Psyllid ID: psy1204

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-
Protein Sequence
MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQESGN
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHcccccHHHHccEEEEEEccccccEEEEEEEEEccccccccccccEEcccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHcccccHHHcccEEEEEEcccccccEEEEEEEEEEccccccccccEccccccccccc
Coil and Loop (DISEMBL)
mdmtplwrqmdeeiastpmpeeyKNVILYVLCKDCHKESKVLYHIIGlkcehcgsyntcrikkpngqesgn
Flexible Loop (DISEMBL)
mdmtplwrQMDEeiastpmpeeYKNVILYVLCKDCHKESKVLYHIIGLKcehcgsyntcrikkpngqesgn
Low Complexity Region (SEG)
MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQESGN
Disordered region (IsUnstruct)
*********************EYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI**********
Disordered Region (DISOPRED)
MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC************
Disordered Region (DISEMBL)
MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQESGN
Disordered Region (DISPRO)
MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQESGN
Positional Conservation
no confident homologs detected

---

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	71	2.2.26 [Sep-21-2011]
Q9CR50	261	RING finger and CHY zinc	yes	N/A	0.816	0.222	0.568	5e-15
Q96PM5	261	RING finger and CHY zinc	yes	N/A	0.816	0.222	0.551	1e-14
O14099	425	Uncharacterized RING fing	yes	N/A	0.901	0.150	0.409	6e-07

>sp|Q9CR50|ZN363_MOUSE RING finger and CHY zinc finger domain-containing protein 1 OS=Mus musculus GN=Rchy1 PE=1 SV=1

 Score = 79.7 bits (195), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 33/58 (56%), Positives = 44/58 (75%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58
           +DMT  WRQ+D E+A TPMP EY+NV + +LC DC+  S V +HI+G+KC+ C SYNT
Sbjct: 191 LDMTRYWRQLDTEVAQTPMPSEYQNVTVDILCNDCNGRSTVQFHILGMKCKLCDSYNT 248

Mediates E3-dependent ubiquitination and proteasomal degradation of target proteins, including p53/TP53, HDAC1 and CDKN1B. Preferentially acts on tetrameric p53/TP53. Increases AR transcription factor activity (By similarity). Contributes to the regulation of CDKN1B and p53/TP53 levels, and thereby contributes to the regulation of the cell cycle progression.
Mus musculus (taxid: 10090)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q96PM5|ZN363_HUMAN RING finger and CHY zinc finger domain-containing protein 1 OS=Homo sapiens GN=RCHY1 PE=1 SV=1

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 45/58 (77%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNT 58
           +DMT  WRQ+D+E+A TPMP EY+N+ + +LC DC+  S V +HI+G+KC+ C SYNT
Sbjct: 191 LDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNT 248

Mediates E3-dependent ubiquitination and proteasomal degradation of target proteins, including p53/TP53, HDAC1 and CDKN1B. Preferentially acts on tetrameric p53/TP53. Contributes to the regulation of CDKN1B and p53/TP53 levels, and thereby contributes to the regulation of the cell cycle progression. Increases AR transcription factor activity.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|O14099|YERG_SCHPO Uncharacterized RING finger protein C2F3.16 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC2F3.16 PE=4 SV=1

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 27/66 (40%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC- 59
           +++  L+R +D EI   PMP  Y   I  + C DC+      YH +G KC  C SYNTC 
Sbjct: 317 INVNSLFRILDMEIERQPMPYPYNTWISTIRCNDCNSRCDTKYHFLGHKCNSCHSYNTCI 376

Query: 60  -RIKKP 64
             I KP
Sbjct: 377 SSIYKP 382

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

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	71
405974062	875	Tyrosine-protein kinase SYK [Crassostrea	0.957	0.077	0.573	1e-19
312377279	430	hypothetical protein AND_11479 [Anophele	0.873	0.144	0.645	3e-19
158300042	219	AGAP009258-PA [Anopheles gambiae str. PE	0.915	0.296	0.615	4e-19
170039223	360	vitellogenin [Culex quinquefasciatus] gi	0.873	0.172	0.645	5e-19
157110713	373	vitellogenin, putative [Aedes aegypti] g	0.873	0.166	0.645	6e-19
91086835	293	PREDICTED: similar to vitellogenin, puta	1.0	0.242	0.581	5e-18
48094508	278	PREDICTED: RING finger and CHY zinc fing	0.873	0.223	0.645	7e-18
340715599	278	PREDICTED: RING finger and CHY zinc fing	0.873	0.223	0.645	1e-17
350417974	278	PREDICTED: RING finger and CHY zinc fing	0.873	0.223	0.645	1e-17
307171009	367	RING finger and CHY zinc finger domain-c	0.873	0.168	0.645	2e-17

>gi|405974062|gb|EKC38732.1| Tyrosine-protein kinase SYK [Crassostrea gigas]

 Score =  100 bits (249), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/68 (57%), Positives = 56/68 (82%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
           +DM  +W+ +DEE++  PMPEEY+N  + +LCKDCH+ES+VL+H++GLKC+ CGSYNTCR
Sbjct: 738 LDMKEVWQNVDEEVSQCPMPEEYQNYYVQILCKDCHEESRVLFHVLGLKCQQCGSYNTCR 797

Query: 61  IKKPNGQE 68
            ++P G E
Sbjct: 798 TQEPEGAE 805

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|312377279|gb|EFR24148.1| hypothetical protein AND_11479 [Anopheles darlingi]

 Score = 99.0 bits (245), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 40/62 (64%), Positives = 51/62 (82%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
           MDM  LW  +D E+A+TPMP+EY+N I+ +LCKDCHKES V +H++GLKC HCG+YNTCR
Sbjct: 169 MDMNQLWEFLDAEVAATPMPKEYENYIVDILCKDCHKESTVKFHVVGLKCTHCGAYNTCR 228

Query: 61  IK 62
            K
Sbjct: 229 TK 230

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158300042|ref|XP_320050.4| AGAP009258-PA [Anopheles gambiae str. PEST] gi|157013810|gb|EAA15075.4| AGAP009258-PA [Anopheles gambiae str. PEST]

 Score = 99.0 bits (245), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 40/65 (61%), Positives = 50/65 (76%)

Query: 1  MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
          MDM  LW  +D E+A+TPMP+EY N  + +LCKDCHKES V +H++GLKC HCG+YNTCR
Sbjct: 2  MDMNQLWEYLDAEVAATPMPKEYANYFVDILCKDCHKESTVKFHVVGLKCTHCGAYNTCR 61

Query: 61 IKKPN 65
           K  N
Sbjct: 62 TKTKN 66

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170039223|ref|XP_001847442.1| vitellogenin [Culex quinquefasciatus] gi|167862812|gb|EDS26195.1| vitellogenin [Culex quinquefasciatus]

 Score = 98.2 bits (243), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 40/62 (64%), Positives = 51/62 (82%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
           MDM  LW  +D E+A+TPMP+EY+N I+ +LCKDCHKES V +H++GLKC HCG+YNTCR
Sbjct: 167 MDMNQLWEYLDSEVAATPMPKEYENYIVDILCKDCHKESTVKFHVVGLKCTHCGAYNTCR 226

Query: 61  IK 62
            K
Sbjct: 227 TK 228

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157110713|ref|XP_001651215.1| vitellogenin, putative [Aedes aegypti] gi|108878629|gb|EAT42854.1| AAEL005646-PA [Aedes aegypti]

 Score = 98.2 bits (243), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 40/62 (64%), Positives = 51/62 (82%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
           MDM  LW  +D E+A+TPMP+EY+N I+ +LCKDCHKES V +H++GLKC HCG+YNTCR
Sbjct: 196 MDMNQLWEYLDAEVAATPMPKEYENYIVDILCKDCHKESTVKFHVVGLKCSHCGAYNTCR 255

Query: 61  IK 62
            K
Sbjct: 256 TK 257

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91086835|ref|XP_974078.1| PREDICTED: similar to vitellogenin, putative [Tribolium castaneum] gi|270010454|gb|EFA06902.1| hypothetical protein TcasGA2_TC009851 [Tribolium castaneum]

 Score = 94.7 bits (234), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 43/74 (58%), Positives = 54/74 (72%), Gaps = 3/74 (4%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
           MDMT LW+ +D E+A TPMP +Y   ++ +LCKDCHKE  V +H+IG KC HCGSYNTCR
Sbjct: 195 MDMTQLWKYLDNEVAHTPMPPQYNCYLVQILCKDCHKEGTVKFHVIGCKCIHCGSYNTCR 254

Query: 61  IK---KPNGQESGN 71
           IK   KP+G+   N
Sbjct: 255 IKGPFKPSGRNRQN 268

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|48094508|ref|XP_392132.1| PREDICTED: RING finger and CHY zinc finger domain-containing protein 1-like [Apis mellifera] gi|380019216|ref|XP_003693509.1| PREDICTED: RING finger and CHY zinc finger domain-containing protein 1-like [Apis florea]

 Score = 94.4 bits (233), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 40/62 (64%), Positives = 53/62 (85%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
           +DMT LWR +D E++STPMPEEY++  + +LCKDCH+ES V +HI+GLKC +CGSYNTCR
Sbjct: 205 LDMTDLWRFLDMEVSSTPMPEEYRDYKVDILCKDCHEESTVKFHIVGLKCLNCGSYNTCR 264

Query: 61  IK 62
           +K
Sbjct: 265 VK 266

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340715599|ref|XP_003396298.1| PREDICTED: RING finger and CHY zinc finger domain-containing protein 1-like [Bombus terrestris]

 Score = 93.6 bits (231), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 40/62 (64%), Positives = 53/62 (85%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
           +DMT LW+ +D E++STPMPEEYK+  + +LCKDCH+ES V +HI+GLKC +CGSYNTCR
Sbjct: 205 LDMTDLWKFLDMEVSSTPMPEEYKDYKVDILCKDCHEESTVKFHIVGLKCLNCGSYNTCR 264

Query: 61  IK 62
           +K
Sbjct: 265 VK 266

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350417974|ref|XP_003491672.1| PREDICTED: RING finger and CHY zinc finger domain-containing protein 1-like [Bombus impatiens]

 Score = 93.6 bits (231), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 40/62 (64%), Positives = 53/62 (85%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
           +DMT LW+ +D E++STPMPEEYK+  + +LCKDCH+ES V +HI+GLKC +CGSYNTCR
Sbjct: 205 LDMTDLWKFLDMEVSSTPMPEEYKDYKVDILCKDCHEESTVKFHIVGLKCLNCGSYNTCR 264

Query: 61  IK 62
           +K
Sbjct: 265 VK 266

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307171009|gb|EFN63072.1| RING finger and CHY zinc finger domain-containing protein 1 [Camponotus floridanus]

 Score = 92.8 bits (229), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 40/62 (64%), Positives = 51/62 (82%)

Query: 1   MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
           +DMT LW+ +D E++ TPMPEEYK+    +LCKDCH+ES V +HI+GLKC +CGSYNTCR
Sbjct: 278 LDMTDLWKYLDTEVSLTPMPEEYKDYKADILCKDCHEESTVKFHIVGLKCLNCGSYNTCR 337

Query: 61  IK 62
           IK
Sbjct: 338 IK 339

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	71
UNIPROTKB|J9NZR5	259	RCHY1 "Uncharacterized protein	0.887	0.243	0.523	4.1e-17
MGI|MGI:1915348	261	Rchy1 "ring finger and CHY zin	0.845	0.229	0.55	2.9e-16
UNIPROTKB|E7EMC8	212	RCHY1 "RING finger and CHY zin	0.845	0.283	0.533	3.7e-16
UNIPROTKB|E7ETW5	239	RCHY1 "RING finger and CHY zin	0.845	0.251	0.533	3.7e-16
UNIPROTKB|J3KPI0	221	RCHY1 "RING finger and CHY zin	0.845	0.271	0.533	3.7e-16
UNIPROTKB|Q96PM5	261	RCHY1 "RING finger and CHY zin	0.845	0.229	0.533	3.7e-16
UNIPROTKB|F1P5N8	190	RCHY1 "Uncharacterized protein	0.845	0.315	0.5	4.7e-16
UNIPROTKB|F1RYV2	232	RCHY1 "Uncharacterized protein	0.845	0.258	0.533	4.7e-16
RGD|1359180	261	Rchy1 "ring finger and CHY zin	0.845	0.229	0.55	4.7e-16
UNIPROTKB|A4IFE2	261	RCHY1 "RCHY1 protein" [Bos tau	0.887	0.241	0.507	2e-15

UNIPROTKB|J9NZR5 RCHY1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 210 (79.0 bits), Expect = 4.1e-17, P = 4.1e-17
 Identities = 33/63 (52%), Positives = 48/63 (76%)

Query:     1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
             +DMT  WRQ+D+E+A TPMP EY+N+ + +LC DC++ S V +HI+G+KC  C SYNT +
Sbjct:   191 LDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNRRSTVQFHILGMKCNICESYNTAQ 250

Query:    61 IKK 63
              K+
Sbjct:   251 AKR 253

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1915348 Rchy1 "ring finger and CHY zinc finger domain containing 1" [Mus musculus (taxid:10090)]

 Score = 202 (76.2 bits), Expect = 2.9e-16, P = 2.9e-16
 Identities = 33/60 (55%), Positives = 45/60 (75%)

Query:     1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
             +DMT  WRQ+D E+A TPMP EY+NV + +LC DC+  S V +HI+G+KC+ C SYNT +
Sbjct:   191 LDMTRYWRQLDTEVAQTPMPSEYQNVTVDILCNDCNGRSTVQFHILGMKCKLCDSYNTAQ 250

GO:0000151 "ubiquitin ligase complex" evidence=ISO

GO:0002039 "p53 binding" evidence=ISO

GO:0004842 "ubiquitin-protein ligase activity" evidence=ISO

GO:0005102 "receptor binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0008270 "zinc ion binding" evidence=ISO

GO:0016567 "protein ubiquitination" evidence=ISO

GO:0016874 "ligase activity" evidence=IEA

GO:0031398 "positive regulation of protein ubiquitination" evidence=ISO

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=ISO

GO:0042787 "protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=ISO

GO:0042803 "protein homodimerization activity" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0051865 "protein autoubiquitination" evidence=ISO

UNIPROTKB|E7EMC8 RCHY1 "RING finger and CHY zinc finger domain-containing protein 1" [Homo sapiens (taxid:9606)]

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 32/60 (53%), Positives = 46/60 (76%)

Query:     1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
             +DMT  WRQ+D+E+A TPMP EY+N+ + +LC DC+  S V +HI+G+KC+ C SYNT +
Sbjct:   142 LDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNTAQ 201

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|E7ETW5 RCHY1 "RING finger and CHY zinc finger domain-containing protein 1" [Homo sapiens (taxid:9606)]

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 32/60 (53%), Positives = 46/60 (76%)

Query:     1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
             +DMT  WRQ+D+E+A TPMP EY+N+ + +LC DC+  S V +HI+G+KC+ C SYNT +
Sbjct:   169 LDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNTAQ 228

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|J3KPI0 RCHY1 "RING finger and CHY zinc finger domain-containing protein 1" [Homo sapiens (taxid:9606)]

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 32/60 (53%), Positives = 46/60 (76%)

Query:     1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
             +DMT  WRQ+D+E+A TPMP EY+N+ + +LC DC+  S V +HI+G+KC+ C SYNT +
Sbjct:   151 LDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNTAQ 210

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q96PM5 RCHY1 "RING finger and CHY zinc finger domain-containing protein 1" [Homo sapiens (taxid:9606)]

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 32/60 (53%), Positives = 46/60 (76%)

Query:     1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
             +DMT  WRQ+D+E+A TPMP EY+N+ + +LC DC+  S V +HI+G+KC+ C SYNT +
Sbjct:   191 LDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNTAQ 250

GO:0005102 "receptor binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0008270 "zinc ion binding" evidence=IDA

GO:0002039 "p53 binding" evidence=IPI

GO:0016567 "protein ubiquitination" evidence=IDA

GO:0051865 "protein autoubiquitination" evidence=IDA

GO:0000151 "ubiquitin ligase complex" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IPI

GO:0031398 "positive regulation of protein ubiquitination" evidence=IDA

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IDA

GO:0042787 "protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|F1P5N8 RCHY1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 30/60 (50%), Positives = 46/60 (76%)

Query:     1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
             +DM   WRQ+D+E+A TPMP EY+N+++ +LC DC+  S V +H++G+KC +C SYNT +
Sbjct:   122 LDMRRYWRQLDDEVAQTPMPSEYQNMMVEILCNDCNSRSTVQFHLLGMKCTNCESYNTAQ 181

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000151 "ubiquitin ligase complex" evidence=IEA

GO:0002039 "p53 binding" evidence=IEA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0031398 "positive regulation of protein ubiquitination" evidence=IEA

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0042787 "protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0051865 "protein autoubiquitination" evidence=IEA

UNIPROTKB|F1RYV2 RCHY1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 32/60 (53%), Positives = 45/60 (75%)

Query:     1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
             +DMT  WRQ+D+E+A TPMP EY+N+ + +LC DC+  S V +HI+G+KC  C SYNT +
Sbjct:   162 LDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCNICESYNTAQ 221

GO:0051865 "protein autoubiquitination" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0042787 "protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031398 "positive regulation of protein ubiquitination" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IEA

GO:0002039 "p53 binding" evidence=IEA

GO:0000151 "ubiquitin ligase complex" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

RGD|1359180 Rchy1 "ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase" [Rattus norvegicus (taxid:10116)]

 Score = 200 (75.5 bits), Expect = 4.7e-16, P = 4.7e-16
 Identities = 33/60 (55%), Positives = 45/60 (75%)

Query:     1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
             +DMT  WRQ+D E+A TPMP EY+NV + +LC DC+  S V +HI+G+KC+ C SYNT +
Sbjct:   191 LDMTRYWRQLDIEVAQTPMPSEYQNVTVDILCNDCNGRSTVQFHILGMKCKLCDSYNTAQ 250

GO:0000151 "ubiquitin ligase complex" evidence=IEA;ISO

GO:0002039 "p53 binding" evidence=IEA;ISO

GO:0004842 "ubiquitin-protein ligase activity" evidence=IEA;ISO

GO:0005102 "receptor binding" evidence=IPI

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA;ISO

GO:0016567 "protein ubiquitination" evidence=ISO

GO:0031398 "positive regulation of protein ubiquitination" evidence=IEA;ISO

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA;ISO

GO:0042787 "protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=IEA;ISO

GO:0042803 "protein homodimerization activity" evidence=IEA;ISO

GO:0051865 "protein autoubiquitination" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|A4IFE2 RCHY1 "RCHY1 protein" [Bos taurus (taxid:9913)]

 Score = 194 (73.4 bits), Expect = 2.0e-15, P = 2.0e-15
 Identities = 32/63 (50%), Positives = 45/63 (71%)

Query:     1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
             +DM+  WRQ D+E+A TPMP EY+N+ + +LC DC+  S V +HI+G+KC  C SYNT +
Sbjct:   191 LDMSRSWRQRDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCNICESYNTAQ 250

Query:    61 IKK 63
               K
Sbjct:   251 AGK 253

GO:0051865 "protein autoubiquitination" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0042787 "protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0031398 "positive regulation of protein ubiquitination" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IEA

GO:0002039 "p53 binding" evidence=IEA

GO:0000151 "ubiquitin ligase complex" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9CR50	ZN363_MOUSE	6, ., 3, ., 2, ., -	0.5689	0.8169	0.2222	yes	N/A
Q96PM5	ZN363_HUMAN	6, ., 3, ., 2, ., -	0.5517	0.8169	0.2222	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

No hit with e-value below 0.005

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	71
PF14599	61	zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.	100.0
KOG1940|consensus	276		99.77
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	98.75
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	98.72
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	98.7
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	98.65
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	98.64
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	98.57
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	98.39
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	98.19
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	97.37
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	96.91
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	96.69
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.67
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	96.65
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	96.62
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	96.6
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	96.25
PRK11823	446	DNA repair protein RadA; Provisional	96.18
cd01675	555	RNR_III Class III ribonucleotide reductase. Ribonu	96.02
PF13597	546	NRDD: Anaerobic ribonucleoside-triphosphate reduct	95.94
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	95.83
PF12172	37	DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35	95.65
COG1545	140	Predicted nucleic-acid-binding protein containing	94.75
PRK00415	59	rps27e 30S ribosomal protein S27e; Reviewed	94.54
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	93.92
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	93.78
PF10058	54	DUF2296: Predicted integral membrane metal-binding	93.7
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	93.63
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	93.59
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	93.58
PRK07111	735	anaerobic ribonucleoside triphosphate reductase; P	93.44
PRK09263	711	anaerobic ribonucleoside triphosphate reductase; P	93.44
PRK08271	623	anaerobic ribonucleoside triphosphate reductase; P	93.36
PRK08579	625	anaerobic ribonucleoside triphosphate reductase; P	93.02
COG1327	156	Predicted transcriptional regulator, consists of a	92.97
COG3357	97	Predicted transcriptional regulator containing an	92.93
TIGR02487	579	NrdD anaerobic ribonucleoside-triphosphate reducta	92.86
TIGR00244	147	transcriptional regulator NrdR. Members of this al	92.69
TIGR02827	586	RNR_anaer_Bdell anaerobic ribonucleoside-triphosph	92.6
PRK11788	389	tetratricopeptide repeat protein; Provisional	92.41
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	92.2
TIGR02159	146	PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subu	92.1
PRK14704	618	anaerobic ribonucleoside triphosphate reductase; P	92.1
TIGR01031	55	rpmF_bact ribosomal protein L32. This protein desc	92.09
PF10122	51	Mu-like_Com: Mu-like prophage protein Com; InterPr	92.06
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	91.91
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	91.05
KOG3507|consensus	62		90.89
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	90.83
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	90.66
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	90.53
smart00531	147	TFIIE Transcription initiation factor IIE.	90.38
PRK06266	178	transcription initiation factor E subunit alpha; V	90.19
PF14369	35	zf-RING_3: zinc-finger	90.03
PF09567	314	RE_MamI: MamI restriction endonuclease; InterPro:	89.98
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	89.63
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	89.49
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	88.84
PRK06260	397	threonine synthase; Validated	88.82
PF02701	63	zf-Dof: Dof domain, zinc finger; InterPro: IPR0038	88.8
PF09082	68	DUF1922: Domain of unknown function (DUF1922); Int	88.76
PLN00209	86	ribosomal protein S27; Provisional	88.75
PF13248	26	zf-ribbon_3: zinc-ribbon domain	88.53
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	88.48
PRK12496	164	hypothetical protein; Provisional	88.35
PTZ00083	85	40S ribosomal protein S27; Provisional	87.76
COG1198	730	PriA Primosomal protein N' (replication factor Y)	87.67
KOG2703|consensus	460		87.65
PRK06450	338	threonine synthase; Validated	87.63
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	87.31
PRK08270	656	anaerobic ribonucleoside triphosphate reductase; P	87.04
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	87.02
PF14952	44	zf-tcix: Putative treble-clef, zinc-finger, Zn-bin	86.89
PRK07591	421	threonine synthase; Validated	86.85
PF01783	56	Ribosomal_L32p: Ribosomal L32p protein family; Int	86.6
PHA00626	59	hypothetical protein	86.59
PF09332	344	Mcm10: Mcm10 replication factor; InterPro: IPR0154	86.4
COG1439	177	Predicted nucleic acid-binding protein, consists o	85.86
TIGR00595	505	priA primosomal protein N'. All proteins in this f	85.85
PRK12775	1006	putative trifunctional 2-polyprenylphenol hydroxyl	85.71
COG1675	176	TFA1 Transcription initiation factor IIE, alpha su	85.67
PF01667	55	Ribosomal_S27e: Ribosomal protein S27; InterPro: I	85.32
COG1096	188	Predicted RNA-binding protein (consists of S1 doma	85.3
PRK06393	64	rpoE DNA-directed RNA polymerase subunit E''; Vali	85.02
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	84.92
PF11023	114	DUF2614: Protein of unknown function (DUF2614); In	84.38
COG4416	60	Com Mu-like prophage protein Com [General function	84.28
TIGR00155	403	pqiA_fam integral membrane protein, PqiA family. T	84.12
PRK14892	99	putative transcription elongation factor Elf1; Pro	83.97
PF09845	131	DUF2072: Zn-ribbon containing protein (DUF2072); I	83.33
PRK01110	60	rpmF 50S ribosomal protein L32; Validated	83.19
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	82.93
PF07295	146	DUF1451: Protein of unknown function (DUF1451); In	81.99
PF06827	30	zf-FPG_IleRS: Zinc finger found in FPG and IleRS;	81.81
PF03367	161	zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004	81.6
COG3058	308	FdhE Uncharacterized protein involved in formate d	81.07
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	80.61
COG1328	700	NrdD Oxygen-sensitive ribonucleoside-triphosphate	80.37
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	80.37
PF14311	55	DUF4379: Domain of unknown function (DUF4379)	80.18

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

Probab=100.00  E-value=7.5e-36  Score=172.87  Aligned_cols=60  Identities=55%  Similarity=1.170  Sum_probs=22.2

Q ss_pred             CChHHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204           1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR   60 (71)
Q Consensus         1 ~dm~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~i   60 (71)
                      +||+.+|++||++|+++|||++|++++|.|+||||+++|.++||++||||++|+||||++
T Consensus         2 ~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT~q   61 (61)
T PF14599_consen    2 VDMSAYWRMLDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNTRQ   61 (61)
T ss_dssp             --------------------------EEEEEESSS--EEEEE--TT----TTTS---EEE
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCcccCC
Confidence            599999999999999999999999999999999999999999999999999999999985

>KOG1940|consensus

Probab=99.77  E-value=3.7e-19  Score=127.29  Aligned_cols=65  Identities=49%  Similarity=0.921  Sum_probs=62.2

Q ss_pred             CChHHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCC
Q psy1204           1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPN   65 (71)
Q Consensus         1 ~dm~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~   65 (71)
                      .||+.+|+++|++|+++|||++|+++.+.|+||||+..+.+.||++++||+.|+||||++++.+.
T Consensus       206 ~d~~~~~~~~d~~l~~~~~p~~y~~~~~~i~cndC~~~~~~k~~~l~~kc~~c~~~~~r~~~~~~  270 (276)
T KOG1940|consen  206 GDMSHYFRKLDKELAGSPMPEEYKNKTQDILCNDCGSGTNVKYHILYHKCGKCGSYNTRMISDPS  270 (276)
T ss_pred             HHHHHHHHHHHHHHhcCCCCchhhchhheeeccCCCCCCccceehhhhhCCCcccceeeeccCCC
Confidence            48999999999999999999999999999999999999999999999999999999999998544

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=98.75  E-value=1.2e-08  Score=64.83  Aligned_cols=57  Identities=12%  Similarity=0.179  Sum_probs=44.0

Q ss_pred             HHHHHHHcCCCCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCCC
Q psy1204           9 QMDEEIASTPMPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQ   67 (71)
Q Consensus         9 ~lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~~   67 (71)
                      .+|...+.+++--.   ....|+.++|++|+..+.+..+.+  .||.|||+++++++|++..
T Consensus        47 af~~~~~~t~~ega~L~I~~~p~~~~C~~Cg~~~~~~~~~~--~CP~Cgs~~~~i~~G~El~  106 (115)
T TIGR00100        47 AFEVVREGTVAEGAKLNIEDEPVECECEDCSEEVSPEIDLY--RCPKCHGIMLQVRAGKELN  106 (115)
T ss_pred             HHHHHhCCCccCCCEEEEEeeCcEEEcccCCCEEecCCcCc--cCcCCcCCCcEEecCCeEE
Confidence            34555556655222   446789999999999999877666  8999999999999999853

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.

>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=98.72  E-value=1.3e-08  Score=64.24  Aligned_cols=56  Identities=20%  Similarity=0.252  Sum_probs=38.7

Q ss_pred             HHHHHHHcCCCCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCC
Q psy1204           9 QMDEEIASTPMPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNG   66 (71)
Q Consensus         9 ~lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~   66 (71)
                      .++...+.++.-..   ....|+..+|++||+.|.+..+.+  .||.|||++.++++|++.
T Consensus        47 ~f~~~~~~T~~e~a~L~Ie~~p~~~~C~~Cg~~~~~~~~~~--~CP~Cgs~~~~i~~G~el  105 (113)
T PF01155_consen   47 AFEVLAEGTILEGAELEIEEVPARARCRDCGHEFEPDEFDF--SCPRCGSPDVEIISGREL  105 (113)
T ss_dssp             HHHHHHCCSTTTT-EEEEEEE--EEEETTTS-EEECHHCCH--H-SSSSSS-EEEEESS-E
T ss_pred             HHHHHhCCCCccCCEEEEEecCCcEECCCCCCEEecCCCCC--CCcCCcCCCcEEccCCeE
Confidence            44555556655333   346689999999999999988776  899999999999999975

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.

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=98.70  E-value=1e-08  Score=64.99  Aligned_cols=56  Identities=14%  Similarity=0.106  Sum_probs=43.1

Q ss_pred             HHHHHHcCCCCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCCC
Q psy1204          10 MDEEIASTPMPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQ   67 (71)
Q Consensus        10 lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~~   67 (71)
                      +|...+.+++--.   -...|+.++|++|++.+.+..+++  .||.|||+++.+++|+|..
T Consensus        48 f~~~~~~T~~egA~L~I~~vp~~~~C~~Cg~~~~~~~~~~--~CP~Cgs~~~~i~~G~El~  106 (113)
T PRK12380         48 FEIVCHGTVAQGCDLHIVYKPAQAWCWDCSQVVEIHQHDA--QCPHCHGERLRVDTGDSLI  106 (113)
T ss_pred             HHHHhCCCccCCCEEEEEeeCcEEEcccCCCEEecCCcCc--cCcCCCCCCcEEccCCeEE
Confidence            4445555654322   335688999999999999887666  7999999999999999853

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=98.65  E-value=3.5e-08  Score=62.60  Aligned_cols=57  Identities=12%  Similarity=0.166  Sum_probs=43.0

Q ss_pred             HHHHHHHcCCCCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCC
Q psy1204           9 QMDEEIASTPMPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNG   66 (71)
Q Consensus         9 ~lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~   66 (71)
                      .+|...+.+++--.   ....|+..+|++|++.+....+.+. .||.|||+++++++|++.
T Consensus        47 ~f~~~~~~t~~egA~L~i~~~p~~~~C~~Cg~~~~~~~~~~~-~CP~Cgs~~~~i~~G~El  106 (114)
T PRK03681         47 CFDLVCRGTVAEGCKLHLEEQEAECWCETCQQYVTLLTQRVR-RCPQCHGDMLRIVADDGL  106 (114)
T ss_pred             HHHHHhCCCccCCCEEEEEeeCcEEEcccCCCeeecCCccCC-cCcCcCCCCcEEccCCeE
Confidence            44555556655322   3456899999999999988765522 899999999999999985

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=98.64  E-value=3.4e-08  Score=62.89  Aligned_cols=58  Identities=19%  Similarity=0.217  Sum_probs=42.8

Q ss_pred             HHHHHHHcCC-CCHh---hhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCCC
Q psy1204           9 QMDEEIASTP-MPEE---YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQ   67 (71)
Q Consensus         9 ~lD~~i~~~p-mP~~---y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~~   67 (71)
                      .+|...+.+| +.-.   ....|+.++|++||..+.+..+.+. .||.|||+++++++|++..
T Consensus        47 af~~~~~~T~~~ega~L~Ie~vp~~~~C~~Cg~~~~~~~~~~~-~CP~Cgs~~~~i~~G~El~  108 (117)
T PRK00564         47 AFETFREESLVCKDAILDIVDEKVELECKDCSHVFKPNALDYG-VCEKCHSKNVIITQGNEMR  108 (117)
T ss_pred             HHHHHhcCCcccCCCEEEEEecCCEEEhhhCCCccccCCccCC-cCcCCCCCceEEecCCEEE
Confidence            4455556663 3221   3466899999999999988754332 7999999999999998853

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=98.57  E-value=8.6e-08  Score=62.36  Aligned_cols=57  Identities=19%  Similarity=0.385  Sum_probs=41.4

Q ss_pred             HHHHHHHcCCCCHh---hhcceeeEEcCCCCCceeec---------------------eEeecccCCCCCCcceeeecCC
Q psy1204           9 QMDEEIASTPMPEE---YKNVILYVLCKDCHKESKVL---------------------YHIIGLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus         9 ~lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~---------------------~h~~g~kCp~C~Synt~ii~g~   64 (71)
                      .++...+.+++-..   ....++..+|++||..+.+.                     ..++  .||.|||+++++++|+
T Consensus        47 afe~l~~gt~~ega~L~i~~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~CP~Cgs~~~~i~~G~  124 (135)
T PRK03824         47 ALNELLKGTILEGAEIIFEEEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFL--KCPKCGSRDFEIVKGR  124 (135)
T ss_pred             HHHHHHcCCcccCCEEEEEecceEEECCCCCCEEecccccccccccccccccccccccccCc--CCcCCCCCCcEEecCc
Confidence            34444455655331   33567899999999999876                     3333  8999999999999998


Q ss_pred             CCC
Q psy1204          65 NGQ   67 (71)
Q Consensus        65 ~~~   67 (71)
                      +..
T Consensus       125 el~  127 (135)
T PRK03824        125 GVY  127 (135)
T ss_pred             eEE
Confidence            853

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

Probab=98.39  E-value=2.2e-07  Score=59.62  Aligned_cols=40  Identities=25%  Similarity=0.340  Sum_probs=36.7

Q ss_pred             cceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCC
Q psy1204          25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNG   66 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~   66 (71)
                      ..|+.++|.+|+..++...|.+  .||.|+|.+.+|++|++.
T Consensus        66 ~~p~~~~C~~C~~~~~~e~~~~--~CP~C~s~~~~i~~G~el  105 (115)
T COG0375          66 EEPAECWCLDCGQEVELEELDY--RCPKCGSINLRIIGGDEL  105 (115)
T ss_pred             EeccEEEeccCCCeecchhhee--ECCCCCCCceEEecCCee
Confidence            5689999999999999999888  699999999999999875

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=98.19  E-value=1.1e-06  Score=56.44  Aligned_cols=57  Identities=16%  Similarity=0.247  Sum_probs=39.4

Q ss_pred             HHHHHHcCCCCHh---hhcceeeEEcCCCCCceeec-e----EeecccCCCCCCcceeeecCCCCC
Q psy1204          10 MDEEIASTPMPEE---YKNVILYVLCKDCHKESKVL-Y----HIIGLKCEHCGSYNTCRIKKPNGQ   67 (71)
Q Consensus        10 lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~-~----h~~g~kCp~C~Synt~ii~g~~~~   67 (71)
                      +|...+.+++--.   ....++..+| +|++.|... +    +.+...||.|||+++.+++|++..
T Consensus        48 f~~~~~gT~~egA~L~I~~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~El~  112 (124)
T PRK00762         48 LDVLAEGTIAEDADLIVEMIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGRECN  112 (124)
T ss_pred             HHHHhCCCCcCCCEEEEEecCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCCeEE
Confidence            3444455554322   3456899999 999997654 1    111237999999999999999864

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=97.37  E-value=0.00035  Score=38.02  Aligned_cols=36  Identities=19%  Similarity=0.358  Sum_probs=26.3

Q ss_pred             eEEcCCCCCceeeceEe---ecccCCCCCCcce-eeecCC
Q psy1204          29 YVLCKDCHKESKVLYHI---IGLKCEHCGSYNT-CRIKKP   64 (71)
Q Consensus        29 ~i~CndC~~~s~v~~h~---~g~kCp~C~Synt-~ii~g~   64 (71)
                      ..+|.+||.+|++....   ....||.|||.++ ++++..
T Consensus         5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s~~   44 (52)
T TIGR02605         5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLSAV   44 (52)
T ss_pred             EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEeccc
Confidence            57899999999875421   1237999999776 677643

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.

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

Probab=96.91  E-value=0.0011  Score=35.59  Aligned_cols=32  Identities=22%  Similarity=0.392  Sum_probs=24.7

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC   59 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~   59 (71)
                      ....|.+||..++.....-..+||.||+.-..
T Consensus         2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~   33 (46)
T PRK00398          2 AEYKCARCGREVELDEYGTGVRCPYCGYRILF   33 (46)
T ss_pred             CEEECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence            46889999999987665424499999986653

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=96.69  E-value=0.0027  Score=32.60  Aligned_cols=34  Identities=26%  Similarity=0.385  Sum_probs=23.8

Q ss_pred             eeEEcCCCCCceeeceE---eecccCCCCCCcceeee
Q psy1204          28 LYVLCKDCHKESKVLYH---IIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h---~~g~kCp~C~Synt~ii   61 (71)
                      -..+|.+||+.|++..-   .....||.||+.-.+++
T Consensus         4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~r~~   40 (41)
T smart00834        4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGDVRRLI   40 (41)
T ss_pred             EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCcceecc
Confidence            36789999999986542   22348999999444443

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.

>TIGR00416 sms DNA repair protein RadA

Probab=96.67  E-value=0.00097  Score=50.49  Aligned_cols=32  Identities=28%  Similarity=0.577  Sum_probs=25.8

Q ss_pred             ceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      .+....|..||.++..   |+| +||.|++|||-+-
T Consensus         4 ~~~~y~C~~Cg~~~~~---~~g-~Cp~C~~w~t~~~   35 (454)
T TIGR00416         4 AKSKFVCQHCGADSPK---WQG-KCPACHAWNTITE   35 (454)
T ss_pred             CCCeEECCcCCCCCcc---ccE-ECcCCCCccccch
Confidence            3567899999986543   666 9999999999875

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

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

Probab=96.65  E-value=0.0012  Score=50.57  Aligned_cols=34  Identities=29%  Similarity=0.589  Sum_probs=27.3

Q ss_pred             ceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecC
Q psy1204          26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKK   63 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g   63 (71)
                      .+....|+.||.+|   -.|+| |||.|+.|||-+-..
T Consensus         4 ~~t~f~C~~CG~~s---~KW~G-kCp~Cg~Wns~vE~~   37 (456)
T COG1066           4 KKTAFVCQECGYVS---PKWLG-KCPACGAWNTLVEEV   37 (456)
T ss_pred             cccEEEcccCCCCC---ccccc-cCCCCCCccceEEee
Confidence            34678999999855   45899 999999999977543

>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=96.62  E-value=0.0034  Score=33.25  Aligned_cols=31  Identities=29%  Similarity=0.518  Sum_probs=22.8

Q ss_pred             eEEcCCCCCceeeceE---eecccCCCCCCccee
Q psy1204          29 YVLCKDCHKESKVLYH---IIGLKCEHCGSYNTC   59 (71)
Q Consensus        29 ~i~CndC~~~s~v~~h---~~g~kCp~C~Synt~   59 (71)
                      ...|.+||..|++...   .....||.||+-+++
T Consensus         5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~   38 (42)
T PF09723_consen    5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR   38 (42)
T ss_pred             EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence            5789999999986432   234589999995543

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.

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=96.60  E-value=0.0017  Score=35.11  Aligned_cols=28  Identities=21%  Similarity=0.673  Sum_probs=22.1

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGSY   56 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~Sy   56 (71)
                      +...|.+||.+++... ....+||.||+.
T Consensus         1 ~~Y~C~~Cg~~~~~~~-~~~irC~~CG~r   28 (44)
T smart00659        1 MIYICGECGRENEIKS-KDVVRCRECGYR   28 (44)
T ss_pred             CEEECCCCCCEeecCC-CCceECCCCCce
Confidence            3578999999998874 344599999874

present in RNA polymerase I, II and III

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

Probab=96.25  E-value=0.0031  Score=35.04  Aligned_cols=30  Identities=27%  Similarity=0.663  Sum_probs=24.8

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSY   56 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy   56 (71)
                      .....|..||++++...-.-+..||.|||-
T Consensus         4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r   33 (49)
T COG1996           4 MMEYKCARCGREVELDQETRGIRCPYCGSR   33 (49)
T ss_pred             eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence            568899999999986666666799999874

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.18  E-value=0.0028  Score=47.86  Aligned_cols=31  Identities=32%  Similarity=0.768  Sum_probs=25.3

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      +....|..||.++.   .|+| +||.|++|||-+-
T Consensus         5 ~~~y~C~~Cg~~~~---~~~g-~Cp~C~~w~t~~e   35 (446)
T PRK11823          5 KTAYVCQECGAESP---KWLG-RCPECGAWNTLVE   35 (446)
T ss_pred             CCeEECCcCCCCCc---ccCe-eCcCCCCccceee
Confidence            56789999998554   3666 9999999999865

>cd01675 RNR_III Class III ribonucleotide reductase

Probab=96.02  E-value=0.0073  Score=46.85  Aligned_cols=53  Identities=23%  Similarity=0.330  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204           4 TPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus         4 ~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~   62 (71)
                      +.+++.++......-++-. -+.++. .|++||....    ..+.+||.|||.++.++.
T Consensus       495 ~al~~lv~~a~~~~~~y~~-~~~p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~~  547 (555)
T cd01675         495 EALEALVKKAAKRGVIYFG-INTPID-ICNDCGYIGE----GEGFKCPKCGSEDVEVIS  547 (555)
T ss_pred             HHHHHHHHHHHHcCCceEE-EecCCc-cCCCCCCCCc----CCCCCCcCCCCcCceEEE
Confidence            3455555554444344433 345667 9999998554    223499999999877664

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

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

Probab=95.94  E-value=0.0073  Score=46.83  Aligned_cols=54  Identities=22%  Similarity=0.214  Sum_probs=26.6

Q ss_pred             hHHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204           3 MTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus         3 m~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~   62 (71)
                      .+.+++.++.......+|-. .-.+..-.|++||.....   ..  +||.|||.|+.+++
T Consensus       466 ~~al~~lv~~~~~~~~i~Y~-~in~~~~~C~~CG~~~~~---~~--~CP~CGs~~~~~~~  519 (546)
T PF13597_consen  466 PEALEKLVRYAMENTGIPYF-TINPPIDICPDCGYIGGE---GD--KCPKCGSENIEVYS  519 (546)
T ss_dssp             HHHHHHHHHHHHH--H-SEE-EEE--EEEETTT---S-----EE--E-CCC----EEEEB
T ss_pred             HHHHHHHHHHHHHhCCCCeE-EEecCcccccCCCcCCCC---CC--CCCCCCCcccceEE
Confidence            34566666666665666654 223567789999986543   23  89999999988875

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=95.83  E-value=0.0043  Score=46.02  Aligned_cols=27  Identities=37%  Similarity=0.853  Sum_probs=22.6

Q ss_pred             EcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          31 LCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        31 ~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      .|.+||.++.   .|+| +||.|++|||-+-
T Consensus         2 ~c~~cg~~~~---~~~g-~cp~c~~w~~~~e   28 (372)
T cd01121           2 VCSECGYVSP---KWLG-KCPECGEWNTLVE   28 (372)
T ss_pred             CCCCCCCCCC---CccE-ECcCCCCceeeee
Confidence            5999998554   4777 9999999999875

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

>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=95.65  E-value=0.012  Score=30.10  Aligned_cols=30  Identities=30%  Similarity=0.538  Sum_probs=15.5

Q ss_pred             cceeeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204          25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNT   58 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt   58 (71)
                      .+-+.-+|.+||...-.+.    ..||+|+|.+.
T Consensus         7 ~~l~~~rC~~Cg~~~~pPr----~~Cp~C~s~~l   36 (37)
T PF12172_consen    7 GRLLGQRCRDCGRVQFPPR----PVCPHCGSDEL   36 (37)
T ss_dssp             T-EEEEE-TTT--EEES------SEETTTT----
T ss_pred             CEEEEEEcCCCCCEecCCC----cCCCCcCcccc
Confidence            3467889999998654444    28999999775

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.

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

Probab=94.75  E-value=0.062  Score=35.04  Aligned_cols=28  Identities=29%  Similarity=0.485  Sum_probs=23.2

Q ss_pred             cceeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204          25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSY   56 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy   56 (71)
                      .+-+-.+|++||+.+-.+..    .||+|+|-
T Consensus        25 ~kl~g~kC~~CG~v~~PPr~----~Cp~C~~~   52 (140)
T COG1545          25 GKLLGTKCKKCGRVYFPPRA----YCPKCGSE   52 (140)
T ss_pred             CcEEEEEcCCCCeEEcCCcc----cCCCCCCC
Confidence            45678999999988776664    89999999

>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed

Probab=94.54  E-value=0.054  Score=31.16  Aligned_cols=41  Identities=27%  Similarity=0.455  Sum_probs=28.8

Q ss_pred             hcceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204          24 KNVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        24 ~~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~   64 (71)
                      +...+.+.|+||+.+..+..|-- -.+|..||..=.+=.+|+
T Consensus         6 ~S~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGK   47 (59)
T PRK00415          6 RSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGK   47 (59)
T ss_pred             CCeEEEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcc
Confidence            45588999999999998765521 228999987655444443

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

Probab=93.92  E-value=0.075  Score=31.28  Aligned_cols=45  Identities=29%  Similarity=0.484  Sum_probs=31.1

Q ss_pred             CHhhhcceeeEEcCCCCCceeeceEe-ecccCCCCCCcceeeecCC
Q psy1204          20 PEEYKNVILYVLCKDCHKESKVLYHI-IGLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        20 P~~y~~~~v~i~CndC~~~s~v~~h~-~g~kCp~C~Synt~ii~g~   64 (71)
                      |.+-+...+.+.|.||+.+..+..|- ...+|..||..=.+=.+|+
T Consensus        10 p~~p~s~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~PTGGk   55 (67)
T COG2051          10 PKEPRSRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEPTGGK   55 (67)
T ss_pred             cCCCCceEEEEECCCCCCEEEEeccCceEEEecccccEEEecCCCe
Confidence            43446678999999999998875542 1238999987655544443

>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=93.78  E-value=0.027  Score=35.65  Aligned_cols=32  Identities=19%  Similarity=0.222  Sum_probs=22.8

Q ss_pred             eeeEEcCCCCCceee-ceEeecccCCCCCCcceee
Q psy1204          27 ILYVLCKDCHKESKV-LYHIIGLKCEHCGSYNTCR   60 (71)
Q Consensus        27 ~v~i~CndC~~~s~v-~~h~~g~kCp~C~Synt~i   60 (71)
                      -..-.|..||++|.- +..-+  .||+||..-...
T Consensus         7 GtKR~Cp~CG~kFYDLnk~Pi--vCP~CG~~~~~~   39 (108)
T PF09538_consen    7 GTKRTCPSCGAKFYDLNKDPI--VCPKCGTEFPPE   39 (108)
T ss_pred             CCcccCCCCcchhccCCCCCc--cCCCCCCccCcc
Confidence            356679999999974 44444  899998754433

The function of members of this family is unknown.

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

Probab=93.70  E-value=0.12  Score=28.89  Aligned_cols=45  Identities=18%  Similarity=0.454  Sum_probs=30.5

Q ss_pred             HHHHHHHHcCCCCHhhhcceeeEEcCCCCCcee------eceEeecccCCCCCCcc
Q psy1204           8 RQMDEEIASTPMPEEYKNVILYVLCKDCHKESK------VLYHIIGLKCEHCGSYN   57 (71)
Q Consensus         8 ~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~------v~~h~~g~kCp~C~Syn   57 (71)
                      +.||.++..-|+.+.-   +..+.|..|....-      ..+..+  +||+|+..|
T Consensus         4 ki~d~L~G~d~~~~~~---r~aLIC~~C~~hNGla~~~~~~~i~y--~C~~Cg~~N   54 (54)
T PF10058_consen    4 KILDVLLGDDPTSPSN---RYALICSKCFSHNGLAPKEEFEEIQY--RCPYCGALN   54 (54)
T ss_pred             HHHHHHhCCCCccccC---ceeEECcccchhhcccccccCCceEE--EcCCCCCcC
Confidence            5688888888844442   33455999986542      233444  999999876

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=93.63  E-value=0.088  Score=26.72  Aligned_cols=28  Identities=21%  Similarity=0.610  Sum_probs=19.4

Q ss_pred             eEEcCCCCCceeece-----EeecccCCCCCCc
Q psy1204          29 YVLCKDCHKESKVLY-----HIIGLKCEHCGSY   56 (71)
Q Consensus        29 ~i~CndC~~~s~v~~-----h~~g~kCp~C~Sy   56 (71)
                      .+.|..|++.+.+..     .-.-..||.|++.
T Consensus         2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~   34 (38)
T TIGR02098         2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV   34 (38)
T ss_pred             EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence            578999999887652     1111389999864

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

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=93.59  E-value=0.058  Score=27.79  Aligned_cols=27  Identities=22%  Similarity=0.642  Sum_probs=19.5

Q ss_pred             eEEcCCCCCceeeceE-----eecccCCCCCC
Q psy1204          29 YVLCKDCHKESKVLYH-----IIGLKCEHCGS   55 (71)
Q Consensus        29 ~i~CndC~~~s~v~~h-----~~g~kCp~C~S   55 (71)
                      .|.|..|+..+.++.-     -.-.+|++|+.
T Consensus         2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~   33 (37)
T PF13719_consen    2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGH   33 (37)
T ss_pred             EEECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence            6889999999976432     22348999975

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=93.58  E-value=0.091  Score=29.75  Aligned_cols=31  Identities=29%  Similarity=0.586  Sum_probs=23.3

Q ss_pred             ceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      .+..+.|..||..  ...|.   .|+.||.|+-+++
T Consensus        24 ~~~l~~C~~CG~~--~~~H~---vC~~CG~Y~gr~v   54 (57)
T PRK12286         24 APGLVECPNCGEP--KLPHR---VCPSCGYYKGREV   54 (57)
T ss_pred             CCcceECCCCCCc--cCCeE---ECCCCCcCCCEEe
Confidence            3667899999962  23343   6999999998875

>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=93.44  E-value=0.1  Score=42.04  Aligned_cols=43  Identities=26%  Similarity=0.336  Sum_probs=28.4

Q ss_pred             HHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204          14 IASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus        14 i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~   62 (71)
                      +..+.||.. .-.+-.-.|++||.....  |   .+||.|||.++.+++
T Consensus       666 ~~~~~i~Y~-sin~~~~~C~~CG~~~~~--~---~~CP~CG~~~~~~~~  708 (735)
T PRK07111        666 MKNTNIGYG-SINHPVDRCPVCGYLGVI--E---DKCPKCGSTNIQRIR  708 (735)
T ss_pred             HHhCCCceE-EeCCCCeecCCCCCCCCc--C---ccCcCCCCccceeee
Confidence            444556654 223557789999965542  2   399999998776664

>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=93.44  E-value=0.048  Score=43.73  Aligned_cols=31  Identities=19%  Similarity=0.454  Sum_probs=21.6

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYN   57 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Syn   57 (71)
                      +..-.|++||.+.+....-.+..||.|||.+
T Consensus       639 ~~~~~C~~CG~~Ge~~~~~~~~~CP~CG~~~  669 (711)
T PRK09263        639 TPIDECYECGFTGEFECTEKGFTCPKCGNHD  669 (711)
T ss_pred             CCCcccCCCCCCccccCCCCCCcCcCCCCCC
Confidence            4567899999865442222234999999977

>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=93.36  E-value=0.059  Score=42.76  Aligned_cols=52  Identities=23%  Similarity=0.347  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204           4 TPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus         4 ~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      +.+++.++... .+.+|-. .-.+..-.|++||.....    .+..||.|||.++.++
T Consensus       543 eal~~lv~~~~-~~~i~Yf-~in~~~~iC~~CG~~~~g----~~~~CP~CGs~~~ev~  594 (623)
T PRK08271        543 EGYRKLLNIAA-KTGCNYF-AFNVKITICNDCHHIDKR----TGKRCPICGSENIDYY  594 (623)
T ss_pred             HHHHHHHHHHH-HcCCceE-EeCCCCccCCCCCCcCCC----CCcCCcCCCCcchhHH
Confidence            34455555443 3556655 223567789999975322    2249999999886654

>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=93.02  E-value=0.055  Score=42.91  Aligned_cols=43  Identities=19%  Similarity=0.329  Sum_probs=28.5

Q ss_pred             HcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204          15 ASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus        15 ~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~   62 (71)
                      ..+.+|-. .-.+..-.|.+||.+....    +..||.|||.++.+++
T Consensus       555 ~~~~i~Y~-~inp~~~~C~~CG~~~~g~----~~~CP~CGs~~~~v~~  597 (625)
T PRK08579        555 MNTKLVYW-SYTPAITVCNKCGRSTTGL----YTRCPRCGSEDVEVWS  597 (625)
T ss_pred             HhcCCceE-EeCCCCccCCCCCCccCCC----CCcCcCCCCchhHHHH
Confidence            34555544 2236788999999855222    2399999998766553

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

Probab=92.97  E-value=0.068  Score=36.01  Aligned_cols=21  Identities=33%  Similarity=0.645  Sum_probs=17.3

Q ss_pred             ccCCCCCCcceeeecCCCCCC
Q psy1204          48 LKCEHCGSYNTCRIKKPNGQE   68 (71)
Q Consensus        48 ~kCp~C~Synt~ii~g~~~~~   68 (71)
                      ++||+|++.+|+|++-+...+
T Consensus         1 M~CPfC~~~~tkViDSR~~ed   21 (156)
T COG1327           1 MKCPFCGHEDTKVIDSRPAEE   21 (156)
T ss_pred             CCCCCCCCCCCeeeecccccc
Confidence            489999999999998665443

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

Probab=92.93  E-value=0.041  Score=34.39  Aligned_cols=32  Identities=22%  Similarity=0.232  Sum_probs=22.6

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNT   58 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt   58 (71)
                      ..-..|++||.+|.....-.--.||.|.|.-.
T Consensus        56 v~Pa~CkkCGfef~~~~ik~pSRCP~CKSE~I   87 (97)
T COG3357          56 VRPARCKKCGFEFRDDKIKKPSRCPKCKSEWI   87 (97)
T ss_pred             ecChhhcccCccccccccCCcccCCcchhhcc
Confidence            34568999999997643332238999999643

>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase

Probab=92.86  E-value=0.11  Score=40.74  Aligned_cols=52  Identities=21%  Similarity=0.236  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204           5 PLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus         5 ~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~   62 (71)
                      .+...++..... .|+.. .-.+..-.|++||......  .  .+||.|||.++.+++
T Consensus       502 al~~lv~~a~~~-~i~Y~-~~n~~~~~C~~CG~~g~~~--~--~~CP~Cgs~~~~~~~  553 (579)
T TIGR02487       502 ALKDITKKAMKN-GIGYF-GINPPVDVCEDCGYTGEGL--N--DKCPKCGSHDIEVIS  553 (579)
T ss_pred             HHHHHHHHHHhc-CCceE-EeccCCccCCCCCCCCCCC--C--CcCcCCCCccceehh
Confidence            334444443333 25544 1224567899999733321  1  399999998876664

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.

>TIGR00244 transcriptional regulator NrdR

Probab=92.69  E-value=0.085  Score=35.22  Aligned_cols=20  Identities=20%  Similarity=0.375  Sum_probs=16.7

Q ss_pred             ccCCCCCCcceeeecCCCCC
Q psy1204          48 LKCEHCGSYNTCRIKKPNGQ   67 (71)
Q Consensus        48 ~kCp~C~Synt~ii~g~~~~   67 (71)
                      ++||+|++.+|+|++-+...
T Consensus         1 M~CP~C~~~dtkViDSR~~~   20 (147)
T TIGR00244         1 MHCPFCQHHNTRVLDSRLVE   20 (147)
T ss_pred             CCCCCCCCCCCEeeeccccC
Confidence            48999999999999865543

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

>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase

Probab=92.60  E-value=0.17  Score=39.99  Aligned_cols=51  Identities=24%  Similarity=0.269  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204           6 LWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus         6 ~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~   62 (71)
                      .++.++.. +...+|-. .-.+..-.|++||..  ...|..  .||.|||.++.+++
T Consensus       511 ~~~lv~~~-~~~~i~Y~-tin~~~siC~~CGy~--~g~~~~--~CP~CGs~~~ev~s  561 (586)
T TIGR02827       511 YRKLLRVA-ADTGCNYF-CFNIKITICNDCHHI--DKRTLH--RCPVCGSANIDYGT  561 (586)
T ss_pred             HHHHHHHH-HhcCCceE-EeCCCCeecCCCCCc--CCCcCC--cCcCCCCccceEEE
Confidence            34444443 33456655 223567789999972  222333  99999998766653

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.

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=92.41  E-value=0.14  Score=35.98  Aligned_cols=27  Identities=19%  Similarity=0.609  Sum_probs=19.3

Q ss_pred             EEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204          30 VLCKDCHKESKVLYHIIGLKCEHCGSYNTCR   60 (71)
Q Consensus        30 i~CndC~~~s~v~~h~~g~kCp~C~Synt~i   60 (71)
                      -.|..||.++.  .+.+  .||.|+|++|-.
T Consensus       355 ~~c~~cg~~~~--~~~~--~c~~c~~~~~~~  381 (389)
T PRK11788        355 YRCRNCGFTAR--TLYW--HCPSCKAWETIK  381 (389)
T ss_pred             EECCCCCCCCc--ccee--ECcCCCCccCcC
Confidence            34999986443  2233  999999999854

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=92.20  E-value=0.13  Score=26.46  Aligned_cols=27  Identities=19%  Similarity=0.621  Sum_probs=19.4

Q ss_pred             eEEcCCCCCceeec-----eEeecccCCCCCC
Q psy1204          29 YVLCKDCHKESKVL-----YHIIGLKCEHCGS   55 (71)
Q Consensus        29 ~i~CndC~~~s~v~-----~h~~g~kCp~C~S   55 (71)
                      .|.|..|+.++.++     ....-.+|+.|+-
T Consensus         2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~   33 (36)
T PF13717_consen    2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH   33 (36)
T ss_pred             EEECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence            68899999999763     2233348999974

>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit

Probab=92.10  E-value=0.08  Score=34.93  Aligned_cols=15  Identities=33%  Similarity=0.762  Sum_probs=13.7

Q ss_pred             ccCCCCCCcceeeec
Q psy1204          48 LKCEHCGSYNTCRIK   62 (71)
Q Consensus        48 ~kCp~C~Synt~ii~   62 (71)
                      ..||+|||.||++++
T Consensus       106 ~~cp~c~s~~t~~~s  120 (146)
T TIGR02159       106 VQCPRCGSADTTITS  120 (146)
T ss_pred             CcCCCCCCCCcEeec
Confidence            499999999999986

Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.

>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=92.10  E-value=0.12  Score=40.96  Aligned_cols=38  Identities=18%  Similarity=0.266  Sum_probs=25.1

Q ss_pred             HHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204          14 IASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYN   57 (71)
Q Consensus        14 i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Syn   57 (71)
                      +..+.||.. .-.+..-.|++||...+.   ..  +||.|||.+
T Consensus       545 ~~~~~i~Y~-sin~~~~~C~~CGy~g~~---~~--~CP~CG~~d  582 (618)
T PRK14704        545 MAEHGVGYG-SINHPVDRCKCCSYHGVI---GN--ECPSCGNED  582 (618)
T ss_pred             HHhcCCceE-EeCCCCeecCCCCCCCCc---Cc--cCcCCCCCC
Confidence            334556655 123567789999985442   23  999999976

>TIGR01031 rpmF_bact ribosomal protein L32

Probab=92.09  E-value=0.15  Score=28.55  Aligned_cols=30  Identities=30%  Similarity=0.671  Sum_probs=22.6

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      +..+.|..||.  ....|.   .|+.||.|+-+++
T Consensus        24 p~l~~C~~cG~--~~~~H~---vc~~cG~Y~gr~v   53 (55)
T TIGR01031        24 PTLVVCPNCGE--FKLPHR---VCPSCGYYKGRQV   53 (55)
T ss_pred             CcceECCCCCC--cccCee---ECCccCeECCEEc
Confidence            56788999996  333343   6999999997765

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

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

Probab=92.06  E-value=0.069  Score=29.92  Aligned_cols=33  Identities=24%  Similarity=0.479  Sum_probs=22.2

Q ss_pred             eEEcCCCCCceee--ceEeecccCCCCCCcceeee
Q psy1204          29 YVLCKDCHKESKV--LYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        29 ~i~CndC~~~s~v--~~h~~g~kCp~C~Synt~ii   61 (71)
                      .|+|..|++.--.  .+..+-.|||.|+..|.--.
T Consensus         4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a   38 (51)
T PF10122_consen    4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA   38 (51)
T ss_pred             ceeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence            5899999964321  23334449999999986543

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=91.91  E-value=0.06  Score=45.32  Aligned_cols=27  Identities=33%  Similarity=0.582  Sum_probs=22.2

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNT   58 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt   58 (71)
                      ..-+|.|||+.++-.  ..  +||.|||.|+
T Consensus       693 tIKrC~dcg~q~~~~--~~--~cP~Cgs~~v  719 (1187)
T COG1110         693 TIKRCRDCGEQFVDS--ED--KCPRCGSRNV  719 (1187)
T ss_pred             HHHHHhhcCceeccc--cc--cCCCCCCccc
Confidence            356899999988766  33  9999999887

>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=91.05  E-value=0.21  Score=25.33  Aligned_cols=27  Identities=22%  Similarity=0.327  Sum_probs=19.0

Q ss_pred             eEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204          29 YVLCKDCHKESKVLYHIIGLKCEHCGSYN   57 (71)
Q Consensus        29 ~i~CndC~~~s~v~~h~~g~kCp~C~Syn   57 (71)
                      .-.|..||.......---  +||.||+..
T Consensus         2 ~~~C~~CG~i~~g~~~p~--~CP~Cg~~~   28 (34)
T cd00729           2 VWVCPVCGYIHEGEEAPE--KCPICGAPK   28 (34)
T ss_pred             eEECCCCCCEeECCcCCC--cCcCCCCch
Confidence            357999998765443233  999998754

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.

>KOG3507|consensus

Probab=90.89  E-value=0.13  Score=29.77  Aligned_cols=38  Identities=18%  Similarity=0.492  Sum_probs=26.8

Q ss_pred             cCCCCHhh--hcceeeEEcCCCCCceeeceEeecccCCCCC
Q psy1204          16 STPMPEEY--KNVILYVLCKDCHKESKVLYHIIGLKCEHCG   54 (71)
Q Consensus        16 ~~pmP~~y--~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~   54 (71)
                      .++.|...  +...+...|-||+++-++..-... .|..||
T Consensus         5 ~s~~~~aa~~r~~~miYiCgdC~~en~lk~~D~i-rCReCG   44 (62)
T KOG3507|consen    5 TSLGDPAAGPRTATMIYICGDCGQENTLKRGDVI-RCRECG   44 (62)
T ss_pred             cCCCCccCCCCcccEEEEeccccccccccCCCcE-ehhhcc
Confidence            34444432  446899999999999887653332 899997

>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=90.83  E-value=0.12  Score=26.21  Aligned_cols=24  Identities=25%  Similarity=0.750  Sum_probs=16.9

Q ss_pred             EcCCCCCceeeceEeecccCCCCCC
Q psy1204          31 LCKDCHKESKVLYHIIGLKCEHCGS   55 (71)
Q Consensus        31 ~CndC~~~s~v~~h~~g~kCp~C~S   55 (71)
                      .|.+|+.++...... ..+|+.||.
T Consensus         2 ~C~~Cg~~~~~~~~~-~irC~~CG~   25 (32)
T PF03604_consen    2 ICGECGAEVELKPGD-PIRCPECGH   25 (32)
T ss_dssp             BESSSSSSE-BSTSS-TSSBSSSS-
T ss_pred             CCCcCCCeeEcCCCC-cEECCcCCC
Confidence            589999999866533 349999985

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 ....

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=90.66  E-value=0.19  Score=33.57  Aligned_cols=19  Identities=26%  Similarity=0.614  Sum_probs=15.6

Q ss_pred             ccCCCCCCcceeeecCCCC
Q psy1204          48 LKCEHCGSYNTCRIKKPNG   66 (71)
Q Consensus        48 ~kCp~C~Synt~ii~g~~~   66 (71)
                      ++||+||+..|.+++-...
T Consensus         1 m~cp~c~~~~~~~~~s~~~   19 (154)
T PRK00464          1 MRCPFCGHPDTRVIDSRPA   19 (154)
T ss_pred             CcCCCCCCCCCEeEecccc
Confidence            4899999999999976543

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

Probab=90.53  E-value=0.19  Score=25.12  Aligned_cols=26  Identities=19%  Similarity=0.294  Sum_probs=18.7

Q ss_pred             EEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204          30 VLCKDCHKESKVLYHIIGLKCEHCGSYN   57 (71)
Q Consensus        30 i~CndC~~~s~v~~h~~g~kCp~C~Syn   57 (71)
                      -.|..||..........  +||.|++..
T Consensus         2 ~~C~~CGy~y~~~~~~~--~CP~Cg~~~   27 (33)
T cd00350           2 YVCPVCGYIYDGEEAPW--VCPVCGAPK   27 (33)
T ss_pred             EECCCCCCEECCCcCCC--cCcCCCCcH
Confidence            46999998765544344  999998743

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.

>smart00531 TFIIE Transcription initiation factor IIE

Probab=90.38  E-value=0.15  Score=33.16  Aligned_cols=30  Identities=27%  Similarity=0.681  Sum_probs=21.1

Q ss_pred             eeeEEcCCCCCceeec---eEe--ec-ccCCCCCCc
Q psy1204          27 ILYVLCKDCHKESKVL---YHI--IG-LKCEHCGSY   56 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~---~h~--~g-~kCp~C~Sy   56 (71)
                      .....|..|+.+++..   ...  -+ ..||.||..
T Consensus        97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~  132 (147)
T smart00531       97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEE  132 (147)
T ss_pred             CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence            5688999999998752   222  00 399999864

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=90.19  E-value=0.2  Score=33.87  Aligned_cols=33  Identities=18%  Similarity=0.541  Sum_probs=23.9

Q ss_pred             cceeeEEcCCCCCceee---ceEeecccCCCCCCccee
Q psy1204          25 NVILYVLCKDCHKESKV---LYHIIGLKCEHCGSYNTC   59 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v---~~h~~g~kCp~C~Synt~   59 (71)
                      ....-..|..|+.+++.   -.+.|  .||.||+.=..
T Consensus       113 ~~~~~Y~Cp~C~~rytf~eA~~~~F--~Cp~Cg~~L~~  148 (178)
T PRK06266        113 ENNMFFFCPNCHIRFTFDEAMEYGF--RCPQCGEMLEE  148 (178)
T ss_pred             cCCCEEECCCCCcEEeHHHHhhcCC--cCCCCCCCCee
Confidence            34578889999999874   23444  99999986443

>PF14369 zf-RING_3: zinc-finger

Probab=90.03  E-value=0.36  Score=24.70  Aligned_cols=32  Identities=13%  Similarity=0.243  Sum_probs=20.9

Q ss_pred             eEEcCCCCCceeeceEeecc-cCCCCCCcceee
Q psy1204          29 YVLCKDCHKESKVLYHIIGL-KCEHCGSYNTCR   60 (71)
Q Consensus        29 ~i~CndC~~~s~v~~h~~g~-kCp~C~Synt~i   60 (71)
                      ...|..|.+...+.-+.... .||.|+|--++.
T Consensus         2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEe   34 (35)
T PF14369_consen    2 RYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEE   34 (35)
T ss_pred             CEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEe
Confidence            35799999877653221222 499999876654

>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV

Probab=89.98  E-value=0.14  Score=37.40  Aligned_cols=32  Identities=28%  Similarity=0.424  Sum_probs=23.2

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~   62 (71)
                      ...-.|++||.  .|...-.  .||.|+|-|....+
T Consensus        80 DQl~~C~~CGa--~V~~~e~--~Cp~C~StnI~r~D  111 (314)
T PF09567_consen   80 DQLGKCNNCGA--NVSRLEE--SCPNCGSTNIKRKD  111 (314)
T ss_pred             hhhhhhccccc--eeeehhh--cCCCCCcccccccC
Confidence            34568999986  4444333  99999999987653

All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=89.63  E-value=0.18  Score=33.09  Aligned_cols=28  Identities=7%  Similarity=-0.096  Sum_probs=21.0

Q ss_pred             eeEEcCCCCCceee-ceEeecccCCCCCCcc
Q psy1204          28 LYVLCKDCHKESKV-LYHIIGLKCEHCGSYN   57 (71)
Q Consensus        28 v~i~CndC~~~s~v-~~h~~g~kCp~C~Syn   57 (71)
                      ..-.|..||++|.- +..-+  .||+||..-
T Consensus         8 tKr~Cp~cg~kFYDLnk~p~--vcP~cg~~~   36 (129)
T TIGR02300         8 TKRICPNTGSKFYDLNRRPA--VSPYTGEQF   36 (129)
T ss_pred             ccccCCCcCccccccCCCCc--cCCCcCCcc
Confidence            45679999999974 44445  999998754

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=89.49  E-value=0.29  Score=32.40  Aligned_cols=31  Identities=13%  Similarity=0.398  Sum_probs=23.1

Q ss_pred             ceeeEEcCCCCCceee---ceEeecccCCCCCCcce
Q psy1204          26 VILYVLCKDCHKESKV---LYHIIGLKCEHCGSYNT   58 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v---~~h~~g~kCp~C~Synt   58 (71)
                      ...-..|..|+.+++.   -.+.|  .||.||+.-.
T Consensus       106 ~~~~Y~Cp~c~~r~tf~eA~~~~F--~Cp~Cg~~L~  139 (158)
T TIGR00373       106 NNMFFICPNMCVRFTFNEAMELNF--TCPRCGAMLD  139 (158)
T ss_pred             CCCeEECCCCCcEeeHHHHHHcCC--cCCCCCCEee
Confidence            3577889999998863   33445  9999998643

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

>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=88.84  E-value=0.23  Score=23.96  Aligned_cols=21  Identities=33%  Similarity=0.724  Sum_probs=13.2

Q ss_pred             EcCCCCCceeeceEeecccCCCCCC
Q psy1204          31 LCKDCHKESKVLYHIIGLKCEHCGS   55 (71)
Q Consensus        31 ~CndC~~~s~v~~h~~g~kCp~C~S   55 (71)
                      .|.+|+++-.+..  -  .||+||-
T Consensus         2 ~CP~C~~~V~~~~--~--~Cp~CG~   22 (26)
T PF10571_consen    2 TCPECGAEVPESA--K--FCPHCGY   22 (26)
T ss_pred             cCCCCcCCchhhc--C--cCCCCCC
Confidence            4788877443332  2  8888874

Several members are annotated as putative helicases.

>PRK06260 threonine synthase; Validated

Probab=88.82  E-value=0.29  Score=36.21  Aligned_cols=26  Identities=31%  Similarity=0.692  Sum_probs=21.0

Q ss_pred             eEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204          29 YVLCKDCHKESKVLYHIIGLKCEHCGSY   56 (71)
Q Consensus        29 ~i~CndC~~~s~v~~h~~g~kCp~C~Sy   56 (71)
                      ...|..||.++......+  .||.|++.
T Consensus         3 ~~~C~~cg~~~~~~~~~~--~Cp~cg~~   28 (397)
T PRK06260          3 WLKCIECGKEYDPDEIIY--TCPECGGL   28 (397)
T ss_pred             EEEECCCCCCCCCCCccc--cCCCCCCe
Confidence            578999999987665445  89999874

>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.80  E-value=0.22  Score=28.99  Aligned_cols=14  Identities=43%  Similarity=0.622  Sum_probs=11.8

Q ss_pred             ccCCCCCCcceeee
Q psy1204          48 LKCEHCGSYNTCRI   61 (71)
Q Consensus        48 ~kCp~C~Synt~ii   61 (71)
                      ++||.|+|.||+--
T Consensus         6 ~~CPRC~S~nTKFc   19 (63)
T PF02701_consen    6 LPCPRCDSTNTKFC   19 (63)
T ss_pred             CCCCCcCCCCCEEE
Confidence            49999999999753

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent

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

Probab=88.76  E-value=0.24  Score=29.20  Aligned_cols=26  Identities=31%  Similarity=0.539  Sum_probs=18.6

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGS   55 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~S   55 (71)
                      ++++| |||..+.+..-.-..+| .||.
T Consensus         2 lifrC-~Cgr~lya~e~~kTkkC-~CG~   27 (68)
T PF09082_consen    2 LIFRC-DCGRYLYAKEGAKTKKC-VCGK   27 (68)
T ss_dssp             EEEEE-TTS--EEEETT-SEEEE-TTTE
T ss_pred             EEEEe-cCCCEEEecCCcceeEe-cCCC
Confidence            67899 99999888776667799 8864

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

>PLN00209 ribosomal protein S27; Provisional

Probab=88.75  E-value=0.61  Score=28.66  Aligned_cols=41  Identities=17%  Similarity=0.344  Sum_probs=28.0

Q ss_pred             hcceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204          24 KNVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        24 ~~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~   64 (71)
                      +...+.+.|.+|+....+..|-- -..|..|+..=.+=.+|.
T Consensus        31 nS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGK   72 (86)
T PLN00209         31 NSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGK   72 (86)
T ss_pred             CCEEEEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCC
Confidence            34578999999999998865421 128999987654444443

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=88.53  E-value=0.15  Score=24.25  Aligned_cols=22  Identities=27%  Similarity=0.781  Sum_probs=14.8

Q ss_pred             EEcCCCCCceeeceEeecccCCCCCC
Q psy1204          30 VLCKDCHKESKVLYHIIGLKCEHCGS   55 (71)
Q Consensus        30 i~CndC~~~s~v~~h~~g~kCp~C~S   55 (71)
                      ++|..||+.  +....-  -||+||.
T Consensus         3 ~~Cp~Cg~~--~~~~~~--fC~~CG~   24 (26)
T PF13248_consen    3 MFCPNCGAE--IDPDAK--FCPNCGA   24 (26)
T ss_pred             CCCcccCCc--CCcccc--cChhhCC
Confidence            578999983  333333  7999985

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

Probab=88.48  E-value=0.26  Score=28.31  Aligned_cols=26  Identities=23%  Similarity=0.566  Sum_probs=15.8

Q ss_pred             eeeEEcCCCCCcee-------eceEeecccCCCCC
Q psy1204          27 ILYVLCKDCHKESK-------VLYHIIGLKCEHCG   54 (71)
Q Consensus        27 ~v~i~CndC~~~s~-------v~~h~~g~kCp~C~   54 (71)
                      -+...|.+||+.-.       ...+.|  +||.||
T Consensus        23 ~~~F~CPnCG~~~I~RC~~CRk~~~~Y--~CP~CG   55 (59)
T PRK14890         23 AVKFLCPNCGEVIIYRCEKCRKQSNPY--TCPKCG   55 (59)
T ss_pred             cCEeeCCCCCCeeEeechhHHhcCCce--ECCCCC
Confidence            46777888876511       123444  788886

>PRK12496 hypothetical protein; Provisional

Probab=88.35  E-value=0.33  Score=32.38  Aligned_cols=28  Identities=36%  Similarity=0.551  Sum_probs=20.4

Q ss_pred             EEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204          30 VLCKDCHKESKVLYHIIGLKCEHCGSYNTC   59 (71)
Q Consensus        30 i~CndC~~~s~v~~h~~g~kCp~C~Synt~   59 (71)
                      ..|..|++.+...+-.-  -||.|||.-.+
T Consensus       128 ~~C~gC~~~~~~~~~~~--~C~~CG~~~~r  155 (164)
T PRK12496        128 KVCKGCKKKYPEDYPDD--VCEICGSPVKR  155 (164)
T ss_pred             EECCCCCccccCCCCCC--cCCCCCChhhh
Confidence            55999999887654223  79999986433

>PTZ00083 40S ribosomal protein S27; Provisional

Probab=87.76  E-value=0.78  Score=28.14  Aligned_cols=41  Identities=20%  Similarity=0.329  Sum_probs=28.0

Q ss_pred             hcceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204          24 KNVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        24 ~~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~   64 (71)
                      +...+.+.|.+|+...++..|-- -..|..|+..=.+=.+|+
T Consensus        30 nS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGK   71 (85)
T PTZ00083         30 NSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGK   71 (85)
T ss_pred             CCeEEEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCC
Confidence            34478999999999998865421 128888876554444443

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

Probab=87.67  E-value=0.4  Score=38.90  Aligned_cols=29  Identities=21%  Similarity=0.466  Sum_probs=18.6

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      -...|+-||....++.     .||.|||...+-.
T Consensus       461 ~~L~CH~Cg~~~~~p~-----~Cp~Cgs~~L~~~  489 (730)
T COG1198         461 GQLRCHYCGYQEPIPQ-----SCPECGSEHLRAV  489 (730)
T ss_pred             CeeEeCCCCCCCCCCC-----CCCCCCCCeeEEe
Confidence            4566666666555544     7899998854433

>KOG2703|consensus

Probab=87.65  E-value=0.23  Score=38.19  Aligned_cols=44  Identities=30%  Similarity=0.582  Sum_probs=32.7

Q ss_pred             eeeEEcCCCCCceee-------ce----EeecccCCCCCCcceeeecCCCCCCCC
Q psy1204          27 ILYVLCKDCHKESKV-------LY----HIIGLKCEHCGSYNTCRIKKPNGQESG   70 (71)
Q Consensus        27 ~v~i~CndC~~~s~v-------~~----h~~g~kCp~C~Synt~ii~g~~~~~~~   70 (71)
                      .+...|..|+...+.       +|    ......|||||--|+.+-.+.+-|.+|
T Consensus        37 EvES~Cm~Cg~nG~TRlllT~IP~fREvVimSF~CpHCG~kN~eiQ~a~~iQ~~G   91 (460)
T KOG2703|consen   37 EVESLCMNCGENGTTRLLLTSIPYFREVVIMSFECPHCGHKNNEIQSAEEIQEGG   91 (460)
T ss_pred             HHHHhhhhcccCCceeEEEeecchhheeeeEEeecCccCCccccccchhccccCc
Confidence            457789999988552       11    112238999999999999988888776

>PRK06450 threonine synthase; Validated

Probab=87.63  E-value=0.34  Score=35.37  Aligned_cols=26  Identities=35%  Similarity=0.902  Sum_probs=19.8

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGSY   56 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~Sy   56 (71)
                      |..+|.+||+++.... .+  .||.|++.
T Consensus         2 ~~~~C~~Cg~~~~~~~-~~--~C~~cg~~   27 (338)
T PRK06450          2 VKEVCMKCGKERESIY-EI--RCKKCGGP   27 (338)
T ss_pred             ceeEECCcCCcCCCcc-cc--cCCcCCCE
Confidence            5679999999986532 23  89999864

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=87.31  E-value=0.23  Score=23.24  Aligned_cols=21  Identities=29%  Similarity=0.727  Sum_probs=13.6

Q ss_pred             EcCCCCCceeeceEeecccCCCCCC
Q psy1204          31 LCKDCHKESKVLYHIIGLKCEHCGS   55 (71)
Q Consensus        31 ~CndC~~~s~v~~h~~g~kCp~C~S   55 (71)
                      +|..||++-.....    -||.||.
T Consensus         1 ~Cp~CG~~~~~~~~----fC~~CG~   21 (23)
T PF13240_consen    1 YCPNCGAEIEDDAK----FCPNCGT   21 (23)
T ss_pred             CCcccCCCCCCcCc----chhhhCC
Confidence            47888876554332    4888875

>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional

Probab=87.04  E-value=0.77  Score=36.69  Aligned_cols=48  Identities=15%  Similarity=0.158  Sum_probs=27.7

Q ss_pred             HHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204           7 WRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus         7 ~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      .+.++.....+.+|-. .-.+-.-.|++||...  ..   +..||.||+. +.+.
T Consensus       605 ~~lv~~~~~~~~i~Y~-~in~~~~~C~~CG~~~--g~---~~~CP~CG~~-~~v~  652 (656)
T PRK08270        605 KKLVKKALENYRLPYI-TITPTFSICPKHGYLS--GE---HEFCPKCGEE-TEVY  652 (656)
T ss_pred             HHHHHHHHHhCCCceE-EeCCCCcccCCCCCcC--CC---CCCCcCCcCc-cceE
Confidence            3333433334456655 1225567899999732  22   2499999975 5443

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

Probab=87.02  E-value=0.4  Score=22.91  Aligned_cols=6  Identities=50%  Similarity=1.647  Sum_probs=4.4

Q ss_pred             cCCCCC
Q psy1204          49 KCEHCG   54 (71)
Q Consensus        49 kCp~C~   54 (71)
                      +||.||
T Consensus        18 ~CPnCG   23 (24)
T PF07754_consen   18 PCPNCG   23 (24)
T ss_pred             eCCCCC
Confidence            777775

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

>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding

Probab=86.89  E-value=0.29  Score=26.61  Aligned_cols=11  Identities=55%  Similarity=1.343  Sum_probs=9.5

Q ss_pred             cCCCCCCccee
Q psy1204          49 KCEHCGSYNTC   59 (71)
Q Consensus        49 kCp~C~Synt~   59 (71)
                      |||+||.||-.
T Consensus        13 kCp~CGt~NG~   23 (44)
T PF14952_consen   13 KCPKCGTYNGT   23 (44)
T ss_pred             cCCcCcCccCc
Confidence            99999999943

>PRK07591 threonine synthase; Validated

Probab=86.85  E-value=0.44  Score=35.70  Aligned_cols=27  Identities=22%  Similarity=0.387  Sum_probs=21.6

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYN   57 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~Syn   57 (71)
                      ...+|..||+++..... +  .||.|++.=
T Consensus        17 ~~l~C~~Cg~~~~~~~~-~--~C~~cg~~l   43 (421)
T PRK07591         17 VALKCRECGAEYPLGPI-H--VCEECFGPL   43 (421)
T ss_pred             eEEEeCCCCCcCCCCCC-c--cCCCCCCeE
Confidence            46899999999987654 4  999998743

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

Probab=86.60  E-value=0.51  Score=26.31  Aligned_cols=30  Identities=27%  Similarity=0.595  Sum_probs=21.4

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      +....|..||.-..  .|   +.|+.||-|+.+++
T Consensus        24 ~~l~~c~~cg~~~~--~H---~vc~~cG~y~~r~v   53 (56)
T PF01783_consen   24 PNLVKCPNCGEPKL--PH---RVCPSCGYYKGRQV   53 (56)
T ss_dssp             TSEEESSSSSSEES--TT---SBCTTTBBSSSSSS
T ss_pred             cceeeeccCCCEec--cc---EeeCCCCeECCEEE
Confidence            45789999995222  22   37999999987764

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....

>PHA00626 hypothetical protein

Probab=86.59  E-value=0.42  Score=27.41  Aligned_cols=34  Identities=18%  Similarity=0.328  Sum_probs=20.9

Q ss_pred             EcCCCCCceeec-------eEeecccCCCCCCcceeeecCCCC
Q psy1204          31 LCKDCHKESKVL-------YHIIGLKCEHCGSYNTCRIKKPNG   66 (71)
Q Consensus        31 ~CndC~~~s~v~-------~h~~g~kCp~C~Synt~ii~g~~~   66 (71)
                      .|.+||+...+.       ...|  +|+.||=..|.-.-|+-|
T Consensus         2 ~CP~CGS~~Ivrcg~cr~~snrY--kCkdCGY~ft~~~~~~~~   42 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRGWSDDY--VCCDCGYNDSKDAFGERG   42 (59)
T ss_pred             CCCCCCCceeeeeceecccCcce--EcCCCCCeechhhhhhcc
Confidence            477787754332       2344  888888777766555443

>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []

Probab=86.40  E-value=0.49  Score=35.32  Aligned_cols=33  Identities=30%  Similarity=0.621  Sum_probs=12.0

Q ss_pred             eEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          29 YVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        29 ~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      .+.|.+|++.+..-+.+-...|++||+.+-+.+
T Consensus       285 FFkC~~C~~Rt~sl~r~P~~~C~~Cg~~~wer~  317 (344)
T PF09332_consen  285 FFKCKDCGNRTISLERLPKKHCSNCGSSKWERT  317 (344)
T ss_dssp             EEE-T-TS-EEEESSSS--S--TTT-S---EEE
T ss_pred             eEECCCCCCeeeecccCCCCCCCcCCcCceeeh
Confidence            456666666655434344456666666655444

; PDB: 2KWQ_A.

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

Probab=85.86  E-value=0.44  Score=32.67  Aligned_cols=26  Identities=23%  Similarity=0.364  Sum_probs=20.8

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSY   56 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy   56 (71)
                      .-.+.|..|.+.|+.+.    ..||.|||.
T Consensus       137 ~w~~rC~GC~~~f~~~~----~~Cp~CG~~  162 (177)
T COG1439         137 KWRLRCHGCKRIFPEPK----DFCPICGSP  162 (177)
T ss_pred             eeeEEEecCceecCCCC----CcCCCCCCc
Confidence            34788999999998333    289999998

>TIGR00595 priA primosomal protein N'

Probab=85.85  E-value=0.56  Score=36.03  Aligned_cols=12  Identities=33%  Similarity=0.805  Sum_probs=8.7

Q ss_pred             cCCCCCCcceee
Q psy1204          49 KCEHCGSYNTCR   60 (71)
Q Consensus        49 kCp~C~Synt~i   60 (71)
                      .||.|+|...+-
T Consensus       255 ~Cp~C~s~~l~~  266 (505)
T TIGR00595       255 TCPQCGSEDLVY  266 (505)
T ss_pred             CCCCCCCCeeEe
Confidence            788898866443

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).

>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional

Probab=85.71  E-value=0.39  Score=39.82  Aligned_cols=41  Identities=24%  Similarity=0.359  Sum_probs=30.3

Q ss_pred             cceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCC
Q psy1204          25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNG   66 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~   66 (71)
                      ...+.-+|.||++.+...-.-|+ .||.||..-.-+-.|...
T Consensus       817 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~  857 (1006)
T PRK12775        817 TSELQWRCDDCGKVSEGFAFPYG-MCPACGGKLQALDRRKVE  857 (1006)
T ss_pred             CcceeeehhhhccccccccCCcC-cCcccccchhhhhccCcc
Confidence            34567899999999987776666 999999875554444443

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

Probab=85.67  E-value=0.3  Score=33.36  Aligned_cols=49  Identities=18%  Similarity=0.341  Sum_probs=29.8

Q ss_pred             HHHHHHcCCCCHhhhcceeeEEcCCCCCceeece-EeecccCCCCCCcce
Q psy1204          10 MDEEIASTPMPEEYKNVILYVLCKDCHKESKVLY-HIIGLKCEHCGSYNT   58 (71)
Q Consensus        10 lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~-h~~g~kCp~C~Synt   58 (71)
                      +.+.+.....--++-....-..|+.|+.+++... .-++..||.|||-=.
T Consensus        94 ~~~~le~Lk~~le~~~~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~  143 (176)
T COG1675          94 KRKILEKLKRKLEKETENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDLE  143 (176)
T ss_pred             HHHHHHHHHHHHHhhccCCceeCCCCCCcccHHHHHHhCCCCCCCCchhh
Confidence            3344444444444444456788999998876432 233349999998543

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

Probab=85.32  E-value=1.5  Score=24.79  Aligned_cols=39  Identities=23%  Similarity=0.389  Sum_probs=23.1

Q ss_pred             ceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204          26 VILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~   64 (71)
                      ..+.+.|.+|+....+..|-- -..|..|+..=.+=.+|+
T Consensus         4 ~Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGGK   43 (55)
T PF01667_consen    4 YFMDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGGK   43 (55)
T ss_dssp             -EEEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SSS
T ss_pred             cEEEEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCcC
Confidence            468899999999998755421 128999987655555554

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

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

Probab=85.30  E-value=1.2  Score=30.88  Aligned_cols=35  Identities=26%  Similarity=0.665  Sum_probs=27.1

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcceeeecC
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKK   63 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g   63 (71)
                      -+..+|..|+..=......+  +||.||-..+|-++-
T Consensus       147 VI~A~CsrC~~~L~~~~~~l--~Cp~Cg~tEkRKia~  181 (188)
T COG1096         147 VIYARCSRCRAPLVKKGNML--KCPNCGNTEKRKIAK  181 (188)
T ss_pred             EEEEEccCCCcceEEcCcEE--ECCCCCCEEeeeecc
Confidence            46789999997665544445  999999988887764

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

Probab=85.02  E-value=0.44  Score=27.76  Aligned_cols=25  Identities=28%  Similarity=0.583  Sum_probs=17.4

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNT   58 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt   58 (71)
                      ...-|.+|+...+      ...||.|||.+|
T Consensus         4 ~~~AC~~C~~i~~------~~~Cp~Cgs~~~   28 (64)
T PRK06393          4 QYRACKKCKRLTP------EKTCPVHGDEKT   28 (64)
T ss_pred             hhhhHhhCCcccC------CCcCCCCCCCcC
Confidence            3456888986442      228999999874

>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=84.92  E-value=0.42  Score=23.58  Aligned_cols=26  Identities=23%  Similarity=0.503  Sum_probs=13.4

Q ss_pred             EcCCCCCceeeceEeecccCCCCCCc
Q psy1204          31 LCKDCHKESKVLYHIIGLKCEHCGSY   56 (71)
Q Consensus        31 ~CndC~~~s~v~~h~~g~kCp~C~Sy   56 (71)
                      +|.-||.......--....||.|+..
T Consensus         5 fC~~CG~~t~~~~~g~~r~C~~Cg~~   30 (32)
T PF09297_consen    5 FCGRCGAPTKPAPGGWARRCPSCGHE   30 (32)
T ss_dssp             B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred             ccCcCCccccCCCCcCEeECCCCcCE
Confidence            68888887765443333488888753

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

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

Probab=84.38  E-value=0.62  Score=29.97  Aligned_cols=32  Identities=31%  Similarity=0.554  Sum_probs=25.4

Q ss_pred             ceeeEEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204          26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC   59 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~   59 (71)
                      +.+.+.|+.|++.+-.-....  .|.+|+..=|-
T Consensus        66 kav~V~CP~C~K~TKmLGr~D--~CM~C~~pLTL   97 (114)
T PF11023_consen   66 KAVQVECPNCGKQTKMLGRVD--ACMHCKEPLTL   97 (114)
T ss_pred             cceeeECCCCCChHhhhchhh--ccCcCCCcCcc
Confidence            457889999999887666666  99999877553

; GO: 0005887 integral to plasma membrane

>COG4416 Com Mu-like prophage protein Com [General function prediction only]

Probab=84.28  E-value=0.39  Score=27.45  Aligned_cols=35  Identities=26%  Similarity=0.453  Sum_probs=23.6

Q ss_pred             eeEEcCCCCCce-eeceE-eecccCCCCCCcceeeec
Q psy1204          28 LYVLCKDCHKES-KVLYH-IIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus        28 v~i~CndC~~~s-~v~~h-~~g~kCp~C~Synt~ii~   62 (71)
                      ..|+|..|++-- .+.+- ++-.|||.|.-.|-.-+.
T Consensus         3 ~tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~~~~   39 (60)
T COG4416           3 QTIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEFYIK   39 (60)
T ss_pred             eeeehHHHhHHHHhcccceeeeecCCccceeeeeecc
Confidence            368999999643 22221 344499999988876665

>TIGR00155 pqiA_fam integral membrane protein, PqiA family

Probab=84.12  E-value=0.73  Score=34.70  Aligned_cols=48  Identities=23%  Similarity=0.443  Sum_probs=29.5

Q ss_pred             CChHHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204           1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYN   57 (71)
Q Consensus         1 ~dm~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Syn   57 (71)
                      +|-...|+.++.+     |++. ......+.|.+|+..... .+..  .||.|++.=
T Consensus       193 ~d~~~lW~~~~~~-----~~~~-~~~~~~~~C~~Cd~~~~~-~~~a--~CpRC~~~L  240 (403)
T TIGR00155       193 LNRRWLWDDFYPE-----MPEL-RQPLKLRSCSACHTTILP-AQEP--VCPRCSTPL  240 (403)
T ss_pred             cCHHHHHHhcccc-----cCCC-CCccCCCcCCCCCCccCC-CCCc--CCcCCCCcc
Confidence            4667899988733     3332 112346679999984422 2233  799998853

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

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=83.97  E-value=2  Score=26.77  Aligned_cols=36  Identities=22%  Similarity=0.529  Sum_probs=25.0

Q ss_pred             ceeeEEcCCCCCceeec--e--EeecccCCCCCCcceeeec
Q psy1204          26 VILYVLCKDCHKESKVL--Y--HIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v~--~--h~~g~kCp~C~Synt~ii~   62 (71)
                      .+..+.|..|+.. .+.  .  ...-+.|+.||-|..+.+.
T Consensus        18 lpt~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~~~~V~   57 (99)
T PRK14892         18 LPKIFECPRCGKV-SISVKIKKNIAIITCGNCGLYTEFEVP   57 (99)
T ss_pred             CCcEeECCCCCCe-EeeeecCCCcceEECCCCCCccCEECC
Confidence            3678999999953 332  1  1122389999999988874

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

Probab=83.33  E-value=0.44  Score=31.29  Aligned_cols=32  Identities=19%  Similarity=0.317  Sum_probs=22.8

Q ss_pred             EcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204          31 LCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus        31 ~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~   62 (71)
                      .|-.||+.|....-.+-.-||.||+---.-+.
T Consensus         3 ~Ct~Cg~~f~dgs~eil~GCP~CGg~kF~yv~   34 (131)
T PF09845_consen    3 QCTKCGRVFEDGSKEILSGCPECGGNKFQYVP   34 (131)
T ss_pred             ccCcCCCCcCCCcHHHHccCcccCCcceEEcC
Confidence            59999999986552333489999986555444

>PRK01110 rpmF 50S ribosomal protein L32; Validated

Probab=83.19  E-value=1.3  Score=25.16  Aligned_cols=30  Identities=17%  Similarity=0.058  Sum_probs=21.5

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~   62 (71)
                      +..+.|..||..  ..-|.   .|+ ||.|+.+.+-
T Consensus        25 ~~~~~c~~cg~~--~~pH~---vc~-cG~Y~gr~v~   54 (60)
T PRK01110         25 PTLSVDKTTGEY--HLPHH---VSP-KGYYKGRKVL   54 (60)
T ss_pred             CceeEcCCCCce--eccce---ecC-CcccCCeEee
Confidence            457889999852  22232   599 9999998774

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

Probab=82.93  E-value=1.2  Score=22.51  Aligned_cols=28  Identities=25%  Similarity=0.364  Sum_probs=19.9

Q ss_pred             eEEcCCCCCceee-ceEeecccCCCCCCcc
Q psy1204          29 YVLCKDCHKESKV-LYHIIGLKCEHCGSYN   57 (71)
Q Consensus        29 ~i~CndC~~~s~v-~~h~~g~kCp~C~Syn   57 (71)
                      .+.|..|+..-.+ ....+ ..|+.|++..
T Consensus         3 ~~~C~~C~~~~i~~~~~~~-~~C~~Cg~~~   31 (33)
T PF08792_consen    3 LKKCSKCGGNGIVNKEDDY-EVCIFCGSSF   31 (33)
T ss_pred             ceEcCCCCCCeEEEecCCe-EEcccCCcEe
Confidence            4679999987776 44333 3899998753

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

Probab=81.99  E-value=1.2  Score=29.49  Aligned_cols=48  Identities=17%  Similarity=0.508  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHcCCCCHhhhc----ceeeEEcCCCCCceeec--eEeecccCCCCCCcc
Q psy1204           5 PLWRQMDEEIASTPMPEEYKN----VILYVLCKDCHKESKVL--YHIIGLKCEHCGSYN   57 (71)
Q Consensus         5 ~~~~~lD~~i~~~pmP~~y~~----~~v~i~CndC~~~s~v~--~h~~g~kCp~C~Syn   57 (71)
                      ..|+.|-+.+....   .|+-    -+....|..||.+-...  .+.-  .||+|++..
T Consensus        87 vEw~el~~d~~h~g---~Y~sGE~~g~G~l~C~~Cg~~~~~~~~~~l~--~Cp~C~~~~  140 (146)
T PF07295_consen   87 VEWAELAQDLEHHG---VYHSGEVVGPGTLVCENCGHEVELTHPERLP--PCPKCGHTE  140 (146)
T ss_pred             HHHHHHHHHHHhcC---CeecCcEecCceEecccCCCEEEecCCCcCC--CCCCCCCCe
Confidence            35666666666655   4442    25688999999877653  3444  999998754

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.

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

Probab=81.81  E-value=1.2  Score=21.41  Aligned_cols=17  Identities=29%  Similarity=0.403  Sum_probs=10.5

Q ss_pred             cccCCCCCCcceeeecC
Q psy1204          47 GLKCEHCGSYNTCRIKK   63 (71)
Q Consensus        47 g~kCp~C~Synt~ii~g   63 (71)
                      |.+|+.|+.+-+.+..+
T Consensus         1 G~~C~rC~~~~~~~~~~   17 (30)
T PF06827_consen    1 GEKCPRCWNYIEDIGIN   17 (30)
T ss_dssp             TSB-TTT--BBEEEEET
T ss_pred             CCcCccCCCcceEeEec
Confidence            57999999997777653

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....

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

Probab=81.60  E-value=2.2  Score=28.40  Aligned_cols=39  Identities=28%  Similarity=0.531  Sum_probs=23.0

Q ss_pred             EEcCCCCCceeece-----------EeecccCCCCCCcceeeecCCCCCC
Q psy1204          30 VLCKDCHKESKVLY-----------HIIGLKCEHCGSYNTCRIKKPNGQE   68 (71)
Q Consensus        30 i~CndC~~~s~v~~-----------h~~g~kCp~C~Synt~ii~g~~~~~   68 (71)
                      ..|..|++......           ......|++||=-|+.|..|...+.
T Consensus         2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~   51 (161)
T PF03367_consen    2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQP   51 (161)
T ss_dssp             EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-S
T ss_pred             CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCC
Confidence            57999998875421           1122389999999999987766553

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

>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]

Probab=81.07  E-value=0.27  Score=36.22  Aligned_cols=12  Identities=17%  Similarity=0.313  Sum_probs=6.2

Q ss_pred             eeEEcCCCCCce
Q psy1204          28 LYVLCKDCHKES   39 (71)
Q Consensus        28 v~i~CndC~~~s   39 (71)
                      .+-+|.-||..-
T Consensus       184 ~~~~CPvCGS~P  195 (308)
T COG3058         184 SRQYCPVCGSMP  195 (308)
T ss_pred             ccccCCCcCCCC
Confidence            445566665443

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=80.61  E-value=1.3  Score=24.77  Aligned_cols=29  Identities=24%  Similarity=0.461  Sum_probs=19.1

Q ss_pred             EEcCCCCCceeeceEe--ecccCCCCCCcce
Q psy1204          30 VLCKDCHKESKVLYHI--IGLKCEHCGSYNT   58 (71)
Q Consensus        30 i~CndC~~~s~v~~h~--~g~kCp~C~Synt   58 (71)
                      ..|..||.+.+++.-.  -...||.||+.--
T Consensus         3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGaele   33 (54)
T TIGR01206         3 FECPDCGAEIELENPELGELVICDECGAELE   33 (54)
T ss_pred             cCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence            5789999888765411  1238999976543

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

>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]

Probab=80.37  E-value=2.3  Score=34.51  Aligned_cols=52  Identities=15%  Similarity=0.164  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeec
Q psy1204           5 PLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIK   62 (71)
Q Consensus         5 ~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~   62 (71)
                      ..|...+.... +.+|--- -.+-.-.|++||..-.  +..-  +||.|||.++.+++
T Consensus       619 al~~l~k~~~~-~ri~Y~~-~n~~i~~C~~cg~~~~--~~~~--~Cp~CG~~dve~~~  670 (700)
T COG1328         619 ALMDLTKYIYK-TRIGYWG-YTTPISVCNRCGYSGE--GLRT--RCPKCGSEDVEVFS  670 (700)
T ss_pred             HHHHHHHHHHh-cCcceEe-cCCCceeeccCCcccc--cccc--cCCCCCCccceeee
Confidence            44555554444 5555542 2345678999997432  2112  59999999987775

>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=80.37  E-value=1.2  Score=25.04  Aligned_cols=26  Identities=23%  Similarity=0.551  Sum_probs=19.2

Q ss_pred             eEEcCCCCCceee--ceEeecccCCCCCCc
Q psy1204          29 YVLCKDCHKESKV--LYHIIGLKCEHCGSY   56 (71)
Q Consensus        29 ~i~CndC~~~s~v--~~h~~g~kCp~C~Sy   56 (71)
                      .-.|..||.....  ..+.+  .||.||-.
T Consensus        28 Sq~C~~CG~~~~~~~~~r~~--~C~~Cg~~   55 (69)
T PF07282_consen   28 SQTCPRCGHRNKKRRSGRVF--TCPNCGFE   55 (69)
T ss_pred             ccCccCcccccccccccceE--EcCCCCCE
Confidence            4569999987765  45555  99999864

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

>PF14311 DUF4379: Domain of unknown function (DUF4379)

Probab=80.18  E-value=1.9  Score=23.45  Aligned_cols=29  Identities=28%  Similarity=0.467  Sum_probs=21.6

Q ss_pred             cceeeEEcCCCCCceee--ceE-eecccCCCC
Q psy1204          25 NVILYVLCKDCHKESKV--LYH-IIGLKCEHC   53 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v--~~h-~~g~kCp~C   53 (71)
                      +..+.=.|..||.++..  ..+ ..+..||.|
T Consensus        24 ~~~v~W~C~~Cgh~w~~~v~~R~~~~~~CP~C   55 (55)
T PF14311_consen   24 NKKVWWKCPKCGHEWKASVNDRTRRGKGCPYC   55 (55)
T ss_pred             CCEEEEECCCCCCeeEccHhhhccCCCCCCCC
Confidence            45788999999988853  333 356789988

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	71
2k2d_A	79	Solution Nmr Structure Of C-Terminal Domain Of Huma		2e-16

>pdb|2K2D|A Chain A, Solution Nmr Structure Of C-Terminal Domain Of Human Pirh2. Northeast Structural Genomics Consortium (Nesg) Target Ht2c Length = 79

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 46/60 (76%)
Query: 1  MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
          +DMT  WRQ+D+E+A TPMP EY+N+ + +LC DC+  S V +HI+G+KC+ C SYNT +
Sbjct: 9  LDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNTAQ 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	71
2k2d_A	79	Ring finger and CHY zinc finger domain- containing	8e-29
1nff_A	260	Putative oxidoreductase RV2002; directed evolution	8e-04

>2k2d_A Ring finger and CHY zinc finger domain- containing protein 1; zinc-binding protein, cytoplasm, metal-binding, nucleus, metal binding protein; NMR {Homo sapiens} Length = 79

 Score = 96.9 bits (241), Expect = 8e-29
 Identities = 32/65 (49%), Positives = 46/65 (70%)

Query: 1  MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR 60
          +DMT  WRQ+D+E+A TPMP EY+N+ + +LC DC+  S V +HI+G+KC+ C SYNT +
Sbjct: 9  LDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNTAQ 68

Query: 61 IKKPN 65
               
Sbjct: 69 AGGRR 73

>1nff_A Putative oxidoreductase RV2002; directed evolution, GFP, SDR, hydroxysteroid dehydrogenase, structural genomics, PSI; HET: NAD; 1.80A {Mycobacterium tuberculosis} SCOP: c.2.1.2 PDB: 1nfq_A* 1nfr_A* Length = 260

 Score = 34.4 bits (80), Expect = 8e-04
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 9/42 (21%)

Query: 4   TPLWRQMDEEIASTPM-----PEEYKNVILYVLCKDCHKESK 40
           TP+   + E+I  T +     P E  N+++Y L  D   ES 
Sbjct: 188 TPMTDWVPEDIFQTALGRAAEPVEVSNLVVY-LASD---ESS 225

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	71
2k2d_A	79	Ring finger and CHY zinc finger domain- containing	100.0
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	98.56
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	98.54
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	96.55
1twf_L	70	ABC10-alpha, DNA-directed RNA polymerases I, II, a	95.25
3irb_A	145	Uncharacterized protein from DUF35 family; 1381535	94.98
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	94.49
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	94.22
2gnr_A	145	Conserved hypothetical protein; 13815350, structur	93.13
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	91.53
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	91.37
3v2d_5	60	50S ribosomal protein L32; ribosome associated inh	90.52
3j20_W	63	30S ribosomal protein S27E; archaea, archaeal, KIN	89.37
2zjr_Z	60	50S ribosomal protein L32; ribosome, large ribosom	88.98
1qxf_A	66	GR2, 30S ribosomal protein S27E; structural genomi	88.73
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	87.62
1h7b_A	605	Anaerobic ribonucleotide-triphosphate reductase la	86.93
1k81_A	36	EIF-2-beta, probable translation initiation factor	86.47
3u5c_b	82	RP61, YS20, 40S ribosomal protein S27-A; translati	86.43
2kwq_A	92	Protein MCM10 homolog; DNA replication, DNA bindin	85.71
2avu_E	192	Flagellar transcriptional activator FLHC; C4-type	85.58
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	85.29
3iz6_X	86	40S ribosomal protein S27 (S27E); eukaryotic ribos	84.09
1lko_A	191	Rubrerythrin all-iron(II) form; reduced form, DIIR	83.77
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	82.68

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

Probab=100.00  E-value=2.9e-35  Score=176.64  Aligned_cols=69  Identities=46%  Similarity=0.934  Sum_probs=43.0

Q ss_pred             CChHHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCCCCC
Q psy1204           1 MDMTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQES   69 (71)
Q Consensus         1 ~dm~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~~~~   69 (71)
                      +||+.+|++||++||++|||++|++++|.|+||||+++|.+.||++|||||.|+||||++++|+..|.+
T Consensus         9 ~dm~~~~~~lD~~ia~~pmP~~y~~~~v~I~CnDC~~~s~v~~h~lg~kC~~C~SyNTr~~~G~~~~~~   77 (79)
T 2k2d_A            9 LDMTRYWRQLDDEVAQTPMPSEYQNMTVDILCNDCNGRSTVQFHILGMKCKICESYNTAQAGGRRISLD   77 (79)
T ss_dssp             ------------------------CCEEEEEESSSCCEEEEECCTTCCCCTTTSCCCEEESCCCCCCCC
T ss_pred             HHHHHHHHHHHHHHHhCCCCHHHhCCEeEEECCCCCCCccCCceeecccCcCCCCcCeEecCCCCCCCC
Confidence            599999999999999999999999999999999999999999999999999999999999999987754

>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=98.56  E-value=7.1e-08  Score=61.95  Aligned_cols=59  Identities=24%  Similarity=0.332  Sum_probs=42.7

Q ss_pred             HHHHHHHcCCCCHh---hhcceeeEEcCCCCCceeece-----------E--ee------cccCCCCCCcceeeecCCCC
Q psy1204           9 QMDEEIASTPMPEE---YKNVILYVLCKDCHKESKVLY-----------H--II------GLKCEHCGSYNTCRIKKPNG   66 (71)
Q Consensus         9 ~lD~~i~~~pmP~~---y~~~~v~i~CndC~~~s~v~~-----------h--~~------g~kCp~C~Synt~ii~g~~~   66 (71)
                      .+|...+.+.+-..   ....++..+|++||+.+....           .  ++      ..+||.|||.++.+++|++.
T Consensus        47 af~~~~~gt~~e~A~L~i~~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~h~~p~~~~~~~~CP~Cgs~~~~i~~G~el  126 (139)
T 3a43_A           47 AMEQLFAGTIAEGAEIEFVEEEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEVVKGRGV  126 (139)
T ss_dssp             HHHHHHTTSTTTTCEEEEEEECCEEEETTTCCEEEGGGCTTCCSCCCGGGCCCCGGGCGGGCSCSSSSCCCEEEEESSCE
T ss_pred             HHHHHHcCCcccCCEEEEEecCCcEECCCCCCEEecccccccccccccccccccccccccCCcCccccCCccEEecCCeE
Confidence            45555556655321   235688999999999998755           4  11      23999999999999999985


Q ss_pred             C
Q psy1204          67 Q   67 (71)
Q Consensus        67 ~   67 (71)
                      .
T Consensus       127 ~  127 (139)
T 3a43_A          127 Y  127 (139)
T ss_dssp             E
T ss_pred             E
Confidence            3

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

Probab=98.54  E-value=2.9e-08  Score=61.90  Aligned_cols=43  Identities=26%  Similarity=0.311  Sum_probs=36.0

Q ss_pred             hcceeeEEcCCCCCceeeceEeecccCCCCCCcceeeecCCCCC
Q psy1204          24 KNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRIKKPNGQ   67 (71)
Q Consensus        24 ~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii~g~~~~   67 (71)
                      ...++..+|.+||+.+++.....+ +||.|||.++++++|++..
T Consensus        68 ~~~p~~~~C~~CG~~~e~~~~~~~-~CP~Cgs~~~~i~~G~el~  110 (119)
T 2kdx_A           68 VDEKVELECKDCSHVFKPNALDYG-VCEKCHSKNVIITQGNEMR  110 (119)
T ss_dssp             EEECCEEECSSSSCEECSCCSTTC-CCSSSSSCCCEEEESSCCE
T ss_pred             EeccceEEcCCCCCEEeCCCCCCC-cCccccCCCcEEecCCeEE
Confidence            356889999999999998654332 8999999999999999864

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

Probab=96.55  E-value=0.00083  Score=41.68  Aligned_cols=36  Identities=22%  Similarity=0.217  Sum_probs=24.8

Q ss_pred             hcceeeEEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204          24 KNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR   60 (71)
Q Consensus        24 ~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~i   60 (71)
                      +-......|.+||.+|. .....--+||.|+|.|+..
T Consensus        62 ~L~v~p~~C~~CG~~F~-~~~~kPsrCP~CkSe~Ie~   97 (105)
T 2gmg_A           62 VLLIKPAQCRKCGFVFK-AEINIPSRCPKCKSEWIEE   97 (105)
T ss_dssp             EEEECCCBBTTTCCBCC-CCSSCCSSCSSSCCCCBCC
T ss_pred             EEEEECcChhhCcCeec-ccCCCCCCCcCCCCCccCC
Confidence            33355778999999992 2212223999999999863

>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=95.25  E-value=0.0062  Score=35.04  Aligned_cols=29  Identities=21%  Similarity=0.659  Sum_probs=23.4

Q ss_pred             ceeeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204          26 VILYVLCKDCHKESKVLYHIIGLKCEHCGS   55 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~S   55 (71)
                      .++...|.+||.+++..... ...||.||+
T Consensus        25 ~~v~Y~C~~CG~~~e~~~~d-~irCp~CG~   53 (70)
T 1twf_L           25 ATLKYICAECSSKLSLSRTD-AVRCKDCGH   53 (70)
T ss_dssp             CCCCEECSSSCCEECCCTTS-TTCCSSSCC
T ss_pred             ceEEEECCCCCCcceeCCCC-CccCCCCCc
Confidence            57899999999998876433 248999998

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

Probab=94.98  E-value=0.022  Score=36.19  Aligned_cols=33  Identities=24%  Similarity=0.319  Sum_probs=24.8

Q ss_pred             cceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      .+-+.-+|.+||+.+-.+.    ..||+|+|.++.-+
T Consensus        43 grL~~~rC~~CG~~~~PPr----~~Cp~C~s~~~~~v   75 (145)
T 3irb_A           43 NKIIGSKCSKCGRIFVPAR----SYCEHCFVKIENYV   75 (145)
T ss_dssp             TCCEEEECTTTCCEEESCC----SEETTTTEECCEEE
T ss_pred             CeEEEEEeCCCCcEEcCch----hhCcCCCCCceeee
Confidence            4567889999998665443    27999999987543

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

Probab=94.49  E-value=0.0096  Score=33.75  Aligned_cols=30  Identities=23%  Similarity=0.658  Sum_probs=23.4

Q ss_pred             ceeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204          26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSY   56 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy   56 (71)
                      +++...|.+|+.++.+... -..+||.||..
T Consensus        18 ~~v~Y~C~~Cg~~~~l~~~-~~iRC~~CG~R   47 (63)
T 3h0g_L           18 ATMIYLCADCGARNTIQAK-EVIRCRECGHR   47 (63)
T ss_dssp             -CCCCBCSSSCCBCCCCSS-SCCCCSSSCCC
T ss_pred             CCeEEECCCCCCeeecCCC-CceECCCCCcE
Confidence            3788999999999987753 33499999863

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

Probab=94.22  E-value=0.019  Score=36.65  Aligned_cols=27  Identities=30%  Similarity=0.586  Sum_probs=21.0

Q ss_pred             eEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204          29 YVLCKDCHKESKVLYHIIGLKCEHCGSYN   57 (71)
Q Consensus        29 ~i~CndC~~~s~v~~h~~g~kCp~C~Syn   57 (71)
                      ...|..||+.|+...-  ...||.|||.-
T Consensus       132 ~y~C~~Cg~~~~~~~~--~~~Cp~CG~~~  158 (165)
T 2lcq_A          132 RYVCIGCGRKFSTLPP--GGVCPDCGSKV  158 (165)
T ss_dssp             CEEESSSCCEESSCCG--GGBCTTTCCBE
T ss_pred             EEECCCCCCcccCCCC--CCcCCCCCCcc
Confidence            6899999999986521  22799999973

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

Probab=93.13  E-value=0.071  Score=34.01  Aligned_cols=33  Identities=24%  Similarity=0.319  Sum_probs=23.9

Q ss_pred             cceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      .+-..-+|.+||+.+-.+.    ..||+|+|.+..-+
T Consensus        43 g~L~~~rC~~CG~~~fPPr----~~Cp~C~s~~~e~v   75 (145)
T 2gnr_A           43 NKIIGSKCSKCGRIFVPAR----SYCEHCFVKIENYV   75 (145)
T ss_dssp             TCCEEEECTTTCCEEESCC----SEETTTTEECCEEE
T ss_pred             CEEEEEEECCCCcEEeCCC----CCCCCCCCCccEEE
Confidence            4567889999997554333    27999999875544

>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=91.53  E-value=0.069  Score=30.69  Aligned_cols=26  Identities=23%  Similarity=0.485  Sum_probs=20.9

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGS   55 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~S   55 (71)
                      +++.|. |+.-+.+..-.-.++|| ||.
T Consensus         3 ~vv~C~-C~~~~~~~~~~kT~~C~-CG~   28 (71)
T 1gh9_A            3 IIFRCD-CGRALYSREGAKTRKCV-CGR   28 (71)
T ss_dssp             EEEEET-TSCCEEEETTCSEEEET-TTE
T ss_pred             EEEECC-CCCEEEEcCCCcEEECC-CCC
Confidence            689999 99988877655566999 975

>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=91.37  E-value=0.075  Score=28.62  Aligned_cols=26  Identities=27%  Similarity=0.595  Sum_probs=19.0

Q ss_pred             eEEcCCCCCceeece--EeecccCCCCC
Q psy1204          29 YVLCKDCHKESKVLY--HIIGLKCEHCG   54 (71)
Q Consensus        29 ~i~CndC~~~s~v~~--h~~g~kCp~C~   54 (71)
                      ...|..||++|...+  ..-+.+||.||
T Consensus         3 iY~C~rCg~~fs~~el~~lP~IrCpyCG   30 (48)
T 4ayb_P            3 VYRCGKCWKTFTDEQLKVLPGVRCPYCG   30 (48)
T ss_dssp             --CCCCTTTTCCCCCSCCCSSSCCTTTC
T ss_pred             EEEeeccCCCccHHHHhhCCCcccCccC
Confidence            467999999997654  34566999996

>3v2d_5 50S ribosomal protein L32; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_4 2hgj_4 2hgu_4 2j03_5 2jl6_5 2jl8_5 2v47_5 2v49_5 2wdi_5 2wdj_5 2wdl_5 2wdn_5 2wh2_5 2wh4_5 2wrj_5 2wrl_5 2wro_5 2wrr_5 2x9s_5 2x9u_5 ...

Probab=90.52  E-value=0.16  Score=28.27  Aligned_cols=31  Identities=26%  Similarity=0.568  Sum_probs=22.8

Q ss_pred             ceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      .+..+.|..||.  ....|   +.|+.||-|+-+.+
T Consensus        27 ~p~l~~c~~cGe--~~~~H---~vc~~CG~Y~gr~V   57 (60)
T 3v2d_5           27 PPTLVPCPECKA--MKPPH---TVCPECGYYAGRKV   57 (60)
T ss_dssp             CCCCEECTTTCC--EECTT---SCCTTTCEETTEEC
T ss_pred             CCceeECCCCCC--eecce---EEcCCCCcCCCEEe
Confidence            366899999996  22223   36999999988755

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

Probab=89.37  E-value=0.37  Score=27.17  Aligned_cols=41  Identities=27%  Similarity=0.455  Sum_probs=28.5

Q ss_pred             hcceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204          24 KNVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        24 ~~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~   64 (71)
                      +...+.+.|.+|+....+..|-- -..|..|+..=.+=.+|+
T Consensus        10 nS~Fm~VkCp~C~~~q~VFSha~t~V~C~~Cgt~L~~PTGGK   51 (63)
T 3j20_W           10 RSRFLRVKCIDCGNEQIVFSHPATKVRCLICGATLVEPTGGK   51 (63)
T ss_dssp             SCCEEEEECSSSCCEEEEESSCSSCEECSSSCCEEEECCSSS
T ss_pred             CCcEEEEECCCCCCeeEEEecCCeEEEccCcCCEEecCCCCc
Confidence            44578999999999998865421 127888887655544444

>2zjr_Z 50S ribosomal protein L32; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: g.41.8.5 PDB: 1j5a_M* 1jzy_M* 1jzz_M* 1k01_M* 1nkw_Z 1ond_Z* 1sm1_Z* 1yl3_5 2b66_5 2b9n_5 2b9p_5 2zjp_Y* 2zjq_Z 1jzx_M 3cf5_Y* 3dll_Y* 3pio_Z* 3pip_Z* 1nwy_Z* 1nwx_Z* ...

Probab=88.98  E-value=0.25  Score=27.35  Aligned_cols=31  Identities=23%  Similarity=0.613  Sum_probs=23.0

Q ss_pred             ceeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          26 VILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        26 ~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      .+..+.|..||..     +.--+.||.||-|+-+.+
T Consensus        27 ~p~l~~c~~cG~~-----~~pH~vc~~CG~Y~gr~v   57 (60)
T 2zjr_Z           27 APNLTECPQCHGK-----KLSHHICPNCGYYDGRQV   57 (60)
T ss_dssp             CCCCEECTTTCCE-----ECTTBCCTTTCBSSSBCS
T ss_pred             CCCceECCCCCCE-----eCCceEcCCCCcCCCEEe
Confidence            4678899999974     222237999999987655

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

Probab=88.73  E-value=0.43  Score=27.18  Aligned_cols=40  Identities=25%  Similarity=0.411  Sum_probs=27.1

Q ss_pred             cceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204          25 NVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~   64 (71)
                      ...+.++|++|++...+..|-- -..|..|+..=.+=.+|+
T Consensus         3 S~Fm~VKCp~C~niq~VFShA~tvV~C~~Cg~~L~~PTGGK   43 (66)
T 1qxf_A            3 SRFVKVKCPDCEHEQVIFDHPSTIVKCIICGRTVAEPTGGK   43 (66)
T ss_dssp             CCEEEEECTTTCCEEEEESSCSSCEECSSSCCEEEECCSSS
T ss_pred             ceeEEEECCCCCCceEEEecCceEEEcccCCCEEeecCCcc
Confidence            3468999999999998865421 127888876554444443

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

Probab=87.62  E-value=0.3  Score=26.05  Aligned_cols=28  Identities=21%  Similarity=0.388  Sum_probs=19.2

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCC
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGS   55 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~S   55 (71)
                      ..-+|..||.......|.-.+.|+.||-
T Consensus        18 ~~k~CP~CG~~~fm~~~~~R~~C~kCG~   45 (50)
T 3j20_Y           18 KNKFCPRCGPGVFMADHGDRWACGKCGY   45 (50)
T ss_dssp             SSEECSSSCSSCEEEECSSEEECSSSCC
T ss_pred             ecccCCCCCCceEEecCCCeEECCCCCC
Confidence            4578999987544444555668998873

>1h7b_A Anaerobic ribonucleotide-triphosphate reductase large chain; oxidoreductase, allosteric regulation, substrate specificity; 2.45A {Bacteriophage T4} SCOP: c.7.1.3 PDB: 1h79_A* 1h7a_A* 1h78_A 1hk8_A*

Probab=86.93  E-value=0.21  Score=38.36  Aligned_cols=31  Identities=19%  Similarity=0.429  Sum_probs=4.5

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYN   57 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Syn   57 (71)
                      +..-.|++||......-..-+.+||.|||.+
T Consensus       538 ~~~~~C~~CGy~~~~~~~~~~~~CP~Cg~~~  568 (605)
T 1h7b_A          538 MPVDKCFTCGSTHEMTPTENGFVCSICGETD  568 (605)
T ss_dssp             CCEEET-------------------------
T ss_pred             CCCccCcccCCcCccCccccCCcCCCCCCCc
Confidence            5577899999866432110123899999977

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

Probab=86.47  E-value=0.32  Score=24.23  Aligned_cols=14  Identities=43%  Similarity=0.762  Sum_probs=12.9

Q ss_pred             cCCCCCCcceeeec
Q psy1204          49 KCEHCGSYNTCRIK   62 (71)
Q Consensus        49 kCp~C~Synt~ii~   62 (71)
                      .|+.|+|.+|.++.
T Consensus         2 lC~~C~~peT~l~~   15 (36)
T 1k81_A            2 ICRECGKPDTKIIK   15 (36)
T ss_dssp             CCSSSCSCEEEEEE
T ss_pred             CCcCCCCCCcEEEE
Confidence            69999999999986

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

Probab=86.43  E-value=0.77  Score=27.11  Aligned_cols=41  Identities=22%  Similarity=0.446  Sum_probs=29.0

Q ss_pred             hcceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204          24 KNVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        24 ~~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~   64 (71)
                      +...+.+.|.+|+...++..|-- -..|..|+..=.+=.+|.
T Consensus        29 nS~Fm~VkCp~C~~~q~VFSha~t~V~C~~Cg~~L~~PTGGK   70 (82)
T 3u5c_b           29 RSYFLDVKCPGCLNITTVFSHAQTAVTCESCSTILCTPTGGK   70 (82)
T ss_dssp             CCCEEEEECTTSCSCEEEESBCSSCCCCSSSCCCCEECCSSB
T ss_pred             CCcEEEEECCCCCCeeEEEecCCeEEEccccCCEEeccCCCC
Confidence            34478999999999998866532 127888887655555554

>2kwq_A Protein MCM10 homolog; DNA replication, DNA binding, zinc motif, zinc ribbon binding protein; NMR {Xenopus laevis}

Probab=85.71  E-value=1  Score=26.92  Aligned_cols=41  Identities=22%  Similarity=0.532  Sum_probs=28.8

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCCcceeee---cCCCCCCC
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI---KKPNGQES   69 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii---~g~~~~~~   69 (71)
                      -...|. |++....-..+-...|++||+.+=+..   .++.||.-
T Consensus        47 RFFkC~-C~~Rt~sl~r~P~~~C~~Cg~~~wer~~M~~ek~g~~~   90 (92)
T 2kwq_A           47 RFFKCP-CGNRTISLDRLPKKHCSTCGLFKWERVGMLKEKTGPKL   90 (92)
T ss_dssp             EEEECT-TSCEEEESSSSCCSCCTTTCSCCCEEECCCSSSCCSCC
T ss_pred             EEEECC-CCCceeEeeeCCCCCCCCCCCCceEEeeccccCcCCCC
Confidence            356796 998886655566668999999886555   36666643

>2avu_E Flagellar transcriptional activator FLHC; C4-type zinc finger, transcription activator; 3.00A {Escherichia coli} SCOP: e.64.1.1

Probab=85.58  E-value=1.5  Score=29.45  Aligned_cols=29  Identities=17%  Similarity=0.372  Sum_probs=22.1

Q ss_pred             eeeEEcCCCCCceeeceEee--cccCCCCCC
Q psy1204          27 ILYVLCKDCHKESKVLYHII--GLKCEHCGS   55 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~--g~kCp~C~S   55 (71)
                      -....|..|+..|.+..|..  ..+||.|..
T Consensus       132 L~l~~C~~Cgg~fv~~~~~~~~~f~Cp~C~~  162 (192)
T 2avu_E          132 LQLSSCNCCGGNFITHAHQPVGSFACSLCQP  162 (192)
T ss_dssp             EEEEECTTTCCEEEEESSCCSSCCCCTTC--
T ss_pred             eeeCcCCCCCCCeeCccCCCCCCCcCCCCCC
Confidence            56789999999998876654  559999973

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

Probab=85.29  E-value=0.91  Score=26.74  Aligned_cols=41  Identities=15%  Similarity=0.352  Sum_probs=28.2

Q ss_pred             hcceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204          24 KNVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        24 ~~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~   64 (71)
                      +...+.+.|.+|+...++..|-- -..|..|+..=.+=.+|.
T Consensus        27 nS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGK   68 (81)
T 2xzm_6           27 NSYFMDVKCAQCQNIQMIFSNAQSTIICEKCSAILCKPTGGK   68 (81)
T ss_dssp             SCCEEEEECSSSCCEEEEETTCSSCEECSSSCCEEEEECSSC
T ss_pred             CCcEEEeECCCCCCeeEEEecCccEEEccCCCCEEeecCCCC
Confidence            44578999999999998865421 127888877654444443

>3iz6_X 40S ribosomal protein S27 (S27E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=84.09  E-value=1.1  Score=26.61  Aligned_cols=41  Identities=17%  Similarity=0.336  Sum_probs=27.4

Q ss_pred             hcceeeEEcCCCCCceeeceEee-cccCCCCCCcceeeecCC
Q psy1204          24 KNVILYVLCKDCHKESKVLYHII-GLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        24 ~~~~v~i~CndC~~~s~v~~h~~-g~kCp~C~Synt~ii~g~   64 (71)
                      +...+.+.|++|+....+..|-- -..|..|+..=.+=.+|.
T Consensus        31 nS~Fm~VkCp~C~~~~~VFShA~t~V~C~~CgtvL~~PTGGK   72 (86)
T 3iz6_X           31 NSFFMDVKCQGCFNITTVFSHSQTVVVCPGCQTVLCQPTGGK   72 (86)
T ss_dssp             --CEEEEECTTTCCEEEEETTCSSCCCCSSSCCCCSCCCSSS
T ss_pred             CCcEeEEECCCCCCeeEEEecCCcEEEccCCCCEeecCCCCC
Confidence            34578999999999998765421 127888877655555554

>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=83.77  E-value=0.82  Score=29.88  Aligned_cols=30  Identities=13%  Similarity=0.201  Sum_probs=21.3

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcce
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNT   58 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt   58 (71)
                      +....|..||.........  -+||.|++...
T Consensus       153 ~~~~~C~~CG~~~~g~~~p--~~CP~C~~~k~  182 (191)
T 1lko_A          153 ATKWRCRNCGYVHEGTGAP--ELCPACAHPKA  182 (191)
T ss_dssp             EEEEEETTTCCEEEEEECC--SBCTTTCCBGG
T ss_pred             CceEEECCCCCEeeCCCCC--CCCCCCcCCHH
Confidence            4578899999886533222  29999998643

>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=82.68  E-value=1.1  Score=28.92  Aligned_cols=28  Identities=18%  Similarity=0.273  Sum_probs=18.8

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcc
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYN   57 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Syn   57 (71)
                      ...-.|..||..... .-.  -+||.||...
T Consensus       136 ~~~~~C~~CG~i~~~-~~p--~~CP~Cg~~~  163 (170)
T 3pwf_A          136 KKVYICPICGYTAVD-EAP--EYCPVCGAPK  163 (170)
T ss_dssp             SCEEECTTTCCEEES-CCC--SBCTTTCCBG
T ss_pred             CCeeEeCCCCCeeCC-CCC--CCCCCCCCCH
Confidence            345569999987652 111  2999998643

---

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	71
d2gmga1	105	Hypothetical protein PF0610 {Pyrococcus furiosus [	95.27
d2gnra1	137	Hypothetical protein SSO2064 {Sulfolobus solfatari	95.04
d1neea2	37	Zinc-binding domain of translation initiation fact	90.92
d1hk8a_	561	Class III anaerobic ribonucleotide reductase NRDD	90.88
d1lkoa2	44	Rubrerythrin, C-terminal domain {Desulfovibrio vul	90.62
d1k81a_	36	Zinc-binding domain of translation initiation fact	90.49
d1qxfa_	58	Ribosomal protein S27e {Archaeon Archaeoglobus ful	89.49
d2zjrz1	58	Ribosomal protein L32p {Deinococcus radiodurans [T	88.9
d1wjva1	35	Cell growth regulating nucleolar protein LyaR {Mou	88.81
d2j0151	59	Ribosomal protein L32p {Thermus thermophilus [TaxI	88.12
d2dkta1	74	RING finger and CHY zinc finger domain-containing	86.65
d2apob1	55	Ribosome biogenesis protein Nop10 {Archaeon Methan	83.25
d1twfl_	46	RBP12 subunit of RNA polymerase II {Baker's yeast	82.86
d2ey4e1	52	Ribosome biogenesis protein Nop10 {Archaeon Pyroco	82.09

>d2gmga1 a.4.5.82 (A:1-105) Hypothetical protein PF0610 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF0610-like
domain: Hypothetical protein PF0610
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.27  E-value=0.0031  Score=37.61  Aligned_cols=36  Identities=22%  Similarity=0.287  Sum_probs=25.0

Q ss_pred             hhcceeeEEcCCCCCceeeceEeecccCCCCCCccee
Q psy1204          23 YKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTC   59 (71)
Q Consensus        23 y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~   59 (71)
                      ++-...-..|.+||..|......-+ +||.|+|....
T Consensus        61 ~~L~v~Pp~CrkCGfvFr~~~kkPS-RCP~CKSE~Ie   96 (105)
T d2gmga1          61 MVLLIKPAQCRKCGFVFKAEINIPS-RCPKCKSEWIE   96 (105)
T ss_dssp             EEEEECCCBBTTTCCBCCCCSSCCS-SCSSSCCCCBC
T ss_pred             CeEEEeChhhhhcCCeecccCCCCC-CCCCCCCcccc
Confidence            3333445689999999954333344 99999997653

>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=95.04  E-value=0.008  Score=36.39  Aligned_cols=42  Identities=19%  Similarity=0.290  Sum_probs=30.6

Q ss_pred             hHHHHHHHHHHHHcCCCCHhhhcceeeEEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204           3 MTPLWRQMDEEIASTPMPEEYKNVILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR   60 (71)
Q Consensus         3 m~~~~~~lD~~i~~~pmP~~y~~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~i   60 (71)
                      ++.+|+.|.+            ++-+--+|.+||..+-.+..    .||+|+|.+..-
T Consensus        25 ~~~F~~al~e------------grL~~~~C~~CG~v~~Ppr~----~Cp~C~s~~~e~   66 (137)
T d2gnra1          25 GEQFFNGLKQ------------NKIIGSKCSKCGRIFVPARS----YCEHCFVKIENY   66 (137)
T ss_dssp             HHHHHHHHHT------------TCCEEEECTTTCCEEESCCS----EETTTTEECCEE
T ss_pred             HHHHHHHhhc------------CeEEEEEcCCCCCEEeCccc----cCCCCCCCccee
Confidence            4566766654            45678899999987665542    699999988654

>d1neea2 g.59.1.1 (A:99-135) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=90.92  E-value=0.022  Score=27.97  Aligned_cols=15  Identities=27%  Similarity=0.609  Sum_probs=13.3

Q ss_pred             ccCCCCCCcceeeec
Q psy1204          48 LKCEHCGSYNTCRIK   62 (71)
Q Consensus        48 ~kCp~C~Synt~ii~   62 (71)
                      ..|+.|+|.+|+++.
T Consensus         2 V~C~~C~spDT~l~k   16 (37)
T d1neea2           2 VICHECNRPDTRIIR   16 (37)
T ss_dssp             HHHTCCSSCSSCCEE
T ss_pred             eECCCCCCCCCEEEE
Confidence            379999999999985

>d1hk8a_ c.7.1.3 (A:) Class III anaerobic ribonucleotide reductase NRDD subunit {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: PFL-like glycyl radical enzymes
superfamily: PFL-like glycyl radical enzymes
family: Class III anaerobic ribonucleotide reductase NRDD subunit
domain: Class III anaerobic ribonucleotide reductase NRDD subunit
species: Bacteriophage T4 [TaxId: 10665]

Probab=90.88  E-value=0.057  Score=39.14  Aligned_cols=29  Identities=17%  Similarity=0.405  Sum_probs=20.2

Q ss_pred             eeeEEcCCCCCceee--ceEeecccCCCCCCcc
Q psy1204          27 ILYVLCKDCHKESKV--LYHIIGLKCEHCGSYN   57 (71)
Q Consensus        27 ~v~i~CndC~~~s~v--~~h~~g~kCp~C~Syn   57 (71)
                      +-.-.|++||.+...  ..|.+  .||.|||.+
T Consensus       513 ~~~~~C~~Cg~~~~~~~~~~~~--~CP~CGs~~  543 (561)
T d1hk8a_         513 MPVDKCFTCGSTHEMTPTENGF--VCSICGETD  543 (561)
T ss_dssp             CCEEEETTTCCCSCCEECSSSE--ECSSSCCCC
T ss_pred             CCCccCCCCCCcCccccCCCCc--cCcCCCCCC
Confidence            345569999986543  33333  899999976

>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=90.62  E-value=0.09  Score=26.49  Aligned_cols=30  Identities=13%  Similarity=0.180  Sum_probs=22.2

Q ss_pred             cceeeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204          25 NVILYVLCKDCHKESKVLYHIIGLKCEHCGSY   56 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v~~h~~g~kCp~C~Sy   56 (71)
                      +.++.-.|..||...+...---  +||.|+..
T Consensus         4 ~~~~~W~C~~CGyi~~g~~aP~--~CPvC~~p   33 (44)
T d1lkoa2           4 EQATKWRCRNCGYVHEGTGAPE--LCPACAHP   33 (44)
T ss_dssp             EEEEEEEETTTCCEEEEEECCS--BCTTTCCB
T ss_pred             CCCeEEEcCCCCcEEECCCCCC--cCCCCCCc
Confidence            3467889999998877554333  99999754

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

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

Probab=90.49  E-value=0.059  Score=26.16  Aligned_cols=14  Identities=43%  Similarity=0.762  Sum_probs=12.8

Q ss_pred             cCCCCCCcceeeec
Q psy1204          49 KCEHCGSYNTCRIK   62 (71)
Q Consensus        49 kCp~C~Synt~ii~   62 (71)
                      .|+.|+|.+|+++.
T Consensus         2 ~C~~C~spDT~l~k   15 (36)
T d1k81a_           2 ICRECGKPDTKIIK   15 (36)
T ss_dssp             CCSSSCSCEEEEEE
T ss_pred             CCCCCCCCCCEEEE
Confidence            69999999999985

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

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

Probab=89.49  E-value=0.17  Score=26.82  Aligned_cols=40  Identities=25%  Similarity=0.421  Sum_probs=28.3

Q ss_pred             cceeeEEcCCCCCceeeceEe-ecccCCCCCCcceeeecCC
Q psy1204          25 NVILYVLCKDCHKESKVLYHI-IGLKCEHCGSYNTCRIKKP   64 (71)
Q Consensus        25 ~~~v~i~CndC~~~s~v~~h~-~g~kCp~C~Synt~ii~g~   64 (71)
                      ...+.+.|.||+....+..|- .-..|..|+..=.+=.+|+
T Consensus         3 S~F~~VkC~~C~n~~ivFsha~t~V~C~~Cg~~L~~PtGGK   43 (58)
T d1qxfa_           3 SRFVKVKCPDCEHEQVIFDHPSTIVKCIICGRTVAEPTGGK   43 (58)
T ss_dssp             CCEEEEECTTTCCEEEEESSCSSCEECSSSCCEEEECCSSS
T ss_pred             ceeEEeECCCCCCeEEEEecCceEEEccccCCEEeccCCCe
Confidence            346899999999998876542 1128999987666555554

>d2zjrz1 g.41.8.5 (Z:2-59) Ribosomal protein L32p {Deinococcus radiodurans [TaxId: 1299]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Deinococcus radiodurans [TaxId: 1299]

Probab=88.90  E-value=0.11  Score=27.44  Aligned_cols=30  Identities=33%  Similarity=0.723  Sum_probs=21.8

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      +..+.|..||.  ...-|   +.|+.||-|+-+++
T Consensus        27 p~l~~C~~CG~--~~lpH---rvC~~CG~YkGr~V   56 (58)
T d2zjrz1          27 PNLTECPQCHG--KKLSH---HICPNCGYYDGRQV   56 (58)
T ss_dssp             CCCEECTTTCC--EECTT---BCCTTTCBSSSBCS
T ss_pred             CceeECCCCCC--Cccce---eeCCCCCcCCCEEe
Confidence            56788999996  22223   37999999987654

>d1wjva1 g.37.1.2 (A:1-35) Cell growth regulating nucleolar protein LyaR {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: C2HC finger
domain: Cell growth regulating nucleolar protein LyaR
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.81  E-value=0.023  Score=27.38  Aligned_cols=26  Identities=23%  Similarity=0.770  Sum_probs=20.2

Q ss_pred             ceeeEEcCCCCCce---eeceEeecccCCCC
Q psy1204          26 VILYVLCKDCHKES---KVLYHIIGLKCEHC   53 (71)
Q Consensus        26 ~~v~i~CndC~~~s---~v~~h~~g~kCp~C   53 (71)
                      .+|..-||.||..-   .|..|..  +|..|
T Consensus         7 ~MVfFtCn~CGEs~KK~qVekH~~--~CR~C   35 (35)
T d1wjva1           7 GMVFFTCNACGESVKKIQVEKHVS--NCRNC   35 (35)
T ss_dssp             CCCEEEESSSCCEEETTHHHHHHH--HCTTC
T ss_pred             eEEEEEcchhHHHHhHHHHHHHHH--hccCC
Confidence            47889999999543   4677887  89887

>d2j0151 g.41.8.5 (5:2-60) Ribosomal protein L32p {Thermus thermophilus [TaxId: 274]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L32p
domain: Ribosomal protein L32p
species: Thermus thermophilus [TaxId: 274]

Probab=88.12  E-value=0.075  Score=28.18  Aligned_cols=30  Identities=27%  Similarity=0.608  Sum_probs=22.0

Q ss_pred             eeeEEcCCCCCceeeceEeecccCCCCCCcceeee
Q psy1204          27 ILYVLCKDCHKESKVLYHIIGLKCEHCGSYNTCRI   61 (71)
Q Consensus        27 ~v~i~CndC~~~s~v~~h~~g~kCp~C~Synt~ii   61 (71)
                      +..+.|..||+.  ..-|.   .|+.||-|+-+++
T Consensus        27 p~l~~C~~CG~~--~~pHr---vC~~CG~YkGr~V   56 (59)
T d2j0151          27 PTLVPCPECKAM--KPPHT---VCPECGYYAGRKV   56 (59)
T ss_dssp             CCCBCCSSSSSC--BCTTC---BCTTTCCSSSCCS
T ss_pred             CceeECCCCCCc--cccee---ECCCCCeECCEEe
Confidence            567889999972  22232   6999999987665

>d2dkta1 g.89.1.1 (A:8-81) RING finger and CHY zinc finger domain-containing protein 1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: CHY zinc finger-like
superfamily: CHY zinc finger-like
family: CHY zinc finger
domain: RING finger and CHY zinc finger domain-containing protein 1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.65  E-value=0.16  Score=27.44  Aligned_cols=12  Identities=17%  Similarity=0.149  Sum_probs=5.9

Q ss_pred             eeEEcCCCCCce
Q psy1204          28 LYVLCKDCHKES   39 (71)
Q Consensus        28 v~i~CndC~~~s   39 (71)
                      +.+.|.+||...
T Consensus        19 ~~l~C~~Cg~~~   30 (74)
T d2dkta1          19 CLLKAPCCDKLY   30 (74)
T ss_dssp             EEEEETTTTEEE
T ss_pred             eEEEcCcCcCee
Confidence            445555555433

>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=83.25  E-value=0.4  Score=25.02  Aligned_cols=26  Identities=19%  Similarity=0.459  Sum_probs=18.2

Q ss_pred             eEEcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204          29 YVLCKDCHKESKVLYHIIGLKCEHCGSYNTCR   60 (71)
Q Consensus        29 ~i~CndC~~~s~v~~h~~g~kCp~C~Synt~i   60 (71)
                      .-.|.+|+.      ..|...||.||+.....
T Consensus         4 lrkC~~C~~------YTL~~~CP~CG~~t~~a   29 (55)
T d2apob1           4 MKKCPKCGL------YTLKEICPKCGEKTVIP   29 (55)
T ss_dssp             CEECTTTCC------EESSSBCSSSCSBCBCC
T ss_pred             eeeCCcccc------eeccccCcCCCCccCcc
Confidence            347889986      34556899998865543

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

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

Probab=82.86  E-value=0.22  Score=25.23  Aligned_cols=28  Identities=21%  Similarity=0.651  Sum_probs=21.4

Q ss_pred             eeEEcCCCCCceeeceEeecccCCCCCCc
Q psy1204          28 LYVLCKDCHKESKVLYHIIGLKCEHCGSY   56 (71)
Q Consensus        28 v~i~CndC~~~s~v~~h~~g~kCp~C~Sy   56 (71)
                      |...|-+|+....+..... ..|..||+.
T Consensus         3 v~YiCgeCg~~~~l~~~d~-irCreCG~R   30 (46)
T d1twfl_           3 LKYICAECSSKLSLSRTDA-VRCKDCGHR   30 (46)
T ss_dssp             CCEECSSSCCEECCCTTST-TCCSSSCCC
T ss_pred             eEEEcccCCCceEeCCCCc-EEeccCCcE
Confidence            5678999999888765443 389999863

>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=82.09  E-value=0.47  Score=24.49  Aligned_cols=24  Identities=21%  Similarity=0.580  Sum_probs=16.6

Q ss_pred             EcCCCCCceeeceEeecccCCCCCCcceee
Q psy1204          31 LCKDCHKESKVLYHIIGLKCEHCGSYNTCR   60 (71)
Q Consensus        31 ~CndC~~~s~v~~h~~g~kCp~C~Synt~i   60 (71)
                      .|.+|+.      ..|...||.||+.....
T Consensus         4 kC~~C~~------YTL~~~CP~CG~~t~~a   27 (52)
T d2ey4e1           4 KCPKCGR------YTLKEVCPVCGEKTKVA   27 (52)
T ss_dssp             ECTTTCC------EESSSBCTTTCCBCEES
T ss_pred             cCCcccc------eeccccCcCCCCccccc
Confidence            6888875      24455899998865543