Citrus Sinensis ID: 033276

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120---
Protein Sequence
MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLYIQVDTEMPCLLHYHC
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHccccccEEEEEEHHHHHHHHHHHHccEEEccccEEEEEEHHHHHHcccccccccccEEEccccccccEEcHHHEEEEEEEEEEEcccccEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEEcccccHHHHHHcccccccEEEEEHHHHHHHHHHHHcccEEccccHHHHHHHHHHHHHHHHHHccccccEEEEcccccEEEcHHHHHHHHHHHEEEccccccEEEccc
Coil and Loop (DISEMBL)
meissknneivdvsyvddecseqswMLRSLSESTVACITGDYAMQNVILQMGLRllapggmqirQLHRYIVDKCLklfsspfplviciksnheirisPVFMLILICLYIqvdtempcllhyhc
Flexible Loop (DISEMBL)
meissknneivdvsyVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLYIQVDTEMPCLLHYHC
Low Complexity Region (SEG)
MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLYIQVDTEMPCLLHYHC
Disordered region (IsUnstruct)
*********IVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLYIQVDTEMPCLLHY**
Disordered Region (DISOPRED)
*********************************TVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLYIQVDTEMPCLLHYHC
Disordered Region (DISEMBL)
MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLYIQVDTEMPCLLHYHC
Disordered Region (DISPRO)
*******NEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLYIQVDTEMPCLLHYHC
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLYIQVDTEMPCLLHYHC
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	123	2.2.26 [Sep-21-2011]
Q5RBB3	411	RNA-binding protein NOB1	yes	no	0.365	0.109	0.521	1e-06
Q4R537	412	RNA-binding protein NOB1	N/A	no	0.365	0.109	0.521	1e-06
Q3T042	413	RNA-binding protein NOB1	yes	no	0.365	0.108	0.521	1e-06
Q9ULX3	412	RNA-binding protein NOB1	yes	no	0.365	0.109	0.521	2e-06
Q6VEU1	410	RNA-binding protein NOB1	yes	no	0.365	0.109	0.5	2e-06
Q8BW10	403	RNA-binding protein NOB1	yes	no	0.365	0.111	0.5	2e-06
Q9UTK0	388	20S-pre-rRNA D-site endon	yes	no	0.300	0.095	0.459	0.0001
Q08444	459	20S-pre-rRNA D-site endon	yes	no	0.406	0.108	0.415	0.0005

>sp|Q5RBB3|NOB1_PONAB RNA-binding protein NOB1 OS=Pongo abelii GN=NOB1 PE=2 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/46 (52%), Positives = 32/46 (69%), Gaps = 1/46 (2%)

Query: 35  VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS 80
           V C+T D+AMQNV+LQMGL +LA  GM IR+   YI+ +C   F +
Sbjct: 231 VGCVTTDFAMQNVLLQMGLHVLAVNGMLIREARSYIL-RCHGCFKT 275

May play a role in mRNA degradation.
Pongo abelii (taxid: 9601)

>sp|Q4R537|NOB1_MACFA RNA-binding protein NOB1 OS=Macaca fascicularis GN=NOB1 PE=2 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/46 (52%), Positives = 32/46 (69%), Gaps = 1/46 (2%)

Query: 35  VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS 80
           V C+T D+AMQNV+LQMGL +LA  GM IR+   YI+ +C   F +
Sbjct: 232 VGCVTTDFAMQNVLLQMGLHVLAVNGMLIREARSYIL-RCHGCFKT 276

May play a role in mRNA degradation.

Macaca fascicularis (taxid: 9541)

>sp|Q3T042|NOB1_BOVIN RNA-binding protein NOB1 OS=Bos taurus GN=NOB1 PE=2 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/46 (52%), Positives = 32/46 (69%), Gaps = 1/46 (2%)

Query: 35  VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS 80
           V C+T D+AMQNV+LQMGL +LA  GM IR+   YI+ +C   F +
Sbjct: 233 VGCVTTDFAMQNVLLQMGLHVLAVNGMLIREARSYIL-RCHGCFKT 277

May play a role in mRNA degradation.

Bos taurus (taxid: 9913)

>sp|Q9ULX3|NOB1_HUMAN RNA-binding protein NOB1 OS=Homo sapiens GN=NOB1 PE=1 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/46 (52%), Positives = 32/46 (69%), Gaps = 1/46 (2%)

Query: 35  VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS 80
           V C+T D+AMQNV+LQMGL +LA  GM IR+   YI+ +C   F +
Sbjct: 232 VGCLTTDFAMQNVLLQMGLHVLAVNGMLIREARSYIL-RCHGCFKT 276

May play a role in mRNA degradation.

Homo sapiens (taxid: 9606)

>sp|Q6VEU1|NOB1_RAT RNA-binding protein NOB1 OS=Rattus norvegicus GN=Nob1 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/46 (50%), Positives = 32/46 (69%), Gaps = 1/46 (2%)

Query: 35  VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS 80
           V C+T D+AMQNV+LQMGL +LA  GM +R+   YI+ +C   F +
Sbjct: 230 VGCVTTDFAMQNVLLQMGLHVLAVNGMLVREARSYIL-RCHGCFKT 274

May play a role in mRNA degradation.

Rattus norvegicus (taxid: 10116)

>sp|Q8BW10|NOB1_MOUSE RNA-binding protein NOB1 OS=Mus musculus GN=Nob1 PE=1 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/46 (50%), Positives = 32/46 (69%), Gaps = 1/46 (2%)

Query: 35  VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS 80
           V C+T D+AMQNV+LQMGL +LA  GM +R+   YI+ +C   F +
Sbjct: 223 VGCVTTDFAMQNVLLQMGLHVLAVNGMLVREARSYIL-RCHGCFKT 267

May play a role in mRNA degradation.

Mus musculus (taxid: 10090)

>sp|Q9UTK0|NOB1_SCHPO 20S-pre-rRNA D-site endonuclease nob1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=nob1 PE=3 SV=1

 Score = 45.1 bits (105), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 17/37 (45%), Positives = 29/37 (78%)

Query: 35  VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIV 71
           VAC T D++MQNV+LQ+GL L++  G +I+ + R+++
Sbjct: 218 VACATTDFSMQNVLLQIGLNLVSSDGFKIQNVKRFVL 254

Required for the synthesis of 40S ribosome subunits. Has a role in processing 20S pre-rRNA into the mature 18S rRNA, where it is required for cleavage at the 3' end of the mature 18S rRNA (D-site). Accompanies the 20S pre-rRNA from the nucleus to the cytoplasm.

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

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q08444|NOB1_YEAST 20S-pre-rRNA D-site endonuclease NOB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NOB1 PE=1 SV=1

 Score = 43.1 bits (100), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/53 (41%), Positives = 34/53 (64%), Gaps = 3/53 (5%)

Query: 32  ESTVACITGDYAMQNVILQMGLRLLA-PGGMQIRQLHRYIV--DKCLKLFSSP 81
           E+ VA  TGD+A+QNV LQM L L+    G++I+++  Y++    C K+F  P
Sbjct: 262 ENQVALATGDFAVQNVALQMNLNLMNFMSGLKIKRIRNYMLRCHACFKIFPLP 314

Required for the synthesis of 40S ribosome subunits. Has a role in processing 20S pre-rRNA into the mature 18S rRNA, where it is required for cleavage at the 3' end of the mature 18S rRNA (D-site). Accompanies the 20S pre-rRNA from the nucleus to the cytoplasm. In association with NIN1, may promote the recruitment of the proteasome to the ribosomal subunits stalled in maturation.

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

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

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	123
359474015	633	PREDICTED: RNA-binding protein NOB1-like	0.593	0.115	0.770	2e-27
297742539	560	unnamed protein product [Vitis vinifera]	0.593	0.130	0.770	2e-27
147800398	621	hypothetical protein VITISV_020978 [Viti	0.593	0.117	0.770	2e-27
449495836	617	PREDICTED: LOW QUALITY PROTEIN: RNA-bind	0.593	0.118	0.783	7e-27
449452344	617	PREDICTED: RNA-binding protein NOB1-like	0.593	0.118	0.783	7e-27
255537423	628	RNA-binding protein nob1, putative [Rici	0.593	0.116	0.756	4e-26
357138448	598	PREDICTED: RNA-binding protein NOB1-like	0.577	0.118	0.746	2e-25
357520491	613	RNA-binding protein NOB1 [Medicago trunc	0.617	0.123	0.730	6e-25
356513405	632	PREDICTED: uncharacterized protein LOC10	0.593	0.115	0.716	1e-24
326517786	588	predicted protein [Hordeum vulgare subsp	0.577	0.120	0.739	5e-24

>gi|359474015|ref|XP_002269627.2| PREDICTED: RNA-binding protein NOB1-like [Vitis vinifera]

 Score =  126 bits (316), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 57/74 (77%), Positives = 69/74 (93%), Gaps = 1/74 (1%)

Query: 1   MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGG 60
           +EISS+ +E VDVSY+DDE SEQSWML+SLS+S+VAC+T D+AMQNV+LQMGLRLLAPGG
Sbjct: 422 LEISSQMSESVDVSYIDDESSEQSWMLKSLSDSSVACVTSDFAMQNVLLQMGLRLLAPGG 481

Query: 61  MQIRQLHRYIVDKC 74
           MQIRQLHR+I+ KC
Sbjct: 482 MQIRQLHRWIL-KC 494

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297742539|emb|CBI34688.3| unnamed protein product [Vitis vinifera]

 Score =  126 bits (316), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 57/74 (77%), Positives = 69/74 (93%), Gaps = 1/74 (1%)

Query: 1   MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGG 60
           +EISS+ +E VDVSY+DDE SEQSWML+SLS+S+VAC+T D+AMQNV+LQMGLRLLAPGG
Sbjct: 349 LEISSQMSESVDVSYIDDESSEQSWMLKSLSDSSVACVTSDFAMQNVLLQMGLRLLAPGG 408

Query: 61  MQIRQLHRYIVDKC 74
           MQIRQLHR+I+ KC
Sbjct: 409 MQIRQLHRWIL-KC 421

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147800398|emb|CAN66411.1| hypothetical protein VITISV_020978 [Vitis vinifera]

 Score =  126 bits (316), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 57/74 (77%), Positives = 69/74 (93%), Gaps = 1/74 (1%)

Query: 1   MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGG 60
           +EISS+ +E VDVSY+DDE SEQSWML+SLS+S+VAC+T D+AMQNV+LQMGLRLLAPGG
Sbjct: 410 LEISSQMSESVDVSYIDDESSEQSWMLKSLSDSSVACVTSDFAMQNVLLQMGLRLLAPGG 469

Query: 61  MQIRQLHRYIVDKC 74
           MQIRQLHR+I+ KC
Sbjct: 470 MQIRQLHRWIL-KC 482

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449495836|ref|XP_004159959.1| PREDICTED: LOW QUALITY PROTEIN: RNA-binding protein NOB1-like [Cucumis sativus]

 Score =  124 bits (311), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 58/74 (78%), Positives = 67/74 (90%), Gaps = 1/74 (1%)

Query: 1   MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGG 60
           ME +S+ NE VD+S VDD  S+QSWMLRSLSES+VAC+TGDYAMQNV+LQMGLRLLAPGG
Sbjct: 404 MEDASQTNESVDMSNVDDVSSDQSWMLRSLSESSVACVTGDYAMQNVLLQMGLRLLAPGG 463

Query: 61  MQIRQLHRYIVDKC 74
           MQIRQLHR+I+ KC
Sbjct: 464 MQIRQLHRWIL-KC 476

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452344|ref|XP_004143919.1| PREDICTED: RNA-binding protein NOB1-like [Cucumis sativus]

 Score =  124 bits (311), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 58/74 (78%), Positives = 67/74 (90%), Gaps = 1/74 (1%)

Query: 1   MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGG 60
           ME +S+ NE VD+S VDD  S+QSWMLRSLSES+VAC+TGDYAMQNV+LQMGLRLLAPGG
Sbjct: 404 MEDASQTNESVDMSNVDDVSSDQSWMLRSLSESSVACVTGDYAMQNVLLQMGLRLLAPGG 463

Query: 61  MQIRQLHRYIVDKC 74
           MQIRQLHR+I+ KC
Sbjct: 464 MQIRQLHRWIL-KC 476

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255537423|ref|XP_002509778.1| RNA-binding protein nob1, putative [Ricinus communis] gi|223549677|gb|EEF51165.1| RNA-binding protein nob1, putative [Ricinus communis]

 Score =  122 bits (305), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 56/74 (75%), Positives = 66/74 (89%), Gaps = 1/74 (1%)

Query: 1   MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGG 60
           ++I S+  E VDVS+ DD+ SEQSWMLRSLSES+VAC+T DYAMQNV+LQMGLRLLAPGG
Sbjct: 417 LDILSETTETVDVSHGDDDASEQSWMLRSLSESSVACVTSDYAMQNVLLQMGLRLLAPGG 476

Query: 61  MQIRQLHRYIVDKC 74
           MQIRQLHR+I+ KC
Sbjct: 477 MQIRQLHRWIL-KC 489

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357138448|ref|XP_003570804.1| PREDICTED: RNA-binding protein NOB1-like [Brachypodium distachyon]

 Score =  119 bits (299), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/71 (74%), Positives = 63/71 (88%)

Query: 1   MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGG 60
           ++I S+  E V+ S+VDDE SEQSW LRSLSESTVAC+T DYAMQNVILQ+GLRLLAPGG
Sbjct: 388 LDIKSETEESVEASFVDDESSEQSWALRSLSESTVACVTSDYAMQNVILQIGLRLLAPGG 447

Query: 61  MQIRQLHRYIV 71
           MQIRQLHR+++
Sbjct: 448 MQIRQLHRWVL 458

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357520491|ref|XP_003630534.1| RNA-binding protein NOB1 [Medicago truncatula] gi|355524556|gb|AET05010.1| RNA-binding protein NOB1 [Medicago truncatula]

 Score =  118 bits (295), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 57/78 (73%), Positives = 67/78 (85%), Gaps = 2/78 (2%)

Query: 2   EISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGM 61
           +I+S+++E  DVSY DD  SEQSWMLRSLSESTVACITGD+AMQNV+LQMGLRLLAPGG 
Sbjct: 405 DIASQSSEAADVSYADD-ASEQSWMLRSLSESTVACITGDFAMQNVLLQMGLRLLAPGGS 463

Query: 62  QIRQLHRYIVDKCLKLFS 79
           QI QLHR+I+ KC   F+
Sbjct: 464 QIHQLHRWIL-KCHACFT 480

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513405|ref|XP_003525404.1| PREDICTED: uncharacterized protein LOC100800291 [Glycine max]

 Score =  117 bits (293), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/74 (71%), Positives = 65/74 (87%), Gaps = 1/74 (1%)

Query: 1   MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGG 60
           +EI+S+ +E  D SY DD+ S+QSWM+RSLSES+VACITGD+AMQNV+LQMGLRLLAPGG
Sbjct: 422 LEIASQTSEAADFSYADDDDSDQSWMVRSLSESSVACITGDFAMQNVLLQMGLRLLAPGG 481

Query: 61  MQIRQLHRYIVDKC 74
            QI QLHR+I+ KC
Sbjct: 482 TQIHQLHRWIL-KC 494

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326517786|dbj|BAK03811.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  115 bits (287), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 54/73 (73%), Positives = 63/73 (86%), Gaps = 2/73 (2%)

Query: 1   MEISSKNNEIVDVS--YVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAP 58
           ++I S+  E V VS  +VDDE SEQSW LRSLSESTVAC+T DYAMQNVILQ+GLRLLAP
Sbjct: 376 LDIKSETEEGVSVSASFVDDESSEQSWALRSLSESTVACVTSDYAMQNVILQIGLRLLAP 435

Query: 59  GGMQIRQLHRYIV 71
           GGMQIRQLHR+++
Sbjct: 436 GGMQIRQLHRWVL 448

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

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	123
TAIR|locus:2163071	602	NOB1 [Arabidopsis thaliana (ta	0.593	0.121	0.72	5.7e-22
UNIPROTKB|Q3T042	413	NOB1 "RNA-binding protein NOB1	0.422	0.125	0.490	1.1e-06
UNIPROTKB|Q9ULX3	412	NOB1 "RNA-binding protein NOB1	0.422	0.126	0.490	1.4e-06
MGI|MGI:1914869	403	Nob1 "NIN1/RPN12 binding prote	0.422	0.129	0.472	1.7e-06
RGD|735222	410	Nob1 "NIN1/RPN12 binding prote	0.422	0.126	0.472	1.7e-06
SGD|S000005582	459	NOB1 "Protein involved in prot	0.512	0.137	0.373	0.00011
POMBASE|SPAC1486.09	388	SPAC1486.09 "ribosome biogenes	0.317	0.100	0.45	0.00011
FB|FBgn0030177	472	CG2972 [Drosophila melanogaste	0.365	0.095	0.456	0.00015
WB|WBGene00021843	364	Y54E10BR.4 [Caenorhabditis ele	0.365	0.123	0.413	0.00021

TAIR|locus:2163071 NOB1 [Arabidopsis thaliana (taxid:3702)]

 Score = 264 (98.0 bits), Expect = 5.7e-22, P = 5.7e-22
 Identities = 54/75 (72%), Positives = 64/75 (85%)

Query:     1 MEISSKNNEIVDVSYV-DDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPG 59
             +EI+S+  +  + S + DD  SEQSW LR+LSES+VACITGDYAMQNVILQMGLRLLAPG
Sbjct:   389 LEIASEAEDTFEASSIGDDGSSEQSWSLRALSESSVACITGDYAMQNVILQMGLRLLAPG 448

Query:    60 GMQIRQLHRYIVDKC 74
             GMQIRQLHR+I+ KC
Sbjct:   449 GMQIRQLHRWIL-KC 462

GO:0005634 "nucleus" evidence=ISM

GO:0006606 "protein import into nucleus" evidence=RCA

GO:0000469 "cleavage involved in rRNA processing" evidence=IDA

GO:0004521 "endoribonuclease activity" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006364 "rRNA processing" evidence=IMP

GO:0009553 "embryo sac development" evidence=IMP

GO:0009555 "pollen development" evidence=IMP

UNIPROTKB|Q3T042 NOB1 "RNA-binding protein NOB1" [Bos taurus (taxid:9913)]

 Score = 120 (47.3 bits), Expect = 1.1e-06, P = 1.1e-06
 Identities = 27/55 (49%), Positives = 35/55 (63%)

Query:    35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLF--SSPFPLVIC 87
             V C+T D+AMQNV+LQMGL +LA  GM IR+   YI+ +C   F  +S    V C
Sbjct:   233 VGCVTTDFAMQNVLLQMGLHVLAVNGMLIREARSYIL-RCHGCFKTTSDMSRVFC 286

GO:0005634 "nucleus" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q9ULX3 NOB1 "RNA-binding protein NOB1" [Homo sapiens (taxid:9606)]

 Score = 119 (46.9 bits), Expect = 1.4e-06, P = 1.4e-06
 Identities = 27/55 (49%), Positives = 35/55 (63%)

Query:    35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLF--SSPFPLVIC 87
             V C+T D+AMQNV+LQMGL +LA  GM IR+   YI+ +C   F  +S    V C
Sbjct:   232 VGCLTTDFAMQNVLLQMGLHVLAVNGMLIREARSYIL-RCHGCFKTTSDMSRVFC 285

GO:0046872 "metal ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:1914869 Nob1 "NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 118 (46.6 bits), Expect = 1.7e-06, P = 1.7e-06
 Identities = 26/55 (47%), Positives = 35/55 (63%)

Query:    35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLF--SSPFPLVIC 87
             V C+T D+AMQNV+LQMGL +LA  GM +R+   YI+ +C   F  +S    V C
Sbjct:   223 VGCVTTDFAMQNVLLQMGLHVLAVNGMLVREARSYIL-RCHGCFKTTSDMNRVFC 276

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISA

GO:0005730 "nucleolus" evidence=ISA

GO:0005737 "cytoplasm" evidence=ISA

GO:0030490 "maturation of SSU-rRNA" evidence=ISA

GO:0042274 "ribosomal small subunit biogenesis" evidence=ISA

GO:0046872 "metal ion binding" evidence=IEA

RGD|735222 Nob1 "NIN1/RPN12 binding protein 1 homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 118 (46.6 bits), Expect = 1.7e-06, P = 1.7e-06
 Identities = 26/55 (47%), Positives = 35/55 (63%)

Query:    35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLF--SSPFPLVIC 87
             V C+T D+AMQNV+LQMGL +LA  GM +R+   YI+ +C   F  +S    V C
Sbjct:   230 VGCVTTDFAMQNVLLQMGLHVLAVNGMLVREARSYIL-RCHGCFKTTSDMNRVFC 283

GO:0005634 "nucleus" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

SGD|S000005582 NOB1 "Protein involved in proteasomal and 40S ribosomal subunit biogenesis" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 102 (41.0 bits), Expect = 0.00011, P = 0.00011
 Identities = 25/67 (37%), Positives = 40/67 (59%)

Query:    19 ECSEQS-WMLRSLSESTVACITGDYAMQNVILQMGLRLLA-PGGMQIRQLHRYIV--DKC 74
             E SE+   +  +  E+ VA  TGD+A+QNV LQM L L+    G++I+++  Y++    C
Sbjct:   248 EASEEDRHVALNRPENQVALATGDFAVQNVALQMNLNLMNFMSGLKIKRIRNYMLRCHAC 307

Query:    75 LKLFSSP 81
              K+F  P
Sbjct:   308 FKIFPLP 314

GO:0042274 "ribosomal small subunit biogenesis" evidence=IDA;IPI

GO:0070181 "SSU rRNA binding" evidence=IDA

GO:0043248 "proteasome assembly" evidence=IMP;IPI

GO:0000462 "maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IEP;IMP

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0005730 "nucleolus" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0030688 "preribosome, small subunit precursor" evidence=IDA

GO:0090305 "nucleic acid phosphodiester bond hydrolysis" evidence=IEA

GO:0004521 "endoribonuclease activity" evidence=IDA

GO:0030490 "maturation of SSU-rRNA" evidence=IDA

POMBASE|SPAC1486.09 SPAC1486.09 "ribosome biogenesis protein Nob1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 101 (40.6 bits), Expect = 0.00011, P = 0.00011
 Identities = 18/40 (45%), Positives = 31/40 (77%)

Query:    35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKC 74
             VAC T D++MQNV+LQ+GL L++  G +I+ + R+++ +C
Sbjct:   218 VACATTDFSMQNVLLQIGLNLVSSDGFKIQNVKRFVL-RC 256

GO:0003723 "RNA binding" evidence=ISO

GO:0004521 "endoribonuclease activity" evidence=ISO

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005730 "nucleolus" evidence=IEA

GO:0005829 "cytosol" evidence=IDA

GO:0030688 "preribosome, small subunit precursor" evidence=ISO

GO:0042274 "ribosomal small subunit biogenesis" evidence=ISO

GO:0043248 "proteasome assembly" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

FB|FBgn0030177 CG2972 [Drosophila melanogaster (taxid:7227)]

 Score = 101 (40.6 bits), Expect = 0.00015, P = 0.00015
 Identities = 21/46 (45%), Positives = 30/46 (65%)

Query:    35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS 80
             VAC+T DYA+QNV+ Q+ L L A  G  I+QL  YI+ +C   + +
Sbjct:   291 VACMTTDYALQNVLKQLNLHLAALNGRIIKQLRTYIL-RCYACYKT 335

GO:0022008 "neurogenesis" evidence=IMP

WB|WBGene00021843 Y54E10BR.4 [Caenorhabditis elegans (taxid:6239)]

 Score = 98 (39.6 bits), Expect = 0.00021, P = 0.00021
 Identities = 19/46 (41%), Positives = 32/46 (69%)

Query:    35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS 80
             V C+T D+A+QNV+L M L L++  G +IR+L  +++ +C   FS+
Sbjct:   196 VGCLTTDFALQNVLLAMNLSLVSLSGYRIRKLKSFVL-RCRTCFST 240


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.327   0.140   0.432    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      123       123   0.00091  102 3  11 22  0.42    30
                                                     29  0.50    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  9
  No. of states in DFA:  598 (64 KB)
  Total size of DFA:  141 KB (2086 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  12.97u 0.10s 13.07t   Elapsed:  00:00:01
  Total cpu time:  12.97u 0.10s 13.07t   Elapsed:  00:00:01
  Start:  Fri May 10 21:22:13 2013   End:  Fri May 10 21:22:14 2013

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0008340 "determination of adult lifespan" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0071688 "striated muscle myosin thick filament assembly" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00000393001	SubName- Full=Chromosome chr2 scaffold_105, whole genome shotgun sequence; (611 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00020673001	SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (607 aa)				•					0.427
	GSVIVG00035100001	SubName- Full=Chromosome chr1 scaffold_75, whole genome shotgun sequence; (207 aa)					•				0.408

---

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	123
COG1439	177	COG1439, COG1439, Predicted nucleic acid-binding p	4e-06

>gnl|CDD|224356 COG1439, COG1439, Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]

 Score = 43.2 bits (102), Expect = 4e-06
 Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 32  ESTVACITGDYAMQNVILQMGLRLLAP---GGMQIRQLHRYIVDKCLKLFSSPFPLVICI 88
           E  VA  T DY++QNV LQ+GL + +    G ++  +  R     C ++F  P P   C 
Sbjct: 100 EVQVALATDDYSVQNVALQLGLNVRSISYKGKIKKVRKWRLRCHGCKRIF--PEPKDFCP 157

Query: 89  KSNHEIRISPV 99
                ++   V
Sbjct: 158 ICGSPLKRKRV 168

Length = 177

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	123
KOG2463	376	consensus Predicted RNA-binding protein Nob1p invo	100.0
COG1439	177	Predicted nucleic acid-binding protein, consists o	99.89
PRK12496	164	hypothetical protein; Provisional	99.79
PF08772	73	NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon lik	99.65
TIGR03875	206	RNA_lig_partner RNA ligase partner, MJ_0950 family	97.89
PRK04358	217	hypothetical protein; Provisional	97.74
PF13248	26	zf-ribbon_3: zinc-ribbon domain	97.15
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	96.96
PF08745	205	UPF0278: UPF0278 family; InterPro: IPR022785 This	96.84
PF15017	87	AF1Q: Drug resistance and apoptosis regulator	96.34
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	96.16
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	96.05
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	95.85
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	95.83
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	95.75
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	95.54
PF12172	37	DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35	95.51
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	95.41
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	95.34
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	95.33
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	95.31
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	95.24
COG1545	140	Predicted nucleic-acid-binding protein containing	94.66
PF12773	50	DZR: Double zinc ribbon	93.94
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	93.57
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	93.46
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	93.35
PF12773	50	DZR: Double zinc ribbon	92.91
PF10263	157	SprT-like: SprT-like family; InterPro: IPR006640 T	92.86
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	92.51
COG2093	64	DNA-directed RNA polymerase, subunit E'' [Transcri	92.51
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	92.48
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	91.94
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	91.81
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	91.21
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	91.2
COG1592	166	Rubrerythrin [Energy production and conversion]	91.05
PRK13130	56	H/ACA RNA-protein complex component Nop10p; Review	90.59
PRK00420	112	hypothetical protein; Validated	90.44
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	89.74
PRK14559	645	putative protein serine/threonine phosphatase; Pro	89.29
PRK04351	149	hypothetical protein; Provisional	89.19
COG1579	239	Zn-ribbon protein, possibly nucleic acid-binding [	88.96
PF07295	146	DUF1451: Protein of unknown function (DUF1451); In	88.75
COG5257	415	GCD11 Translation initiation factor 2, gamma subun	88.6
COG1656	165	Uncharacterized conserved protein [Function unknow	88.5
PRK14559	645	putative protein serine/threonine phosphatase; Pro	88.15
COG2260	59	Predicted Zn-ribbon RNA-binding protein [Translati	87.76
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	87.71
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	87.63
PRK11032	160	hypothetical protein; Provisional	86.57
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	86.24
PF14369	35	zf-RING_3: zinc-finger	85.97
PF14205	55	Cys_rich_KTR: Cysteine-rich KTR	85.94
COG1198	730	PriA Primosomal protein N' (replication factor Y)	85.9
TIGR02827	586	RNR_anaer_Bdell anaerobic ribonucleoside-triphosph	85.84
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	85.36
PF14205	55	Cys_rich_KTR: Cysteine-rich KTR	85.22
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	85.15
PF13638	133	PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_	85.1
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	84.94
PRK08351	61	DNA-directed RNA polymerase subunit E''; Validated	84.81
PF04135	53	Nop10p: Nucleolar RNA-binding protein, Nop10p fami	84.73
COG2331	82	Uncharacterized protein conserved in bacteria [Fun	84.61
cd01675	555	RNR_III Class III ribonucleotide reductase. Ribonu	84.6
TIGR02487	579	NrdD anaerobic ribonucleoside-triphosphate reducta	84.5
PRK14714	1337	DNA polymerase II large subunit; Provisional	84.45
smart00731	146	SprT SprT homologues. Predicted to have roles in t	84.06
PRK06393	64	rpoE DNA-directed RNA polymerase subunit E''; Vali	83.85
PRK07111	735	anaerobic ribonucleoside triphosphate reductase; P	83.66
TIGR00595	505	priA primosomal protein N'. All proteins in this f	83.33
PRK02935	110	hypothetical protein; Provisional	82.93
PF13597	546	NRDD: Anaerobic ribonucleoside-triphosphate reduct	82.23
PRK08270	656	anaerobic ribonucleoside triphosphate reductase; P	81.89
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	81.75
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	81.71
PF14319	111	Zn_Tnp_IS91: Transposase zinc-binding domain	81.61
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	81.13
cd04476	166	RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds cor	81.1
PRK08271	623	anaerobic ribonucleoside triphosphate reductase; P	81.1
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	81.01
PRK06260	397	threonine synthase; Validated	80.92

>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.4e-34  Score=241.61  Aligned_cols=86  Identities=36%  Similarity=0.665  Sum_probs=77.7

Q ss_pred             CCCCCCceeccCC--------------CCceeEEecccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc--c
Q 033276           18 DECSEQSWMLRSL--------------SESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS--P   81 (123)
Q Consensus        18 ~~~~~~~WIt~~~--------------~~~~va~vTdDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~--~   81 (123)
                      ||.++++||||+|              ....|||+|+||||||||+||||+++++.|++|+++|+|++ ||+|||++  +
T Consensus       176 ed~DdDgwitp~ni~~~~~e~~al~~pe~~~Vac~TtDfamQNVlLqm~L~l~~~~G~~Ir~~r~~iL-RCh~Cfsit~~  254 (376)
T KOG2463|consen  176 EDADDDGWITPSNITEAIIELGALNRPENQLVACLTTDFAMQNVLLQMNLNLLAMSGMKIRSVRSYIL-RCHGCFSITSE  254 (376)
T ss_pred             cccccccccccchHHHHHHhhhcccccccceeeeecccHHHHHHHHHhcccccCccchhhhhhhhhee-EeeeeeEecCc
Confidence            4444444999995              36679999999999999999999999999999999999999 99999998  7


Q ss_pred             cCccccccCCCCCeeeEEEEEeeE
Q 033276           82 FPLVICIKSNHEIRISPVFMLILI  105 (123)
Q Consensus        82 ~~~~fCp~CG~~~tl~rV~~~~~~  105 (123)
                      +++.|||+||++ ||+||+|+++.
T Consensus       255 m~k~FCp~CG~~-TL~K~aVsv~~  277 (376)
T KOG2463|consen  255 MPKDFCPSCGHK-TLTKCAVSVDE  277 (376)
T ss_pred             cchhcccccCCC-eeeEEEEEecC
Confidence            899999999999 99999998864

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

Probab=99.89  E-value=3.6e-24  Score=167.33  Aligned_cols=78  Identities=23%  Similarity=0.310  Sum_probs=65.0

Q ss_pred             CCCCceeccCC-----------CCceeEEecccHHHHHHHHHhCceeeCCC-CCcceeeeEEeeccccCCccc-ccCccc
Q 033276           20 CSEQSWMLRSL-----------SESTVACITGDYAMQNVILQMGLRLLAPG-GMQIRQLHRYIVDKCLKLFSS-PFPLVI   86 (123)
Q Consensus        20 ~~~~~WIt~~~-----------~~~~va~vTdDyAmQNVllqlGL~l~sv~-g~~I~~v~~wvl~rC~gC~k~-~~~~~f   86 (123)
                      .++-.|++++.           .+.+|+++||||||||||+||||+|+++. +.+|+++++|++ ||+||+++ +++.+|
T Consensus        77 tgd~~~LS~tDi~VlalAlel~~~~~v~l~TdDysvQNVa~~Lgi~~~~~~~~~~I~~v~~w~~-rC~GC~~~f~~~~~~  155 (177)
T COG1439          77 TGDLGNLSPTDIEVLALALELGEEVQVALATDDYSVQNVALQLGLNVRSISYKGKIKKVRKWRL-RCHGCKRIFPEPKDF  155 (177)
T ss_pred             hCcccccChhhHHHHHHHHhhccccceeEEecchHHHHHHHHhCceEEeeeccCccceEeeeeE-EEecCceecCCCCCc
Confidence            34445787762           23458999999999999999999999854 566999999999 99999999 888999


Q ss_pred             cccCCCCCeeeEE
Q 033276           87 CIKSNHEIRISPV   99 (123)
Q Consensus        87 Cp~CG~~~tl~rV   99 (123)
                      ||.||++ ++++.
T Consensus       156 Cp~CG~~-~~~~~  167 (177)
T COG1439         156 CPICGSP-LKRKR  167 (177)
T ss_pred             CCCCCCc-eEEee
Confidence            9999999 44443

>PRK12496 hypothetical protein; Provisional

Probab=99.79  E-value=5.1e-20  Score=140.68  Aligned_cols=67  Identities=19%  Similarity=0.320  Sum_probs=60.0

Q ss_pred             CceeEEecccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc-c--cCccccccCCCCCeeeEE
Q 033276           32 ESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-P--FPLVICIKSNHEIRISPV   99 (123)
Q Consensus        32 ~~~va~vTdDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~--~~~~fCp~CG~~~tl~rV   99 (123)
                      ++.+.++||||++||||++|||++.++++++|+++++|++ +|+||++. +  .+.+|||+||+++.++++
T Consensus        89 el~~~lvtDD~~~~~vA~~lgi~v~~~~~~~i~~~~~w~~-~C~gC~~~~~~~~~~~~C~~CG~~~~r~~~  158 (164)
T PRK12496         89 ELNGTLYTDDYGIQNVAKKLNIKFENIKTKGIKKVIKWRK-VCKGCKKKYPEDYPDDVCEICGSPVKRKMV  158 (164)
T ss_pred             HhCCcEECcHHHHHHHHHHcCCeEeccccccchhheeeeE-ECCCCCccccCCCCCCcCCCCCChhhhcch
Confidence            3457999999999999999999999999999999999999 99999998 4  467999999999655544

>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=99.65  E-value=4.6e-17  Score=111.73  Aligned_cols=41  Identities=15%  Similarity=0.406  Sum_probs=19.5

Q ss_pred             cceeeeEEeeccccCCccc--ccCccccccCCCCCeeeEEEEEee
Q 033276           62 QIRQLHRYIVDKCLKLFSS--PFPLVICIKSNHEIRISPVFMLIL  104 (123)
Q Consensus        62 ~I~~v~~wvl~rC~gC~k~--~~~~~fCp~CG~~~tl~rV~~~~~  104 (123)
                      +|+++|+|++ ||+|||++  ++++.|||+|||+ ||+||+|++.
T Consensus         1 rIk~~k~~vl-rC~aCf~~t~~~~k~FCp~CGn~-TL~rvsvsv~   43 (73)
T PF08772_consen    1 RIKRVKTWVL-RCHACFKITKDMTKQFCPKCGNA-TLKRVSVSVD   43 (73)
T ss_dssp             -------EEE-E-SSS--EES-SS--S-SSS--S---EEEE-B--
T ss_pred             CcchhheeeE-EccccccCcCCCCceeCcccCCC-cceEEEEEEC
Confidence            6899999999 99999998  7999999999999 9999999876

; PDB: 2CON_A.

>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family

Probab=97.89  E-value=7.7e-06  Score=65.89  Aligned_cols=27  Identities=22%  Similarity=0.416  Sum_probs=25.1

Q ss_pred             CceeEEecccHHHHHHHHHhCceeeCC
Q 033276           32 ESTVACITGDYAMQNVILQMGLRLLAP   58 (123)
Q Consensus        32 ~~~va~vTdDyAmQNVllqlGL~l~sv   58 (123)
                      +++++++||||+|||+|.+|||++++.
T Consensus       169 ELda~lvTdD~giqn~A~~Lgi~~~~~  195 (206)
T TIGR03875       169 ELDAAVVSADEGIRKWAERLGLRFVDA  195 (206)
T ss_pred             HcCcEEEeCcHHHHHHHHHcCCeeecH
Confidence            678999999999999999999999974

This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.

>PRK04358 hypothetical protein; Provisional

Probab=97.74  E-value=1.6e-05  Score=64.43  Aligned_cols=27  Identities=22%  Similarity=0.416  Sum_probs=25.0

Q ss_pred             CceeEEecccHHHHHHHHHhCceeeCC
Q 033276           32 ESTVACITGDYAMQNVILQMGLRLLAP   58 (123)
Q Consensus        32 ~~~va~vTdDyAmQNVllqlGL~l~sv   58 (123)
                      +++++++|+||+|||+|.+|||++++.
T Consensus       173 ELda~lvTdD~giqn~A~~LGI~~~~~  199 (217)
T PRK04358        173 ELDAAVVSADEGIRKWAERLGLRFVDA  199 (217)
T ss_pred             HhCCEEEeCCHHHHHHHHHcCCeeecH
Confidence            568899999999999999999999985

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=97.15  E-value=0.00019  Score=40.01  Aligned_cols=21  Identities=10%  Similarity=0.078  Sum_probs=19.1

Q ss_pred             cccCCccc-ccCccccccCCCC
Q 033276           73 KCLKLFSS-PFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~-~~~~~fCp~CG~~   93 (123)
                      .|+.|++. +....|||.||.+
T Consensus         4 ~Cp~Cg~~~~~~~~fC~~CG~~   25 (26)
T PF13248_consen    4 FCPNCGAEIDPDAKFCPNCGAK   25 (26)
T ss_pred             CCcccCCcCCcccccChhhCCC
Confidence            79999998 7778999999987

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=96.96  E-value=0.00037  Score=38.22  Aligned_cols=21  Identities=10%  Similarity=0.070  Sum_probs=18.3

Q ss_pred             cccCCccc-ccCccccccCCCC
Q 033276           73 KCLKLFSS-PFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~-~~~~~fCp~CG~~   93 (123)
                      +|+-|++. +..-.|||.||.+
T Consensus         1 ~Cp~CG~~~~~~~~fC~~CG~~   22 (23)
T PF13240_consen    1 YCPNCGAEIEDDAKFCPNCGTP   22 (23)
T ss_pred             CCcccCCCCCCcCcchhhhCCc
Confidence            59999998 6667999999987

>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains

Probab=96.84  E-value=0.00055  Score=55.27  Aligned_cols=28  Identities=29%  Similarity=0.523  Sum_probs=16.9

Q ss_pred             CceeEEecccHHHHHHHHHhCceeeCCC
Q 033276           32 ESTVACITGDYAMQNVILQMGLRLLAPG   59 (123)
Q Consensus        32 ~~~va~vTdDyAmQNVllqlGL~l~sv~   59 (123)
                      +++++++|+||+|||++.+|||+++...
T Consensus       166 El~a~lvt~D~gi~~~A~~lGi~~i~~~  193 (205)
T PF08745_consen  166 ELDAVLVTDDYGIQNWAEKLGIRFIDAR  193 (205)
T ss_dssp             HHT--EE---HHHHHHHHHTT--EE---
T ss_pred             HcCCEEEeCCHhHHHHHHHCCCEEEecc
Confidence            5678999999999999999999999874

Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.

>PF15017 AF1Q: Drug resistance and apoptosis regulator

Probab=96.34  E-value=0.0019  Score=46.03  Aligned_cols=18  Identities=11%  Similarity=0.213  Sum_probs=13.3

Q ss_pred             ccccCCCCCCCceeccCC
Q 033276           13 VSYVDDECSEQSWMLRSL   30 (123)
Q Consensus        13 ~~~~~~~~~~~~WIt~~~   30 (123)
                      .+++++++++|+||||+|
T Consensus        63 ~eee~~ddD~gGWITPsN   80 (87)
T PF15017_consen   63 EEEEEEDDDGGGWITPSN   80 (87)
T ss_pred             cccccccCCCCccccchh
Confidence            344456677899999996

>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=96.16  E-value=0.0057  Score=37.30  Aligned_cols=30  Identities=17%  Similarity=0.184  Sum_probs=23.0

Q ss_pred             EEeeccccCCccc--------ccCccccccCCCCCeeeEE
Q 033276           68 RYIVDKCLKLFSS--------PFPLVICIKSNHEIRISPV   99 (123)
Q Consensus        68 ~wvl~rC~gC~k~--------~~~~~fCp~CG~~~tl~rV   99 (123)
                      .|.| +|..|+..        +.....||.||+. .++|+
T Consensus         3 ~Yey-~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~-~~~r~   40 (42)
T PF09723_consen    3 IYEY-RCEECGHEFEVLQSISEDDPVPCPECGST-EVRRV   40 (42)
T ss_pred             CEEE-EeCCCCCEEEEEEEcCCCCCCcCCCCCCC-ceEEe
Confidence            4788 99999954        2346889999996 66665

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.

>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=96.05  E-value=0.0033  Score=35.50  Aligned_cols=21  Identities=14%  Similarity=0.284  Sum_probs=19.0

Q ss_pred             cccCCccc-ccCccccccCCCC
Q 033276           73 KCLKLFSS-PFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~-~~~~~fCp~CG~~   93 (123)
                      .|+.|++. +..-.+||.||+.
T Consensus         2 ~CP~C~~~V~~~~~~Cp~CG~~   23 (26)
T PF10571_consen    2 TCPECGAEVPESAKFCPHCGYD   23 (26)
T ss_pred             cCCCCcCCchhhcCcCCCCCCC
Confidence            79999998 7778999999987

Several members are annotated as putative helicases.

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=95.85  E-value=0.008  Score=43.59  Aligned_cols=41  Identities=10%  Similarity=-0.039  Sum_probs=29.6

Q ss_pred             eeEEeeccccCCccc-c--cCccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276           66 LHRYIVDKCLKLFSS-P--FPLVICIKSNHEIRISPVFMLILICLYIQV  111 (123)
Q Consensus        66 v~~wvl~rC~gC~k~-~--~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~  111 (123)
                      ...=+. +|..|+.. .  .....||.||+.    .+.++-|.-+||++
T Consensus        66 ~vp~~~-~C~~Cg~~~~~~~~~~~CP~Cgs~----~~~i~~G~El~i~~  109 (113)
T PRK12380         66 YKPAQA-WCWDCSQVVEIHQHDAQCPHCHGE----RLRVDTGDSLIVKS  109 (113)
T ss_pred             eeCcEE-EcccCCCEEecCCcCccCcCCCCC----CcEEccCCeEEEEE
Confidence            334466 99999987 3  234559999988    35667788888874

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=95.83  E-value=0.0074  Score=43.82  Aligned_cols=40  Identities=10%  Similarity=-0.007  Sum_probs=28.8

Q ss_pred             eEEeeccccCCccc-ccC--c-cccccCCCCCeeeEEEEEeeEEEEEee
Q 033276           67 HRYIVDKCLKLFSS-PFP--L-VICIKSNHEIRISPVFMLILICLYIQV  111 (123)
Q Consensus        67 ~~wvl~rC~gC~k~-~~~--~-~fCp~CG~~~tl~rV~~~~~~~~~~~~  111 (123)
                      ..=.. +|..|+.. +..  . ..||.||+. .   +.++-|.-++|++
T Consensus        67 ~p~~~-~C~~Cg~~~~~~~~~~~~CP~Cgs~-~---~~i~~G~El~i~~  110 (114)
T PRK03681         67 QEAEC-WCETCQQYVTLLTQRVRRCPQCHGD-M---LRIVADDGLQIRR  110 (114)
T ss_pred             eCcEE-EcccCCCeeecCCccCCcCcCcCCC-C---cEEccCCeEEEEE
Confidence            34456 89999987 432  2 449999988 2   5566788888874

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=95.75  E-value=0.011  Score=43.07  Aligned_cols=39  Identities=10%  Similarity=-0.004  Sum_probs=28.1

Q ss_pred             EEeeccccCCccc-cc--Cccc-cccCCCCCeeeEEEEEeeEEEEEee
Q 033276           68 RYIVDKCLKLFSS-PF--PLVI-CIKSNHEIRISPVFMLILICLYIQV  111 (123)
Q Consensus        68 ~wvl~rC~gC~k~-~~--~~~f-Cp~CG~~~tl~rV~~~~~~~~~~~~  111 (123)
                      .-.. +|..|++. +.  ...+ ||.||++ .   +.++-|.-+||++
T Consensus        69 p~~~-~C~~Cg~~~~~~~~~~~~CP~Cgs~-~---~~i~~G~El~I~~  111 (117)
T PRK00564         69 KVEL-ECKDCSHVFKPNALDYGVCEKCHSK-N---VIITQGNEMRLLS  111 (117)
T ss_pred             CCEE-EhhhCCCccccCCccCCcCcCCCCC-c---eEEecCCEEEEEE
Confidence            4456 89999987 33  2234 9999998 3   5556688888874

>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=95.54  E-value=0.011  Score=42.68  Aligned_cols=42  Identities=12%  Similarity=-0.043  Sum_probs=26.6

Q ss_pred             eeeEEeeccccCCccc---ccCccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276           65 QLHRYIVDKCLKLFSS---PFPLVICIKSNHEIRISPVFMLILICLYIQV  111 (123)
Q Consensus        65 ~v~~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~  111 (123)
                      ....-+. +|..|++.   +.....||.||+. .   +.++-|.-+||++
T Consensus        65 e~~p~~~-~C~~Cg~~~~~~~~~~~CP~Cgs~-~---~~i~~G~el~i~~  109 (113)
T PF01155_consen   65 EEVPARA-RCRDCGHEFEPDEFDFSCPRCGSP-D---VEIISGRELRIKS  109 (113)
T ss_dssp             EEE--EE-EETTTS-EEECHHCCHH-SSSSSS-----EEEEESS-EEEEE
T ss_pred             EecCCcE-ECCCCCCEEecCCCCCCCcCCcCC-C---cEEccCCeEEEEE
Confidence            3445567 99999987   2344669999999 3   4556788888875

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.

>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=95.51  E-value=0.0081  Score=35.30  Aligned_cols=25  Identities=12%  Similarity=0.109  Sum_probs=15.0

Q ss_pred             EEeeccccCCccc-ccCccccccCCCC
Q 033276           68 RYIVDKCLKLFSS-PFPLVICIKSNHE   93 (123)
Q Consensus        68 ~wvl~rC~gC~k~-~~~~~fCp~CG~~   93 (123)
                      -... ||..|++. -+++.+||.||+.
T Consensus         9 l~~~-rC~~Cg~~~~pPr~~Cp~C~s~   34 (37)
T PF12172_consen    9 LLGQ-RCRDCGRVQFPPRPVCPHCGSD   34 (37)
T ss_dssp             EEEE-E-TTT--EEES--SEETTTT--
T ss_pred             EEEE-EcCCCCCEecCCCcCCCCcCcc
Confidence            3445 99999999 6778999999976

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.

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

Probab=95.41  E-value=0.014  Score=35.84  Aligned_cols=24  Identities=21%  Similarity=0.085  Sum_probs=18.7

Q ss_pred             eeccccCCccc---c--cCccccccCCCCC
Q 033276           70 IVDKCLKLFSS---P--FPLVICIKSNHEI   94 (123)
Q Consensus        70 vl~rC~gC~k~---~--~~~~fCp~CG~~~   94 (123)
                      .+ +|..|+..   +  .....||.||+++
T Consensus         3 ~y-~C~~CG~~~~~~~~~~~~~Cp~CG~~~   31 (46)
T PRK00398          3 EY-KCARCGREVELDEYGTGVRCPYCGYRI   31 (46)
T ss_pred             EE-ECCCCCCEEEECCCCCceECCCCCCeE
Confidence            46 99999986   2  2258899999994

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=95.34  E-value=0.013  Score=34.22  Aligned_cols=25  Identities=20%  Similarity=0.349  Sum_probs=19.5

Q ss_pred             EEeeccccCCccc-c-------cCccccccCCCC
Q 033276           68 RYIVDKCLKLFSS-P-------FPLVICIKSNHE   93 (123)
Q Consensus        68 ~wvl~rC~gC~k~-~-------~~~~fCp~CG~~   93 (123)
                      .|.+ +|..|++. .       .....||.||.+
T Consensus         3 ~Y~y-~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~   35 (41)
T smart00834        3 IYEY-RCEDCGHTFEVLQKISDDPLATCPECGGD   35 (41)
T ss_pred             CEEE-EcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence            4788 99999985 1       235679999996

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.

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=95.33  E-value=0.018  Score=42.93  Aligned_cols=38  Identities=16%  Similarity=0.267  Sum_probs=28.1

Q ss_pred             EeeccccCCccc-cc-----------------------CccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276           69 YIVDKCLKLFSS-PF-----------------------PLVICIKSNHEIRISPVFMLILICLYIQV  111 (123)
Q Consensus        69 wvl~rC~gC~k~-~~-----------------------~~~fCp~CG~~~tl~rV~~~~~~~~~~~~  111 (123)
                      =.+ +|..|+.. ..                       ....||.||+. .   +.++-|.-+||++
T Consensus        69 ~~~-~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~-~---~~i~~G~el~i~~  130 (135)
T PRK03824         69 AVL-KCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR-D---FEIVKGRGVYIEE  130 (135)
T ss_pred             eEE-ECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC-C---cEEecCceEEEEE
Confidence            456 89999987 32                       23449999988 2   5667799999984

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=95.31  E-value=0.018  Score=41.83  Aligned_cols=40  Identities=13%  Similarity=0.006  Sum_probs=28.9

Q ss_pred             eEEeeccccCCccc-cc--CccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276           67 HRYIVDKCLKLFSS-PF--PLVICIKSNHEIRISPVFMLILICLYIQV  111 (123)
Q Consensus        67 ~~wvl~rC~gC~k~-~~--~~~fCp~CG~~~tl~rV~~~~~~~~~~~~  111 (123)
                      ..=.. +|..|++. +.  ....||.||++ .   +.++-|.-++|++
T Consensus        67 ~p~~~-~C~~Cg~~~~~~~~~~~CP~Cgs~-~---~~i~~G~El~I~~  109 (115)
T TIGR00100        67 EPVEC-ECEDCSEEVSPEIDLYRCPKCHGI-M---LQVRAGKELNLKS  109 (115)
T ss_pred             eCcEE-EcccCCCEEecCCcCccCcCCcCC-C---cEEecCCeEEEEE
Confidence            34456 89999987 33  24559999998 3   5566788888874

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.

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=95.24  E-value=0.029  Score=34.72  Aligned_cols=32  Identities=19%  Similarity=0.342  Sum_probs=22.7

Q ss_pred             EEeeccccCCccc-c-------cCccccccCCCCCeeeEEEE
Q 033276           68 RYIVDKCLKLFSS-P-------FPLVICIKSNHEIRISPVFM  101 (123)
Q Consensus        68 ~wvl~rC~gC~k~-~-------~~~~fCp~CG~~~tl~rV~~  101 (123)
                      .|.| +|..|+.. .       .....||.||+. .++|+--
T Consensus         3 ~Yey-~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~-~~~r~~s   42 (52)
T TIGR02605         3 IYEY-RCTACGHRFEVLQKMSDDPLATCPECGGE-KLRRLLS   42 (52)
T ss_pred             CEEE-EeCCCCCEeEEEEecCCCCCCCCCCCCCC-ceeEEec
Confidence            4789 99999984 1       123479999996 5666543

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.

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

Probab=94.66  E-value=0.031  Score=41.88  Aligned_cols=33  Identities=24%  Similarity=0.121  Sum_probs=25.5

Q ss_pred             eeEEeeccccCCccc-ccCccccccCCCCCeeeEE
Q 033276           66 LHRYIVDKCLKLFSS-PFPLVICIKSNHEIRISPV   99 (123)
Q Consensus        66 v~~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV   99 (123)
                      -+-..- ||..|+++ -+++.+||.||+++.+.-|
T Consensus        25 ~kl~g~-kC~~CG~v~~PPr~~Cp~C~~~~~~E~v   58 (140)
T COG1545          25 GKLLGT-KCKKCGRVYFPPRAYCPKCGSETELEWV   58 (140)
T ss_pred             CcEEEE-EcCCCCeEEcCCcccCCCCCCCCceEEE
Confidence            344555 99999999 7889999999999543444

>PF12773 DZR: Double zinc ribbon

Probab=93.94  E-value=0.028  Score=34.41  Aligned_cols=21  Identities=14%  Similarity=0.279  Sum_probs=13.8

Q ss_pred             ccCCccc-ccCccccccCCCCC
Q 033276           74 CLKLFSS-PFPLVICIKSNHEI   94 (123)
Q Consensus        74 C~gC~k~-~~~~~fCp~CG~~~   94 (123)
                      |+.|++. +....|||.||.++
T Consensus         1 Cp~Cg~~~~~~~~fC~~CG~~l   22 (50)
T PF12773_consen    1 CPHCGTPNPDDAKFCPHCGTPL   22 (50)
T ss_pred             CCCcCCcCCccccCChhhcCCh
Confidence            5667766 55567777777764

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

Probab=93.57  E-value=0.072  Score=39.62  Aligned_cols=42  Identities=14%  Similarity=-0.074  Sum_probs=30.4

Q ss_pred             eeeEEeeccccCCccc---ccCccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276           65 QLHRYIVDKCLKLFSS---PFPLVICIKSNHEIRISPVFMLILICLYIQV  111 (123)
Q Consensus        65 ~v~~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~  111 (123)
                      +...=.. +|.-|...   ......||+||++    ++.+.-|..++|++
T Consensus        65 e~~p~~~-~C~~C~~~~~~e~~~~~CP~C~s~----~~~i~~G~el~i~~  109 (115)
T COG0375          65 EEEPAEC-WCLDCGQEVELEELDYRCPKCGSI----NLRIIGGDELIIKS  109 (115)
T ss_pred             EEeccEE-EeccCCCeecchhheeECCCCCCC----ceEEecCCeeEEEE
Confidence            3344556 89999776   3345569999999    35567789998875

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=93.46  E-value=0.074  Score=33.14  Aligned_cols=24  Identities=21%  Similarity=0.204  Sum_probs=19.3

Q ss_pred             eeccccCCccc----ccCccccccCCCCC
Q 033276           70 IVDKCLKLFSS----PFPLVICIKSNHEI   94 (123)
Q Consensus        70 vl~rC~gC~k~----~~~~~fCp~CG~~~   94 (123)
                      .| +|..|++.    ......||.||+++
T Consensus         2 ~Y-~C~~Cg~~~~~~~~~~irC~~CG~rI   29 (44)
T smart00659        2 IY-ICGECGRENEIKSKDVVRCRECGYRI   29 (44)
T ss_pred             EE-ECCCCCCEeecCCCCceECCCCCceE
Confidence            47 89999986    24468899999994

present in RNA polymerase I, II and III

>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=93.35  E-value=0.063  Score=31.63  Aligned_cols=22  Identities=9%  Similarity=-0.173  Sum_probs=17.5

Q ss_pred             eccccCCccc---ccCccccccCCCC
Q 033276           71 VDKCLKLFSS---PFPLVICIKSNHE   93 (123)
Q Consensus        71 l~rC~gC~k~---~~~~~fCp~CG~~   93 (123)
                      + +|.-|+.+   +..-..||.||.+
T Consensus         3 ~-~C~~CG~i~~g~~~p~~CP~Cg~~   27 (34)
T cd00729           3 W-VCPVCGYIHEGEEAPEKCPICGAP   27 (34)
T ss_pred             E-ECCCCCCEeECCcCCCcCcCCCCc
Confidence            5 89999988   2234789999987

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.

>PF12773 DZR: Double zinc ribbon

Probab=92.91  E-value=0.053  Score=33.14  Aligned_cols=19  Identities=16%  Similarity=0.242  Sum_probs=10.4

Q ss_pred             cccCCccc-ccCccccccCC
Q 033276           73 KCLKLFSS-PFPLVICIKSN   91 (123)
Q Consensus        73 rC~gC~k~-~~~~~fCp~CG   91 (123)
                      +|+.|++. +....||+.||
T Consensus        31 ~C~~Cg~~~~~~~~fC~~CG   50 (50)
T PF12773_consen   31 ICPNCGAENPPNAKFCPNCG   50 (50)
T ss_pred             CCcCCcCCCcCCcCccCccc
Confidence            45555555 44445555555

>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=92.86  E-value=0.11  Score=37.92  Aligned_cols=51  Identities=12%  Similarity=0.234  Sum_probs=34.2

Q ss_pred             HHHHHHHHhCceee----CC---CCCcce--eeeEEeeccccCCccc---c----cCccccccCCCCC
Q 033276           43 AMQNVILQMGLRLL----AP---GGMQIR--QLHRYIVDKCLKLFSS---P----FPLVICIKSNHEI   94 (123)
Q Consensus        43 AmQNVllqlGL~l~----sv---~g~~I~--~v~~wvl~rC~gC~k~---~----~~~~fCp~CG~~~   94 (123)
                      +=|.++.++|..+.    .+   +...|.  +.++|.+ +|..|+..   .    ..+..|+.||.++
T Consensus        87 ~fk~~~~~ig~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~C~~C~~~~~r~~~~~~~~~~C~~C~~~l  153 (157)
T PF10263_consen   87 EFKQWARRIGASPPRGRPNPTTCHSYEIEGKEYKKYVY-RCPSCGREYKRHRRSKRKRYRCGRCGGPL  153 (157)
T ss_pred             HHHHHHHHHCCcccccccccccccccccccccccceEE-EcCCCCCEeeeecccchhhEECCCCCCEE
Confidence            67889999998542    11   222232  2368999 99999965   1    2245799999773

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.

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

Probab=92.51  E-value=0.072  Score=40.50  Aligned_cols=21  Identities=19%  Similarity=0.145  Sum_probs=18.1

Q ss_pred             cccCCccc---ccCccccccCCCC
Q 033276           73 KCLKLFSS---PFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~---~~~~~fCp~CG~~   93 (123)
                      -|+.|+.+   .....|||+||..
T Consensus        30 hCp~Cg~PLF~KdG~v~CPvC~~~   53 (131)
T COG1645          30 HCPKCGTPLFRKDGEVFCPVCGYR   53 (131)
T ss_pred             hCcccCCcceeeCCeEECCCCCce
Confidence            79999987   4668999999975

>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]

Probab=92.51  E-value=0.059  Score=36.62  Aligned_cols=21  Identities=19%  Similarity=0.222  Sum_probs=18.7

Q ss_pred             cccCCccc-ccCccccccCCCC
Q 033276           73 KCLKLFSS-PFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~-~~~~~fCp~CG~~   93 (123)
                      .|.-|++. +...+.||+||++
T Consensus         6 AC~~Ck~l~~~d~e~CP~Cgs~   27 (64)
T COG2093           6 ACKNCKRLTPEDTEICPVCGST   27 (64)
T ss_pred             HHhhccccCCCCCccCCCCCCc
Confidence            69999998 7777889999998

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=92.48  E-value=0.13  Score=37.86  Aligned_cols=39  Identities=10%  Similarity=0.072  Sum_probs=27.0

Q ss_pred             eEEeeccccCCccc-cc---C------ccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276           67 HRYIVDKCLKLFSS-PF---P------LVICIKSNHEIRISPVFMLILICLYIQV  111 (123)
Q Consensus        67 ~~wvl~rC~gC~k~-~~---~------~~fCp~CG~~~tl~rV~~~~~~~~~~~~  111 (123)
                      ..=.. +| .|++. ..   .      ...||.||+. .   +.++-|.-+||++
T Consensus        67 vp~~~-~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~-~---~~i~~G~El~i~~  115 (124)
T PRK00762         67 IPVEI-EC-ECGYEGVVDEDEIDHYAAVIECPVCGNK-R---AHILGGRECNVKN  115 (124)
T ss_pred             cCeeE-Ee-eCcCcccccccchhccccCCcCcCCCCC-C---CEEecCCeEEEEE
Confidence            34456 89 99977 22   1      1459999988 3   5566788888874

>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=91.94  E-value=0.2  Score=29.53  Aligned_cols=25  Identities=16%  Similarity=0.212  Sum_probs=17.8

Q ss_pred             cccCCccc----ccCccccccCCCCCeeeE
Q 033276           73 KCLKLFSS----PFPLVICIKSNHEIRISP   98 (123)
Q Consensus        73 rC~gC~k~----~~~~~fCp~CG~~~tl~r   98 (123)
                      .|..|++.    .....-||.||+. .|.|
T Consensus         2 ~C~~Cg~~~~~~~~~~irC~~CG~R-IlyK   30 (32)
T PF03604_consen    2 ICGECGAEVELKPGDPIRCPECGHR-ILYK   30 (32)
T ss_dssp             BESSSSSSE-BSTSSTSSBSSSS-S-EEBE
T ss_pred             CCCcCCCeeEcCCCCcEECCcCCCe-EEEe
Confidence            78999986    3345789999999 4443

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 ....

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

Probab=91.81  E-value=0.11  Score=30.04  Aligned_cols=22  Identities=9%  Similarity=-0.099  Sum_probs=17.6

Q ss_pred             eccccCCccc-cc--CccccccCCCC
Q 033276           71 VDKCLKLFSS-PF--PLVICIKSNHE   93 (123)
Q Consensus        71 l~rC~gC~k~-~~--~~~fCp~CG~~   93 (123)
                      + +|..|+.+ +.  .-..||.||.+
T Consensus         2 ~-~C~~CGy~y~~~~~~~~CP~Cg~~   26 (33)
T cd00350           2 Y-VCPVCGYIYDGEEAPWVCPVCGAP   26 (33)
T ss_pred             E-ECCCCCCEECCCcCCCcCcCCCCc
Confidence            5 89999988 32  35789999987

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.

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

Probab=91.21  E-value=0.1  Score=31.08  Aligned_cols=11  Identities=9%  Similarity=0.350  Sum_probs=5.2

Q ss_pred             cccccCCCCCe
Q 033276           85 VICIKSNHEIR   95 (123)
Q Consensus        85 ~fCp~CG~~~t   95 (123)
                      .|||.||+++.
T Consensus         1 kfC~~CG~~l~   11 (34)
T PF14803_consen    1 KFCPQCGGPLE   11 (34)
T ss_dssp             -B-TTT--B-E
T ss_pred             CccccccChhh
Confidence            59999999943

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

Probab=91.20  E-value=0.13  Score=33.22  Aligned_cols=26  Identities=15%  Similarity=0.105  Sum_probs=20.5

Q ss_pred             EEeeccccCCccc-c----cCccccccCCCCC
Q 033276           68 RYIVDKCLKLFSS-P----FPLVICIKSNHEI   94 (123)
Q Consensus        68 ~wvl~rC~gC~k~-~----~~~~fCp~CG~~~   94 (123)
                      .-.| +|.-|++. .    .....||.||+++
T Consensus         4 ~~~Y-~C~~Cg~~~~~~~~~~~irCp~Cg~rI   34 (49)
T COG1996           4 MMEY-KCARCGREVELDQETRGIRCPYCGSRI   34 (49)
T ss_pred             eEEE-EhhhcCCeeehhhccCceeCCCCCcEE
Confidence            3568 99999987 2    3467899999994

>COG1592 Rubrerythrin [Energy production and conversion]

Probab=91.05  E-value=0.14  Score=40.05  Aligned_cols=23  Identities=9%  Similarity=-0.014  Sum_probs=19.5

Q ss_pred             eeccccCCccc--ccCccccccCCCC
Q 033276           70 IVDKCLKLFSS--PFPLVICIKSNHE   93 (123)
Q Consensus        70 vl~rC~gC~k~--~~~~~fCp~CG~~   93 (123)
                      ++ +|+-|+.+  ..+-..||+||.+
T Consensus       134 ~~-vC~vCGy~~~ge~P~~CPiCga~  158 (166)
T COG1592         134 VW-VCPVCGYTHEGEAPEVCPICGAP  158 (166)
T ss_pred             EE-EcCCCCCcccCCCCCcCCCCCCh
Confidence            78 99999998  5445889999987

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

Probab=90.59  E-value=0.12  Score=33.99  Aligned_cols=20  Identities=25%  Similarity=0.261  Sum_probs=17.6

Q ss_pred             cccCCcccccCccccccCCCC
Q 033276           73 KCLKLFSSPFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~~~~~~fCp~CG~~   93 (123)
                      +|..|+.... +..||.||.+
T Consensus         7 ~C~~CgvYTL-k~~CP~CG~~   26 (56)
T PRK13130          7 KCPKCGVYTL-KEICPVCGGK   26 (56)
T ss_pred             ECCCCCCEEc-cccCcCCCCC
Confidence            8999998844 7899999998

>PRK00420 hypothetical protein; Validated

Probab=90.44  E-value=0.17  Score=37.39  Aligned_cols=21  Identities=14%  Similarity=0.047  Sum_probs=18.1

Q ss_pred             cccCCccc----ccCccccccCCCC
Q 033276           73 KCLKLFSS----PFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~----~~~~~fCp~CG~~   93 (123)
                      .|+.|+.+    .....|||.||..
T Consensus        25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~~   49 (112)
T PRK00420         25 HCPVCGLPLFELKDGEVVCPVHGKV   49 (112)
T ss_pred             CCCCCCCcceecCCCceECCCCCCe
Confidence            89999987    3567999999998

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

Probab=89.74  E-value=0.19  Score=37.54  Aligned_cols=33  Identities=12%  Similarity=0.316  Sum_probs=25.3

Q ss_pred             eeeEEeeccccCCccc-cc--CccccccCCCCCeeeE
Q 033276           65 QLHRYIVDKCLKLFSS-PF--PLVICIKSNHEIRISP   98 (123)
Q Consensus        65 ~v~~wvl~rC~gC~k~-~~--~~~fCp~CG~~~tl~r   98 (123)
                      ..+.... +|+.|.|. .+  ..+-|+.|+.|+|+.|
T Consensus        64 Stkav~V-~CP~C~K~TKmLGr~D~CM~C~~pLTLd~   99 (114)
T PF11023_consen   64 STKAVQV-ECPNCGKQTKMLGRVDACMHCKEPLTLDP   99 (114)
T ss_pred             cccceee-ECCCCCChHhhhchhhccCcCCCcCccCc
Confidence            3445667 99999998 32  2478999999998876

; GO: 0005887 integral to plasma membrane

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=89.29  E-value=0.15  Score=46.95  Aligned_cols=27  Identities=15%  Similarity=0.192  Sum_probs=20.3

Q ss_pred             cccCCccc-ccCccccccCCCCCeeeEEE
Q 033276           73 KCLKLFSS-PFPLVICIKSNHEIRISPVF  100 (123)
Q Consensus        73 rC~gC~k~-~~~~~fCp~CG~~~tl~rV~  100 (123)
                      .|+.|++. +..-.|||.||.+ +-++-.
T Consensus        29 ~Cp~CG~~~~~~~~fC~~CG~~-~~~~~~   56 (645)
T PRK14559         29 PCPQCGTEVPVDEAHCPNCGAE-TGTIWW   56 (645)
T ss_pred             cCCCCCCCCCcccccccccCCc-ccchhh
Confidence            68899987 7777899999988 444433

>PRK04351 hypothetical protein; Provisional

Probab=89.19  E-value=0.54  Score=35.80  Aligned_cols=50  Identities=18%  Similarity=0.206  Sum_probs=34.4

Q ss_pred             cHHHHHHHHHhCc-eeeCCCCCcceeeeEEeeccccCCccc-------ccCccccccCCCCC
Q 033276           41 DYAMQNVILQMGL-RLLAPGGMQIRQLHRYIVDKCLKLFSS-------PFPLVICIKSNHEI   94 (123)
Q Consensus        41 DyAmQNVllqlGL-~l~sv~g~~I~~v~~wvl~rC~gC~k~-------~~~~~fCp~CG~~~   94 (123)
                      |-.=|-+|.++|- +..+ +-..  .-++|.| +|.+|+..       +..+..|-.||+.+
T Consensus        85 g~~fk~~~~~v~~~r~~~-~~~~--~~~~y~Y-~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L  142 (149)
T PRK04351         85 DRDFKELLKQVGGPRYCP-PLPS--QKKNYLY-ECQSCGQQYLRKRRINTKRYRCGKCRGKL  142 (149)
T ss_pred             CHHHHHHHHHhCCCcccC-CCCC--CCceEEE-ECCCCCCEeeeeeecCCCcEEeCCCCcEe
Confidence            4445888888863 3222 2222  2357999 99999974       45678999999985

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

Probab=88.96  E-value=0.26  Score=40.57  Aligned_cols=21  Identities=19%  Similarity=0.262  Sum_probs=16.4

Q ss_pred             cccCCccc-c----------cCccccccCCCC
Q 033276           73 KCLKLFSS-P----------FPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~-~----------~~~~fCp~CG~~   93 (123)
                      +|.||+=. +          .+..|||.||.=
T Consensus       199 ~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI  230 (239)
T COG1579         199 VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI  230 (239)
T ss_pred             cccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence            99999954 2          346899999964

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

Probab=88.75  E-value=0.31  Score=37.26  Aligned_cols=29  Identities=21%  Similarity=0.230  Sum_probs=22.7

Q ss_pred             eeccccCCccc-----ccCccccccCCCCCeeeEEE
Q 033276           70 IVDKCLKLFSS-----PFPLVICIKSNHEIRISPVF  100 (123)
Q Consensus        70 vl~rC~gC~k~-----~~~~~fCp~CG~~~tl~rV~  100 (123)
                      .| +|..|+..     +....-||+||+. .-+|.+
T Consensus       112 ~l-~C~~Cg~~~~~~~~~~l~~Cp~C~~~-~F~R~~  145 (146)
T PF07295_consen  112 TL-VCENCGHEVELTHPERLPPCPKCGHT-EFTRQP  145 (146)
T ss_pred             eE-ecccCCCEEEecCCCcCCCCCCCCCC-eeeeCC
Confidence            57 99999985     3446789999999 676654

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.

>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]

Probab=88.60  E-value=0.46  Score=41.85  Aligned_cols=32  Identities=19%  Similarity=0.194  Sum_probs=24.5

Q ss_pred             EEeeccccCCccc--ccCccccccCCCCC-eeeEEE
Q 033276           68 RYIVDKCLKLFSS--PFPLVICIKSNHEI-RISPVF  100 (123)
Q Consensus        68 ~wvl~rC~gC~k~--~~~~~fCp~CG~~~-tl~rV~  100 (123)
                      .=.+ +|+.|++.  ......||.||.++ -+||||
T Consensus        55 ~~i~-kC~~c~~~~~y~~~~~C~~cg~~~~l~R~VS   89 (415)
T COG5257          55 AKIY-KCPECYRPECYTTEPKCPNCGAETELVRRVS   89 (415)
T ss_pred             CceE-eCCCCCCCcccccCCCCCCCCCCccEEEEEE
Confidence            3467 99999986  45678899999874 357787

>COG1656 Uncharacterized conserved protein [Function unknown]

Probab=88.50  E-value=0.11  Score=40.87  Aligned_cols=23  Identities=13%  Similarity=0.278  Sum_probs=12.9

Q ss_pred             ceeEEecccHHHHHHHHHhCceee
Q 033276           33 STVACITGDYAMQNVILQMGLRLL   56 (123)
Q Consensus        33 ~~va~vTdDyAmQNVllqlGL~l~   56 (123)
                      .+.+++|.|+.+=-=+ .+|++-+
T Consensus        47 e~rIllTRDr~L~~r~-k~g~~~i   69 (165)
T COG1656          47 EGRILLTRDRELYKRA-KLGIKAI   69 (165)
T ss_pred             CCeEEEeccHHHHHHh-hccCceE
Confidence            3456777777665444 4555433

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=88.15  E-value=0.18  Score=46.39  Aligned_cols=23  Identities=17%  Similarity=0.252  Sum_probs=19.4

Q ss_pred             cccCCccc-ccCccccccCCCCCe
Q 033276           73 KCLKLFSS-PFPLVICIKSNHEIR   95 (123)
Q Consensus        73 rC~gC~k~-~~~~~fCp~CG~~~t   95 (123)
                      +|+.|+.. +..-.|||.||.+++
T Consensus         3 ~Cp~Cg~~n~~~akFC~~CG~~l~   26 (645)
T PRK14559          3 ICPQCQFENPNNNRFCQKCGTSLT   26 (645)
T ss_pred             cCCCCCCcCCCCCccccccCCCCC
Confidence            79999988 666789999999864

>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]

Probab=87.76  E-value=0.25  Score=33.11  Aligned_cols=23  Identities=17%  Similarity=0.226  Sum_probs=17.9

Q ss_pred             eccccCCcccccCccccccCCCCC
Q 033276           71 VDKCLKLFSSPFPLVICIKSNHEI   94 (123)
Q Consensus        71 l~rC~gC~k~~~~~~fCp~CG~~~   94 (123)
                      +-+|..|+..... +.||+||..+
T Consensus         5 ~rkC~~cg~YTLk-e~Cp~CG~~t   27 (59)
T COG2260           5 IRKCPKCGRYTLK-EKCPVCGGDT   27 (59)
T ss_pred             hhcCcCCCceeec-ccCCCCCCcc
Confidence            3389999987433 7899999993

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

Probab=87.71  E-value=0.32  Score=28.79  Aligned_cols=10  Identities=10%  Similarity=0.361  Sum_probs=7.6

Q ss_pred             cccccCCCCC
Q 033276           85 VICIKSNHEI   94 (123)
Q Consensus        85 ~fCp~CG~~~   94 (123)
                      .|||.|||=+
T Consensus         2 ~FCp~C~nlL   11 (35)
T PF02150_consen    2 RFCPECGNLL   11 (35)
T ss_dssp             -BETTTTSBE
T ss_pred             eeCCCCCccc
Confidence            6899999874

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 ....

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

Probab=87.63  E-value=0.74  Score=29.66  Aligned_cols=44  Identities=11%  Similarity=0.179  Sum_probs=32.0

Q ss_pred             HHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc--c---cCccccccCCCC
Q 033276           43 AMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS--P---FPLVICIKSNHE   93 (123)
Q Consensus        43 AmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~--~---~~~~fCp~CG~~   93 (123)
                      .|+-.+..-|+.++.++-..-.+       .|+.|+..  .   ...-.||.||..
T Consensus         7 ~L~yka~~~G~~v~~v~~~~TSq-------~C~~CG~~~~~~~~~r~~~C~~Cg~~   55 (69)
T PF07282_consen    7 RLEYKAEEYGIQVVEVDEAYTSQ-------TCPRCGHRNKKRRSGRVFTCPNCGFE   55 (69)
T ss_pred             HHHHHHHHhCCEEEEECCCCCcc-------CccCcccccccccccceEEcCCCCCE
Confidence            35666778899998887554444       89999987  2   225789999975

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

>PRK11032 hypothetical protein; Provisional

Probab=86.57  E-value=0.48  Score=36.87  Aligned_cols=29  Identities=24%  Similarity=0.362  Sum_probs=23.2

Q ss_pred             eeccccCCccc-----ccCccccccCCCCCeeeEEE
Q 033276           70 IVDKCLKLFSS-----PFPLVICIKSNHEIRISPVF  100 (123)
Q Consensus        70 vl~rC~gC~k~-----~~~~~fCp~CG~~~tl~rV~  100 (123)
                      .+ +|..|+..     +....-||+||+. .-+|.+
T Consensus       124 ~L-vC~~Cg~~~~~~~p~~i~pCp~C~~~-~F~R~~  157 (160)
T PRK11032        124 NL-VCEKCHHHLAFYTPEVLPLCPKCGHD-QFQRRP  157 (160)
T ss_pred             eE-EecCCCCEEEecCCCcCCCCCCCCCC-eeeeCC
Confidence            47 99999985     4557889999999 777765

>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=86.24  E-value=0.39  Score=27.43  Aligned_cols=11  Identities=9%  Similarity=0.166  Sum_probs=6.5

Q ss_pred             ccccccCCCCC
Q 033276           84 LVICIKSNHEI   94 (123)
Q Consensus        84 ~~fCp~CG~~~   94 (123)
                      ..|||.||+++
T Consensus         3 ~rfC~~CG~~t   13 (32)
T PF09297_consen    3 HRFCGRCGAPT   13 (32)
T ss_dssp             TSB-TTT--BE
T ss_pred             CcccCcCCccc
Confidence            47999999994

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

>PF14369 zf-RING_3: zinc-finger

Probab=85.97  E-value=0.8  Score=27.16  Aligned_cols=22  Identities=14%  Similarity=0.051  Sum_probs=16.1

Q ss_pred             eccccCCccc-c-----cCccccccCCCC
Q 033276           71 VDKCLKLFSS-P-----FPLVICIKSNHE   93 (123)
Q Consensus        71 l~rC~gC~k~-~-----~~~~fCp~CG~~   93 (123)
                      | .|+.|.+. .     ....+||.|++.
T Consensus         3 y-wCh~C~~~V~~~~~~~~~~~CP~C~~g   30 (35)
T PF14369_consen    3 Y-WCHQCNRFVRIAPSPDSDVACPRCHGG   30 (35)
T ss_pred             E-eCccCCCEeEeCcCCCCCcCCcCCCCc
Confidence            5 79999975 1     233469999998

>PF14205 Cys_rich_KTR: Cysteine-rich KTR

Probab=85.94  E-value=1  Score=29.86  Aligned_cols=30  Identities=20%  Similarity=0.244  Sum_probs=21.1

Q ss_pred             EEeeccccCCccc-------cc----CccccccCCCCCeeeEEE
Q 033276           68 RYIVDKCLKLFSS-------PF----PLVICIKSNHEIRISPVF  100 (123)
Q Consensus        68 ~wvl~rC~gC~k~-------~~----~~~fCp~CG~~~tl~rV~  100 (123)
                      .|++  |+-|+..       |.    --.|||+|-++ +|-.|.
T Consensus         3 ~Wi~--CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E-tlI~v~   43 (55)
T PF14205_consen    3 EWIL--CPICGNKTRLKIREDTVLKNFPLYCPKCKQE-TLIDVK   43 (55)
T ss_pred             eEEE--CCCCCCccceeeecCceeccccccCCCCCce-EEEEee
Confidence            6887  9999932       21    13799999999 665554

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

Probab=85.90  E-value=0.62  Score=43.68  Aligned_cols=27  Identities=19%  Similarity=0.348  Sum_probs=20.1

Q ss_pred             EeeccccCCccc-ccCccccccCCCCCeeeE
Q 033276           69 YIVDKCLKLFSS-PFPLVICIKSNHEIRISP   98 (123)
Q Consensus        69 wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~r   98 (123)
                      =.+ +||=|++. +.+ ..||.||+. .|+-
T Consensus       461 ~~L-~CH~Cg~~~~~p-~~Cp~Cgs~-~L~~  488 (730)
T COG1198         461 GQL-RCHYCGYQEPIP-QSCPECGSE-HLRA  488 (730)
T ss_pred             Cee-EeCCCCCCCCCC-CCCCCCCCC-eeEE
Confidence            356 78888877 555 789999999 6654

>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase

Probab=85.84  E-value=0.62  Score=42.57  Aligned_cols=53  Identities=11%  Similarity=0.025  Sum_probs=33.2

Q ss_pred             HHHHHHHHHh---CceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCCCeeeEEEEEee
Q 033276           42 YAMQNVILQM---GLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHEIRISPVFMLIL  104 (123)
Q Consensus        42 yAmQNVllql---GL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV~~~~~  104 (123)
                      -|+.++.+.+   |+...++.-         ..++|..|+.+ ......||+||++ .+...+=++|
T Consensus       509 ea~~~lv~~~~~~~i~Y~tin~---------~~siC~~CGy~~g~~~~~CP~CGs~-~~ev~sRv~G  565 (586)
T TIGR02827       509 DGYRKLLRVAADTGCNYFCFNI---------KITICNDCHHIDKRTLHRCPVCGSA-NIDYGTRVIG  565 (586)
T ss_pred             HHHHHHHHHHHhcCCceEEeCC---------CCeecCCCCCcCCCcCCcCcCCCCc-cceEEEeecc
Confidence            4666666554   566665532         33589999986 3334789999987 4444444444

Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.

>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=85.36  E-value=0.47  Score=34.63  Aligned_cols=25  Identities=16%  Similarity=0.295  Sum_probs=18.4

Q ss_pred             cccCCccc--ccCc--cccccCCCCCeee
Q 033276           73 KCLKLFSS--PFPL--VICIKSNHEIRIS   97 (123)
Q Consensus        73 rC~gC~k~--~~~~--~fCp~CG~~~tl~   97 (123)
                      .|+.|++.  ++.|  ..||+||....+.
T Consensus        11 ~Cp~CG~kFYDLnk~PivCP~CG~~~~~~   39 (108)
T PF09538_consen   11 TCPSCGAKFYDLNKDPIVCPKCGTEFPPE   39 (108)
T ss_pred             cCCCCcchhccCCCCCccCCCCCCccCcc
Confidence            89999986  4332  5699999875444

The function of members of this family is unknown.

>PF14205 Cys_rich_KTR: Cysteine-rich KTR

Probab=85.22  E-value=0.45  Score=31.53  Aligned_cols=14  Identities=7%  Similarity=0.320  Sum_probs=10.6

Q ss_pred             cccccCCCCCeeeEE
Q 033276           85 VICIKSNHEIRISPV   99 (123)
Q Consensus        85 ~fCp~CG~~~tl~rV   99 (123)
                      ..||+||++ |..|+
T Consensus         5 i~CP~CgnK-TR~ki   18 (55)
T PF14205_consen    5 ILCPICGNK-TRLKI   18 (55)
T ss_pred             EECCCCCCc-cceee
Confidence            469999999 55544

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=85.15  E-value=0.24  Score=32.51  Aligned_cols=35  Identities=14%  Similarity=0.133  Sum_probs=25.6

Q ss_pred             cccCCccc---ccCccccccCCCCCeeeEEEEEeeEEEE
Q 033276           73 KCLKLFSS---PFPLVICIKSNHEIRISPVFMLILICLY  108 (123)
Q Consensus        73 rC~gC~k~---~~~~~fCp~CG~~~tl~rV~~~~~~~~~  108 (123)
                      +|..|++.   .....+||.||.+ -=|..-...|.|++
T Consensus         7 ~C~~Cg~~~~~~dDiVvCp~Cgap-yHR~C~~~~g~C~~   44 (54)
T PF14446_consen    7 KCPVCGKKFKDGDDIVVCPECGAP-YHRDCWEKAGGCIN   44 (54)
T ss_pred             cChhhCCcccCCCCEEECCCCCCc-ccHHHHhhCCceEe
Confidence            89999987   4568999999998 55555545555544

>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J

Probab=85.10  E-value=1.1  Score=31.49  Aligned_cols=27  Identities=15%  Similarity=0.137  Sum_probs=19.5

Q ss_pred             CceeEEecccHHHHHHHHHhCceeeCC
Q 033276           32 ESTVACITGDYAMQNVILQMGLRLLAP   58 (123)
Q Consensus        32 ~~~va~vTdDyAmQNVllqlGL~l~sv   58 (123)
                      ..+|+++|.|..|++.|...||+..+.
T Consensus       106 ~~~vvLvT~D~~l~~~A~~~gi~~~~~  132 (133)
T PF13638_consen  106 GRKVVLVTNDKNLRLKARAEGIPAVSY  132 (133)
T ss_dssp             CEEEEEEE--HHHHHHHHHTT--EE--
T ss_pred             CCeEEEEeCCHHHHHHHhhcccccccC
Confidence            568999999999999999999998865

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

Probab=84.94  E-value=0.82  Score=27.33  Aligned_cols=22  Identities=23%  Similarity=0.230  Sum_probs=17.1

Q ss_pred             cccCCccc-------ccCccccccCCCCC
Q 033276           73 KCLKLFSS-------PFPLVICIKSNHEI   94 (123)
Q Consensus        73 rC~gC~k~-------~~~~~fCp~CG~~~   94 (123)
                      .|+.|+++       +.....|.+||+++
T Consensus         3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L   31 (36)
T PF05191_consen    3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL   31 (36)
T ss_dssp             EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred             CcCCCCCccccccCCCCCCCccCCCCCee
Confidence            69999987       12358999999983

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 ....

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

Probab=84.81  E-value=0.49  Score=31.68  Aligned_cols=21  Identities=10%  Similarity=0.009  Sum_probs=16.2

Q ss_pred             cccCCcccccCccccccCCCCC
Q 033276           73 KCLKLFSSPFPLVICIKSNHEI   94 (123)
Q Consensus        73 rC~gC~k~~~~~~fCp~CG~~~   94 (123)
                      .|.-|.++. +.+.||+||+..
T Consensus         5 AC~~C~~i~-~~~~CP~Cgs~~   25 (61)
T PRK08351          5 ACRHCHYIT-TEDRCPVCGSRD   25 (61)
T ss_pred             hhhhCCccc-CCCcCCCCcCCc
Confidence            699999882 234799999983

>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs

Probab=84.73  E-value=1.2  Score=29.09  Aligned_cols=25  Identities=20%  Similarity=0.195  Sum_probs=18.9

Q ss_pred             EEeeccccCCcccccCccccccCCCCC
Q 033276           68 RYIVDKCLKLFSSPFPLVICIKSNHEI   94 (123)
Q Consensus        68 ~wvl~rC~gC~k~~~~~~fCp~CG~~~   94 (123)
                      .++. .|.+|...... +-||.||.++
T Consensus         3 ~~~r-~c~~~~~YTLk-~~cp~cG~~T   27 (53)
T PF04135_consen    3 YYIR-KCPGCRVYTLK-DKCPPCGGPT   27 (53)
T ss_dssp             EEEE-ECTTTCEEESS-SBBTTTSSBS
T ss_pred             cccc-cCCCCCcEeCC-CccCCCCCCC
Confidence            4455 89999976333 6899999993

More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....

>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.61  E-value=0.74  Score=32.62  Aligned_cols=42  Identities=14%  Similarity=0.196  Sum_probs=30.0

Q ss_pred             eeeEEeeccccCCccc--------ccCccccccCCCCC--eeeEEEEEeeEEE
Q 033276           65 QLHRYIVDKCLKLFSS--------PFPLVICIKSNHEI--RISPVFMLILICL  107 (123)
Q Consensus        65 ~v~~wvl~rC~gC~k~--------~~~~~fCp~CG~~~--tl~rV~~~~~~~~  107 (123)
                      -+-.|.| +|..|+..        +.+...||.||.++  ++.||.++.+-+=
T Consensus         7 lMPtY~Y-~c~~cg~~~dvvq~~~ddplt~ce~c~a~~kk~l~~vgi~fKGSG   58 (82)
T COG2331           7 LMPTYSY-ECTECGNRFDVVQAMTDDPLTTCEECGARLKKLLNAVGIVFKGSG   58 (82)
T ss_pred             cccceEE-eecccchHHHHHHhcccCccccChhhChHHHHhhccceEEEecce
Confidence            3457899 99999975        45688999999752  4556666665443

>cd01675 RNR_III Class III ribonucleotide reductase

Probab=84.60  E-value=0.89  Score=40.82  Aligned_cols=58  Identities=12%  Similarity=0.032  Sum_probs=33.3

Q ss_pred             ccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCCCeeeEEEEEee
Q 033276           40 GDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHEIRISPVFMLIL  104 (123)
Q Consensus        40 dDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV~~~~~  104 (123)
                      +=-|+.++.+.+ .    -.|..--....=.. +|..|+.. ......||+||+. -+.+++=++|
T Consensus       493 n~~al~~lv~~a-~----~~~~~y~~~~~p~~-~C~~CG~~~~~~~~~CP~CGs~-~~~~~~Rv~G  551 (555)
T cd01675         493 NPEALEALVKKA-A----KRGVIYFGINTPID-ICNDCGYIGEGEGFKCPKCGSE-DVEVISRITG  551 (555)
T ss_pred             CHHHHHHHHHHH-H----HcCCceEEEecCCc-cCCCCCCCCcCCCCCCcCCCCc-CceEEEeeee
Confidence            445677766653 0    01222223334455 89999987 3556899999987 3444433333

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

>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase

Probab=84.50  E-value=0.49  Score=42.72  Aligned_cols=43  Identities=16%  Similarity=0.124  Sum_probs=27.7

Q ss_pred             HHHHHHHHHh---CceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCC
Q 033276           42 YAMQNVILQM---GLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHE   93 (123)
Q Consensus        42 yAmQNVllql---GL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~   93 (123)
                      =|+.++.+.+   |++..++.         ..+++|..|+.. ......||+||++
T Consensus       501 eal~~lv~~a~~~~i~Y~~~n---------~~~~~C~~CG~~g~~~~~~CP~Cgs~  547 (579)
T TIGR02487       501 EALKDITKKAMKNGIGYFGIN---------PPVDVCEDCGYTGEGLNDKCPKCGSH  547 (579)
T ss_pred             HHHHHHHHHHHhcCCceEEec---------cCCccCCCCCCCCCCCCCcCcCCCCc
Confidence            4666665543   44555442         234599999987 3333689999986

This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=84.45  E-value=0.97  Score=45.04  Aligned_cols=32  Identities=6%  Similarity=0.043  Sum_probs=23.9

Q ss_pred             CcceeeeEEeeccccCCcccccCccccccCCCCC
Q 033276           61 MQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEI   94 (123)
Q Consensus        61 ~~I~~v~~wvl~rC~gC~k~~~~~~fCp~CG~~~   94 (123)
                      .++-++.-... +|+.|++... ..|||.||+++
T Consensus       658 ~G~ieVEV~~r-kCPkCG~~t~-~~fCP~CGs~t  689 (1337)
T PRK14714        658 GGVIEVEVGRR-RCPSCGTETY-ENRCPDCGTHT  689 (1337)
T ss_pred             CCeEEEEEEEE-ECCCCCCccc-cccCcccCCcC
Confidence            44456777888 9999998722 24999999884

>smart00731 SprT SprT homologues

Probab=84.06  E-value=1.1  Score=33.03  Aligned_cols=52  Identities=12%  Similarity=0.092  Sum_probs=33.0

Q ss_pred             HHHHHHHHHhCceeeC-CCCCcceeeeEEeeccccCCccc--------ccCccccccCCCCC
Q 033276           42 YAMQNVILQMGLRLLA-PGGMQIRQLHRYIVDKCLKLFSS--------PFPLVICIKSNHEI   94 (123)
Q Consensus        42 yAmQNVllqlGL~l~s-v~g~~I~~v~~wvl~rC~gC~k~--------~~~~~fCp~CG~~~   94 (123)
                      -.=|..+.++|-..-. -+...+..+++|.+ +|.+|+..        +..+..|-+||+++
T Consensus        83 ~~f~~~~~~~~~~~~~~~h~~~~~~~~~~~y-~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l  143 (146)
T smart00731       83 DEWKRWMRQVNGLFPERCHTFLIESVKKYPY-RCTGCGQRYLRVRRSNNVSRYRCGKCGGKL  143 (146)
T ss_pred             HHHHHHHHHHcCCCcceEcCCcccccceEEE-ECCCCCCCCceEccccCcceEEcCCCCCEE
Confidence            3446666666543111 12333444478999 99999975        12458899999984

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

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

Probab=83.85  E-value=0.52  Score=31.92  Aligned_cols=20  Identities=25%  Similarity=0.320  Sum_probs=16.2

Q ss_pred             cccCCcccccCccccccCCCC
Q 033276           73 KCLKLFSSPFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~~~~~~fCp~CG~~   93 (123)
                      .|..|.++. +...||.||+.
T Consensus         7 AC~~C~~i~-~~~~Cp~Cgs~   26 (64)
T PRK06393          7 ACKKCKRLT-PEKTCPVHGDE   26 (64)
T ss_pred             hHhhCCccc-CCCcCCCCCCC
Confidence            699999982 23589999998

>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=83.66  E-value=0.64  Score=43.33  Aligned_cols=33  Identities=18%  Similarity=0.079  Sum_probs=21.5

Q ss_pred             eccccCCcccccCccccccCCCCCeeeEEEEEee
Q 033276           71 VDKCLKLFSSPFPLVICIKSNHEIRISPVFMLIL  104 (123)
Q Consensus        71 l~rC~gC~k~~~~~~fCp~CG~~~tl~rV~~~~~  104 (123)
                      +++|..|+........||+||+. .+.+.+=++|
T Consensus       680 ~~~C~~CG~~~~~~~~CP~CG~~-~~~~~~Ri~G  712 (735)
T PRK07111        680 VDRCPVCGYLGVIEDKCPKCGST-NIQRIRRITG  712 (735)
T ss_pred             CeecCCCCCCCCcCccCcCCCCc-cceeeehhhh
Confidence            45899999763234789999986 3444433333

>TIGR00595 priA primosomal protein N'

Probab=83.33  E-value=0.93  Score=40.07  Aligned_cols=26  Identities=19%  Similarity=0.361  Sum_probs=18.2

Q ss_pred             eeccccCCccc-ccCccccccCCCCCeeeE
Q 033276           70 IVDKCLKLFSS-PFPLVICIKSNHEIRISP   98 (123)
Q Consensus        70 vl~rC~gC~k~-~~~~~fCp~CG~~~tl~r   98 (123)
                      .+ +||-|+.. +.+ ..||.||++ .++.
T Consensus       240 ~l-~Ch~Cg~~~~~~-~~Cp~C~s~-~l~~  266 (505)
T TIGR00595       240 KL-RCHYCGYQEPIP-KTCPQCGSE-DLVY  266 (505)
T ss_pred             eE-EcCCCcCcCCCC-CCCCCCCCC-eeEe
Confidence            45 67777776 444 679999998 5553

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

>PRK02935 hypothetical protein; Provisional

Probab=82.93  E-value=0.79  Score=34.07  Aligned_cols=31  Identities=13%  Similarity=0.271  Sum_probs=24.0

Q ss_pred             eEEeeccccCCccc-cc--CccccccCCCCCeeeE
Q 033276           67 HRYIVDKCLKLFSS-PF--PLVICIKSNHEIRISP   98 (123)
Q Consensus        67 ~~wvl~rC~gC~k~-~~--~~~fCp~CG~~~tl~r   98 (123)
                      |.-.. .|+.|.|. .+  ..+-|..|+.|+||.+
T Consensus        67 kavqV-~CP~C~K~TKmLGrvD~CM~C~~PLTLd~  100 (110)
T PRK02935         67 KAVQV-ICPSCEKPTKMLGRVDACMHCNQPLTLDR  100 (110)
T ss_pred             cceee-ECCCCCchhhhccceeecCcCCCcCCcCc
Confidence            34455 89999998 32  3478999999998865

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

Probab=82.23  E-value=0.49  Score=42.43  Aligned_cols=24  Identities=21%  Similarity=0.026  Sum_probs=11.6

Q ss_pred             eeccccCCcccccCccccccCCCC
Q 033276           70 IVDKCLKLFSSPFPLVICIKSNHE   93 (123)
Q Consensus        70 vl~rC~gC~k~~~~~~fCp~CG~~   93 (123)
                      ..++|..|+........||+||++
T Consensus       490 ~~~~C~~CG~~~~~~~~CP~CGs~  513 (546)
T PF13597_consen  490 PIDICPDCGYIGGEGDKCPKCGSE  513 (546)
T ss_dssp             -EEEETTT---S--EEE-CCC---
T ss_pred             CcccccCCCcCCCCCCCCCCCCCc
Confidence            345899999983237899999999

>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=81.89  E-value=0.99  Score=41.59  Aligned_cols=44  Identities=16%  Similarity=0.093  Sum_probs=31.0

Q ss_pred             HHHHHHHHHh----CceeeCCCCCcceeeeEEeeccccCCcccccCccccccCCCCC
Q 033276           42 YAMQNVILQM----GLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEI   94 (123)
Q Consensus        42 yAmQNVllql----GL~l~sv~g~~I~~v~~wvl~rC~gC~k~~~~~~fCp~CG~~~   94 (123)
                      =|+.++.+.+    ++...++..         .+++|..|+........||+||+++
T Consensus       602 ~a~~~lv~~~~~~~~i~Y~~in~---------~~~~C~~CG~~~g~~~~CP~CG~~~  649 (656)
T PRK08270        602 EACKKLVKKALENYRLPYITITP---------TFSICPKHGYLSGEHEFCPKCGEET  649 (656)
T ss_pred             HHHHHHHHHHHHhCCCceEEeCC---------CCcccCCCCCcCCCCCCCcCCcCcc
Confidence            5777777754    566666632         2358999998633357899999873

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

Probab=81.75  E-value=1  Score=36.69  Aligned_cols=27  Identities=11%  Similarity=0.118  Sum_probs=14.3

Q ss_pred             cccCCccc-ccCccccccCCCCCeeeEEE
Q 033276           73 KCLKLFSS-PFPLVICIKSNHEIRISPVF  100 (123)
Q Consensus        73 rC~gC~k~-~~~~~fCp~CG~~~tl~rV~  100 (123)
                      .|.-|++. ...+.-||.||+. --.+..
T Consensus       199 ~Cs~C~t~W~~~R~~Cp~Cg~~-~~~~l~  226 (290)
T PF04216_consen  199 HCSLCGTEWRFVRIKCPYCGNT-DHEKLE  226 (290)
T ss_dssp             EETTT--EEE--TTS-TTT----SS-EEE
T ss_pred             EcCCCCCeeeecCCCCcCCCCC-CCccee
Confidence            59999988 8888999999988 455554

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

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

Probab=81.71  E-value=0.87  Score=26.81  Aligned_cols=21  Identities=24%  Similarity=0.297  Sum_probs=15.4

Q ss_pred             cccCCccc-----ccCccccccCCCC
Q 033276           73 KCLKLFSS-----PFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~-----~~~~~fCp~CG~~   93 (123)
                      +|.+|+..     .....||+.||.-
T Consensus         5 ~C~~C~~~~i~~~~~~~~~C~~Cg~~   30 (33)
T PF08792_consen    5 KCSKCGGNGIVNKEDDYEVCIFCGSS   30 (33)
T ss_pred             EcCCCCCCeEEEecCCeEEcccCCcE
Confidence            68888875     3457888888864

>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain

Probab=81.61  E-value=0.96  Score=32.69  Aligned_cols=25  Identities=8%  Similarity=-0.025  Sum_probs=18.4

Q ss_pred             eeccccCCccc---ccC--ccccccCCCCCe
Q 033276           70 IVDKCLKLFSS---PFP--LVICIKSNHEIR   95 (123)
Q Consensus        70 vl~rC~gC~k~---~~~--~~fCp~CG~~~t   95 (123)
                      .+ +|..|+..   ..+  ..+||.||+..+
T Consensus        42 ~~-~C~~Cg~~~~~~~SCk~R~CP~C~~~~~   71 (111)
T PF14319_consen   42 RY-RCEDCGHEKIVYNSCKNRHCPSCQAKAT   71 (111)
T ss_pred             ee-ecCCCCceEEecCcccCcCCCCCCChHH
Confidence            46 99999986   221  459999998743

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

Probab=81.13  E-value=0.97  Score=30.26  Aligned_cols=26  Identities=19%  Similarity=0.220  Sum_probs=18.3

Q ss_pred             cccCCccc--c---cCccccccCCCCCeeeEE
Q 033276           73 KCLKLFSS--P---FPLVICIKSNHEIRISPV   99 (123)
Q Consensus        73 rC~gC~k~--~---~~~~fCp~CG~~~tl~rV   99 (123)
                      .|.+|+..  +   ..+-.||.||.. ++.|.
T Consensus         9 ~CtSCg~~i~~~~~~~~F~CPnCG~~-~I~RC   39 (59)
T PRK14890          9 KCTSCGIEIAPREKAVKFLCPNCGEV-IIYRC   39 (59)
T ss_pred             cccCCCCcccCCCccCEeeCCCCCCe-eEeec
Confidence            68888876  2   235679999887 56664

>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70)

Probab=81.10  E-value=2.6  Score=31.31  Aligned_cols=26  Identities=15%  Similarity=0.130  Sum_probs=21.1

Q ss_pred             EEeeccccCCccc--cc--CccccccCCCC
Q 033276           68 RYIVDKCLKLFSS--PF--PLVICIKSNHE   93 (123)
Q Consensus        68 ~wvl~rC~gC~k~--~~--~~~fCp~CG~~   93 (123)
                      .|-|..|+.|.+.  +.  ..-+|++|+..
T Consensus        31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~   60 (166)
T cd04476          31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKS   60 (166)
T ss_pred             CeEEccccccCcccEeCCCCcEECCCCCCc
Confidence            5777799999987  22  56899999987

RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun

>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=81.10  E-value=0.89  Score=41.83  Aligned_cols=43  Identities=12%  Similarity=0.040  Sum_probs=29.0

Q ss_pred             HHHHHHHHH---hCceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCC
Q 033276           42 YAMQNVILQ---MGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHE   93 (123)
Q Consensus        42 yAmQNVllq---lGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~   93 (123)
                      -|+.++++.   .|+...++..         ..++|..|+.. ......||+||++
T Consensus       543 eal~~lv~~~~~~~i~Yf~in~---------~~~iC~~CG~~~~g~~~~CP~CGs~  589 (623)
T PRK08271        543 EGYRKLLNIAAKTGCNYFAFNV---------KITICNDCHHIDKRTGKRCPICGSE  589 (623)
T ss_pred             HHHHHHHHHHHHcCCceEEeCC---------CCccCCCCCCcCCCCCcCCcCCCCc
Confidence            455555444   3566665532         33589999987 5567899999976

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=81.01  E-value=1.1  Score=25.98  Aligned_cols=22  Identities=27%  Similarity=0.209  Sum_probs=16.5

Q ss_pred             cccCCccc---c-------cCccccccCCCCC
Q 033276           73 KCLKLFSS---P-------FPLVICIKSNHEI   94 (123)
Q Consensus        73 rC~gC~k~---~-------~~~~fCp~CG~~~   94 (123)
                      .|+.|++.   +       ..+..||+||+.+
T Consensus         4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            79999984   2       1247999999983

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.

>PRK06260 threonine synthase; Validated

Probab=80.92  E-value=1  Score=38.12  Aligned_cols=25  Identities=16%  Similarity=0.312  Sum_probs=18.7

Q ss_pred             EeeccccCCccc-cc--CccccccCCCCC
Q 033276           69 YIVDKCLKLFSS-PF--PLVICIKSNHEI   94 (123)
Q Consensus        69 wvl~rC~gC~k~-~~--~~~fCp~CG~~~   94 (123)
                      +.+ +|..|++. +.  ....||.||..+
T Consensus         2 ~~~-~C~~cg~~~~~~~~~~~Cp~cg~~l   29 (397)
T PRK06260          2 YWL-KCIECGKEYDPDEIIYTCPECGGLL   29 (397)
T ss_pred             CEE-EECCCCCCCCCCCccccCCCCCCeE
Confidence            357 99999998 32  335699999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	123
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	1e-05

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii} Length = 165

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 18/89 (20%), Positives = 41/89 (46%), Gaps = 9/89 (10%)

Query: 1   MEISSKNNEIVDVSYVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGG 60
           ++++ +  E+ ++S  D E    ++ L+          + DY +QN+   +GLR      
Sbjct: 70  IQVAKETGEVNELSKADIEVLALAYELK------GEIFSDDYNVQNIASLLGLRFRTL-K 122

Query: 61  MQIRQLHRYIV--DKCLKLFSSPFPLVIC 87
             I+++ ++      C + FS+  P  +C
Sbjct: 123 RGIKKVIKWRYVCIGCGRKFSTLPPGGVC 151

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	123
2con_A	79	RUH-035 protein, NIN one binding protein; ribosome	99.72
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	99.66
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	96.06
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	96.06
3i8o_A	142	KH domain-containing protein MJ1533; APC89320.5, m	95.49
3irb_A	145	Uncharacterized protein from DUF35 family; 1381535	95.03
2gnr_A	145	Conserved hypothetical protein; 13815350, structur	94.05
3ix7_A	134	Uncharacterized protein TTHA0540; unknown function	93.81
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	92.49
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	91.47
2aus_D	60	NOP10, ribosome biogenesis protein NOP10; isomeras	90.78
2apo_B	60	Ribosome biogenesis protein NOP10; protein-protein	90.77
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	90.18
1lko_A	191	Rubrerythrin all-iron(II) form; reduced form, DIIR	88.22
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	88.09
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	87.88
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	85.49
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	85.05
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	84.8
3na7_A	256	HP0958; flagellar biogenesis, flagellum export, C4	83.58
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	81.12
1yuz_A	202	Nigerythrin; rubrythrin, rubredoxin, hemerythrin,	80.6

>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=99.72  E-value=1.5e-18  Score=119.60  Aligned_cols=46  Identities=22%  Similarity=0.460  Sum_probs=43.1

Q ss_pred             CCCCCcceeeeEEeeccccCCccc--ccCccccccCCCCCeeeEEEEEee
Q 033276           57 APGGMQIRQLHRYIVDKCLKLFSS--PFPLVICIKSNHEIRISPVFMLIL  104 (123)
Q Consensus        57 sv~g~~I~~v~~wvl~rC~gC~k~--~~~~~fCp~CG~~~tl~rV~~~~~  104 (123)
                      |++|++|+++|+|++ ||+|||++  ++++.|||+|||+ ||+||+|++.
T Consensus         2 s~~G~~Ir~~k~~iL-rC~aCf~~t~~~~k~FCp~CGn~-TL~Rvsvsvd   49 (79)
T 2con_A            2 SSGSSGVREARSYIL-RCHGCFKTTSDMNRVFCGHCGNK-TLKKVSVTIN   49 (79)
T ss_dssp             CCCCCCCCCCCCEEE-ECSSSCCEESCSSCCSCSSSCCS-CCEEEECBCC
T ss_pred             CCCceEeeeeeeeee-EecccceECCCcccccccccCcc-cceEEEEEEC
Confidence            689999999999999 99999998  8899999999999 9999998653

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

Probab=99.66  E-value=3.6e-17  Score=121.15  Aligned_cols=59  Identities=19%  Similarity=0.305  Sum_probs=54.1

Q ss_pred             ceeEEecccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc-c--cCccccccCCCC
Q 033276           33 STVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-P--FPLVICIKSNHE   93 (123)
Q Consensus        33 ~~va~vTdDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~--~~~~fCp~CG~~   93 (123)
                      ..+.++|+||++||||+++||+++++. .+|++++.|.| +|.+|++. +  .+..|||.||++
T Consensus        96 l~~~lvT~D~~l~~vA~~~Gv~v~~~~-~~i~~~~~~~y-~C~~Cg~~~~~~~~~~~Cp~CG~~  157 (165)
T 2lcq_A           96 LKGEIFSDDYNVQNIASLLGLRFRTLK-RGIKKVIKWRY-VCIGCGRKFSTLPPGGVCPDCGSK  157 (165)
T ss_dssp             HTCCEECCCHHHHHHHHHTTCCEECCS-CCCSSCCCCCE-EESSSCCEESSCCGGGBCTTTCCB
T ss_pred             hCCeEEcCcHHHHHHHHHCCCeEEchh-hhccccccEEE-ECCCCCCcccCCCCCCcCCCCCCc
Confidence            356899999999999999999999998 99999999999 99999997 3  346799999999

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

Probab=96.06  E-value=0.0033  Score=44.26  Aligned_cols=40  Identities=8%  Similarity=0.047  Sum_probs=29.0

Q ss_pred             eEEeeccccCCccc---ccCcc-ccccCCCCCeeeEEEEEeeEEEEEee
Q 033276           67 HRYIVDKCLKLFSS---PFPLV-ICIKSNHEIRISPVFMLILICLYIQV  111 (123)
Q Consensus        67 ~~wvl~rC~gC~k~---~~~~~-fCp~CG~~~tl~rV~~~~~~~~~~~~  111 (123)
                      ..=.+ +|..|++.   +.... .||.||++ .++   ++-|.-+||++
T Consensus        70 ~p~~~-~C~~CG~~~e~~~~~~~~CP~Cgs~-~~~---i~~G~el~i~~  113 (119)
T 2kdx_A           70 EKVEL-ECKDCSHVFKPNALDYGVCEKCHSK-NVI---ITQGNEMRLLS  113 (119)
T ss_dssp             ECCEE-ECSSSSCEECSCCSTTCCCSSSSSC-CCE---EEESSCCEEEE
T ss_pred             ccceE-EcCCCCCEEeCCCCCCCcCccccCC-CcE---EecCCeEEEEE
Confidence            34467 99999987   33445 79999999 443   56688888874

>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=96.06  E-value=0.0038  Score=45.52  Aligned_cols=39  Identities=13%  Similarity=0.144  Sum_probs=28.8

Q ss_pred             EEeeccccCCccc---cc-----------C----------ccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276           68 RYIVDKCLKLFSS---PF-----------P----------LVICIKSNHEIRISPVFMLILICLYIQV  111 (123)
Q Consensus        68 ~wvl~rC~gC~k~---~~-----------~----------~~fCp~CG~~~tl~rV~~~~~~~~~~~~  111 (123)
                      .=+. +|..|+..   ..           .          ...||.||++ .   +.++-|.-+||++
T Consensus        68 p~~~-~C~~CG~~~~~~~~~~~~~~~~~~~~h~~p~~~~~~~~CP~Cgs~-~---~~i~~G~el~I~~  130 (139)
T 3a43_A           68 EAVF-KCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSH-D---FEVVKGRGVYVAG  130 (139)
T ss_dssp             CCEE-EETTTCCEEEGGGCTTCCSCCCGGGCCCCGGGCGGGCSCSSSSCC-C---EEEEESSCEEEEE
T ss_pred             CCcE-ECCCCCCEEecccccccccccccccccccccccccCCcCccccCC-c---cEEecCCeEEEEE
Confidence            3356 89999987   23           3          4669999999 3   4467788888875

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

Probab=95.49  E-value=0.0092  Score=44.28  Aligned_cols=29  Identities=17%  Similarity=0.214  Sum_probs=26.0

Q ss_pred             CceeEEecccHHHHHHHHHhCceeeCCCC
Q 033276           32 ESTVACITGDYAMQNVILQMGLRLLAPGG   60 (123)
Q Consensus        32 ~~~va~vTdDyAmQNVllqlGL~l~sv~g   60 (123)
                      ...+.++|+||.+++||..+|++++.+..
T Consensus       104 ~~~a~lvTnD~~l~kvA~~~GI~V~~l~~  132 (142)
T 3i8o_A          104 ETNSILLTSDWIQYNLAKAQGIEAYFLEA  132 (142)
T ss_dssp             HTTCEEEESCHHHHHHHHHTTCCEEECCC
T ss_pred             HhCCEEEcCCHHHHHHHHHcCCEEEEecc
Confidence            35679999999999999999999999865

>3irb_A Uncharacterized protein from DUF35 family; 13815350, protein with unknown function from DUF35 family, S genomics; 1.80A {Sulfolobus solfataricus}

Probab=95.03  E-value=0.0071  Score=44.22  Aligned_cols=34  Identities=15%  Similarity=-0.123  Sum_probs=26.8

Q ss_pred             eEEeeccccCCccc-ccCccccccCCCCCeeeEEEEE
Q 033276           67 HRYIVDKCLKLFSS-PFPLVICIKSNHEIRISPVFML  102 (123)
Q Consensus        67 ~~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV~~~  102 (123)
                      +-... ||..|++. -+++.+||.||+. .+..+.++
T Consensus        44 rL~~~-rC~~CG~~~~PPr~~Cp~C~s~-~~~~ve~s   78 (145)
T 3irb_A           44 KIIGS-KCSKCGRIFVPARSYCEHCFVK-IENYVEIN   78 (145)
T ss_dssp             CCEEE-ECTTTCCEEESCCSEETTTTEE-CCEEEECC
T ss_pred             eEEEE-EeCCCCcEEcCchhhCcCCCCC-ceeeeeec
Confidence            34556 99999999 6778999999998 66666544

>2gnr_A Conserved hypothetical protein; 13815350, structural genomics, PSI, protein structure initiative; 1.80A {Sulfolobus solfataricus P2} PDB: 3irb_A

Probab=94.05  E-value=0.016  Score=42.54  Aligned_cols=33  Identities=15%  Similarity=-0.133  Sum_probs=26.1

Q ss_pred             EEeeccccCCccc-ccCccccccCCCCCeeeEEEEE
Q 033276           68 RYIVDKCLKLFSS-PFPLVICIKSNHEIRISPVFML  102 (123)
Q Consensus        68 ~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV~~~  102 (123)
                      -... ||..|++. .+++.+||.||+. .+..+.+.
T Consensus        45 L~~~-rC~~CG~~~fPPr~~Cp~C~s~-~~e~v~ls   78 (145)
T 2gnr_A           45 IIGS-KCSKCGRIFVPARSYCEHCFVK-IENYVEIN   78 (145)
T ss_dssp             CEEE-ECTTTCCEEESCCSEETTTTEE-CCEEEECC
T ss_pred             EEEE-EECCCCcEEeCCCCCCCCCCCC-ccEEEEcc
Confidence            4456 99999999 6778999999998 56666544

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

Probab=93.81  E-value=0.025  Score=41.33  Aligned_cols=28  Identities=21%  Similarity=0.266  Sum_probs=24.7

Q ss_pred             CceeEEecccHHHHHHHHHhCceeeCCC
Q 033276           32 ESTVACITGDYAMQNVILQMGLRLLAPG   59 (123)
Q Consensus        32 ~~~va~vTdDyAmQNVllqlGL~l~sv~   59 (123)
                      +..+.++|.||.++++|..+|++++.++
T Consensus        96 ~~~~~lvTnD~~L~kvA~~~GI~Vl~l~  123 (134)
T 3ix7_A           96 DLEAALVTNDHALLQMARIYGVKALSIQ  123 (134)
T ss_dssp             HTTCEEEESCHHHHHHHHHTTCCEEEHH
T ss_pred             HhCCEEEeCCHHHHHHHHHCCCeEEehH
Confidence            3468999999999999999999998763

>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=92.49  E-value=0.043  Score=36.33  Aligned_cols=27  Identities=22%  Similarity=0.248  Sum_probs=21.6

Q ss_pred             eEEeeccccCCccc----ccCccccccCCCCC
Q 033276           67 HRYIVDKCLKLFSS----PFPLVICIKSNHEI   94 (123)
Q Consensus        67 ~~wvl~rC~gC~k~----~~~~~fCp~CG~~~   94 (123)
                      ....| +|..|+..    +.....||.||+.+
T Consensus        25 ~~v~Y-~C~~CG~~~e~~~~d~irCp~CG~RI   55 (70)
T 1twf_L           25 ATLKY-ICAECSSKLSLSRTDAVRCKDCGHRI   55 (70)
T ss_dssp             CCCCE-ECSSSCCEECCCTTSTTCCSSSCCCC
T ss_pred             ceEEE-ECCCCCCcceeCCCCCccCCCCCceE
Confidence            46788 99999986    34457899999973

>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=91.47  E-value=0.092  Score=33.00  Aligned_cols=28  Identities=25%  Similarity=0.371  Sum_probs=19.6

Q ss_pred             eeccccCCccc-c------cCccccccCCCCCeeeEE
Q 033276           70 IVDKCLKLFSS-P------FPLVICIKSNHEIRISPV   99 (123)
Q Consensus        70 vl~rC~gC~k~-~------~~~~fCp~CG~~~tl~rV   99 (123)
                      +| +|.-|++. .      .+..-||.||.+ .+.+|
T Consensus         3 iY-~C~rCg~~fs~~el~~lP~IrCpyCGyr-ii~Kv   37 (48)
T 4ayb_P            3 VY-RCGKCWKTFTDEQLKVLPGVRCPYCGYK-IIFMV   37 (48)
T ss_dssp             ---CCCCTTTTCCCCCSCCCSSSCCTTTCCS-CEECC
T ss_pred             EE-EeeccCCCccHHHHhhCCCcccCccCcE-EEEEe
Confidence            46 89999987 1      456789999999 44443

>2aus_D NOP10, ribosome biogenesis protein NOP10; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_B 3lwo_B* 3lwq_B* 3lwp_B 3lwv_B 3hax_C* 2hvy_C* 3hay_C* 2ey4_E 3hjw_B* 2rfk_B* 3hjy_B 3mqk_B

Probab=90.78  E-value=0.1  Score=33.91  Aligned_cols=21  Identities=19%  Similarity=0.208  Sum_probs=17.5

Q ss_pred             cccCCcccccCccccccCCCCC
Q 033276           73 KCLKLFSSPFPLVICIKSNHEI   94 (123)
Q Consensus        73 rC~gC~k~~~~~~fCp~CG~~~   94 (123)
                      +|..|+.... +..||.||.++
T Consensus         7 ~C~~Cg~YTL-k~~CP~CG~~t   27 (60)
T 2aus_D            7 KCPKCGRYTL-KETCPVCGEKT   27 (60)
T ss_dssp             ECTTTCCEES-SSBCTTTCSBC
T ss_pred             ECCCCCCEEc-cccCcCCCCcc
Confidence            8999998733 68899999993

>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A

Probab=90.77  E-value=0.098  Score=33.97  Aligned_cols=20  Identities=30%  Similarity=0.354  Sum_probs=17.1

Q ss_pred             cccCCcccccCccccccCCCC
Q 033276           73 KCLKLFSSPFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~~~~~~fCp~CG~~   93 (123)
                      +|..|+.... +..||.||.+
T Consensus         8 ~C~~CgvYTL-k~~CP~CG~~   27 (60)
T 2apo_B            8 KCPKCGLYTL-KEICPKCGEK   27 (60)
T ss_dssp             ECTTTCCEES-SSBCSSSCSB
T ss_pred             eCCCCCCEec-cccCcCCCCc
Confidence            8999997744 6889999999

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

Probab=90.18  E-value=0.14  Score=33.49  Aligned_cols=25  Identities=16%  Similarity=0.331  Sum_probs=19.8

Q ss_pred             EeeccccCCccc-c---cCccccccCCCCC
Q 033276           69 YIVDKCLKLFSS-P---FPLVICIKSNHEI   94 (123)
Q Consensus        69 wvl~rC~gC~k~-~---~~~~fCp~CG~~~   94 (123)
                      -.| +|..|++. +   ....-||.||+.+
T Consensus        20 v~Y-~C~~Cg~~~~l~~~~~iRC~~CG~RI   48 (63)
T 3h0g_L           20 MIY-LCADCGARNTIQAKEVIRCRECGHRV   48 (63)
T ss_dssp             CCC-BCSSSCCBCCCCSSSCCCCSSSCCCC
T ss_pred             eEE-ECCCCCCeeecCCCCceECCCCCcEE
Confidence            457 99999987 2   3457899999995

>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=88.22  E-value=0.33  Score=36.47  Aligned_cols=23  Identities=13%  Similarity=0.082  Sum_probs=17.7

Q ss_pred             eeccccCCccc-c--cCccccccCCCC
Q 033276           70 IVDKCLKLFSS-P--FPLVICIKSNHE   93 (123)
Q Consensus        70 vl~rC~gC~k~-~--~~~~fCp~CG~~   93 (123)
                      ++ +|+-|+.+ +  ..-..||.||.+
T Consensus       155 ~~-~C~~CG~~~~g~~~p~~CP~C~~~  180 (191)
T 1lko_A          155 KW-RCRNCGYVHEGTGAPELCPACAHP  180 (191)
T ss_dssp             EE-EETTTCCEEEEEECCSBCTTTCCB
T ss_pred             eE-EECCCCCEeeCCCCCCCCCCCcCC
Confidence            56 99999988 2  222589999987

>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=88.09  E-value=0.23  Score=37.13  Aligned_cols=22  Identities=14%  Similarity=0.131  Sum_probs=17.3

Q ss_pred             eeccccCCccc---ccCccccccCCCC
Q 033276           70 IVDKCLKLFSS---PFPLVICIKSNHE   93 (123)
Q Consensus        70 vl~rC~gC~k~---~~~~~fCp~CG~~   93 (123)
                      .+ +|+-|+.+   +.| ..||.||.+
T Consensus       138 ~~-~C~~CG~i~~~~~p-~~CP~Cg~~  162 (170)
T 3pwf_A          138 VY-ICPICGYTAVDEAP-EYCPVCGAP  162 (170)
T ss_dssp             EE-ECTTTCCEEESCCC-SBCTTTCCB
T ss_pred             ee-EeCCCCCeeCCCCC-CCCCCCCCC
Confidence            45 79999997   333 589999987

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

Probab=87.88  E-value=0.2  Score=30.68  Aligned_cols=22  Identities=9%  Similarity=-0.133  Sum_probs=16.4

Q ss_pred             eccccCCccc-ccC----------cc--ccccCCCC
Q 033276           71 VDKCLKLFSS-PFP----------LV--ICIKSNHE   93 (123)
Q Consensus        71 l~rC~gC~k~-~~~----------~~--fCp~CG~~   93 (123)
                      + +|..|+.+ ++.          -+  .||.||.+
T Consensus         5 y-~C~vCGyvyd~~~Gd~t~f~~lP~dw~CP~Cg~~   39 (46)
T 6rxn_A            5 Y-VCNVCGYEYDPAEHDNVPFDQLPDDWCCPVCGVS   39 (46)
T ss_dssp             E-EETTTCCEECGGGGTTCCGGGSCTTCBCTTTCCB
T ss_pred             E-ECCCCCeEEeCCcCCCcchhhCCCCCcCcCCCCc
Confidence            5 89999987 521          11  79999986

>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=85.49  E-value=0.1  Score=34.71  Aligned_cols=28  Identities=11%  Similarity=0.179  Sum_probs=20.8

Q ss_pred             eeccccCCccc-----ccCccccccCCCCCeeeEEE
Q 033276           70 IVDKCLKLFSS-----PFPLVICIKSNHEIRISPVF  100 (123)
Q Consensus        70 vl~rC~gC~k~-----~~~~~fCp~CG~~~tl~rV~  100 (123)
                      +. +|+ |++.     .....-|| ||..+.++++.
T Consensus         4 vv-~C~-C~~~~~~~~~~kT~~C~-CG~~~~~~k~r   36 (71)
T 1gh9_A            4 IF-RCD-CGRALYSREGAKTRKCV-CGRTVNVKDRR   36 (71)
T ss_dssp             EE-EET-TSCCEEEETTCSEEEET-TTEEEECCSSS
T ss_pred             EE-ECC-CCCEEEEcCCCcEEECC-CCCeeeeceEE
Confidence            56 999 9986     23457899 99887666655

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

Probab=85.05  E-value=0.62  Score=29.20  Aligned_cols=27  Identities=26%  Similarity=0.501  Sum_probs=22.3

Q ss_pred             eeccccCCccc-ccCccccccCCCCCeeeE
Q 033276           70 IVDKCLKLFSS-PFPLVICIKSNHEIRISP   98 (123)
Q Consensus        70 vl~rC~gC~k~-~~~~~fCp~CG~~~tl~r   98 (123)
                      .+ .|+-|+.. +.....|.+||+. .|+.
T Consensus        14 k~-iCpkC~a~~~~gaw~CrKCG~~-~lr~   41 (51)
T 3j21_g           14 KY-VCLRCGATNPWGAKKCRKCGYK-RLRP   41 (51)
T ss_dssp             EE-ECTTTCCEECTTCSSCSSSSSC-CCEE
T ss_pred             Cc-cCCCCCCcCCCCceecCCCCCc-cccc
Confidence            45 89999988 7778999999998 5654

>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=84.80  E-value=0.4  Score=30.25  Aligned_cols=22  Identities=9%  Similarity=-0.102  Sum_probs=16.4

Q ss_pred             eccccCCccc-ccCc-------------------cccccCCCC
Q 033276           71 VDKCLKLFSS-PFPL-------------------VICIKSNHE   93 (123)
Q Consensus        71 l~rC~gC~k~-~~~~-------------------~fCp~CG~~   93 (123)
                      + +|..|+.+ ++.+                   -.||.||.+
T Consensus         4 y-~C~vCGyvYd~~~Gdp~~gi~pGt~fe~lP~dw~CP~Cg~~   45 (54)
T 4rxn_A            4 Y-TCTVCGYIYDPEDGDPDDGVNPGTDFKDIPDDWVCPLCGVG   45 (54)
T ss_dssp             E-EETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCB
T ss_pred             e-ECCCCCeEECCCcCCcccCcCCCCChhHCCCCCcCcCCCCc
Confidence            5 89999987 4321                   169999986

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

Probab=83.58  E-value=0.43  Score=37.06  Aligned_cols=21  Identities=14%  Similarity=0.205  Sum_probs=16.5

Q ss_pred             cccCCccc-c----------cCccccccCCCC
Q 033276           73 KCLKLFSS-P----------FPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~-~----------~~~~fCp~CG~~   93 (123)
                      +|.|||-. |          ....+||+||-=
T Consensus       200 ~C~GC~~~lppq~~~~i~~~~~Iv~Cp~CgRI  231 (256)
T 3na7_A          200 ACGGCFIRLNDKIYTEVLTSGDMITCPYCGRI  231 (256)
T ss_dssp             BCTTTCCBCCHHHHHHHHHSSSCEECTTTCCE
T ss_pred             ccCCCCeeeCHHHHHHHHCCCCEEECCCCCee
Confidence            99999975 3          235799999975

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

Probab=81.12  E-value=0.54  Score=32.08  Aligned_cols=21  Identities=10%  Similarity=0.392  Sum_probs=15.2

Q ss_pred             cccCCccc-ccCccccccCCCCC
Q 033276           73 KCLKLFSS-PFPLVICIKSNHEI   94 (123)
Q Consensus        73 rC~gC~k~-~~~~~fCp~CG~~~   94 (123)
                      .|..|.+. +.. -|||.||.++
T Consensus        20 ~C~~C~~~~~~~-afCPeCgq~L   41 (81)
T 2jrp_A           20 HCETCAKDFSLQ-ALCPDCRQPL   41 (81)
T ss_dssp             ECTTTCCEEEEE-EECSSSCSCC
T ss_pred             ECccccccCCCc-ccCcchhhHH
Confidence            58888876 433 3888888883

>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=80.60  E-value=0.79  Score=34.92  Aligned_cols=23  Identities=9%  Similarity=-0.138  Sum_probs=17.6

Q ss_pred             eeccccCCccc-c-cCccccccCCCC
Q 033276           70 IVDKCLKLFSS-P-FPLVICIKSNHE   93 (123)
Q Consensus        70 vl~rC~gC~k~-~-~~~~fCp~CG~~   93 (123)
                      ++ +|.-|+.+ + ..-..||.||.+
T Consensus       171 ~~-~C~~CG~i~~g~~p~~CP~C~~~  195 (202)
T 1yuz_A          171 FH-LCPICGYIHKGEDFEKCPICFRP  195 (202)
T ss_dssp             EE-ECSSSCCEEESSCCSBCTTTCCB
T ss_pred             EE-EECCCCCEEcCcCCCCCCCCCCC
Confidence            45 89999988 3 222689999987

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	123
d2cona1	66	RNA-binding protein NOB1 (Nin one binding) {Mouse	99.63
d2gnra1	137	Hypothetical protein SSO2064 {Sulfolobus solfatari	93.95
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	92.89
d1lkoa2	44	Rubrerythrin, C-terminal domain {Desulfovibrio vul	92.19
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	92.08
d2apob1	55	Ribosome biogenesis protein Nop10 {Archaeon Methan	91.92
d2ey4e1	52	Ribosome biogenesis protein Nop10 {Archaeon Pyroco	91.62
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	85.12
d1e4va2	35	Microbial and mitochondrial ADK, insert "zinc fing	84.95
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	80.53

>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=99.63  E-value=3.5e-17  Score=107.97  Aligned_cols=40  Identities=23%  Similarity=0.478  Sum_probs=37.4

Q ss_pred             ceeeeEEeeccccCCccc--ccCccccccCCCCCeeeEEEEEee
Q 033276           63 IRQLHRYIVDKCLKLFSS--PFPLVICIKSNHEIRISPVFMLIL  104 (123)
Q Consensus        63 I~~v~~wvl~rC~gC~k~--~~~~~fCp~CG~~~tl~rV~~~~~  104 (123)
                      |+++|+|++ ||+|||++  ++++.|||+||++ ||+||+|++.
T Consensus         1 Ir~vr~~~L-rC~aCf~~t~~~~k~FCpkCGn~-TL~rvsvsvd   42 (66)
T d2cona1           1 VREARSYIL-RCHGCFKTTSDMNRVFCGHCGNK-TLKKVSVTIN   42 (66)
T ss_dssp             CCCCCCEEE-ECSSSCCEESCSSCCSCSSSCCS-CCEEEECBCC
T ss_pred             Chhhheeee-EeeecCcCcCCcccccCcccCCC-ceeEEEEEEC
Confidence            789999999 99999998  8899999999999 9999998764

>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=93.95  E-value=0.0088  Score=41.52  Aligned_cols=34  Identities=15%  Similarity=-0.165  Sum_probs=26.8

Q ss_pred             EeeccccCCccc-ccCccccccCCCCCeeeEEEEEee
Q 033276           69 YIVDKCLKLFSS-PFPLVICIKSNHEIRISPVFMLIL  104 (123)
Q Consensus        69 wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV~~~~~  104 (123)
                      ... +|..|++. -+++.+||+||+. .+.-+.+.-|
T Consensus        38 ~~~-~C~~CG~v~~Ppr~~Cp~C~s~-~~e~~e~s~g   72 (137)
T d2gnra1          38 IGS-KCSKCGRIFVPARSYCEHCFVK-IENYVEINKD   72 (137)
T ss_dssp             EEE-ECTTTCCEEESCCSEETTTTEE-CCEEEECCGG
T ss_pred             EEE-EcCCCCCEEeCccccCCCCCCC-cceeEEecCC
Confidence            344 99999999 6678999999999 7777665543

>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=92.89  E-value=0.026  Score=32.03  Aligned_cols=23  Identities=9%  Similarity=-0.040  Sum_probs=18.0

Q ss_pred             eeccccCCccc--ccCccccccCCCC
Q 033276           70 IVDKCLKLFSS--PFPLVICIKSNHE   93 (123)
Q Consensus        70 vl~rC~gC~k~--~~~~~fCp~CG~~   93 (123)
                      ++ +|.-|+.+  ...-+.||+||.+
T Consensus         5 ~~-~C~vCG~i~~g~~P~~CPvCg~~   29 (37)
T d1nnqa2           5 VY-ICPICGYTAVDEAPEYCPVCGAP   29 (37)
T ss_dssp             EE-ECTTTCCEEESCCCSBCTTTCCB
T ss_pred             EE-ECCCCCCEecCCCCCcCCCCCCc
Confidence            45 89999988  3333789999987

>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=92.19  E-value=0.049  Score=32.04  Aligned_cols=25  Identities=12%  Similarity=0.050  Sum_probs=19.1

Q ss_pred             EEeeccccCCccc---ccCccccccCCCC
Q 033276           68 RYIVDKCLKLFSS---PFPLVICIKSNHE   93 (123)
Q Consensus        68 ~wvl~rC~gC~k~---~~~~~fCp~CG~~   93 (123)
                      .-.. +|.-|+.+   +..-+.||.||++
T Consensus         6 ~~~W-~C~~CGyi~~g~~aP~~CPvC~~p   33 (44)
T d1lkoa2           6 ATKW-RCRNCGYVHEGTGAPELCPACAHP   33 (44)
T ss_dssp             EEEE-EETTTCCEEEEEECCSBCTTTCCB
T ss_pred             CeEE-EcCCCCcEEECCCCCCcCCCCCCc
Confidence            3355 89999987   3334689999997

>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=92.08  E-value=0.04  Score=31.14  Aligned_cols=21  Identities=10%  Similarity=-0.151  Sum_probs=16.9

Q ss_pred             cccCCccc--ccCccccccCCCC
Q 033276           73 KCLKLFSS--PFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~--~~~~~fCp~CG~~   93 (123)
                      +|.-|+.+  ...-+.||+||.+
T Consensus         7 vC~vCGyi~~g~~Pe~CPvCg~~   29 (36)
T d1yuza2           7 LCPICGYIHKGEDFEKCPICFRP   29 (36)
T ss_dssp             ECSSSCCEEESSCCSBCTTTCCB
T ss_pred             ECCCCCCEeeCCCCCcCCCCCCc
Confidence            89999988  3334789999987

>d2apob1 g.41.16.1 (B:403-457) Ribosome biogenesis protein Nop10 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Nop10-like SnoRNP
family: Nucleolar RNA-binding protein Nop10-like
domain: Ribosome biogenesis protein Nop10
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=91.92  E-value=0.03  Score=34.47  Aligned_cols=20  Identities=30%  Similarity=0.354  Sum_probs=17.4

Q ss_pred             cccCCcccccCccccccCCCC
Q 033276           73 KCLKLFSSPFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~~~~~~fCp~CG~~   93 (123)
                      +|..|+.... +..||.||.+
T Consensus         6 kC~~C~~YTL-~~~CP~CG~~   25 (55)
T d2apob1           6 KCPKCGLYTL-KEICPKCGEK   25 (55)
T ss_dssp             ECTTTCCEES-SSBCSSSCSB
T ss_pred             eCCcccceec-cccCcCCCCc
Confidence            8999998744 5889999998

>d2ey4e1 g.41.16.1 (E:4-55) Ribosome biogenesis protein Nop10 {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Nop10-like SnoRNP
family: Nucleolar RNA-binding protein Nop10-like
domain: Ribosome biogenesis protein Nop10
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.62  E-value=0.039  Score=33.62  Aligned_cols=20  Identities=20%  Similarity=0.290  Sum_probs=17.2

Q ss_pred             cccCCcccccCccccccCCCC
Q 033276           73 KCLKLFSSPFPLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~~~~~~fCp~CG~~   93 (123)
                      +|..|+.... ++.||.||++
T Consensus         4 kC~~C~~YTL-~~~CP~CG~~   23 (52)
T d2ey4e1           4 KCPKCGRYTL-KEVCPVCGEK   23 (52)
T ss_dssp             ECTTTCCEES-SSBCTTTCCB
T ss_pred             cCCcccceec-cccCcCCCCc
Confidence            8999998744 5889999998

>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=85.12  E-value=0.2  Score=28.18  Aligned_cols=22  Identities=9%  Similarity=-0.200  Sum_probs=17.5

Q ss_pred             cccCCccc-----ccC--ccccccCCCCC
Q 033276           73 KCLKLFSS-----PFP--LVICIKSNHEI   94 (123)
Q Consensus        73 rC~gC~k~-----~~~--~~fCp~CG~~~   94 (123)
                      .|++|+++     .++  ...|.+||.++
T Consensus         4 vc~~cG~~Yh~~~~pPk~~g~CD~cg~~L   32 (37)
T d2ak3a2           4 IHPGSGRVYNIEFNPPKTMGIDDLTGEPL   32 (37)
T ss_dssp             EETTTTEEEETTTBCCSSTTBCTTTCCBC
T ss_pred             eeCCcCChhhhccCCccccCCccCCCCcC
Confidence            79999987     222  57899999995

>d1e4va2 g.41.2.1 (A:122-156) Microbial and mitochondrial ADK, insert "zinc finger" domain {Escherichia coli [TaxId: 562]}

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: Escherichia coli [TaxId: 562]

Probab=84.95  E-value=0.24  Score=27.43  Aligned_cols=22  Identities=5%  Similarity=-0.420  Sum_probs=17.4

Q ss_pred             cccCCccc-----cc--CccccccCCCCC
Q 033276           73 KCLKLFSS-----PF--PLVICIKSNHEI   94 (123)
Q Consensus        73 rC~gC~k~-----~~--~~~fCp~CG~~~   94 (123)
                      .|++|+++     .+  ....|..||.++
T Consensus         4 ~c~~cG~~Yh~~~~PPk~~g~CD~cg~~L   32 (35)
T d1e4va2           4 VHAPSGRVYHVKFNPPKVEGKDDVTGEEL   32 (35)
T ss_dssp             EETTTTEEEETTTBCCSSTTBCTTTCCBC
T ss_pred             CCcCcCChhhhccCccccCCcccCCCCEe
Confidence            69999986     22  257899999995

>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=80.53  E-value=0.46  Score=26.21  Aligned_cols=21  Identities=19%  Similarity=0.153  Sum_probs=16.6

Q ss_pred             cccCCccc-----cc--CccccccCCCC
Q 033276           73 KCLKLFSS-----PF--PLVICIKSNHE   93 (123)
Q Consensus        73 rC~gC~k~-----~~--~~~fCp~CG~~   93 (123)
                      .|+.|+++     .+  ....|..||.+
T Consensus         4 ~C~~CG~~Yh~~~~pPk~~g~CD~cG~~   31 (35)
T d1zina2           4 ICRNCGATYHLIFHPPAKPGVCDKCGGE   31 (35)
T ss_dssp             EETTTCCEEETTTBCCSSTTBCTTTCCB
T ss_pred             CCcCcCchhccccCCCCCCCcCCCCCCC
Confidence            68999986     12  25789999998