Citrus Sinensis ID: 041240

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110---
Protein Sequence
MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQKVEYEGLPNTSFLCGKYGHSKDICPNRTEEDHALGFQPHLDGANESVEMNSNL
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHccccEEEEEccccccccccEEEEEEEEccccccEEEEEEccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHcccEEEEEccccccccccEEEEEEEEEcccccccEEEEEccEEEEEEEccccHHHccccccccccccccccHHHHHcccccccccccccccccccc
Coil and Loop (DISEMBL)
MALHYYNKKILRMLGQIFGRVfktdyntesasrdkFGRLaveidpnkplisqffldgklqkveyeglpntsflcgkyghskdicpnrteedhalgfqphldganesvemnsnl
Flexible Loop (DISEMBL)
MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQKVEYEGLPNTSFLCGKYGHSKDICPNRTEEDHALGfqphldganesvemnsnl
Low Complexity Region (SEG)
MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQKVEYEGLPNTSFLCGKYGHSKDICPNRTEEDHALGFQPHLDGANESVEMNSNL
Disordered region (IsUnstruct)
**LHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQKVEYEGLPNTSFLCGKYGHSKDIC*****************************
Disordered Region (DISOPRED)
MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQKVEYEGLPNTSFLCGKYGHSKDICP****************************
Disordered Region (DISEMBL)
MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQKVEYEGLPNTSFLCGKYGHSKDICPNRTEEDHALGFQPHLDGANE********
Disordered Region (DISPRO)
MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQKVEYEGLPNTSFLCGKYGHSKDICP****************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQKVEYEGLPNTSFLCGKYGHSKDICPNRTEEDHALGFQPHLDGANESVEMNSNL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

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	113
332322109	678	hypothetical protein [Beta vulgaris subs	0.743	0.123	0.428	5e-14
255578245	182	hypothetical protein RCOM_1264690 [Ricin	0.867	0.538	0.378	4e-12
332322101	744	hypothetical protein [Beta vulgaris subs	0.805	0.122	0.371	2e-11
87116463	1898	unnamed protein product [Ipomoea batatas	0.752	0.044	0.376	5e-11
87116458	532	unnamed protein product [Ipomoea batatas	0.752	0.159	0.364	9e-11
87116461	532	unnamed protein product [Ipomoea batatas	0.752	0.159	0.364	1e-10
356562050	470	PREDICTED: uncharacterized protein LOC10	0.752	0.180	0.423	2e-10
357506591	189	hypothetical protein MTR_7g072780 [Medic	0.955	0.571	0.342	3e-10
255555973	87	hypothetical protein RCOM_0935160 [Ricin	0.663	0.862	0.426	4e-10
255549926	753	conserved hypothetical protein [Ricinus	0.504	0.075	0.526	5e-10

>gi|332322109|emb|CCA66008.1| hypothetical protein [Beta vulgaris subsp. vulgaris]

 Score = 82.0 bits (201), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/84 (42%), Positives = 55/84 (65%)

Query: 1   MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQ 60
           +++ Y++K+ L  +G   G+V K D NTES  R ++ R  +E+D +KPL+S+F L+GK+ 
Sbjct: 232 LSVEYFDKQFLHSIGSKIGKVIKIDRNTESMDRGQYVRFCIEVDLSKPLLSKFRLNGKVW 291

Query: 61  KVEYEGLPNTSFLCGKYGHSKDIC 84
            V+YEGL    F CG  GH +D C
Sbjct: 292 IVQYEGLRLICFKCGHLGHKEDTC 315

Source: Beta vulgaris subsp. vulgaris

Species: Beta vulgaris

Genus: Beta

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255578245|ref|XP_002529990.1| hypothetical protein RCOM_1264690 [Ricinus communis] gi|223530513|gb|EEF32395.1| hypothetical protein RCOM_1264690 [Ricinus communis]

 Score = 75.5 bits (184), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 39/103 (37%), Positives = 55/103 (53%), Gaps = 5/103 (4%)

Query: 5   YYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQKVEY 64
           Y  + +LR +  + GR  K DYNT++  + KF R+AVE+D  +P IS+  +DG  Q VEY
Sbjct: 26  YLLRNVLRTIDNLIGRPLKIDYNTQAGDKGKFARVAVELDLRRPFISRVKVDGNTQSVEY 85

Query: 65  EGLPNTSFLCGKYGHSKDICPNRTEEDHAL-----GFQPHLDG 102
           E L    +   KYGH  D+C     +  +L     G  P  DG
Sbjct: 86  EALLMIYYRYKKYGHVNDLCKENLRDRVSLEIVRSGTLPEKDG 128

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|332322101|emb|CCA65996.1| hypothetical protein [Beta vulgaris subsp. vulgaris]

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/97 (37%), Positives = 53/97 (54%), Gaps = 6/97 (6%)

Query: 1   MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQ 60
           + L YY+K+ L  +    G+  K DY T+  +R ++ R+ +E+D  K L+S+ ++    Q
Sbjct: 218 LPLEYYDKEALFAIAGKVGKPIKVDYATDHMARGRYARVCIELDLAKALVSKVWVARAWQ 277

Query: 61  KVEYEGLPNTSFLCGKYGHSKDICPNRTEEDHALGFQ 97
            VEYE L    FLCGK GH +D C       H LG Q
Sbjct: 278 NVEYENLSLVCFLCGKIGHRRDQC------SHGLGEQ 308

Source: Beta vulgaris subsp. vulgaris

Species: Beta vulgaris

Genus: Beta

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|87116463|dbj|BAE79384.1| unnamed protein product [Ipomoea batatas]

 Score = 71.6 bits (174), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 32/85 (37%), Positives = 50/85 (58%)

Query: 1   MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQ 60
           +++ Y+    ++ + +  G+    D  T +  R +F R AVEID +KPL+S+ ++ G +Q
Sbjct: 196 LSMEYFRDDTIKAILENIGKPLGLDRTTMARERGRFARAAVEIDLDKPLVSEIWVMGDVQ 255

Query: 61  KVEYEGLPNTSFLCGKYGHSKDICP 85
           KVEYEGL    F CG  GH +  CP
Sbjct: 256 KVEYEGLHVVCFGCGVVGHREQACP 280

Source: Ipomoea batatas

Species: Ipomoea batatas

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|87116458|dbj|BAE79381.1| unnamed protein product [Ipomoea batatas]

 Score = 70.9 bits (172), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 31/85 (36%), Positives = 51/85 (60%)

Query: 1   MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQ 60
           +++ Y+    ++ + +  G+  + D  T +  + +F R AVEID +KPL+S+ ++ G +Q
Sbjct: 196 LSMEYFRDDTIKAILENIGKPLRLDRTTMAREKGRFARAAVEIDLDKPLVSEIWVMGDVQ 255

Query: 61  KVEYEGLPNTSFLCGKYGHSKDICP 85
           KVEYEGL    F CG  GH +  CP
Sbjct: 256 KVEYEGLHVVCFGCGVVGHREQACP 280

Source: Ipomoea batatas

Species: Ipomoea batatas

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|87116461|dbj|BAE79383.1| unnamed protein product [Ipomoea batatas]

 Score = 70.5 bits (171), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 31/85 (36%), Positives = 50/85 (58%)

Query: 1   MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQ 60
           +++ Y+    ++ + +  G+  + D  T +  + +F R AVEID  KPL+S+ ++ G +Q
Sbjct: 196 LSMEYFRDDTIKAILENIGKPLRLDRTTMAREKGRFARAAVEIDLGKPLVSEIWVMGDVQ 255

Query: 61  KVEYEGLPNTSFLCGKYGHSKDICP 85
           KVEYEGL    F CG  GH +  CP
Sbjct: 256 KVEYEGLHVVCFGCGVVGHREQACP 280

Source: Ipomoea batatas

Species: Ipomoea batatas

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562050|ref|XP_003549288.1| PREDICTED: uncharacterized protein LOC100791212 [Glycine max]

 Score = 70.1 bits (170), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/85 (42%), Positives = 45/85 (52%)

Query: 1   MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQ 60
           + L YY++ IL  L +  G   K D NT    R  F R+ V+ID NKP++ +  L G   
Sbjct: 186 LNLIYYDENILLALARAIGTPIKVDSNTLDVRRGHFARICVQIDLNKPVVGKVGLKGYWY 245

Query: 61  KVEYEGLPNTSFLCGKYGHSKDICP 85
           KVEYEGL      CG YGH    CP
Sbjct: 246 KVEYEGLHRICSSCGCYGHLARECP 270

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357506591|ref|XP_003623584.1| hypothetical protein MTR_7g072780 [Medicago truncatula] gi|355498599|gb|AES79802.1| hypothetical protein MTR_7g072780 [Medicago truncatula]

 Score = 69.3 bits (168), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 37/108 (34%), Positives = 52/108 (48%)

Query: 1   MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQ 60
           + L YY++  L  +    GR  K D NT    R +F R+ VE+D   P + + +++G L 
Sbjct: 79  LNLVYYDEIFLLAIASTIGRPIKVDTNTLKVERGRFSRVCVEVDLTVPAVGKIWVNGHLY 138

Query: 61  KVEYEGLPNTSFLCGKYGHSKDICPNRTEEDHALGFQPHLDGANESVE 108
           KV++EGL      CG YGH    CP  T E  A     H    N + E
Sbjct: 139 KVQHEGLHLICTNCGCYGHLSRNCPLDTTESKAAAPPLHNSSQNRNQE 186

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555973|ref|XP_002519021.1| hypothetical protein RCOM_0935160 [Ricinus communis] gi|223541684|gb|EEF43232.1| hypothetical protein RCOM_0935160 [Ricinus communis]

 Score = 68.6 bits (166), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 32/75 (42%), Positives = 48/75 (64%)

Query: 1  MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQ 60
          M + YY++ IL+ + ++     K D NT+ A+R KF R+AV+++   PL+++  LDG  Q
Sbjct: 13 MPVKYYHENILQAIDKVVRTTVKVDMNTQLANRGKFTRVAVKLNLVNPLVTKIHLDGFNQ 72

Query: 61 KVEYEGLPNTSFLCG 75
           VEYEGLP   F CG
Sbjct: 73 HVEYEGLPKIFFTCG 87

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255549926|ref|XP_002516014.1| conserved hypothetical protein [Ricinus communis] gi|223544919|gb|EEF46434.1| conserved hypothetical protein [Ricinus communis]

 Score = 68.2 bits (165), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 39/57 (68%)

Query: 1   MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDG 57
           M +HYY+ KILR  G I GR  K D+N E  + D+F R+AVE+D +KPLI+   LDG
Sbjct: 88  MPMHYYHNKILRTNGNIVGRTVKIDFNIEEVNHDRFARVAVELDLSKPLIAHCILDG 144

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	113
TAIR|locus:2045756	515	AT2G01050 [Arabidopsis thalian	0.964	0.211	0.302	8.2e-09

TAIR|locus:2045756 AT2G01050 [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 8.2e-09, P = 8.2e-09
 Identities = 33/109 (30%), Positives = 51/109 (46%)

Query:     4 HYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVEIDPNKPLISQFFLDGKLQKVE 63
             +YY++ +L  + +  GR  K D NT +  + +F R+ +E++  KPL     ++G    V 
Sbjct:   176 NYYHRCLLMEIARGLGRPLKVDMNTINFDKGRFARVCIEVNLAKPLKGTVLINGDRYFVA 235

Query:    64 YEGLPNTSFLCGKYGHSKDICPNRTEEDHALGFQPHLDGANESVEMNSN 112
             YEGL      CG YGH    CP       + G +   D A   V M  +
Sbjct:   236 YEGLSKICSSCGIYGHLVHSCPRNVVVKVSAGAETVTDRAVVPVGMEGD 284


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.319   0.138   0.410    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      113       113   0.00091  102 3  11 22  0.48    30
                                                     29  0.44    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  548 (58 KB)
  Total size of DFA:  119 KB (2078 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  11.70u 0.16s 11.86t   Elapsed:  00:00:01
  Total cpu time:  11.70u 0.16s 11.86t   Elapsed:  00:00:01
  Start:  Fri May 10 04:25:24 2013   End:  Fri May 10 04:25:25 2013

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	113
pfam14392	49	pfam14392, zf-CCHC_4, Zinc knuckle	8e-07
pfam14111	153	pfam14111, DUF4283, Domain of unknown function (DU	2e-04

>gnl|CDD|222730 pfam14392, zf-CCHC_4, Zinc knuckle

 Score = 42.2 bits (100), Expect = 8e-07
 Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 5/48 (10%)

Query: 43 IDPNKPLISQFFLDGK-----LQKVEYEGLPNTSFLCGKYGHSKDICP 85
          +D +KPL  +  +        + KV YE LPN  F CG+ GHS   CP
Sbjct: 1  LDVSKPLRFEVNVKFPSGEEAVVKVRYERLPNFCFHCGRLGHSDKECP 48

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. This particular family is found in plant proteins. Length = 49

>gnl|CDD|222549 pfam14111, DUF4283, Domain of unknown function (DUF4283)

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 13/40 (32%), Positives = 23/40 (57%)

Query: 3   LHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVE 42
           LH ++++IL+ +G   G     D +TE   R +F R+ V+
Sbjct: 114 LHLWSEEILKRIGSACGGFVAVDEDTEGRERLQFARILVK 153

This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region. There are two highly conserved tryptophan residues. Length = 153

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	113
PF14392	49	zf-CCHC_4: Zinc knuckle	99.67
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	99.09
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	97.43
PF13696	32	zf-CCHC_2: Zinc knuckle	95.54
PF15288	40	zf-CCHC_6: Zinc knuckle	95.02
smart00343	26	ZnF_C2HC zinc finger.	94.61
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	91.0
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	90.98
PF13917	42	zf-CCHC_3: Zinc knuckle	89.71
PTZ00368	148	universal minicircle sequence binding protein (UMS	88.95
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	84.5
PF10083	158	DUF2321: Uncharacterized protein conserved in bact	81.87
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	80.61

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=99.67  E-value=3.6e-17  Score=98.29  Aligned_cols=44  Identities=45%  Similarity=0.859  Sum_probs=40.2

Q ss_pred             ecCCCCceeEEEEc---Ce--EEEEEEccccccccccCccccCCCCCCC
Q 041240           43 IDPNKPLISQFFLD---GK--LQKVEYEGLPNTSFLCGKYGHSKDICPN   86 (113)
Q Consensus        43 iDl~kpL~~~v~v~---g~--~~~v~YE~Lp~fC~~Cg~iGH~~~~C~~   86 (113)
                      ||++|||.+++.|+   |.  ++.|+|||||.||++||.+||..++|++
T Consensus         1 id~~kPL~~~i~v~~~~g~~~~~~v~YE~lp~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen    1 IDVSKPLRREIKVKFPEGESFWVKVKYERLPRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             CCCCCcccceEEEEeCCCcEEEEEEEECCcChhhcCCCCcCcCHhHcCC
Confidence            69999999999884   32  8999999999999999999999999985

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=99.09  E-value=9.4e-11  Score=82.59  Aligned_cols=42  Identities=33%  Similarity=0.592  Sum_probs=41.0

Q ss_pred             CCcccccHHHHHHHhhccCceEEEecCCCcccccceeEEEEE
Q 041240            1 MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVE   42 (113)
Q Consensus         1 LP~~y~~~~~l~~I~~~iG~~l~vD~~t~~~~~g~faRV~Ve   42 (113)
                      ||+.||+++++++||+.+|+|+++|.+|.+..+++||||+|+
T Consensus       112 lP~~~~~~~~~~~i~~~iG~~i~vD~~t~~~~~~~~~Rv~V~  153 (153)
T PF14111_consen  112 LPLHLWSEEILKAIGSKIGEPIEVDENTLKRTRLDFARVRVE  153 (153)
T ss_pred             CCHHHhhhHHHHHHHHhcCCeEEEEcCCCCcccccEEEEEEC
Confidence            799999999999999999999999999999999999999996

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=97.43  E-value=6.6e-05  Score=36.32  Aligned_cols=17  Identities=41%  Similarity=0.913  Sum_probs=15.8

Q ss_pred             cccccCccccCCCCCCC
Q 041240           70 TSFLCGKYGHSKDICPN   86 (113)
Q Consensus        70 fC~~Cg~iGH~~~~C~~   86 (113)
                      .||+||..||...+||.
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            69999999999999984

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=95.54  E-value=0.0063  Score=33.58  Aligned_cols=20  Identities=30%  Similarity=0.637  Sum_probs=17.9

Q ss_pred             ccccccCccccCCCCCCCCC
Q 041240           69 NTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        69 ~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      ..|+.|+.-||..++||...
T Consensus         9 Y~C~~C~~~GH~i~dCP~~~   28 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPTNK   28 (32)
T ss_pred             CEeecCCCCCccHhHCCCCC
Confidence            47999999999999999943

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=95.02  E-value=0.023  Score=32.82  Aligned_cols=20  Identities=30%  Similarity=0.685  Sum_probs=17.0

Q ss_pred             ccccccCccccCC--CCCCCCC
Q 041240           69 NTSFLCGKYGHSK--DICPNRT   88 (113)
Q Consensus        69 ~fC~~Cg~iGH~~--~~C~~~~   88 (113)
                      ..|..||-+||..  +.||...
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             ccccccccccccccCccCCCCC
Confidence            4699999999987  6899864

>smart00343 ZnF_C2HC zinc finger

Probab=94.61  E-value=0.015  Score=29.93  Aligned_cols=18  Identities=39%  Similarity=0.866  Sum_probs=16.0

Q ss_pred             cccccCccccCCCCCCCC
Q 041240           70 TSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        70 fC~~Cg~iGH~~~~C~~~   87 (113)
                      .|+.||..||..++|+..
T Consensus         1 ~C~~CG~~GH~~~~C~~~   18 (26)
T smart00343        1 KCYNCGKEGHIARDCPKX   18 (26)
T ss_pred             CCccCCCCCcchhhCCcc
Confidence            599999999999999843

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=91.00  E-value=0.12  Score=39.17  Aligned_cols=16  Identities=31%  Similarity=0.802  Sum_probs=8.7

Q ss_pred             ccccccCccccCCCCC
Q 041240           69 NTSFLCGKYGHSKDIC   84 (113)
Q Consensus        69 ~fC~~Cg~iGH~~~~C   84 (113)
                      ..|++||..||..++|
T Consensus        98 ~~C~~Cg~~GH~~~dC  113 (190)
T COG5082          98 KKCYNCGETGHLSRDC  113 (190)
T ss_pred             cccccccccCcccccc
Confidence            4455555555555555

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=90.98  E-value=0.099  Score=39.57  Aligned_cols=22  Identities=32%  Similarity=0.679  Sum_probs=18.9

Q ss_pred             EccccccccccCccccCCCCCC
Q 041240           64 YEGLPNTSFLCGKYGHSKDICP   85 (113)
Q Consensus        64 YE~Lp~fC~~Cg~iGH~~~~C~   85 (113)
                      +-.-..+||+||..||..++||
T Consensus        56 ~~~~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          56 IREENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             ccccccccchhcccCcccccCC
Confidence            3344579999999999999999

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=89.71  E-value=0.18  Score=29.37  Aligned_cols=19  Identities=37%  Similarity=0.639  Sum_probs=17.4

Q ss_pred             cccccccCccccCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPN   86 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~   86 (113)
                      ...|..|+..||...+|+.
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            4689999999999999996

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=88.95  E-value=0.23  Score=35.17  Aligned_cols=18  Identities=39%  Similarity=0.944  Sum_probs=10.5

Q ss_pred             ccccccCccccCCCCCCC
Q 041240           69 NTSFLCGKYGHSKDICPN   86 (113)
Q Consensus        69 ~fC~~Cg~iGH~~~~C~~   86 (113)
                      .+|++||..||..++||.
T Consensus       130 ~~C~~Cg~~gH~~~dCp~  147 (148)
T PTZ00368        130 KTCYNCGQTGHLSRDCPD  147 (148)
T ss_pred             CccccCCCcCcccccCCC
Confidence            456666666666666654

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=84.50  E-value=0.45  Score=36.75  Aligned_cols=25  Identities=32%  Similarity=0.678  Sum_probs=20.3

Q ss_pred             EEEccccccccccCccccCCCCCCCC
Q 041240           62 VEYEGLPNTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        62 v~YE~Lp~fC~~Cg~iGH~~~~C~~~   87 (113)
                      +.+.+- .+||.||..||....|+..
T Consensus       138 ~~~~~~-~~Cy~Cg~~GH~s~~C~~~  162 (261)
T KOG4400|consen  138 VDGPKP-AKCYSCGEQGHISDDCPEN  162 (261)
T ss_pred             ccCCCC-CccCCCCcCCcchhhCCCC
Confidence            344444 7899999999999999964

>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454

Probab=81.87  E-value=0.54  Score=34.62  Aligned_cols=31  Identities=26%  Similarity=0.503  Sum_probs=23.5

Q ss_pred             CCCCceeEEEEcCe-EEEEEEccccccccccCc
Q 041240           45 PNKPLISQFFLDGK-LQKVEYEGLPNTSFLCGK   76 (113)
Q Consensus        45 l~kpL~~~v~v~g~-~~~v~YE~Lp~fC~~Cg~   76 (113)
                      -+-|++....++|. .+.-.|+ .|.||++||.
T Consensus        45 C~~~IrG~y~v~gv~~~g~~~~-~PsYC~~CGk   76 (158)
T PF10083_consen   45 CSTPIRGDYHVEGVFGLGGHYE-APSYCHNCGK   76 (158)
T ss_pred             CCCCCCCceecCCeeeeCCCCC-CChhHHhCCC
Confidence            45566777777775 4557888 9999999996

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=80.61  E-value=1.2  Score=25.17  Aligned_cols=25  Identities=32%  Similarity=0.452  Sum_probs=14.7

Q ss_pred             cccccccCccccCCCCCCCCCcccc
Q 041240           68 PNTSFLCGKYGHSKDICPNRTEEDH   92 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~~~~~~   92 (113)
                      |..|+.||+-.|-.++|......++
T Consensus         2 ~~~CprC~kg~Hwa~~C~sk~d~~G   26 (36)
T PF14787_consen    2 PGLCPRCGKGFHWASECRSKTDVDG   26 (36)
T ss_dssp             --C-TTTSSSCS-TTT---TCCCCC
T ss_pred             CccCcccCCCcchhhhhhhhhcccC
Confidence            5679999999999999998754443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	113
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.28
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	97.12
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.03
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	96.95
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	95.88
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	95.5
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	95.48
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	95.45
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	95.42
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	95.39
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	95.34
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	95.33
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	95.33
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	95.31
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	95.15
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	94.79
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	94.78
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	94.73
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	94.59
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	94.48
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	94.3
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	94.19
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	92.79
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	92.28
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	92.06
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	92.01
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	91.62
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	90.65
2pzo_E	42	CAP-Gly domain-containing linker protein 1; struct	87.93
3e2u_E	42	CAP-Gly domain-containing linker protein 1; struct	82.79

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=97.28  E-value=0.00014  Score=41.15  Aligned_cols=26  Identities=19%  Similarity=0.474  Sum_probs=21.3

Q ss_pred             cccccccCccccCCCCCCCCCccccc
Q 041240           68 PNTSFLCGKYGHSKDICPNRTEEDHA   93 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~~~~~~~   93 (113)
                      ...||.||..||...+||.....+..
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~~~~r~   35 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKPRGPRG   35 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCCCTTC
T ss_pred             CCeeeECCCCCcchhhCcCCcccCCC
Confidence            36899999999999999997654433

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=97.03  E-value=0.00022  Score=37.36  Aligned_cols=21  Identities=33%  Similarity=0.570  Sum_probs=18.3

Q ss_pred             cccccccCccccCCCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      +..||+||..||..++|+.+.
T Consensus         6 ~~~C~nCgk~GH~ar~C~~pr   26 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSS
T ss_pred             CCEEEECCccccCHhHCcccc
Confidence            467999999999999998753

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=96.95  E-value=0.00039  Score=41.98  Aligned_cols=26  Identities=19%  Similarity=0.474  Sum_probs=21.2

Q ss_pred             cccccccCccccCCCCCCCCCccccc
Q 041240           68 PNTSFLCGKYGHSKDICPNRTEEDHA   93 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~~~~~~~   93 (113)
                      ...||.||..||..++||.....+..
T Consensus        23 ~~~C~~Cge~GH~ardCp~~~~~~~~   48 (56)
T 1u6p_A           23 RDQCAYCKEKGHWAKDCPKKPRGPRG   48 (56)
T ss_dssp             TTBCSSSCCBSSCGGGCTTCCCSSCS
T ss_pred             CCcceeCCCCCcccccCcCCccccCC
Confidence            46799999999999999997654433

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=95.88  E-value=0.0038  Score=36.05  Aligned_cols=21  Identities=33%  Similarity=0.540  Sum_probs=17.8

Q ss_pred             ccccccccCccccCCCCCCCC
Q 041240           67 LPNTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        67 Lp~fC~~Cg~iGH~~~~C~~~   87 (113)
                      -+..||+||..||...+|+..
T Consensus         5 r~~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            5 KVIRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CCCBCTTTCCBTCCTTTCCCS
T ss_pred             CcCeeeecCCCCcChhhCcCC
Confidence            356899999999999999875

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=95.50  E-value=0.0051  Score=37.03  Aligned_cols=20  Identities=30%  Similarity=0.830  Sum_probs=14.1

Q ss_pred             cccccccCccccCCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~   87 (113)
                      +..||+||..||..++|+..
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~   23 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKK   23 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTT
T ss_pred             CCcccccCCCCeehhhCcCC
Confidence            45677777777777777765

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.48  E-value=0.0037  Score=37.49  Aligned_cols=19  Identities=47%  Similarity=0.884  Sum_probs=17.0

Q ss_pred             ccccccCccccCCCCCCCC
Q 041240           69 NTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        69 ~fC~~Cg~iGH~~~~C~~~   87 (113)
                      ..||.||..||..++||..
T Consensus         8 ~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             CCCTTTCCTTSCGGGCSGG
T ss_pred             CccccCCCcCcccccCCCC
Confidence            4799999999999999843

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=95.45  E-value=0.0069  Score=33.27  Aligned_cols=18  Identities=44%  Similarity=0.945  Sum_probs=16.1

Q ss_pred             cccccCccccCCCCCCCC
Q 041240           70 TSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        70 fC~~Cg~iGH~~~~C~~~   87 (113)
                      .||+||..||..++|+..
T Consensus         2 ~C~~Cg~~GH~a~~C~~~   19 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQP   19 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSC
T ss_pred             eeeccCCCCcccccCCCC
Confidence            599999999999999975

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=95.42  E-value=0.0065  Score=33.39  Aligned_cols=19  Identities=26%  Similarity=0.628  Sum_probs=17.0

Q ss_pred             cccccccCccccCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPN   86 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~   86 (113)
                      ...|+.||..||..++||+
T Consensus        21 ~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           21 QEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             CSSCTTTCCSSSCTTTSCC
T ss_pred             CCccccCCCCCCccCcCcC
Confidence            3689999999999999985

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=95.39  E-value=0.0061  Score=39.25  Aligned_cols=21  Identities=29%  Similarity=0.578  Sum_probs=19.2

Q ss_pred             cccccccCccccCCCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      ..+|++||.-||..++|+...
T Consensus        46 ~~~CYnCG~~GH~~rdC~~~r   66 (83)
T 3nyb_B           46 TIYCYNCGGKGHFGDDCKEKR   66 (83)
T ss_dssp             CCBCSSSSCBSSCGGGCSSCC
T ss_pred             CCeecccCCCCcCcccCCccc
Confidence            379999999999999999875

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=95.34  E-value=0.0065  Score=33.01  Aligned_cols=18  Identities=39%  Similarity=0.768  Sum_probs=13.9

Q ss_pred             cccccCccccCCCCCCCC
Q 041240           70 TSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        70 fC~~Cg~iGH~~~~C~~~   87 (113)
                      .||+||..||..++|+..
T Consensus         2 ~C~~Cg~~GH~~~~C~~~   19 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP   19 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB
T ss_pred             cccccCCCCcchhhCcCc
Confidence            588888888888888763

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=95.33  E-value=0.0055  Score=33.30  Aligned_cols=19  Identities=32%  Similarity=0.740  Sum_probs=17.0

Q ss_pred             cccccccCccccCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPN   86 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~   86 (113)
                      +..|+.||..||..++||.
T Consensus        19 ~~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           19 PKVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             BTTCSSCCCTTGGGGTTCC
T ss_pred             cCeEccCCCcCCccCcCcC
Confidence            3689999999999999984

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=95.33  E-value=0.0092  Score=35.58  Aligned_cols=23  Identities=22%  Similarity=0.466  Sum_probs=19.9

Q ss_pred             ccccccccCccccCCCCCCCCCc
Q 041240           67 LPNTSFLCGKYGHSKDICPNRTE   89 (113)
Q Consensus        67 Lp~fC~~Cg~iGH~~~~C~~~~~   89 (113)
                      ....|+.||..||..++|+....
T Consensus        29 ~~~~C~~Cg~~GH~ar~C~~~~~   51 (60)
T 1cl4_A           29 VPGLCPRCKRGKHWANECKSKTD   51 (60)
T ss_dssp             CCCSCSSCSSCSSCSTTCCCTTS
T ss_pred             CCcceeECCCCCCccCcCCCccc
Confidence            45789999999999999998754

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=95.31  E-value=0.0059  Score=35.82  Aligned_cols=21  Identities=33%  Similarity=0.574  Sum_probs=17.7

Q ss_pred             ccccccccCccccCCCCCCCC
Q 041240           67 LPNTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        67 Lp~fC~~Cg~iGH~~~~C~~~   87 (113)
                      -+..||.||..||...+|+..
T Consensus        11 ~~~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           11 KTVKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             GTCBCTTTCCBSSCGGGCSSC
T ss_pred             CCcceeeeCCCCcChhhcCCC
Confidence            356899999999999999875

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=95.15  E-value=0.0077  Score=34.73  Aligned_cols=20  Identities=40%  Similarity=0.884  Sum_probs=17.9

Q ss_pred             ccccccCccccCCCCCCCCC
Q 041240           69 NTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        69 ~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      ..|+.||..||..++|+...
T Consensus        28 ~~C~~Cg~~GH~~~~C~~~~   47 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCPERQ   47 (49)
T ss_dssp             CSCSSSCCSSCCGGGCCSSC
T ss_pred             CeeCcCCCcCCccCCCcCCC
Confidence            57999999999999999753

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=94.79  E-value=0.012  Score=35.44  Aligned_cols=22  Identities=27%  Similarity=0.590  Sum_probs=18.9

Q ss_pred             cccccccCccccCCCCCCCCCc
Q 041240           68 PNTSFLCGKYGHSKDICPNRTE   89 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~~~   89 (113)
                      ...||.||..||..++|+....
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~~   51 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKRDG   51 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCCC-
T ss_pred             CCeeCCCCCCCCCcCCCcCCCc
Confidence            4679999999999999998754

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.78  E-value=0.013  Score=35.52  Aligned_cols=21  Identities=19%  Similarity=0.442  Sum_probs=15.9

Q ss_pred             ccccccccCccccCCCCCCCC
Q 041240           67 LPNTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        67 Lp~fC~~Cg~iGH~~~~C~~~   87 (113)
                      .+..||+||..||..++|+..
T Consensus         6 r~~~C~~Cg~~GH~a~~C~~~   26 (63)
T 2cqf_A            6 SGDRCYNCGGLDHHAKECKLP   26 (63)
T ss_dssp             SCCCCSSSCCSSSCTTTCCSC
T ss_pred             CCCcccccCCCCcChhhCCCC
Confidence            356788888888888888754

>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}

Probab=94.73  E-value=0.011  Score=30.30  Aligned_cols=20  Identities=20%  Similarity=0.472  Sum_probs=17.4

Q ss_pred             cccccccCccccCCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~   87 (113)
                      ..+|..|..+||...+|+..
T Consensus         3 RpYCe~CE~FGH~t~~C~d~   22 (26)
T 2hqh_E            3 RPYCEICEMFGHWATNCNDD   22 (26)
T ss_dssp             -CEETTTTEESSCGGGCCTT
T ss_pred             CccchHHHHhCcccccCCcc
Confidence            36899999999999999764

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.59  E-value=0.019  Score=34.80  Aligned_cols=21  Identities=24%  Similarity=0.651  Sum_probs=18.8

Q ss_pred             cccccccCccccCCCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      +..||.||..||..++|+...
T Consensus        29 ~~~C~~Cg~~GH~ar~Cp~~~   49 (63)
T 2cqf_A           29 PKKCHFCQSISHMVASCPLKA   49 (63)
T ss_dssp             SSCCTTTCCSSSCTTTCTGGG
T ss_pred             CCccCCcCCcCCccCcCCCcc
Confidence            578999999999999999764

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=94.48  E-value=0.013  Score=34.33  Aligned_cols=20  Identities=35%  Similarity=0.753  Sum_probs=18.0

Q ss_pred             ccccccCccccCCCCCCCCC
Q 041240           69 NTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        69 ~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      ..|+.||..||..++|+...
T Consensus        34 ~~C~~Cg~~GH~~~~C~~~~   53 (55)
T 1a1t_A           34 KGCWKCGKEGHQMKDCTERQ   53 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSSSC
T ss_pred             CEeCCCCCcCCccCCCcCcC
Confidence            57999999999999999754

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=94.30  E-value=0.016  Score=36.38  Aligned_cols=21  Identities=19%  Similarity=0.442  Sum_probs=18.6

Q ss_pred             ccccccccCccccCCCCCCCC
Q 041240           67 LPNTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        67 Lp~fC~~Cg~iGH~~~~C~~~   87 (113)
                      .+..||+||..||..++|+..
T Consensus        23 r~~~C~~Cg~~GH~a~~C~~~   43 (74)
T 2li8_A           23 KGDRCYNCGGLDHHAKECKLP   43 (74)
T ss_dssp             TTSCCTTTCCSSSCTTTCSSC
T ss_pred             CCCcccccCCcCcCcccCCCC
Confidence            567899999999999999964

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=94.19  E-value=0.0084  Score=35.76  Aligned_cols=19  Identities=37%  Similarity=0.795  Sum_probs=0.0

Q ss_pred             cccccCccccCCCCCCCCC
Q 041240           70 TSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        70 fC~~Cg~iGH~~~~C~~~~   88 (113)
                      .||+||..||..++|+...
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~~   21 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEHA   21 (60)
T ss_dssp             -------------------
T ss_pred             ccccCCCCCcCHhhCcCCC
Confidence            6999999999999999864

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=92.79  E-value=0.023  Score=36.47  Aligned_cols=21  Identities=33%  Similarity=0.534  Sum_probs=17.0

Q ss_pred             ccccccccCccccCCCCCCCC
Q 041240           67 LPNTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        67 Lp~fC~~Cg~iGH~~~~C~~~   87 (113)
                      -..+|+.||..||..+.||..
T Consensus         4 k~~~C~~Cg~~GH~~~~Cp~~   24 (83)
T 3nyb_B            4 KKVQCTLCKSKKHSKERCPSI   24 (83)
T ss_dssp             ---CCSSSCCSSSCGGGCGGG
T ss_pred             ccCCCCCCCCCCCccccCCCc
Confidence            457899999999999999975

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=92.28  E-value=0.048  Score=38.25  Aligned_cols=20  Identities=20%  Similarity=0.527  Sum_probs=17.0

Q ss_pred             ccccccCccccCCCCCCCCC
Q 041240           69 NTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        69 ~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      ..||+||..||..++|+...
T Consensus        98 ~~C~~Cg~~GH~a~~C~~~~  117 (148)
T 3ts2_A           98 DRCYNCGGLDHHAKECKLPP  117 (148)
T ss_dssp             CCCTTTCCSSCCGGGCCSCC
T ss_pred             CcccEeCCccchhhhCCCCC
Confidence            35999999999999999843

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=92.06  E-value=0.056  Score=37.88  Aligned_cols=21  Identities=24%  Similarity=0.651  Sum_probs=19.0

Q ss_pred             cccccccCccccCCCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      +..|+.||..||..+.||...
T Consensus       119 ~~~C~~Cg~~GH~~r~Cp~~~  139 (148)
T 3ts2_A          119 PKKCHFCQSINHMVASCPLKA  139 (148)
T ss_dssp             CCCCTTTCCSSCCGGGCTTTT
T ss_pred             CCcccccCCcCCEeccCcCCC
Confidence            578999999999999999863

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=92.01  E-value=0.049  Score=34.12  Aligned_cols=21  Identities=24%  Similarity=0.651  Sum_probs=18.7

Q ss_pred             cccccccCccccCCCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      +..|+.||..||..++|+...
T Consensus        46 ~~~C~~Cg~~GH~ar~Cp~~~   66 (74)
T 2li8_A           46 PKKCHFCQSISHMVASCPLKA   66 (74)
T ss_dssp             CCCCTTTCCTTSCGGGCTTGG
T ss_pred             CCccCCcCCcCCccCcCcCCc
Confidence            578999999999999999753

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=91.62  E-value=0.076  Score=35.62  Aligned_cols=21  Identities=29%  Similarity=0.551  Sum_probs=18.5

Q ss_pred             ccccccccCccccCCCCCCCC
Q 041240           67 LPNTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        67 Lp~fC~~Cg~iGH~~~~C~~~   87 (113)
                      -..+|++||..||..++||..
T Consensus       104 ~~~~Cy~Cg~~GH~a~dCp~~  124 (124)
T 2lli_A          104 HTIYCYNCGGKGHFGDDCKEK  124 (124)
T ss_dssp             CCCCTTTTSSSCTTTTTSCCC
T ss_pred             CCCCcCCCCCCCcCcccCcCC
Confidence            357999999999999999963

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=90.65  E-value=0.1  Score=35.00  Aligned_cols=17  Identities=35%  Similarity=0.714  Sum_probs=8.2

Q ss_pred             cccccCccccCCCCCCC
Q 041240           70 TSFLCGKYGHSKDICPN   86 (113)
Q Consensus        70 fC~~Cg~iGH~~~~C~~   86 (113)
                      .||+|+..||..++||.
T Consensus         6 ~C~~C~~~GH~~~~Cp~   22 (124)
T 2lli_A            6 KCNNCSQRGHLKKDCPH   22 (124)
T ss_dssp             CCSSCSSSSCCTTTTTS
T ss_pred             cccCCCCCCcCcccCcC
Confidence            44555555555444443

>3e2u_E CAP-Gly domain-containing linker protein 1; structural protein microtubule binding, dynactin, cytoskelet associated protein, P150glued; 2.60A {Homo sapiens}

Probab=82.79  E-value=0.48  Score=26.77  Aligned_cols=20  Identities=20%  Similarity=0.472  Sum_probs=18.3

Q ss_pred             cccccccCccccCCCCCCCC
Q 041240           68 PNTSFLCGKYGHSKDICPNR   87 (113)
Q Consensus        68 p~fC~~Cg~iGH~~~~C~~~   87 (113)
                      ..+|..|-.+||-..+|...
T Consensus        20 RpYCe~CEVFGH~t~eC~dd   39 (42)
T 3e2u_E           20 RPYCEICEMFGHWATNCNDD   39 (42)
T ss_dssp             CCEETTTTEESSCGGGCCTT
T ss_pred             CcccccceecccccccCCcc
Confidence            57999999999999999875

---

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	113
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.25
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.08
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	96.1
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	95.89
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	91.95
d1hmja_	68	RNA polymerase subunit RBP5 (RNA polymerase subuni	91.15
d1dzfa2	72	Eukaryotic RPB5 C-terminal domain {Baker's yeast (	88.14
d1eika_	77	RNA polymerase subunit RBP5 (RNA polymerase subuni	83.79

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=97.25  E-value=5.6e-05  Score=38.41  Aligned_cols=22  Identities=32%  Similarity=0.513  Sum_probs=19.0

Q ss_pred             ccccccccCccccCCCCCCCCC
Q 041240           67 LPNTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        67 Lp~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      -...||+||+.||..++|.-+.
T Consensus         5 ~~ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           5 KVIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSS
T ss_pred             ceeEeecCCccchhhhhccCcc
Confidence            4578999999999999998753

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=96.10  E-value=0.0013  Score=35.95  Aligned_cols=17  Identities=35%  Similarity=0.778  Sum_probs=8.4

Q ss_pred             cccccCccccCCCCCCC
Q 041240           70 TSFLCGKYGHSKDICPN   86 (113)
Q Consensus        70 fC~~Cg~iGH~~~~C~~   86 (113)
                      .|+.||..||...+||.
T Consensus        24 ~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1          24 GCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             SCSSSCCSSSCTTTCCS
T ss_pred             ccccCCCCCeecccCCC
Confidence            35555555555555543

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=95.89  E-value=0.0016  Score=35.48  Aligned_cols=20  Identities=35%  Similarity=0.674  Sum_probs=17.8

Q ss_pred             ccccccCccccCCCCCCCCC
Q 041240           69 NTSFLCGKYGHSKDICPNRT   88 (113)
Q Consensus        69 ~fC~~Cg~iGH~~~~C~~~~   88 (113)
                      ..||+||..||...+||.+.
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~   21 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR   21 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC
T ss_pred             CccccCCCcCcCcccCcCCC
Confidence            47999999999999999753

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=91.95  E-value=0.053  Score=28.92  Aligned_cols=22  Identities=23%  Similarity=0.567  Sum_probs=18.9

Q ss_pred             ccccccCccccCCCCCCCCCcc
Q 041240           69 NTSFLCGKYGHSKDICPNRTEE   90 (113)
Q Consensus        69 ~fC~~Cg~iGH~~~~C~~~~~~   90 (113)
                      .-|..|..-||-.++||+....
T Consensus        11 DQCAyCke~GHW~~dCPkkprg   32 (40)
T d1a6bb_          11 DQCAYCKEKGHWAKDCPKKPRG   32 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSSCCC
T ss_pred             hhhHHHhhcCchhhhCccCCCC
Confidence            4699999999999999987543

>d1hmja_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: RNA polymerase subunit RBP5 (RNA polymerase subunit H)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=91.15  E-value=0.16  Score=29.78  Aligned_cols=42  Identities=17%  Similarity=0.246  Sum_probs=38.1

Q ss_pred             CCcccccHHHHHHHhhccCceEEEecCCCcccccceeEEEEE
Q 041240            1 MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVE   42 (113)
Q Consensus         1 LP~~y~~~~~l~~I~~~iG~~l~vD~~t~~~~~g~faRV~Ve   42 (113)
                      ||.-++++-+.+.+|-.-|.++++...+......-|-|++|+
T Consensus        25 LP~I~~~DPva~~~g~k~GdvvkI~R~S~tag~~i~YR~vv~   66 (68)
T d1hmja_          25 LPKIYEDDPVIQEIGAKEGDVVRVIRKSPTAGVSIAYRLVIK   66 (68)
T ss_pred             CCcccccCHHHHHhCCCCCcEEEEEEcCCCCCCceEEEEEEE
Confidence            788999999999999999999999998877777788899986

>d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: Eukaryotic RPB5 C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.14  E-value=0.33  Score=28.67  Aligned_cols=41  Identities=20%  Similarity=0.154  Sum_probs=36.8

Q ss_pred             CCcccccHHHHHHHhhccCceEEEecCCCcccccceeEEEE
Q 041240            1 MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAV   41 (113)
Q Consensus         1 LP~~y~~~~~l~~I~~~iG~~l~vD~~t~~~~~g~faRV~V   41 (113)
                      ||.-++++-+.+.++-.-|.++++-..+......-|-|+||
T Consensus        32 LP~I~~~DPva~~~g~~~GdvikI~R~s~tag~~~~YR~~V   72 (72)
T d1dzfa2          32 LPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM   72 (72)
T ss_dssp             SCEECTTCHHHHHHTCCTTCEEEEECTTCSSSTTCEEEEEC
T ss_pred             CCeecccCHhhhhcCCCCCCEEEEEEcCCCCCceeEEEEeC
Confidence            78899999999999999999999999887777778888886

>d1eika_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: RPB5-like RNA polymerase subunit
superfamily: RPB5-like RNA polymerase subunit
family: RPB5
domain: RNA polymerase subunit RBP5 (RNA polymerase subunit H)
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=83.79  E-value=0.24  Score=29.72  Aligned_cols=42  Identities=14%  Similarity=0.109  Sum_probs=35.7

Q ss_pred             CCcccccHHHHHHHhhccCceEEEecCCCcccccceeEEEEE
Q 041240            1 MALHYYNKKILRMLGQIFGRVFKTDYNTESASRDKFGRLAVE   42 (113)
Q Consensus         1 LP~~y~~~~~l~~I~~~iG~~l~vD~~t~~~~~g~faRV~Ve   42 (113)
                      ||.-++++-+.+.+|-.-|.++++...+......-|-|++|+
T Consensus        36 LP~I~~~DPva~~~g~k~GdvvkI~R~S~tag~~~~YR~vv~   77 (77)
T d1eika_          36 LPKIKTTDPVAKAIGAKRGDIVKIIRKSPTAEEFVTYRLVQD   77 (77)
T ss_dssp             SCCCBTTSHHHHGGGCCTTCEEEEEEEETTTEEEEEEEECBC
T ss_pred             CCeecccCHhhhhhCCcCCcEEEEEEcCCCCCCceEEEEEeC
Confidence            788999999999999999999999988766666667777764