSCEESS
T ss_pred             CccCCCcChhhCC
Confidence            3889999988753

>1m2k_A Silent information regulator 2; protein-ligand complex, gene regulation; HET: APR; 1.47A {Archaeoglobus fulgidus} SCOP: c.31.1.5 PDB: 1m2g_A* 1m2h_A* 1m2j_A* 1m2n_A* 1ici_A*

Probab=83.40  E-value=0.97  Score=28.92  Aligned_cols=29  Identities=17%  Similarity=0.485  Sum_probs=20.9

Q ss_pred             eEEEcCCCCCeeecCC----CCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLKP----GDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~----~~~irC~~CG~RI   36 (51)
                      ....|..|+...+.+.    ...-+||.||..+
T Consensus       120 ~~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~l  152 (249)
T 1m2k_A          120 RVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLL  152 (249)
T ss_dssp             EEEEESSSSCEEECSSCCCSSSCCBCSSSSSBE
T ss_pred             ceeEeCCCCCcccchhhccCCCCCCCCCCCCCc
Confidence            3567999999876532    2246999999864

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

Probab=83.37  E-value=0.88  Score=25.46  Aligned_cols=18  Identities=28%  Similarity=0.521  Sum_probs=13.0

Q ss_pred             cCCCCeeEcCCCCCcEEE
Q 035461           21 LKPGDVIQCRECGYRILY   38 (51)
Q Consensus        21 ~~~~~~irC~~CG~RIly   38 (51)
                      +..+.+-||++||+-...
T Consensus        51 l~~g~~~RC~eCG~~fkL   68 (80)
T 2odx_A           51 PTVNEVARCWECGSVYKL   68 (80)
T ss_dssp             CCTTCEEECSSSCCEEEE
T ss_pred             ecCCCCeECCCCCeEEEE
Confidence            456677899999985443

>2eme_A Zinc finger protein 473; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=82.99  E-value=0.65  Score=20.91  Aligned_cols=14  Identities=36%  Similarity=0.831  Sum_probs=11.3

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 k~~~C~~C~k~f~~   24 (46)
T 2eme_A           11 KPYVCDYCGKAFGL   24 (46)
T ss_dssp             CSEECSSSCCEESS
T ss_pred             CCeECCCCChhhCC
Confidence            45999999998864

>1f2i_G Fusion of N-terminal 17-MER peptide extension to ZIF12; zinc finger, dimer, protein-DNA complex, cooperativity, transcription/DNA complex; 2.35A {Mus musculus} SCOP: g.37.1.1 g.37.1.1

Probab=82.80  E-value=1.2  Score=21.81  Aligned_cols=29  Identities=24%  Similarity=0.497  Sum_probs=21.8

Q ss_pred             eEEEcC--CCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            8 VSYICG--DCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~--~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      -.|.|.  .||+.|...           ...+..|+.||...
T Consensus        18 ~~~~C~~~~C~k~f~~~~~l~~H~~~h~~~~~~~C~~C~~~f   59 (73)
T 1f2i_G           18 RPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNF   59 (73)
T ss_dssp             CCEECSSTTBCCEESSHHHHHHHHHHHHCCCCEECTTTCCEE
T ss_pred             CccCCcCCCCCCccCCHHHHHHHHHhhCCCCCeECCCCCchh
Confidence            459996  799998642           23568999999754

>2kvf_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}

Probab=82.73  E-value=0.72  Score=18.36  Aligned_cols=12  Identities=42%  Similarity=0.958  Sum_probs=9.9

Q ss_pred             EEcCCCCCeeec
Q 035461           10 YICGDCGMENTL   21 (51)
Q Consensus        10 Y~C~~Cg~~~~~   21 (51)
                      |.|..||+.|..
T Consensus         4 ~~C~~C~k~f~~   15 (28)
T 2kvf_A            4 YSCSVCGKRFSL   15 (28)
T ss_dssp             EECSSSCCEESC
T ss_pred             ccCCCCCcccCC
Confidence            889999988764

>3p2a_A Thioredoxin 2, putative thioredoxin-like protein; structural genomics, center for structural genomics of infec diseases, csgid; 2.19A {Yersinia pestis}

Probab=82.67  E-value=1.1  Score=25.01  Aligned_cols=31  Identities=26%  Similarity=0.626  Sum_probs=24.2

Q ss_pred             CceEEEcCCCCCeeecC---CCCeeEcCCCCCcE
Q 035461            6 EPVSYICGDCGMENTLK---PGDVIQCRECGYRI   36 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~---~~~~irC~~CG~RI   36 (51)
                      +.+.+.|..||+.+++.   ..+...|..||..+
T Consensus         2 ~~~~~~c~~c~~~n~~p~~~~~~~~~~~~~~~~~   35 (148)
T 3p2a_A            2 NAMNTVCTACMATNRLPEERIDDGAKCGRCGHSL   35 (148)
T ss_dssp             CEEEEECTTTCCEEEEESSCSCSCCBCTTTCCBT
T ss_pred             CccEEECcccccccCCCCcccccCCcchhcCCcc
Confidence            45789999999999875   34567799998764

>2m0f_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}

Probab=82.28  E-value=0.73  Score=18.19  Aligned_cols=11  Identities=36%  Similarity=0.875  Sum_probs=9.2

Q ss_pred             EEcCCCCCeee
Q 035461           10 YICGDCGMENT   20 (51)
Q Consensus        10 Y~C~~Cg~~~~   20 (51)
                      |.|..||+.|.
T Consensus         3 ~~C~~C~k~f~   13 (29)
T 2m0f_A            3 LKCRECGKQFT   13 (29)
T ss_dssp             EECTTTSCEES
T ss_pred             ccCCCCCCccC
Confidence            88999998875

>2yso_A ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=82.16  E-value=0.77  Score=20.72  Aligned_cols=14  Identities=29%  Similarity=0.385  Sum_probs=11.5

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 ~~~~C~~C~k~f~~   24 (46)
T 2yso_A           11 KSHQCRECGEIFFQ   24 (46)
T ss_dssp             CCEECTTTCCEESS
T ss_pred             CCEEccccChhhCC
Confidence            45999999998874

>1x6h_A Transcriptional repressor CTCF; zinc finger protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.37.1.1 g.37.1.1

Probab=82.03  E-value=1.6  Score=21.74  Aligned_cols=29  Identities=24%  Similarity=0.606  Sum_probs=21.0

Q ss_pred             eEEEcCCCCCeeecC-----------CC----CeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK-----------PG----DVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-----------~~----~~irC~~CG~RI   36 (51)
                      ..|.|..|++.|...           ..    .+..|+.||...
T Consensus        14 k~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~C~~C~~~f   57 (86)
T 1x6h_A           14 KPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSKCGKTF   57 (86)
T ss_dssp             CCEECSSSSCEESSHHHHHHHHHHTTCSSCCCCCEECSSSCCEE
T ss_pred             CCCcCCCCCCccCCHHHHHHHHHHhcCCcCCCcceECCCCCChh
Confidence            459999999988632           11    358999999754

>2gnr_A Conserved hypothetical protein; 13815350, structural genomics, PSI, protein structure initiative; 1.80A {Sulfolobus solfataricus P2} PDB: 3irb_A

Probab=81.97  E-value=1  Score=27.14  Aligned_cols=28  Identities=21%  Similarity=0.408  Sum_probs=21.5

Q ss_pred             ceEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461            7 PVSYICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      -..-+|.+||+..-...   ..||.||..-+
T Consensus        45 L~~~rC~~CG~~~fPPr---~~Cp~C~s~~~   72 (145)
T 2gnr_A           45 IIGSKCSKCGRIFVPAR---SYCEHCFVKIE   72 (145)
T ss_dssp             CEEEECTTTCCEEESCC---SEETTTTEECC
T ss_pred             EEEEEECCCCcEEeCCC---CCCCCCCCCcc
Confidence            36789999999875543   47999998743

>2em5_A ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.87  E-value=0.7  Score=20.93  Aligned_cols=14  Identities=43%  Similarity=0.672  Sum_probs=11.4

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 ~~~~C~~C~k~f~~   24 (46)
T 2em5_A           11 KSHQCHECGRGFTL   24 (46)
T ss_dssp             CSEECSSSCCEESS
T ss_pred             CCeECCcCCCccCC
Confidence            45999999999874

>2ene_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.69  E-value=0.81  Score=20.64  Aligned_cols=14  Identities=29%  Similarity=0.681  Sum_probs=11.4

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 k~~~C~~C~k~f~~   24 (46)
T 2ene_A           11 KPYKCNECGKVFRH   24 (46)
T ss_dssp             SSEECSSSCCEESS
T ss_pred             CCeECCCCCchhCC
Confidence            45999999998874

>1rik_A E6APC1 peptide; E6-binding domain, zinc finger, human papillomavirus, HPV E6 protein, de novo protein; NMR {Synthetic} SCOP: k.12.1.1 PDB: 1sp1_A 1va3_A

Probab=81.60  E-value=0.81  Score=18.20  Aligned_cols=13  Identities=15%  Similarity=0.513  Sum_probs=10.2

Q ss_pred             EEcCCCCCeeecC
Q 035461           10 YICGDCGMENTLK   22 (51)
Q Consensus        10 Y~C~~Cg~~~~~~   22 (51)
                      |.|..||+.|...
T Consensus         3 ~~C~~C~k~f~~~   15 (29)
T 1rik_A            3 FACPECPKRFMRS   15 (29)
T ss_dssp             EECSSSSCEESCS
T ss_pred             ccCCCCCchhCCH
Confidence            8899999887643

>1ptq_A Protein kinase C delta type; phosphotransferase; 1.95A {Mus musculus} SCOP: g.49.1.1 PDB: 1ptr_A*

Probab=81.46  E-value=1.5  Score=21.23  Aligned_cols=26  Identities=23%  Similarity=0.626  Sum_probs=18.7

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      .|.-|+..+---...+.+|..|+..+
T Consensus        13 ~C~~C~~~l~g~~~qg~~C~~C~~~~   38 (50)
T 1ptq_A           13 FCDHCGSLLWGLVKQGLKCEDCGMNV   38 (50)
T ss_dssp             BCTTTCCBCCSSSSCEEEETTTCCEE
T ss_pred             CcCCCCceeeccCCccCEeCCCCCeE
Confidence            48888887643345789999998753

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

Probab=81.36  E-value=1.3  Score=22.48  Aligned_cols=11  Identities=36%  Similarity=1.017  Sum_probs=5.3

Q ss_pred             eEEEcCCCCCe
Q 035461            8 VSYICGDCGME   18 (51)
Q Consensus         8 ~~Y~C~~Cg~~   18 (51)
                      ..|.|.+||..
T Consensus        42 ~fy~C~~Cg~~   52 (57)
T 1qyp_A           42 IFYKCTKCGHT   52 (57)
T ss_dssp             EEEEESSSCCE
T ss_pred             EEEEcCCCCCE
Confidence            44555555443

>2em8_A Zinc finger protein 224; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.27  E-value=1.1  Score=20.29  Aligned_cols=15  Identities=27%  Similarity=0.605  Sum_probs=11.8

Q ss_pred             ceEEEcCCCCCeeec
Q 035461            7 PVSYICGDCGMENTL   21 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~   21 (51)
                      ...|.|..||+.|..
T Consensus        10 ~k~~~C~~C~k~f~~   24 (46)
T 2em8_A           10 EKPYKCVECGKGYKR   24 (46)
T ss_dssp             CCSEECSSSCCEESS
T ss_pred             CCCeECcccCchhCC
Confidence            345999999998874

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

Probab=81.20  E-value=2.2  Score=23.19  Aligned_cols=29  Identities=14%  Similarity=0.347  Sum_probs=20.9

Q ss_pred             EEEcCCCCCeeecCCC-CeeEcCCCCCcEE
Q 035461            9 SYICGDCGMENTLKPG-DVIQCRECGYRIL   37 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~-~~irC~~CG~RIl   37 (51)
                      .+-|.+|+..+..... ..+.||.||+..=
T Consensus        25 ~~wCP~C~~~~~~~~~~~~v~C~~C~~~FC   54 (86)
T 2ct7_A           25 FLWCAQCSFGFIYEREQLEATCPQCHQTFC   54 (86)
T ss_dssp             EECCSSSCCCEECCCSCSCEECTTTCCEEC
T ss_pred             EeECcCCCchheecCCCCceEeCCCCCccc
Confidence            4448899998766543 4589999998653

>2eml_A Zinc finger protein 28 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=81.07  E-value=0.82  Score=20.62  Aligned_cols=14  Identities=29%  Similarity=0.619  Sum_probs=11.4

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 k~~~C~~C~k~f~~   24 (46)
T 2eml_A           11 KPYECSVCGKAFSH   24 (46)
T ss_dssp             CSEECSSSCCEESS
T ss_pred             CCeeCCCcCCccCC
Confidence            45999999998874

>2kvg_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}

Probab=81.06  E-value=0.62  Score=18.78  Aligned_cols=12  Identities=25%  Similarity=0.459  Sum_probs=9.7

Q ss_pred             EEcCCCCCeeec
Q 035461           10 YICGDCGMENTL   21 (51)
Q Consensus        10 Y~C~~Cg~~~~~   21 (51)
                      |.|..||+.|..
T Consensus         4 ~~C~~C~k~f~~   15 (27)
T 2kvg_A            4 YRCPLCRAGCPS   15 (27)
T ss_dssp             EEETTTTEEESC
T ss_pred             cCCCCCCcccCC
Confidence            889999988753

>2wbt_A B-129; zinc finger; 2.70A {Sulfolobus virus 1}

Probab=80.93  E-value=0.7  Score=25.23  Aligned_cols=29  Identities=17%  Similarity=0.383  Sum_probs=21.6

Q ss_pred             eEEEcCCCCCeeecCC---------CCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLKP---------GDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~---------~~~irC~~CG~RI   36 (51)
                      -.|.|..||+.|....         ..+-.|+.||...
T Consensus        73 ~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~C~~C~k~f  110 (129)
T 2wbt_A           73 SQFVCPLCLMPFSSSVSLKQHIRYTEHTKVCPVCKKEF  110 (129)
T ss_dssp             CSEECTTTCCEESSHHHHHHHHHHTCCCCBCTTTCCBC
T ss_pred             CCeECCCCCcccCCHhHHHHHHHHCCCCCCCCCCCccc
Confidence            3499999999986431         3557899999754

>2i13_A AART; DNA binding, zinc finger, DNA binding protein-DNA complex; 1.96A {Mus musculus} SCOP: k.12.1.1 PDB: 1mey_C*

Probab=80.85  E-value=1.4  Score=25.46  Aligned_cols=11  Identities=36%  Similarity=1.017  Sum_probs=6.0

Q ss_pred             EEcCCCCCeee
Q 035461           10 YICGDCGMENT   20 (51)
Q Consensus        10 Y~C~~Cg~~~~   20 (51)
                      |.|..||..|.
T Consensus       134 ~~C~~C~~~f~  144 (190)
T 2i13_A          134 YKCPECGKSFS  144 (190)
T ss_dssp             EECTTTCCEES
T ss_pred             eECCCCCcccC
Confidence            55555555554

>2eoo_A ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.80  E-value=0.8  Score=20.74  Aligned_cols=14  Identities=29%  Similarity=0.655  Sum_probs=11.5

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 k~~~C~~C~k~F~~   24 (46)
T 2eoo_A           11 RPYGCNECGKNFGR   24 (46)
T ss_dssp             CCEECSSSCCEESS
T ss_pred             CCEEccccCcccCC
Confidence            45999999998874

>2emm_A ZFP-95, zinc finger protein 95 homolog; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.76  E-value=0.69  Score=20.82  Aligned_cols=14  Identities=21%  Similarity=0.484  Sum_probs=11.3

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 k~~~C~~C~k~f~~   24 (46)
T 2emm_A           11 RPHKCNECGKSFIQ   24 (46)
T ss_dssp             CSEECSSSCCEESS
T ss_pred             CCeeCCCCChhhCC
Confidence            45899999998874

>2elm_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.74  E-value=1.8  Score=18.66  Aligned_cols=15  Identities=20%  Similarity=0.518  Sum_probs=11.2

Q ss_pred             ceEEEcCCCCCeeec
Q 035461            7 PVSYICGDCGMENTL   21 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~   21 (51)
                      ...|.|..||+.|..
T Consensus         7 ~k~~~C~~C~k~f~~   21 (37)
T 2elm_A            7 GHLYYCSQCHYSSIT   21 (37)
T ss_dssp             SCEEECSSSSCEEEC
T ss_pred             CcCeECCCCCcccCC
Confidence            346889999888764

>2em9_A Zinc finger protein 224; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1 PDB: 2yrh_A

Probab=80.62  E-value=0.88  Score=20.44  Aligned_cols=14  Identities=29%  Similarity=0.707  Sum_probs=11.3

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 k~~~C~~C~k~f~~   24 (46)
T 2em9_A           11 KPYNCKECGKSFRW   24 (46)
T ss_dssp             CSEECSSSCCEESS
T ss_pred             cCeECCccccccCC
Confidence            45899999998874

>2emp_A Zinc finger protein 347; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.61  E-value=0.9  Score=20.47  Aligned_cols=14  Identities=29%  Similarity=0.964  Sum_probs=11.2

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 k~~~C~~C~k~f~~   24 (46)
T 2emp_A           11 KPYMCNECGKAFSV   24 (46)
T ss_dssp             CSEECSSSCCEESC
T ss_pred             cCeECCCCCchhCC
Confidence            45899999998864

>1ma3_A SIR2-AF2, transcriptional regulatory protein, SIR2 family; enzyme-substrate complex, protein binding, transcription; HET: ALY MES; 2.00A {Archaeoglobus fulgidus} SCOP: c.31.1.5 PDB: 1s7g_A* 1yc2_A*

Probab=80.57  E-value=1.5  Score=28.13  Aligned_cols=27  Identities=30%  Similarity=0.685  Sum_probs=20.1

Q ss_pred             eEEEcCCCCCeeecC-------CCCeeEcCCCCC
Q 035461            8 VSYICGDCGMENTLK-------PGDVIQCRECGY   34 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~-------~~~~irC~~CG~   34 (51)
                      ....|..||.....+       ....-+||.||.
T Consensus       122 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg  155 (253)
T 1ma3_A          122 DKLDCLDCHETYDWSEFVEDFNKGEIPRCRKCGS  155 (253)
T ss_dssp             EEEEETTTCCEEEGGGTHHHHHTTCCCCCTTTCC
T ss_pred             CeeeeCCCCCcCcHHHHHHHhccCCCCCCCCCCC
Confidence            456799999987653       223469999998

>2em7_A Zinc finger protein 224; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.35  E-value=0.85  Score=20.55  Aligned_cols=14  Identities=29%  Similarity=0.679  Sum_probs=11.2

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      -.|.|..||+.|..
T Consensus        11 k~~~C~~C~k~f~~   24 (46)
T 2em7_A           11 KPYKCEECGKGFIC   24 (46)
T ss_dssp             CSEECSSSCCEESC
T ss_pred             cCccCCCccchhCC
Confidence            45899999998874

>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=80.35  E-value=1.3  Score=25.61  Aligned_cols=17  Identities=29%  Similarity=0.741  Sum_probs=12.5

Q ss_pred             cCCCCeeEcCCCCCcEE
Q 035461           21 LKPGDVIQCRECGYRIL   37 (51)
Q Consensus        21 ~~~~~~irC~~CG~RIl   37 (51)
                      +..+.+-|||+||+-..
T Consensus        74 l~~g~~~RC~eCG~~fk   90 (98)
T 1v54_F           74 LHKGEAQRCPSCGTHYK   90 (98)
T ss_dssp             EESSSCEECTTTCCEEE
T ss_pred             EeCCCceECCCCCeEEE
Confidence            34567889999998433

>2ysp_A Zinc finger protein 224; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.34  E-value=0.62  Score=21.06  Aligned_cols=14  Identities=29%  Similarity=0.679  Sum_probs=11.4

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 k~~~C~~C~k~f~~   24 (46)
T 2ysp_A           11 KPYKCEKCGKGYNS   24 (46)
T ss_dssp             CSEEETTTTEEESC
T ss_pred             CCeECCCCCCccCC
Confidence            45999999998874

>1wge_A Hypothetical protein 2610018L09RIK; diphthamide,CSL zinc finger, ADP-ribosylating toxin, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.41.17.1

Probab=80.19  E-value=3.9  Score=22.94  Aligned_cols=34  Identities=32%  Similarity=0.660  Sum_probs=25.5

Q ss_pred             CCCCceEEEcCCCCCeeecC-----CC-CeeEcCCCCCcEE
Q 035461            3 PQPEPVSYICGDCGMENTLK-----PG-DVIQCRECGYRIL   37 (51)
Q Consensus         3 ~~~~~~~Y~C~~Cg~~~~~~-----~~-~~irC~~CG~RIl   37 (51)
                      ...+...|-|- ||..|.+.     .+ ..+.|+.|.-.|-
T Consensus        24 e~~~~y~y~Cr-CGd~F~it~edL~~ge~iv~C~sCSL~I~   63 (83)
T 1wge_A           24 EDSETYFYPCP-CGDNFAITKEDLENGEDVATCPSCSLIIK   63 (83)
T ss_dssp             TTTTEEEECCS-SSSCEEEEHHHHHTTCCEEECTTTCCEEE
T ss_pred             cCCCEEEEeCC-CCCEEEECHHHHhCCCEEEECCCCceEEE
Confidence            34456789995 99999985     22 5799999997653

>2emy_A Zinc finger protein 268; ZF-C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.05  E-value=0.91  Score=20.45  Aligned_cols=14  Identities=29%  Similarity=0.691  Sum_probs=11.4

Q ss_pred             eEEEcCCCCCeeec
Q 035461            8 VSYICGDCGMENTL   21 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~   21 (51)
                      ..|.|..||+.|..
T Consensus        11 k~~~C~~C~k~F~~   24 (46)
T 2emy_A           11 NPYECHECGKAFSR   24 (46)
T ss_dssp             CCEECSSSCCEESS
T ss_pred             cCcCCCCCCcccCc
Confidence            45999999998874

>2lvu_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc finger, transcription; NMR {Homo sapiens}

Probab=81.17  E-value=0.35  Score=19.19  Aligned_cols=14  Identities=29%  Similarity=0.814  Sum_probs=10.6

Q ss_pred             EEEcCCCCCeeecC
Q 035461            9 SYICGDCGMENTLK   22 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~   22 (51)
                      .|.|..||+.|.-.
T Consensus         2 p~~C~~C~k~f~~~   15 (26)
T 2lvu_A            2 PYVCERCGKRFVQS   15 (26)
Confidence            38899998887654

---

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	51
d1twfl_	46	g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {	1e-22

>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 = 78.2 bits (193), Expect = 1e-22
 Identities = 21/45 (46%), Positives = 33/45 (73%)

Query: 7  PVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR 51
           + YIC +C  + +L   D ++C++CG+RIL K RT+R+VQ+EAR
Sbjct: 2  TLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 46

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	51
d1twfl_	46	RBP12 subunit of RNA polymerase II {Baker's yeast	99.94
d1lkoa2	44	Rubrerythrin, C-terminal domain {Desulfovibrio vul	96.46
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	96.38
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	96.29
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	96.0
d2gmga1	105	Hypothetical protein PF0610 {Pyrococcus furiosus [	95.69
d2csha1	53	Zinc finger protein 297b {Human (Homo sapiens) [Ta	93.35
d1s24a_	56	Two-iron rubredoxin {Pseudomonas oleovorans [TaxId	93.23
d2dsxa1	52	Rubredoxin {Desulfovibrio gigas [TaxId: 879]}	93.02
d1dfxa2	36	Desulfoferrodoxin N-terminal domain {Desulfovibrio	92.82
d1brfa_	53	Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2	92.81
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	92.78
d1x6ea2	26	Zinc finger protein 24 {Human (Homo sapiens) [TaxI	92.63
d1vzia2	37	Desulfoferrodoxin N-terminal domain {Desulfoarculu	92.4
d1ltla_	239	DNA replication initiator (cdc21/cdc54) N-terminal	92.21
d6rxna_	45	Rubredoxin {Desulfovibrio desulfuricans, strain 27	92.04
d1dxga_	36	Desulforedoxin {Desulfovibrio gigas [TaxId: 879]}	92.0
d1vd4a_	62	Transcription initiation factor TFIIE-alpha {Human	91.9
d1zbdb_	124	Effector domain of rabphilin-3a {Rat (Rattus norve	91.56
d1iroa_	53	Rubredoxin {Clostridium pasteurianum [TaxId: 1501]	91.36
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	89.86
d2ayja1	56	Ribosomal protein L40e {Sulfolobus solfataricus [T	89.8
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	89.55
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	89.53
d1dx8a_	70	Rubredoxin {Guillardia theta [TaxId: 55529]}	89.25
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	88.46
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	88.2
d1akya2	38	Microbial and mitochondrial ADK, insert "zinc fing	88.05
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	87.73
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	87.43
d1hxra_	115	RabGEF Mss4 {Rat (Rattus norvegicus) [TaxId: 10116	87.15
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	86.6
d2cona1	66	RNA-binding protein NOB1 (Nin one binding) {Mouse	86.2
d1ryqa_	67	putative DNA-directed RNA polymerase subunit E'' (	85.88
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	84.9
d1a1ia2	28	ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}	84.49
d1m2ka_	249	AF1676, Sir2 homolog (Sir2-AF1?) {Archaeon Archaeo	83.66
d1x6ea1	33	Zinc finger protein 24 {Human (Homo sapiens) [TaxI	82.15
d1tbna_	66	Protein kinase c-gamma {Rat (Rattus rattus) [TaxId	81.85
d2gnra1	137	Hypothetical protein SSO2064 {Sulfolobus solfatari	81.49
d1ptqa_	50	Protein kinase C-delta (PKCdelta) {Mouse (Mus musc	81.2
d1wgea1	70	DelGEF-interacting protein 1, DelGIP1 {Mouse (Mus	80.67
d2nn6i1	125	Exosome component 1, EXOSC1 {Human (Homo sapiens)	80.51
d1ywsa1	82	Diphthamide biosynthesis protein 3, DPH3 {Baker's	80.22
d2dkta1	74	RING finger and CHY zinc finger domain-containing	80.06

>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=99.94  E-value=3.9e-29  Score=131.61  Aligned_cols=45  Identities=47%  Similarity=1.020  Sum_probs=44.0

Q ss_pred             ceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEEecCceEEEEcC
Q 035461            7 PVSYICGDCGMENTLKPGDVIQCRECGYRILYKKRTRRIVQYEAR   51 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~R~~~~~~~~Ar   51 (51)
                      +|.|+|++||.+++++++|+|||.+||||||||+||++++|||||
T Consensus         2 ~v~YiCgeCg~~~~l~~~d~irCreCG~RIlYK~RTkr~vqfeAR   46 (46)
T d1twfl_           2 TLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR   46 (46)
T ss_dssp             CCCEECSSSCCEECCCTTSTTCCSSSCCCCCBCCCCSSCEEECCC
T ss_pred             ceEEEcccCCCceEeCCCCcEEeccCCcEEEEeecccceeeEecC
Confidence            588999999999999999999999999999999999999999998

>d1lkoa2 g.41.5.1 (A:148-191) Rubrerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=96.46  E-value=0.00069  Score=33.80  Aligned_cols=30  Identities=17%  Similarity=0.449  Sum_probs=24.2

Q ss_pred             CCceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            5 PEPVSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         5 ~~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .+++.++|..||...+-+. .+-.||-||+-
T Consensus         4 ~~~~~W~C~~CGyi~~g~~-aP~~CPvC~~p   33 (44)
T d1lkoa2           4 EQATKWRCRNCGYVHEGTG-APELCPACAHP   33 (44)
T ss_dssp             EEEEEEEETTTCCEEEEEE-CCSBCTTTCCB
T ss_pred             CCCeEEEcCCCCcEEECCC-CCCcCCCCCCc
Confidence            3568999999999998653 45589999984

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

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

Probab=96.38  E-value=0.00057  Score=33.30  Aligned_cols=25  Identities=32%  Similarity=0.769  Sum_probs=22.4

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|.+|+.+..-..++.+.||+|||-
T Consensus         5 ~CP~C~seytYedg~l~vCPeC~hE   29 (38)
T d2akla2           5 PCPQCNSEYTYEDGALLVCPECAHE   29 (38)
T ss_dssp             CCTTTCCCCCEECSSSEEETTTTEE
T ss_pred             cCCCCCCcceEcCCCEEECCcccCc
Confidence            4889999999999999999999984

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=96.29  E-value=0.0021  Score=30.70  Aligned_cols=28  Identities=21%  Similarity=0.389  Sum_probs=22.6

Q ss_pred             CceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            6 EPVSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      +...|+|..||...+-+  .+-.||-||+.
T Consensus         2 ~~~~~vC~vCGyi~~g~--~Pe~CPvCg~~   29 (36)
T d1yuza2           2 DDKFHLCPICGYIHKGE--DFEKCPICFRP   29 (36)
T ss_dssp             SCCEEECSSSCCEEESS--CCSBCTTTCCB
T ss_pred             CCCEEECCCCCCEeeCC--CCCcCCCCCCc
Confidence            34679999999998764  56689999974

>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.00  E-value=0.0029  Score=30.26  Aligned_cols=27  Identities=30%  Similarity=0.575  Sum_probs=22.1

Q ss_pred             ceEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            7 PVSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      ...|+|..||...+-+  .+-.||-||+.
T Consensus         3 ~~~~~C~vCG~i~~g~--~P~~CPvCg~~   29 (37)
T d1nnqa2           3 KKVYICPICGYTAVDE--APEYCPVCGAP   29 (37)
T ss_dssp             SCEEECTTTCCEEESC--CCSBCTTTCCB
T ss_pred             CcEEECCCCCCEecCC--CCCcCCCCCCc
Confidence            3579999999999853  56789999963

>d2gmga1 a.4.5.82 (A:1-105) Hypothetical protein PF0610 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF0610-like
domain: Hypothetical protein PF0610
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.69  E-value=0.0018  Score=37.26  Aligned_cols=25  Identities=20%  Similarity=0.488  Sum_probs=21.3

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|.+||.+|..+.+-+-|||.|.+-
T Consensus        69 ~CrkCGfvFr~~~kkPSRCP~CKSE   93 (105)
T d2gmga1          69 QCRKCGFVFKAEINIPSRCPKCKSE   93 (105)
T ss_dssp             BBTTTCCBCCCCSSCCSSCSSSCCC
T ss_pred             hhhhcCCeecccCCCCCCCCCCCCc
Confidence            5999999997667788999999864

>d2csha1 g.37.1.1 (A:8-60) Zinc finger protein 297b {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 297b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.35  E-value=0.027  Score=27.09  Aligned_cols=27  Identities=33%  Similarity=0.637  Sum_probs=20.6

Q ss_pred             EEEcCCCCCeeecC-----------CCCeeEcCCCCCcE
Q 035461            9 SYICGDCGMENTLK-----------PGDVIQCRECGYRI   36 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~-----------~~~~irC~~CG~RI   36 (51)
                      .|.| +||+.|.-.           ...+-.|+.||...
T Consensus         3 ~y~C-~Cgk~F~~~~~l~~H~~~Ht~ekpy~C~~C~k~F   40 (53)
T d2csha1           3 LYPC-QCGKSFTHKSQRDRHMSMHLGLRPYGCGVCGKKF   40 (53)
T ss_dssp             CEEC-TTSCEESSHHHHHHHHHHHSCCCSEECTTTSCEE
T ss_pred             CCCC-CCCCeECCHHHhHHHhhccccccCCcCCCcCCEe
Confidence            4999 799999853           23568999999753

>d1s24a_ g.41.5.1 (A:) Two-iron rubredoxin {Pseudomonas oleovorans [TaxId: 301]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Two-iron rubredoxin
species: Pseudomonas oleovorans [TaxId: 301]

Probab=93.23  E-value=0.021  Score=29.26  Aligned_cols=27  Identities=33%  Similarity=0.711  Sum_probs=20.7

Q ss_pred             eEEEcCCCCCeeecCCC----------------CeeEcCCCCC
Q 035461            8 VSYICGDCGMENTLKPG----------------DVIQCRECGY   34 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~   34 (51)
                      ..|+|..||..-+...+                +.-+||.||.
T Consensus         3 kky~C~~CgyiYdp~~Gd~~~gi~pGT~F~~LP~dw~CP~C~a   45 (56)
T d1s24a_           3 LKWICITCGHIYDEALGDEAEGFTPGTRFEDIPDDWCCPDCGA   45 (56)
T ss_dssp             CEEEETTTTEEEETTSCCTTTTCCSCCCGGGCCTTCCCSSSCC
T ss_pred             ccEECCCCCcEECcccCCcccCcCCCCChhhCCCCCCCcCCCC
Confidence            57999999988765432                3459999995

>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio gigas [TaxId: 879]

Probab=93.02  E-value=0.022  Score=28.82  Aligned_cols=26  Identities=38%  Similarity=0.825  Sum_probs=20.3

Q ss_pred             EEEcCCCCCeeecCCC----------------CeeEcCCCCC
Q 035461            9 SYICGDCGMENTLKPG----------------DVIQCRECGY   34 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~   34 (51)
                      .|+|..||.+-+...+                +.-+||.||.
T Consensus         3 ~y~C~~CgyiYdp~~Gd~~~gi~pGT~F~~LP~~w~CP~C~a   44 (52)
T d2dsxa1           3 IYVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGA   44 (52)
T ss_dssp             CEEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCC
T ss_pred             eEEeCCCCeEECcccCCcccCCCCCCCHHHCCCCCCCcCCCC
Confidence            5999999998765432                4569999995

>d1dfxa2 g.41.5.2 (A:1-36) Desulfoferrodoxin N-terminal domain {Desulfovibrio desulfuricans [TaxId: 876]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Desulforedoxin
domain: Desulfoferrodoxin N-terminal domain
species: Desulfovibrio desulfuricans [TaxId: 876]

Probab=92.82  E-value=0.055  Score=25.67  Aligned_cols=24  Identities=33%  Similarity=0.811  Sum_probs=18.4

Q ss_pred             eEEEcCCCCCeeecCC--CCeeEcCCCC
Q 035461            8 VSYICGDCGMENTLKP--GDVIQCRECG   33 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~--~~~irC~~CG   33 (51)
                      -.|+|..||..+++-.  ...+-|  ||
T Consensus         5 evYkC~~CGNiVeV~~~g~G~LvC--Cg   30 (36)
T d1dfxa2           5 EVYKCTHCGNIVEVLHGGGAELVC--CG   30 (36)
T ss_dssp             CEEECTTTCCEEECSSCCSSCCEE--TT
T ss_pred             cEEEecccCcEEEEEECCCccEEE--CC
Confidence            4799999999999863  345777  55

>d1brfa_ g.41.5.1 (A:) Rubredoxin {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.81  E-value=0.038  Score=27.95  Aligned_cols=27  Identities=30%  Similarity=0.663  Sum_probs=20.6

Q ss_pred             EEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPG----------------DVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R   35 (51)
                      .|+|..||..-+...+                +.-+||.||..
T Consensus         2 ky~C~~CgyiYd~~~Gd~~~gi~pGT~f~dLP~dw~CP~C~a~   44 (53)
T d1brfa_           2 KWVCKICGYIYDEDAGDPDNGISPGTKFEELPDDWVCPICGAP   44 (53)
T ss_dssp             EEEETTTCCEEETTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             ceECCCCCcEECcccCCcccCCCCCCCHHHCCCCCCCcCCCCc
Confidence            6999999998765421                45699999953

>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=92.78  E-value=0.031  Score=26.09  Aligned_cols=24  Identities=33%  Similarity=0.875  Sum_probs=17.4

Q ss_pred             cCCCCCeee----cCCCCeeEcCCCCCc
Q 035461           12 CGDCGMENT----LKPGDVIQCRECGYR   35 (51)
Q Consensus        12 C~~Cg~~~~----~~~~~~irC~~CG~R   35 (51)
                      |+.|+...-    +..++.|-|++||.-
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~cgsg   29 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKCGSG   29 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTTTCC
T ss_pred             CccceEEEEeeeeeeccCcEEehhcCCC
Confidence            778865443    335799999999974

>d1x6ea2 g.37.1.1 (A:41-66) Zinc finger protein 24 {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 24
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.63  E-value=0.026  Score=24.94  Aligned_cols=13  Identities=31%  Similarity=0.754  Sum_probs=11.0

Q ss_pred             EEEcCCCCCeeec
Q 035461            9 SYICGDCGMENTL   21 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~   21 (51)
                      .|.|.+||+.|.-
T Consensus         2 Py~C~eCgK~F~~   14 (26)
T d1x6ea2           2 PYKCLECGKAFSQ   14 (26)
T ss_dssp             CEECSSSCCEESS
T ss_pred             CccCCCCcCeecc
Confidence            3999999999864

>d1vzia2 g.41.5.2 (A:1-37) Desulfoferrodoxin N-terminal domain {Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Desulforedoxin
domain: Desulfoferrodoxin N-terminal domain
species: Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887]

Probab=92.40  E-value=0.062  Score=25.61  Aligned_cols=25  Identities=24%  Similarity=0.490  Sum_probs=18.8

Q ss_pred             eEEEcCCCCCeeecC--CCCeeEcCCCCC
Q 035461            8 VSYICGDCGMENTLK--PGDVIQCRECGY   34 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~   34 (51)
                      -.|+|..||..+++-  ....+-|  ||.
T Consensus         5 evYkC~~CGNiVeV~~~g~G~LvC--Cg~   31 (37)
T d1vzia2           5 QVYKCEVCGNIVEVLNGGIGELVC--CNQ   31 (37)
T ss_dssp             CEEECTTTCCEEEEEECCSSCEEE--TTE
T ss_pred             cEEEecccCcEEEEEECCCccEEE--CCC
Confidence            479999999999975  3356777  553

>d1ltla_ b.40.4.11 (A:) DNA replication initiator (cdc21/cdc54) N-terminal domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: DNA replication initiator (cdc21/cdc54) N-terminal domain
domain: DNA replication initiator (cdc21/cdc54) N-terminal domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=92.21  E-value=0.048  Score=33.18  Aligned_cols=32  Identities=22%  Similarity=0.499  Sum_probs=25.6

Q ss_pred             ceEEEcCCCCCeeecC-----CCCeeEcCCCCCcEEE
Q 035461            7 PVSYICGDCGMENTLK-----PGDVIQCRECGYRILY   38 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~-----~~~~irC~~CG~RIly   38 (51)
                      .+.|.|..||..+.+.     ...+..|+.||++-+.
T Consensus       124 ~~~~~C~~C~~~~~~~~~~~~~~~p~~C~~C~~~~f~  160 (239)
T d1ltla_         124 KAVFECRGCMRHHAVTQSTNMITEPSLCSECGGRSFR  160 (239)
T ss_dssp             EEEEEETTTCCEEEEECSSSSCCCCSCCTTTCCCCEE
T ss_pred             EEEEECCCCCceEEEEecCCeecCCccCCCCCCcccE
Confidence            4789999999998874     2367899999987644

>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]

Probab=92.04  E-value=0.039  Score=27.08  Aligned_cols=27  Identities=33%  Similarity=0.721  Sum_probs=20.4

Q ss_pred             EEEcCCCCCeeecCC---------CCeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKP---------GDVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~---------~~~irC~~CG~R   35 (51)
                      .|+|..||..-+...         -+.-+||.||..
T Consensus         3 ~y~C~~CgyiYd~~~Gdgt~Fe~LP~dw~CP~C~a~   38 (45)
T d6rxna_           3 KYVCNVCGYEYDPAEHDNVPFDQLPDDWCCPVCGVS   38 (45)
T ss_dssp             CEEETTTCCEECGGGGTTCCGGGSCTTCBCTTTCCB
T ss_pred             CeEeCCCCeEECcccCCCCCHHHCCCCCCCcCCCCc
Confidence            499999998876532         255799999964

>d1dxga_ g.41.5.2 (A:) Desulforedoxin {Desulfovibrio gigas [TaxId: 879]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Desulforedoxin
domain: Desulforedoxin
species: Desulfovibrio gigas [TaxId: 879]

Probab=92.00  E-value=0.075  Score=25.18  Aligned_cols=26  Identities=31%  Similarity=0.680  Sum_probs=19.4

Q ss_pred             ceEEEcCCCCCeeecC--CCCeeEcCCCCC
Q 035461            7 PVSYICGDCGMENTLK--PGDVIQCRECGY   34 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~--~~~~irC~~CG~   34 (51)
                      .-.|+|..||..+++-  ....+-|  ||.
T Consensus         4 ~evYkC~~CGNiVeV~~~g~G~LvC--Cg~   31 (36)
T d1dxga_           4 GDVYKCELCGQVVKVLEEGGGTLVC--CGE   31 (36)
T ss_dssp             TCEEECTTTCCEEEEEECCSSCEEE--TTE
T ss_pred             ccEEEeccCCcEEEEEECCCceEEE--CCC
Confidence            3579999999999975  3356777  554

>d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=91.90  E-value=0.077  Score=27.50  Aligned_cols=31  Identities=19%  Similarity=0.357  Sum_probs=24.8

Q ss_pred             ceEEEcCCCCCeeec-------C-CCCeeEcCCCCCcEE
Q 035461            7 PVSYICGDCGMENTL-------K-PGDVIQCRECGYRIL   37 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~-------~-~~~~irC~~CG~RIl   37 (51)
                      .-.|+|..|++.++.       . .....+|.+|+.-+.
T Consensus        12 ~~~y~Cp~C~~~ys~Lda~~L~d~~~~~F~C~~C~~el~   50 (62)
T d1vd4a_          12 RASFKCPVCSSTFTDLEANQLFDPMTGTFRCTFCHTEVE   50 (62)
T ss_dssp             SSEEECSSSCCEEEHHHHHHHEETTTTEEBCSSSCCBCE
T ss_pred             CCceECCCCCCCcchhhHHHhcCcCCCeEEecCCCCEEe
Confidence            367999999999983       2 347799999998764

>d1zbdb_ g.50.1.1 (B:) Effector domain of rabphilin-3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Effector domain of rabphilin-3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.56  E-value=0.067  Score=29.92  Aligned_cols=26  Identities=19%  Similarity=0.519  Sum_probs=21.1

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      .|..|+..|.+.......|.+||..+
T Consensus        50 ~C~~C~~~f~~~~~~~~~C~~C~~~~   75 (124)
T d1zbdb_          50 RCILCGEQLGMLGSASVVCEDCKKNV   75 (124)
T ss_dssp             BCSSSCCBCSTTSCCEEECTTTCCEE
T ss_pred             cCcccCCcccCCCCCCCcCccCCccc
Confidence            59999999886555677899999775

>d1iroa_ g.41.5.1 (A:) Rubredoxin {Clostridium pasteurianum [TaxId: 1501]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Clostridium pasteurianum [TaxId: 1501]

Probab=91.36  E-value=0.055  Score=27.29  Aligned_cols=27  Identities=33%  Similarity=0.694  Sum_probs=20.5

Q ss_pred             EEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461            9 SYICGDCGMENTLKPG----------------DVIQCRECGYR   35 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R   35 (51)
                      .|+|..||..-+...+                +.-+||.||..
T Consensus         3 ky~C~~CgyiYd~~~Gd~~~gi~pGT~F~~LP~dw~CP~C~a~   45 (53)
T d1iroa_           3 KYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVG   45 (53)
T ss_dssp             CEEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             CeEcCCCCcEECcccCCcccCCCCCCCHHHCCCCCCCcCCCCc
Confidence            5999999988765422                45699999964

>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=89.86  E-value=0.18  Score=23.31  Aligned_cols=29  Identities=28%  Similarity=0.590  Sum_probs=22.5

Q ss_pred             EEEcCCCCCeeecCC---CCeeEcCCCCCcEE
Q 035461            9 SYICGDCGMENTLKP---GDVIQCRECGYRIL   37 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~---~~~irC~~CG~RIl   37 (51)
                      .++|..||+...+..   ...-.|-.||..++
T Consensus         2 Rr~C~~CG~~Yh~~~~pPk~~g~CD~cG~~L~   33 (35)
T d1zina2           2 RRICRNCGATYHLIFHPPAKPGVCDKCGGELY   33 (35)
T ss_dssp             EEEETTTCCEEETTTBCCSSTTBCTTTCCBEE
T ss_pred             ccCCcCcCchhccccCCCCCCCcCCCCCCCcc
Confidence            368999999998764   34578999998643

>d2ayja1 g.41.8.7 (A:1-56) Ribosomal protein L40e {Sulfolobus solfataricus [TaxId: 2287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L40e
domain: Ribosomal protein L40e
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=89.80  E-value=0.085  Score=27.12  Aligned_cols=27  Identities=30%  Similarity=0.801  Sum_probs=22.3

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCcEE
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYRIL   37 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIl   37 (51)
                      -.-+|-.|++.+.+.+   ..|..|||.-|
T Consensus        18 ~k~ICrkC~AR~p~rA---t~CRKCg~~nL   44 (56)
T d2ayja1          18 LKKVCRKCGALNPIRA---TKCRRCHSTNL   44 (56)
T ss_dssp             CCEEETTTCCEECTTC---SSCTTTCCCCE
T ss_pred             hhHHHhhccccCCccc---cccccCCCCCc
Confidence            4578999999988775   56999999864

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=89.55  E-value=0.041  Score=25.24  Aligned_cols=23  Identities=26%  Similarity=0.749  Sum_probs=17.6

Q ss_pred             EEcCCCCCeeecCC----CCeeEcCCC
Q 035461           10 YICGDCGMENTLKP----GDVIQCREC   32 (51)
Q Consensus        10 Y~C~~Cg~~~~~~~----~~~irC~~C   32 (51)
                      |+|+.||+-.+...    ...|-|.-|
T Consensus         1 frca~cgk~lestt~adkdgeiyck~c   27 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGC   27 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHH
T ss_pred             CccccccCccccceeeccCCcEEEeee
Confidence            68999999988752    366888655

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.53  E-value=0.17  Score=25.88  Aligned_cols=30  Identities=13%  Similarity=0.324  Sum_probs=22.5

Q ss_pred             EEEcCCCCCeeecCCC-CeeEcCCCCCcEEE
Q 035461            9 SYICGDCGMENTLKPG-DVIQCRECGYRILY   38 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~-~~irC~~CG~RIly   38 (51)
                      .=-|..|+..+..+.+ ..+.|+.||+..=|
T Consensus        18 ~k~CP~C~~~~~~~~~~~~~~C~~C~~~fC~   48 (73)
T d2ct7a1          18 FLWCAQCSFGFIYEREQLEATCPQCHQTFCV   48 (73)
T ss_dssp             EECCSSSCCCEECCCSCSCEECTTTCCEECS
T ss_pred             CCCCCCCCCEeEECCCCCEEEcCCCCCeECc
Confidence            4458899998887765 45899999987543

>d1dx8a_ g.41.5.1 (A:) Rubredoxin {Guillardia theta [TaxId: 55529]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Guillardia theta [TaxId: 55529]

Probab=89.25  E-value=0.1  Score=27.59  Aligned_cols=30  Identities=27%  Similarity=0.613  Sum_probs=22.2

Q ss_pred             CceEEEcCCCCCeeecCCC----------------CeeEcCCCCCc
Q 035461            6 EPVSYICGDCGMENTLKPG----------------DVIQCRECGYR   35 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~----------------~~irC~~CG~R   35 (51)
                      +...|+|..||..-+...+                +.-+||.||..
T Consensus         4 ~~~ky~C~~CgyiYDp~~GD~~~gI~pGT~F~dLP~dW~CP~Cga~   49 (70)
T d1dx8a_           4 DEGKYECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSP   49 (70)
T ss_dssp             CSSCEEETTTCCEECTTTCCTTTTCCSSCCGGGSCTTCBCTTTCCB
T ss_pred             cCCeEEcCCCCeEECcccCCcccCCCCCCChHHCCCCCCCcCCCCc
Confidence            3457999999988765432                45689999964

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

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

Probab=88.46  E-value=0.32  Score=24.83  Aligned_cols=29  Identities=31%  Similarity=0.797  Sum_probs=23.6

Q ss_pred             eEEEcCCCCCeeecC--CCCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLK--PGDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~RI   36 (51)
                      +.=+|.+|+.+.-+-  +...+.|..||.-+
T Consensus         6 ~~VkC~~C~n~~ivFsha~t~V~C~~Cg~~L   36 (58)
T d1qxfa_           6 VKVKCPDCEHEQVIFDHPSTIVKCIICGRTV   36 (58)
T ss_dssp             EEEECTTTCCEEEEESSCSSCEECSSSCCEE
T ss_pred             EEeECCCCCCeEEEEecCceEEEccccCCEE
Confidence            566899999998764  56789999999754

>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus globisporus [TaxId: 1459]

Probab=88.20  E-value=0.24  Score=22.80  Aligned_cols=29  Identities=24%  Similarity=0.360  Sum_probs=22.4

Q ss_pred             EEEcCCCCCeeecCCC---CeeEcCCCCCcEE
Q 035461            9 SYICGDCGMENTLKPG---DVIQCRECGYRIL   37 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~---~~irC~~CG~RIl   37 (51)
                      ...|..||+...+..+   ..-.|-.||..++
T Consensus         2 R~~C~~CG~~Yh~~~~pPk~~g~CD~cg~~L~   33 (35)
T d1s3ga2           2 RRICKVCGTSYHLLFNPPQVEGKCDKDGGELY   33 (35)
T ss_dssp             EEEETTTCCEEETTTBCCSBTTBCTTTCCBEE
T ss_pred             ccCCcCcCchhccccCCCCCCCccCCCCCCce
Confidence            3689999999988643   4578999998653

>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.05  E-value=0.19  Score=23.62  Aligned_cols=28  Identities=11%  Similarity=0.008  Sum_probs=21.9

Q ss_pred             EEEcCCCCCeeecCCC---CeeEcCCCCCcE
Q 035461            9 SYICGDCGMENTLKPG---DVIQCRECGYRI   36 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~~---~~irC~~CG~RI   36 (51)
                      ..+|..||+...+..+   ..-.|-.||..+
T Consensus         2 Rr~C~~cG~~Yh~~~~ppk~~g~CD~cg~~L   32 (38)
T d1akya2           2 RLIHPASGRSYHKIFNPPKEDMKDDVTGEAL   32 (38)
T ss_dssp             EEECTTTCCEEETTTBCCSSTTBCTTTCCBC
T ss_pred             ccCCcCccchhhhhccCcCcCCccCCCCCEe
Confidence            3689999999988643   445899999863

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=87.73  E-value=0.12  Score=25.32  Aligned_cols=24  Identities=29%  Similarity=0.826  Sum_probs=17.3

Q ss_pred             EcCCCCCeeecC--CCCeeEcCCCCC
Q 035461           11 ICGDCGMENTLK--PGDVIQCRECGY   34 (51)
Q Consensus        11 ~C~~Cg~~~~~~--~~~~irC~~CG~   34 (51)
                      +|.+||...-+.  ....+-|..||.
T Consensus         7 ~Cp~Cgs~~iv~D~~~Ge~vC~~CG~   32 (50)
T d1pfta_           7 VCPACESAELIYDPERGEIVCAKCGY   32 (50)
T ss_dssp             SCTTTSCCCEEEETTTTEEEESSSCC
T ss_pred             cCcCCCCCcEEEECCCCeEecccCCc
Confidence            688998764332  456799999996

>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=87.43  E-value=0.17  Score=23.65  Aligned_cols=28  Identities=11%  Similarity=0.010  Sum_probs=22.7

Q ss_pred             EEEcCCCCCeeecCC---CCeeEcCCCCCcE
Q 035461            9 SYICGDCGMENTLKP---GDVIQCRECGYRI   36 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~~~---~~~irC~~CG~RI   36 (51)
                      .++|..||+...+..   .-.-.|-.||..+
T Consensus         2 R~vc~~cG~~Yh~~~~pPk~~g~CD~cg~~L   32 (37)
T d2ak3a2           2 RWIHPGSGRVYNIEFNPPKTMGIDDLTGEPL   32 (37)
T ss_dssp             EEEETTTTEEEETTTBCCSSTTBCTTTCCBC
T ss_pred             ceeeCCcCChhhhccCCccccCCccCCCCcC
Confidence            478999999999874   3557899999864

>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=87.15  E-value=0.13  Score=29.46  Aligned_cols=13  Identities=38%  Similarity=1.114  Sum_probs=11.9

Q ss_pred             CeeEcCCCCCcEE
Q 035461           25 DVIQCRECGYRIL   37 (51)
Q Consensus        25 ~~irC~~CG~RIl   37 (51)
                      ..|+|+.|+++||
T Consensus        11 ~~v~C~~C~S~il   23 (115)
T d1hxra_          11 KAVLCQRCGSRVL   23 (115)
T ss_dssp             SCEEETTTCCEEE
T ss_pred             ceEECCCCCCEee
Confidence            6799999999996

>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=86.60  E-value=0.14  Score=25.88  Aligned_cols=28  Identities=18%  Similarity=0.348  Sum_probs=19.2

Q ss_pred             eEEEcCCCCCeeecC--CCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLK--PGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~R   35 (51)
                      ...+|.+||...-+.  ....+.|.+||.=
T Consensus        10 ~~~~Cp~Cgs~~ii~D~~~Ge~vC~~CG~V   39 (58)
T d1dl6a_          10 PRVTCPNHPDAILVEDYRAGDMICPECGLV   39 (58)
T ss_dssp             SCCSBTTBSSSCCEECSSSCCEECTTTCCE
T ss_pred             cccCCCCCCCCCEEEECCCCcEecccCCCE
Confidence            345788998775332  3466889999863

>d2cona1 g.41.15.1 (A:8-73) RNA-binding protein NOB1 (Nin one binding) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: NOB1 zinc finger-like
family: NOB1 zinc finger-like
domain: RNA-binding protein NOB1 (Nin one binding)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.20  E-value=0.4  Score=24.81  Aligned_cols=33  Identities=21%  Similarity=0.426  Sum_probs=25.2

Q ss_pred             CceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461            6 EPVSYICGDCGMENTLKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus         6 ~~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~   40 (51)
                      ..-.++|-.|-....  ...-+-||.||+.-|.|.
T Consensus         5 r~~~LrC~aCf~~t~--~~~k~FCpkCGn~TL~rv   37 (66)
T d2cona1           5 RSYILRCHGCFKTTS--DMNRVFCGHCGNKTLKKV   37 (66)
T ss_dssp             CCEEEECSSSCCEES--CSSCCSCSSSCCSCCEEE
T ss_pred             heeeeEeeecCcCcC--CcccccCcccCCCceeEE
Confidence            456789999988643  235689999999988774

>d1ryqa_ g.41.9.3 (A:) putative DNA-directed RNA polymerase subunit E'' (RpoE2) {Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RpoE2-like
domain: putative DNA-directed RNA polymerase subunit E'' (RpoE2)
species: Pyrococcus furiosus [TaxId: 2261]

Probab=85.88  E-value=0.18  Score=26.32  Aligned_cols=22  Identities=23%  Similarity=0.614  Sum_probs=16.7

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCC
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGY   34 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~   34 (51)
                      .+--|.+|+..++-+     .||+||.
T Consensus         8 ~~rAC~~C~~i~~~~-----~CpnC~s   29 (67)
T d1ryqa_           8 SEKACRHCHYITSED-----RCPVCGS   29 (67)
T ss_dssp             -CEEETTTCBEESSS-----SCTTTCC
T ss_pred             cChhHhhCCCccCCC-----CCCCCcC
Confidence            345699999997754     3999996

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=84.90  E-value=0.37  Score=25.58  Aligned_cols=24  Identities=25%  Similarity=0.509  Sum_probs=18.1

Q ss_pred             eEEEcCCCCCeeecCCCCeeEcCCCCCc
Q 035461            8 VSYICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      -.|-|..|..++.+.    .+||+|+..
T Consensus        17 ~~~~C~~C~~~~~~~----a~CPdC~~~   40 (71)
T d2jnea1          17 GHARCRSCGEFIEMK----ALCPDCHQP   40 (71)
T ss_dssp             TEEEETTTCCEEEEE----EECTTTCSB
T ss_pred             CCEehhhhhhhheeE----EeCCccccH
Confidence            368888888888766    688888764

>d1a1ia2 g.37.1.1 (A:132-159) ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: ZIF268
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=84.49  E-value=0.24  Score=21.69  Aligned_cols=13  Identities=15%  Similarity=0.353  Sum_probs=10.9

Q ss_pred             EEEcCCCCCeeec
Q 035461            9 SYICGDCGMENTL   21 (51)
Q Consensus         9 ~Y~C~~Cg~~~~~   21 (51)
                      .|.|..||+.|.-
T Consensus         3 Py~C~~C~k~F~~   15 (28)
T d1a1ia2           3 PFQCRICMRNFSR   15 (28)
T ss_dssp             CEECTTTCCEESC
T ss_pred             CccCCCCcCEecc
Confidence            3999999998864

>d1m2ka_ c.31.1.5 (A:) AF1676, Sir2 homolog (Sir2-AF1?) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: DHS-like NAD/FAD-binding domain
superfamily: DHS-like NAD/FAD-binding domain
family: Sir2 family of transcriptional regulators
domain: AF1676, Sir2 homolog (Sir2-AF1?)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=83.66  E-value=0.45  Score=28.60  Aligned_cols=29  Identities=17%  Similarity=0.485  Sum_probs=22.4

Q ss_pred             eEEEcCCCCCeeecCC----CCeeEcCCCCCcE
Q 035461            8 VSYICGDCGMENTLKP----GDVIQCRECGYRI   36 (51)
Q Consensus         8 ~~Y~C~~Cg~~~~~~~----~~~irC~~CG~RI   36 (51)
                      ....|..|+..+..+.    ...-+||.||..+
T Consensus       120 ~~~~C~~c~~~~~~~~~~~~~~~p~C~~Cgg~l  152 (249)
T d1m2ka_         120 RVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLL  152 (249)
T ss_dssp             EEEEESSSSCEEECSSCCCSSSCCBCSSSSSBE
T ss_pred             hheeeccCCCcccccccccCCCCCCcccCCCEe
Confidence            4578999999998763    3556899999853

>d1x6ea1 g.37.1.1 (A:8-40) Zinc finger protein 24 {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 24
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.15  E-value=0.33  Score=21.86  Aligned_cols=15  Identities=27%  Similarity=0.563  Sum_probs=11.9

Q ss_pred             ceEEEcCCCCCeeec
Q 035461            7 PVSYICGDCGMENTL   21 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~   21 (51)
                      .-.|.|.+||+.|.-
T Consensus         5 ekpy~C~~Cgk~F~~   19 (33)
T d1x6ea1           5 EKPYGCVECGKAFSR   19 (33)
T ss_dssp             CCCEECSSSCCEESS
T ss_pred             CCCeeCCCCCCEeCc
Confidence            345999999998864

>d1tbna_ g.49.1.1 (A:) Protein kinase c-gamma {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)
domain: Protein kinase c-gamma
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=81.85  E-value=0.54  Score=23.33  Aligned_cols=26  Identities=19%  Similarity=0.464  Sum_probs=19.6

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCcE
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYRI   36 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~RI   36 (51)
                      .|.-|+..+-.-...+.+|..|+..+
T Consensus        21 ~C~~C~~~i~g~~~~g~~C~~C~~~~   46 (66)
T d1tbna_          21 FCDHCGSLLYGLVHQGMKCSCCEMNV   46 (66)
T ss_dssp             BCSSSCCBCCTTSSSCEEETTTCCEE
T ss_pred             CCcCCCCcccCcccCccccCcccCeE
Confidence            59999887754445789999998653

>d2gnra1 b.40.4.15 (A:8-144) Hypothetical protein SSO2064 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: SSO2064-like
domain: Hypothetical protein SSO2064
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=81.49  E-value=0.53  Score=26.52  Aligned_cols=31  Identities=19%  Similarity=0.313  Sum_probs=24.2

Q ss_pred             ceEEEcCCCCCeeecCCCCeeEcCCCCCcEEEEE
Q 035461            7 PVSYICGDCGMENTLKPGDVIQCRECGYRILYKK   40 (51)
Q Consensus         7 ~~~Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK~   40 (51)
                      -+..+|.+||...-...   -.|+.||..-+--.
T Consensus        37 L~~~~C~~CG~v~~Ppr---~~Cp~C~s~~~e~~   67 (137)
T d2gnra1          37 IIGSKCSKCGRIFVPAR---SYCEHCFVKIENYV   67 (137)
T ss_dssp             CEEEECTTTCCEEESCC---SEETTTTEECCEEE
T ss_pred             EEEEEcCCCCCEEeCcc---ccCCCCCCCcceeE
Confidence            37789999999987653   35999999877653

>d1ptqa_ g.49.1.1 (A:) Protein kinase C-delta (PKCdelta) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)
domain: Protein kinase C-delta (PKCdelta)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.20  E-value=0.72  Score=21.63  Aligned_cols=25  Identities=24%  Similarity=0.610  Sum_probs=18.6

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      .|.-|+..+-.-...+.+|.+|+..
T Consensus        13 ~C~~C~~~i~g~~~qg~~C~~C~~~   37 (50)
T d1ptqa_          13 FCDHCGSLLWGLVKQGLKCEDCGMN   37 (50)
T ss_dssp             BCTTTCCBCCSSSSCEEEETTTCCE
T ss_pred             CCcccCCcccCcccCcEECCCCCCe
Confidence            5888988764434578999999864

>d1wgea1 g.41.17.1 (A:8-77) DelGEF-interacting protein 1, DelGIP1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: CSL zinc finger
family: CSL zinc finger
domain: DelGEF-interacting protein 1, DelGIP1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.67  E-value=1.3  Score=23.14  Aligned_cols=34  Identities=35%  Similarity=0.727  Sum_probs=25.0

Q ss_pred             CCCCCceEEEcCCCCCeeecC-----CC-CeeEcCCCCCcE
Q 035461            2 DPQPEPVSYICGDCGMENTLK-----PG-DVIQCRECGYRI   36 (51)
Q Consensus         2 ~~~~~~~~Y~C~~Cg~~~~~~-----~~-~~irC~~CG~RI   36 (51)
                      |+..+...|-|- ||..|.+.     .+ ..+.||-|.=.|
T Consensus        16 dee~~~~~ypCp-CGd~F~it~~dLe~ge~V~~C~sCSL~i   55 (70)
T d1wgea1          16 DEDSETYFYPCP-CGDNFAITKEDLENGEDVATCPSCSLII   55 (70)
T ss_dssp             BTTTTEEEECCS-SSSCEEEEHHHHHTTCCEEECTTTCCEE
T ss_pred             eCCCCEEEeCCC-CCCeEEECHHHHhCCCeEEeCCCCceEE
Confidence            345566889998 99998874     33 457899998544

>d2nn6i1 b.40.4.5 (I:61-185) Exosome component 1, EXOSC1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome component 1, EXOSC1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.51  E-value=0.49  Score=26.51  Aligned_cols=24  Identities=8%  Similarity=-0.089  Sum_probs=16.7

Q ss_pred             EcCCCCCeeecCCCCeeEcCCCCCc
Q 035461           11 ICGDCGMENTLKPGDVIQCRECGYR   35 (51)
Q Consensus        11 ~C~~Cg~~~~~~~~~~irC~~CG~R   35 (51)
                      +|..|+ ..-....+.+.||+||..
T Consensus        97 ~c~~g~-~m~~~~~~~m~cp~~g~~  120 (125)
T d2nn6i1          97 HSESGI-QMVPISWCEMQCPKTHTK  120 (125)
T ss_dssp             BCSSSC-BCEEEETTEEECTTTTCC
T ss_pred             ECCCCC-EeEeecCCEEECCCCCCe
Confidence            676544 444445588999999975

>d1ywsa1 g.41.17.1 (A:1-82) Diphthamide biosynthesis protein 3, DPH3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: CSL zinc finger
family: CSL zinc finger
domain: Diphthamide biosynthesis protein 3, DPH3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.22  E-value=0.72  Score=24.81  Aligned_cols=33  Identities=30%  Similarity=0.709  Sum_probs=24.5

Q ss_pred             CCCCceEEEcCCCCCeeecC-----CC-CeeEcCCCCCcE
Q 035461            3 PQPEPVSYICGDCGMENTLK-----PG-DVIQCRECGYRI   36 (51)
Q Consensus         3 ~~~~~~~Y~C~~Cg~~~~~~-----~~-~~irC~~CG~RI   36 (51)
                      +..+...|-|- ||..|.+.     .+ ..+.|+.|.=.|
T Consensus        16 ed~~~~~ypCr-CGd~F~it~~dLe~ge~v~~C~sCSL~I   54 (82)
T d1ywsa1          16 PENQMFTYPCP-CGDRFQIYLDDMFEGEKVAVCPSCSLMI   54 (82)
T ss_dssp             TTTTEEEECCS-SSSCEEEEHHHHHTTCCEEEETTTTEEE
T ss_pred             CCCCEEEeccc-cCCeEEEcHHHHhCCCeEEeCCCCceEE
Confidence            45567889998 99999875     33 456899998543

>d2dkta1 g.89.1.1 (A:8-81) RING finger and CHY zinc finger domain-containing protein 1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CHY zinc finger-like
superfamily: CHY zinc finger-like
family: CHY zinc finger
domain: RING finger and CHY zinc finger domain-containing protein 1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.06  E-value=0.51  Score=24.17  Aligned_cols=10  Identities=30%  Similarity=0.767  Sum_probs=4.9

Q ss_pred             CeeEcCCCCC
Q 035461           25 DVIQCRECGY   34 (51)
Q Consensus        25 ~~irC~~CG~   34 (51)
                      ..+.|-+||+
T Consensus        50 ~~l~CH~Cg~   59 (74)
T d2dkta1          50 KEVQCINCEK   59 (74)
T ss_dssp             CCEEESSSCC
T ss_pred             CEEEeccCCC
Confidence            4455555554