Citrus Sinensis ID: 036116

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50---
Protein Sequence
VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKSDAADAAMNKE
Secondary Structure (PSIPRED)
cccccccHHHcccccccEEcccccccccccccEEcccccccccHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccEccccccccccccccEEccccccccccccHcccccc
Coil and Loop (DISEMBL)
vceetnslisdsigvsfpikdgipslvpkdgkilgvdddqiksDAADAAMNKE
Flexible Loop (DISEMBL)
vceetnslisdsigvsfpikdgIPSLVPKDGKILGVDDDQIKSDAADAAMNKE
Low Complexity Region (SEG)
VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKSDAADAAMNKE
Disordered region (IsUnstruct)
************IGVSFPIKDGIPSL***************************
Disordered Region (DISOPRED)
*****NSLISDSIGVSFPIKDGIPSLVPKDG**********************
Disordered Region (DISEMBL)
********ISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKSDA********
Disordered Region (DISPRO)
*****NSLISDSIGVSFPIKDGIPSLVPKDGKILG******************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKSDAADAAMNKE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	53	2.2.26 [Sep-21-2011]
Q5M8Z2	122	Protein preY, mitochondri	yes	no	0.660	0.286	0.457	0.0001

>sp|Q5M8Z2|PREY_XENTR Protein preY, mitochondrial OS=Xenopus tropicalis GN=pyurf PE=2 SV=1

 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 28/35 (80%)

Query: 3   EETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVD 37
           E TN LI+D +G+++PI DGIP+++P+D +++  D
Sbjct: 76  ESTNELINDELGIAYPIVDGIPNMIPQDARMIHKD 110

Xenopus tropicalis (taxid: 8364)

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	53
255580651	88	Protein preY, mitochondrial precursor, p	1.0	0.602	0.611	2e-09
356538323	92	PREDICTED: protein preY, mitochondrial-l	0.981	0.565	0.603	2e-08
297798328	77	hypothetical protein ARALYDRAFT_491048 [	0.792	0.545	0.714	4e-08
18419744	77	uncharacterized protein [Arabidopsis tha	0.792	0.545	0.714	4e-08
242039581	86	hypothetical protein SORBIDRAFT_01g02112	0.773	0.476	0.674	6e-08
388514121	90	unknown [Lotus japonicus]	0.792	0.466	0.674	6e-08
357483887	78	Protein preY [Medicago truncatula] gi|35	0.698	0.474	0.729	7e-08
351727250	90	uncharacterized protein LOC100500428 [Gl	0.698	0.411	0.702	7e-08
224132956	76	predicted protein [Populus trichocarpa]	0.716	0.5	0.736	7e-08
115482180	96	Os10g0438700 [Oryza sativa Japonica Grou	0.792	0.437	0.659	3e-07

>gi|255580651|ref|XP_002531148.1| Protein preY, mitochondrial precursor, putative [Ricinus communis] gi|223529261|gb|EEF31233.1| Protein preY, mitochondrial precursor, putative [Ricinus communis]

 Score = 66.6 bits (161), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/54 (61%), Positives = 43/54 (79%), Gaps = 1/54 (1%)

Query: 1  VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIK-SDAADAAMNKE 53
          +CE TNSLISD+IGVS+PIKDGIP LVP DGKIL  D+++ + S A D++  K+
Sbjct: 35 ICEATNSLISDAIGVSYPIKDGIPCLVPLDGKILETDEEKKQDSVATDSSFTKQ 88

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538323|ref|XP_003537653.1| PREDICTED: protein preY, mitochondrial-like [Glycine max]

 Score = 63.2 bits (152), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/53 (60%), Positives = 43/53 (81%), Gaps = 1/53 (1%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDD-DQIKSDAADAAMNKE 53
          CEE+NSLISD+IGV+FPIK+GIP LVP+DGKIL  +D  +  +D   +A+N+E
Sbjct: 32 CEESNSLISDAIGVAFPIKNGIPCLVPRDGKILEEEDASKPDNDTNLSAVNEE 84

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297798328|ref|XP_002867048.1| hypothetical protein ARALYDRAFT_491048 [Arabidopsis lyrata subsp. lyrata] gi|297312884|gb|EFH43307.1| hypothetical protein ARALYDRAFT_491048 [Arabidopsis lyrata subsp. lyrata]

 Score = 62.0 bits (149), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 35/42 (83%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKS 43
          CE+T SL+SD+IGVSFPIKDGIP LVPKDGKIL  + D  K+
Sbjct: 36 CEKTKSLVSDTIGVSFPIKDGIPCLVPKDGKILEEEGDASKA 77

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18419744|ref|NP_567992.1| uncharacterized protein [Arabidopsis thaliana] gi|21536733|gb|AAM61065.1| unknown [Arabidopsis thaliana] gi|62319357|dbj|BAD94651.1| hypothetical protein [Arabidopsis thaliana] gi|88010908|gb|ABD38871.1| At4g35905 [Arabidopsis thaliana] gi|332661187|gb|AEE86587.1| uncharacterized protein [Arabidopsis thaliana]

 Score = 62.0 bits (149), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 35/42 (83%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKS 43
          CE+T SL+SD+IGVSFPIKDGIP LVPKDGKIL  + D  K+
Sbjct: 36 CEKTKSLVSDTIGVSFPIKDGIPCLVPKDGKILEEEGDASKA 77

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242039581|ref|XP_002467185.1| hypothetical protein SORBIDRAFT_01g021120 [Sorghum bicolor] gi|241921039|gb|EER94183.1| hypothetical protein SORBIDRAFT_01g021120 [Sorghum bicolor]

 Score = 61.6 bits (148), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 29/43 (67%), Positives = 36/43 (83%), Gaps = 2/43 (4%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKSD 44
          CE T SL+SD+ GVSFP+ DGIPSLVPKDGK+L  DD ++KS+
Sbjct: 36 CEATGSLVSDAAGVSFPVLDGIPSLVPKDGKLL--DDQEVKSE 76

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388514121|gb|AFK45122.1| unknown [Lotus japonicus]

 Score = 61.6 bits (148), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 29/43 (67%), Positives = 37/43 (86%), Gaps = 1/43 (2%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKSD 44
          CEE+NSLISD+IGVSFP+K+G+P L+PKDG IL  D+D+ K D
Sbjct: 32 CEESNSLISDAIGVSFPVKNGVPCLIPKDGTILE-DEDESKPD 73

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357483887|ref|XP_003612230.1| Protein preY [Medicago truncatula] gi|355513565|gb|AES95188.1| Protein preY [Medicago truncatula] gi|388491964|gb|AFK34048.1| unknown [Medicago truncatula]

 Score = 61.2 bits (147), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 27/37 (72%), Positives = 33/37 (89%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDD 38
          C+E+NSLISD+I VSFPIK+GIP LVP+DGKIL  +D
Sbjct: 32 CQESNSLISDAIAVSFPIKNGIPCLVPRDGKILNEED 68

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727250|ref|NP_001237922.1| uncharacterized protein LOC100500428 [Glycine max] gi|255630315|gb|ACU15514.1| unknown [Glycine max]

 Score = 61.2 bits (147), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 26/37 (70%), Positives = 34/37 (91%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDD 38
          C+E+NSLISD+IGV+FPIK+GIP LVP+DGK+L  +D
Sbjct: 32 CQESNSLISDAIGVAFPIKNGIPCLVPRDGKVLEEED 68

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224132956|ref|XP_002321451.1| predicted protein [Populus trichocarpa] gi|222868447|gb|EEF05578.1| predicted protein [Populus trichocarpa]

 Score = 61.2 bits (147), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 28/38 (73%), Positives = 32/38 (84%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDD 39
          C+ETNSL SDSI VSFPIKDGIP LVP+DGK++   DD
Sbjct: 36 CKETNSLFSDSIAVSFPIKDGIPCLVPRDGKVIETVDD 73

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115482180|ref|NP_001064683.1| Os10g0438700 [Oryza sativa Japonica Group] gi|78708718|gb|ABB47693.1| expressed protein [Oryza sativa Japonica Group] gi|110289140|gb|ABG66096.1| expressed protein [Oryza sativa Japonica Group] gi|113639292|dbj|BAF26597.1| Os10g0438700 [Oryza sativa Japonica Group] gi|215741294|dbj|BAG97789.1| unnamed protein product [Oryza sativa Japonica Group] gi|218184604|gb|EEC67031.1| hypothetical protein OsI_33757 [Oryza sativa Indica Group] gi|222612887|gb|EEE51019.1| hypothetical protein OsJ_31653 [Oryza sativa Japonica Group]

 Score = 59.3 bits (142), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 29/44 (65%), Positives = 36/44 (81%), Gaps = 2/44 (4%)

Query: 1  VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKSD 44
           CE++ SL+SD++GVSFPI DGIP LVPKDGK+L  D DQ KS+
Sbjct: 44 YCEDSGSLVSDAVGVSFPIVDGIPYLVPKDGKLL--DHDQDKSE 85

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	53
TAIR|locus:505006561	77	AT4G35905 "AT4G35905" [Arabido	0.792	0.545	0.714	2.8e-11
ZFIN|ZDB-GENE-050506-109	110	zgc:162634 "zgc:162634" [Danio	0.566	0.272	0.4	0.00027
UNIPROTKB|F1NX15	96	F1NX15 "Uncharacterized protei	0.509	0.281	0.481	0.00045
RGD|1565524	112	Pigy "phosphatidylinositol gly	0.471	0.223	0.48	0.00073

TAIR|locus:505006561 AT4G35905 "AT4G35905" [Arabidopsis thaliana (taxid:3702)]

 Score = 155 (59.6 bits), Expect = 2.8e-11, P = 2.8e-11
 Identities = 30/42 (71%), Positives = 35/42 (83%)

Query:     2 CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKS 43
             CE+T SL+SD+IGVSFPIKDGIP LVPKDGKIL  + D  K+
Sbjct:    36 CEKTKSLVSDTIGVSFPIKDGIPCLVPKDGKILEEEGDASKA 77

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

ZFIN|ZDB-GENE-050506-109 zgc:162634 "zgc:162634" [Danio rerio (taxid:7955)]

 Score = 89 (36.4 bits), Expect = 0.00027, P = 0.00027
 Identities = 12/30 (40%), Positives = 26/30 (86%)

Query:     5 TNSLISDSIGVSFPIKDGIPSLVPKDGKIL 34
             +N LI++ +G+++PI DGIP+++P+D +++
Sbjct:    69 SNELINEELGIAYPIIDGIPNMIPQDARMI 98

GO:0003674 "molecular_function" evidence=ND

UNIPROTKB|F1NX15 F1NX15 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 87 (35.7 bits), Expect = 0.00045, P = 0.00045
 Identities = 13/27 (48%), Positives = 23/27 (85%)

Query:     3 EETNSLISDSIGVSFPIKDGIPSLVPK 29
             E TN LI++ +G+++PI DGIP+++P+
Sbjct:    54 ESTNELINEELGIAYPIIDGIPNMIPE 80

GO:0000506 "glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0006506 "GPI anchor biosynthetic process" evidence=IEA

GO:0009893 "positive regulation of metabolic process" evidence=IEA

RGD|1565524 Pigy "phosphatidylinositol glycan anchor biosynthesis, class Y" [Rattus norvegicus (taxid:10116)]

 Score = 85 (35.0 bits), Expect = 0.00073, P = 0.00072
 Identities = 12/25 (48%), Positives = 22/25 (88%)

Query:     5 TNSLISDSIGVSFPIKDGIPSLVPK 29
             TN LI+D +G+++PI DG+P+++P+
Sbjct:    71 TNELINDELGIAYPIIDGVPNMIPQ 95


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        0.309   0.133   0.364    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       53        53   0.00091  102 3  11 23  0.37    28
                                                     29  0.50    26


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:  4
  No. of states in DFA:  333 (36 KB)
  Total size of DFA:  57 KB (2059 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:  5.73u 0.26s 5.99t   Elapsed:  00:00:00
  Total cpu time:  5.73u 0.26s 5.99t   Elapsed:  00:00:00
  Start:  Sat May 11 00:25:58 2013   End:  Sat May 11 00:25:58 2013

GO:0000506 "glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex" evidence=ISO;ISS

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0005789 "endoplasmic reticulum membrane" evidence=ISO;ISS

GO:0005886 "plasma membrane" evidence=ISO

GO:0006506 "GPI anchor biosynthetic process" evidence=ISO;ISS

GO:0009893 "positive regulation of metabolic process" evidence=ISS

---

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	53
COG2835	60	Uncharacterized conserved protein [Function unknow	99.69
PRK11827	60	hypothetical protein; Provisional	99.68
KOG1088	124	consensus Uncharacterized conserved protein [Funct	99.17
PF03966	68	Trm112p: Trm112p-like protein; InterPro: IPR005651	98.72
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	92.23
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	89.48
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	87.41
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	85.54
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	83.52
COG4391	62	Uncharacterized protein conserved in bacteria [Fun	81.53
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	81.05

>COG2835 Uncharacterized conserved protein [Function unknown]

Probab=99.69  E-value=8.9e-18  Score=95.70  Aligned_cols=39  Identities=36%  Similarity=0.680  Sum_probs=35.7

Q ss_pred             CcccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCcc
Q 036116            1 VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDD   39 (53)
Q Consensus         1 ~~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~   39 (53)
                      |+.++++|+|+.|+++|||+|||||||+++||.++.++.
T Consensus        20 ~~~~~~~L~c~~~~~aYpI~dGIPvlL~~eaR~~~~d~~   58 (60)
T COG2835          20 YDEEKQELICPRCKLAYPIRDGIPVLLPDEARDLSEDES   58 (60)
T ss_pred             EeccCCEEEecccCceeecccCccccCchhhcccchhhc
Confidence            467789999999999999999999999999999988764

>PRK11827 hypothetical protein; Provisional

Probab=99.68  E-value=1e-17  Score=95.11  Aligned_cols=40  Identities=30%  Similarity=0.652  Sum_probs=35.2

Q ss_pred             CcccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCccc
Q 036116            1 VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQ   40 (53)
Q Consensus         1 ~~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~~   40 (53)
                      |+..+++|+|+.|+++|||+|||||||+++||.++.++..
T Consensus        20 ~~~~~~~Lic~~~~laYPI~dgIPVlL~deAr~~~~~~~~   59 (60)
T PRK11827         20 YNQEKQELICKLDNLAFPLRDGIPVLLETEARVLTADESK   59 (60)
T ss_pred             EcCCCCeEECCccCeeccccCCccccCHHHhccCCccccc
Confidence            3556789999999999999999999999999999876543

>KOG1088 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.17  E-value=1.2e-11  Score=78.52  Aligned_cols=31  Identities=29%  Similarity=0.552  Sum_probs=27.8

Q ss_pred             cccCCeEEcCCCCeeeeeeCCccccCCCCCc
Q 036116            2 CEETNSLISDSIGVSFPIKDGIPSLVPKDGK   32 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear   32 (53)
                      +..+|+|+||.||+.|||++|||+||..++.
T Consensus        93 ~v~EG~l~CpetG~vfpI~~GIPNMLL~e~E  123 (124)
T KOG1088|consen   93 DVIEGELVCPETGRVFPISDGIPNMLLSEDE  123 (124)
T ss_pred             hhccceEecCCCCcEeecccCCcccccCccc
Confidence            4578999999999999999999999998753

>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function

Probab=98.72  E-value=7.1e-09  Score=58.41  Aligned_cols=21  Identities=33%  Similarity=0.555  Sum_probs=19.4

Q ss_pred             cccCCeEEcCCCCeeeeeeCC
Q 036116            2 CEETNSLISDSIGVSFPIKDG   22 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~YPI~dG   22 (53)
                      ++.+|.|+|+.|+++|||+||
T Consensus        48 ~i~eg~L~Cp~c~r~YPI~dG   68 (68)
T PF03966_consen   48 EIVEGELICPECGREYPIRDG   68 (68)
T ss_dssp             ETTTTEEEETTTTEEEEEETT
T ss_pred             cccCCEEEcCCCCCEEeCCCC
Confidence            467899999999999999998

The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=92.23  E-value=0.086  Score=26.62  Aligned_cols=16  Identities=13%  Similarity=0.248  Sum_probs=14.4

Q ss_pred             eEEcCCCCeeeeeeCC
Q 036116            7 SLISDSIGVSFPIKDG   22 (53)
Q Consensus         7 ~LiC~~c~~~YPI~dG   22 (53)
                      .+.|+.|+..|.|.|.
T Consensus         2 ~i~Cp~C~~~y~i~d~   17 (36)
T PF13717_consen    2 IITCPNCQAKYEIDDE   17 (36)
T ss_pred             EEECCCCCCEEeCCHH
Confidence            4789999999999987

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

Probab=89.48  E-value=0.19  Score=25.72  Aligned_cols=15  Identities=20%  Similarity=0.313  Sum_probs=11.5

Q ss_pred             cccCCeEEcCCCCee
Q 036116            2 CEETNSLISDSIGVS   16 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~   16 (53)
                      |..+|.++|+.||..
T Consensus        14 D~~~g~~vC~~CG~V   28 (43)
T PF08271_consen   14 DPERGELVCPNCGLV   28 (43)
T ss_dssp             ETTTTEEEETTT-BB
T ss_pred             cCCCCeEECCCCCCE
Confidence            557899999999853

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

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

Probab=87.41  E-value=0.48  Score=23.68  Aligned_cols=17  Identities=29%  Similarity=0.384  Sum_probs=14.3

Q ss_pred             ccCCeEEcCCCCeeeee
Q 036116            3 EETNSLISDSIGVSFPI   19 (53)
Q Consensus         3 ~~~g~LiC~~c~~~YPI   19 (53)
                      .+.+.++|..|+..||+
T Consensus        17 ~~~~~~~C~~Cg~~~~~   33 (33)
T PF08792_consen   17 KEDDYEVCIFCGSSFPY   33 (33)
T ss_pred             ecCCeEEcccCCcEeeC
Confidence            35678999999999985

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=85.54  E-value=0.41  Score=29.47  Aligned_cols=20  Identities=15%  Similarity=0.348  Sum_probs=16.4

Q ss_pred             CcccCCeEEcCCCCeeeeee
Q 036116            1 VCEETNSLISDSIGVSFPIK   20 (53)
Q Consensus         1 ~~~~~g~LiC~~c~~~YPI~   20 (53)
                      |+-.+.-.+||.||..|++.
T Consensus        20 YDLnk~PivCP~CG~~~~~~   39 (108)
T PF09538_consen   20 YDLNKDPIVCPKCGTEFPPE   39 (108)
T ss_pred             ccCCCCCccCCCCCCccCcc
Confidence            45556678999999999998

The function of members of this family is unknown.

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=83.52  E-value=0.79  Score=23.01  Aligned_cols=16  Identities=13%  Similarity=0.248  Sum_probs=13.5

Q ss_pred             eEEcCCCCeeeeeeCC
Q 036116            7 SLISDSIGVSFPIKDG   22 (53)
Q Consensus         7 ~LiC~~c~~~YPI~dG   22 (53)
                      .+.||.|+..|.|.+.
T Consensus         2 ~i~CP~C~~~f~v~~~   17 (37)
T PF13719_consen    2 IITCPNCQTRFRVPDD   17 (37)
T ss_pred             EEECCCCCceEEcCHH
Confidence            3689999999999875

>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=81.53  E-value=1  Score=25.87  Aligned_cols=16  Identities=0%  Similarity=0.246  Sum_probs=14.1

Q ss_pred             cCCeEEcCCCCeeeee
Q 036116            4 ETNSLISDSIGVSFPI   19 (53)
Q Consensus         4 ~~g~LiC~~c~~~YPI   19 (53)
                      .+|+.+||-|+..|..
T Consensus        45 ~~gev~CPYC~t~y~l   60 (62)
T COG4391          45 DEGEVVCPYCSTRYRL   60 (62)
T ss_pred             CCCcEecCccccEEEe
Confidence            5789999999999975

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=81.05  E-value=1.1  Score=21.90  Aligned_cols=16  Identities=19%  Similarity=0.285  Sum_probs=13.2

Q ss_pred             eEEcCCCCeeeeeeCC
Q 036116            7 SLISDSIGVSFPIKDG   22 (53)
Q Consensus         7 ~LiC~~c~~~YPI~dG   22 (53)
                      .+.||.|+..|.|.+.
T Consensus         2 ~~~CP~C~~~~~v~~~   17 (38)
T TIGR02098         2 RIQCPNCKTSFRVVDS   17 (38)
T ss_pred             EEECCCCCCEEEeCHH
Confidence            3789999999998753

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	53
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	6e-07
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	8e-07
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	9e-07
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	1e-06
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	2e-06
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	8e-05

>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1 Length = 69

 Score = 40.4 bits (95), Expect = 6e-07
 Identities = 11/39 (28%), Positives = 22/39 (56%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQ 40
            +   LIS   G+++PI+DGIP ++  + + L  ++  
Sbjct: 21 SADKTELISKGAGLAYPIRDGIPVMLESEARTLTTEERL 59

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis} Length = 68

 Score = 39.9 bits (94), Expect = 8e-07
 Identities = 11/42 (26%), Positives = 25/42 (59%), Gaps = 2/42 (4%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKS 43
           ++   L S    +++PIKDGIP ++  + + L   ++++K+
Sbjct: 21 HQDKQELWSRQAKLAYPIKDGIPYMLENEARPL--SEEELKA 60

>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50} Length = 70

 Score = 39.9 bits (94), Expect = 9e-07
 Identities = 8/50 (16%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIKSDAADAAMN 51
                L+ ++  ++FP++DG+P ++  + + L  D +     + +   +
Sbjct: 21 QRAQAELVCNADRLAFPVRDGVPIMLEAEARSL--DAEAPAQPSLEHHHH 68

>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1 Length = 68

 Score = 39.5 bits (93), Expect = 1e-06
 Identities = 11/37 (29%), Positives = 21/37 (56%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDD 38
           +  + LI     ++FPIKDGIP ++  + + L  ++
Sbjct: 21 DKSKDELICKGDRLAFPIKDGIPMMLESEARELAPEE 57

>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1 Length = 67

 Score = 39.1 bits (92), Expect = 2e-06
 Identities = 8/37 (21%), Positives = 19/37 (51%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDD 38
           E    L+++ + +++ I DGIP L+  +      ++
Sbjct: 23 LESEQLLVNERLNLAYRIDDGIPVLLIDEATEWTPNN 59

>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor} Length = 56

 Score = 34.8 bits (81), Expect = 8e-05
 Identities = 7/33 (21%), Positives = 16/33 (48%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKIL 34
           +          G+++P++DGIP L+  + +  
Sbjct: 23 RDAELICTGQDCGLAYPVRDGIPVLLVDEARRP 55

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	53
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	99.69
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	99.69
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	99.67
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	99.67
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	99.64
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	99.52
2k5r_A	97	Uncharacterized protein XF2673; solution structure	99.52
2j6a_A	141	Protein TRM112; translation termination, methyltra	99.45
3q87_A	125	Putative uncharacterized protein ECU08_1170; SAM-m	99.11
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	96.25
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	91.51
2i5o_A	39	DNA polymerase ETA; zinc finger, DNA polymerase,PO	84.0
2jrr_A	67	Uncharacterized protein; solution structure, SIR90	82.31

>2js4_A UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}

Probab=99.69  E-value=1.1e-17  Score=95.89  Aligned_cols=41  Identities=17%  Similarity=0.473  Sum_probs=36.3

Q ss_pred             cccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCccccC
Q 036116            2 CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQIK   42 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~~~~   42 (53)
                      +..+|+|+|+.|+++|||+|||||||+++++.++.++..+.
T Consensus        21 ~~~~~~LiC~~cg~~YPI~dGIPvmL~~Ear~~~~~e~~~~   61 (70)
T 2js4_A           21 QRAQAELVCNADRLAFPVRDGVPIMLEAEARSLDAEAPAQP   61 (70)
T ss_dssp             ETTTTEEEETTTTEEEEEETTEECCCGGGSEESSSCCCCCC
T ss_pred             eCCCCEEEcCCCCceecCCCCeeeeChhhcccCCchhhhhh
Confidence            45679999999999999999999999999999998775543

>2jny_A Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: b.171.1.1

Probab=99.69  E-value=1.3e-17  Score=95.14  Aligned_cols=39  Identities=21%  Similarity=0.435  Sum_probs=35.6

Q ss_pred             cccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCccc
Q 036116            2 CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQ   40 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~~   40 (53)
                      +..+|+|+|+.|+++|||+|||||||+++++.++..+.+
T Consensus        23 ~~~~g~LvC~~c~~~YPI~dGIPvmL~~Ear~~~~~~~~   61 (67)
T 2jny_A           23 LESEQLLVNERLNLAYRIDDGIPVLLIDEATEWTPNNLE   61 (67)
T ss_dssp             ETTTTEEEETTTTEEEEEETTEECCCSSCCEECCCCCCC
T ss_pred             eCCCCEEEcCCCCccccCCCCEeeeChhHhcCCchhhhh
Confidence            456899999999999999999999999999999987764

>2hf1_A Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthes structural genomics, PSI-2, protein structure initiative; 1.90A {Chromobacterium violaceum} SCOP: b.171.1.1

Probab=99.67  E-value=8.7e-18  Score=95.90  Aligned_cols=40  Identities=28%  Similarity=0.548  Sum_probs=35.4

Q ss_pred             cccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCcccc
Q 036116            2 CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQI   41 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~~~   41 (53)
                      +..+|+|+|+.|+++|||+|||||||+++++.++.++..+
T Consensus        21 ~~~~~~LiC~~cg~~YPI~dGIPvmL~~Ear~~~~~e~~~   60 (68)
T 2hf1_A           21 DKSKDELICKGDRLAFPIKDGIPMMLESEARELAPEEEVK   60 (68)
T ss_dssp             ETTTTEEEETTTTEEEEEETTEECCCGGGCEECCHHHHGG
T ss_pred             eCCCCEEEcCCCCcEecCCCCeeeeChhhccCcCchhhhh
Confidence            4567999999999999999999999999999998766543

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}

Probab=99.67  E-value=1e-17  Score=95.61  Aligned_cols=39  Identities=26%  Similarity=0.547  Sum_probs=34.8

Q ss_pred             cccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCccc
Q 036116            2 CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQ   40 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~~   40 (53)
                      +..+|+|+|+.|+++|||+|||||||+++++.++.++..
T Consensus        21 ~~~~~~LiC~~cg~~YPI~dGIPvmL~~Ear~~~~~e~~   59 (68)
T 2jr6_A           21 HQDKQELWSRQAKLAYPIKDGIPYMLENEARPLSEEELK   59 (68)
T ss_dssp             ETTTTEEEETTTTEEEEEETTEECCCTTTCEECCHHHHH
T ss_pred             eCCCCEEEcCCCCcEecCCCCeeeeChhhccCcCcchhh
Confidence            456799999999999999999999999999999876653

>2pk7_A Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4K structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens} SCOP: b.171.1.1

Probab=99.64  E-value=3.1e-17  Score=93.85  Aligned_cols=38  Identities=29%  Similarity=0.721  Sum_probs=34.3

Q ss_pred             cccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCcc
Q 036116            2 CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDD   39 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~   39 (53)
                      +..+++|+|+.|+++|||+|||||||+++++.++.++.
T Consensus        21 ~~~~~~LiC~~cg~~YPI~dGIPvmL~~ear~~~~~~~   58 (69)
T 2pk7_A           21 SADKTELISKGAGLAYPIRDGIPVMLESEARTLTTEER   58 (69)
T ss_dssp             CTTSSEEEETTTTEEEEEETTEECCCGGGCEECCHHHH
T ss_pred             eCCCCEEEcCCCCcEecCcCCeeeeChhhccccCcccc
Confidence            45679999999999999999999999999999987554

>2kpi_A Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}

Probab=99.52  E-value=5.4e-15  Score=81.47  Aligned_cols=31  Identities=29%  Similarity=0.669  Sum_probs=28.8

Q ss_pred             CCeEEcC--CCCeeeeeeCCccccCCCCCccCC
Q 036116            5 TNSLISD--SIGVSFPIKDGIPSLVPKDGKILG   35 (53)
Q Consensus         5 ~g~LiC~--~c~~~YPI~dGIPvLL~~ear~l~   35 (53)
                      +|+|+|+  .|+++|||+|||||||+++||.++
T Consensus        24 ~~~L~C~~~~c~~~YPI~dGIPvlL~~ear~~~   56 (56)
T 2kpi_A           24 DAELICTGQDCGLAYPVRDGIPVLLVDEARRPE   56 (56)
T ss_dssp             TTEEEECSSSCCCEEEEETTEECCCTTTCBCCC
T ss_pred             CCEEEcCCcCCCcEEeeECCEeeeCHHHcccCC
Confidence            3899999  999999999999999999999864

>2k5r_A Uncharacterized protein XF2673; solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Xylella fastidiosa TEMECULA1}

Probab=99.52  E-value=2.6e-15  Score=90.80  Aligned_cols=33  Identities=27%  Similarity=0.377  Sum_probs=30.7

Q ss_pred             cCCeEEcCCCCeeeeeeCCccccCCCCCccCCC
Q 036116            4 ETNSLISDSIGVSFPIKDGIPSLVPKDGKILGV   36 (53)
Q Consensus         4 ~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~   36 (53)
                      .+|+|+|+.|+++|||+|||||||+++++.++.
T Consensus        50 ~~~~LvC~~c~~~YPI~dGIPvmL~~ear~~~~   82 (97)
T 2k5r_A           50 LHEALITRDRKQVFRIEDSIPVLLPEEAIATIQ   82 (97)
T ss_dssp             CSEEEECTTSCEEEEEETTEEECCGGGEEEGGG
T ss_pred             cCCeEEcCCCCCCccccCCCcccChHHhccccc
Confidence            368999999999999999999999999998875

>2j6a_A Protein TRM112; translation termination, methyltransferase, transferase, ERF1, nuclear protein, protein methylation; 1.7A {Saccharomyces cerevisiae}

Probab=99.45  E-value=1.3e-14  Score=92.38  Aligned_cols=32  Identities=22%  Similarity=0.348  Sum_probs=29.7

Q ss_pred             cccCCeEEcCCCCeeeeeeCCccccCCCCCcc
Q 036116            2 CEETNSLISDSIGVSFPIKDGIPSLVPKDGKI   33 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~   33 (53)
                      ++.+|.|+|+.||++|||+||||+||++++|.
T Consensus       104 ~v~eg~L~C~~cg~~YPI~dGIP~mL~~ear~  135 (141)
T 2j6a_A          104 SIAEGEMKCRNCGHIYYIKNGIPNLLLPPHLV  135 (141)
T ss_dssp             EEEEEEEECTTTCCEEEEETTEESSCCCSSCC
T ss_pred             eccCCEEECCCCCCcccccCCccCcCCcHHHh
Confidence            45789999999999999999999999999985

>3q87_A Putative uncharacterized protein ECU08_1170; SAM-methyltransferase, methyltransferase, methylation, trans activator-transferase complex; HET: SAM; 2.00A {Encephalitozoon cuniculi}

Probab=99.11  E-value=1.4e-11  Score=77.07  Aligned_cols=27  Identities=33%  Similarity=0.415  Sum_probs=24.7

Q ss_pred             ccCCeEEcCCCCeeeeeeCCccccCCC
Q 036116            3 EETNSLISDSIGVSFPIKDGIPSLVPK   29 (53)
Q Consensus         3 ~~~g~LiC~~c~~~YPI~dGIPvLL~~   29 (53)
                      ..+|.|+|+.||+.|||++|||+|+..
T Consensus        95 V~EG~L~Cp~cgr~ypI~~GIPNm~~~  121 (125)
T 3q87_A           95 VVEGSLRCDMCGLIYPIKGSIVETVDT  121 (125)
T ss_dssp             EEEEEEEETTTCCEEEEETTEEECSSC
T ss_pred             EEEEEEECCCCCCEeeccCCcccHHHh
Confidence            468999999999999999999999864

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

Probab=96.25  E-value=0.0014  Score=33.85  Aligned_cols=19  Identities=11%  Similarity=0.111  Sum_probs=15.9

Q ss_pred             CcccCCeEEcCCCCeeeee
Q 036116            1 VCEETNSLISDSIGVSFPI   19 (53)
Q Consensus         1 ~~~~~g~LiC~~c~~~YPI   19 (53)
                      |+...|+|+|+.||+.|+-
T Consensus        18 ~d~~~gelvC~~CG~v~~e   36 (50)
T 1pft_A           18 YDPERGEIVCAKCGYVIEE   36 (50)
T ss_dssp             EETTTTEEEESSSCCBCCC
T ss_pred             EcCCCCeEECcccCCcccc
Confidence            4567799999999999974

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

Probab=91.51  E-value=0.083  Score=28.26  Aligned_cols=17  Identities=12%  Similarity=0.143  Sum_probs=14.0

Q ss_pred             cccCCeEEcCCCCeeee
Q 036116            2 CEETNSLISDSIGVSFP   18 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~YP   18 (53)
                      +...|.++|..||+.+.
T Consensus        25 D~~~ge~vC~~CGlVl~   41 (58)
T 1dl6_A           25 DYRAGDMICPECGLVVG   41 (58)
T ss_dssp             CSSSCCEECTTTCCEEC
T ss_pred             eCCCCeEEeCCCCCEEe
Confidence            45679999999998873

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

Probab=84.00  E-value=0.64  Score=23.39  Aligned_cols=16  Identities=13%  Similarity=0.295  Sum_probs=13.5

Q ss_pred             CCeEEcCCCCeeeeee
Q 036116            5 TNSLISDSIGVSFPIK   20 (53)
Q Consensus         5 ~g~LiC~~c~~~YPI~   20 (53)
                      ...+.|++|+..+|+.
T Consensus         7 ~~~~~C~~C~~~i~~~   22 (39)
T 2i5o_A            7 EDQVPCEKCGSLVPVW   22 (39)
T ss_dssp             CCEEECTTTCCEEEGG
T ss_pred             CCCcccccccCcCCcc
Confidence            4568899999999985

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

Probab=82.31  E-value=1.3  Score=24.63  Aligned_cols=24  Identities=8%  Similarity=0.101  Sum_probs=19.7

Q ss_pred             cCCeEEcCCCCeeeeeeCCccccC
Q 036116            4 ETNSLISDSIGVSFPIKDGIPSLV   27 (53)
Q Consensus         4 ~~g~LiC~~c~~~YPI~dGIPvLL   27 (53)
                      ..+.-.|+-|++.|..+++-..-|
T Consensus        37 ~~g~~~CpYCg~~f~l~~~~~~~~   60 (67)
T 2jrr_A           37 DTGWVECPYCDCKYVLKGSKADAL   60 (67)
T ss_dssp             TTSEEEETTTTEEEEETTSGGGCC
T ss_pred             CCCeEECCCCCCEEEECCCcchhh
Confidence            468999999999999888765544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	53
d2pk7a1	59	b.171.1.1 (A:3-61) Uncharacterized protein PFL1779	1e-06
d2hf1a1	59	b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Ch	1e-06
d2jnya1	59	b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405	3e-05

>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]} Length = 59

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein PFL1779
species: Pseudomonas fluorescens [TaxId: 294]

 Score = 38.4 bits (90), Expect = 1e-06
 Identities = 11/36 (30%), Positives = 22/36 (61%)

Query: 3  EETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDD 38
           +   LIS   G+++PI+DGIP ++  + + L  ++
Sbjct: 20 ADKTELISKGAGLAYPIRDGIPVMLESEARTLTTEE 55

>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]} Length = 59

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Hypothetical protein CV3345
species: Chromobacterium violaceum [TaxId: 536]

 Score = 38.1 bits (89), Expect = 1e-06
 Identities = 11/37 (29%), Positives = 22/37 (59%)

Query: 3  EETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDD 39
          +  + LI     ++FPIKDGIP ++  + + L  +++
Sbjct: 21 KSKDELICKGDRLAFPIKDGIPMMLESEARELAPEEE 57

>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]} Length = 59

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein Cgl1405/cg1592
species: Corynebacterium glutamicum [TaxId: 1718]

 Score = 35.0 bits (81), Expect = 3e-05
 Identities = 8/37 (21%), Positives = 19/37 (51%)

Query: 2  CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDD 38
           E    L+++ + +++ I DGIP L+  +      ++
Sbjct: 23 LESEQLLVNERLNLAYRIDDGIPVLLIDEATEWTPNN 59

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	53
d2pk7a1	59	Uncharacterized protein PFL1779 {Pseudomonas fluor	99.68
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	99.65
d2hf1a1	59	Hypothetical protein CV3345 {Chromobacterium viola	99.65
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	90.25
d1akya2	38	Microbial and mitochondrial ADK, insert "zinc fing	89.37
d1e4va2	35	Microbial and mitochondrial ADK, insert "zinc fing	89.32
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	87.92
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	86.69
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	83.78
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	82.56
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	82.34

>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein PFL1779
species: Pseudomonas fluorescens [TaxId: 294]

Probab=99.68  E-value=2.4e-18  Score=95.12  Aligned_cols=40  Identities=28%  Similarity=0.687  Sum_probs=36.4

Q ss_pred             CcccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCccc
Q 036116            1 VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDDQ   40 (53)
Q Consensus         1 ~~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~~   40 (53)
                      |+..+++|+|+.|+++|||+|||||||+++||.++.+++.
T Consensus        18 ~~~~~~~Lvc~~~~laYPI~dGIPvlL~~eAr~l~~~E~~   57 (59)
T d2pk7a1          18 LSADKTELISKGAGLAYPIRDGIPVMLESEARTLTTEERL   57 (59)
T ss_dssp             ECTTSSEEEETTTTEEEEEETTEECCCGGGCEECCHHHHS
T ss_pred             EeCCCCEEecCCcCccccccCCccccCHHHhccCChhhhc
Confidence            4567899999999999999999999999999999987764

>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein Cgl1405/cg1592
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=99.65  E-value=2.9e-17  Score=90.43  Aligned_cols=36  Identities=22%  Similarity=0.472  Sum_probs=33.3

Q ss_pred             cccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCC
Q 036116            2 CEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVD   37 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~   37 (53)
                      +..+++|+|+.|+++|||+|||||||+++||.++.+
T Consensus        23 ~~~~~~Lvc~~~~~~YPI~dgIPvLL~deA~~l~~~   58 (59)
T d2jnya1          23 LESEQLLVNERLNLAYRIDDGIPVLLIDEATEWTPN   58 (59)
T ss_dssp             ETTTTEEEETTTTEEEEEETTEECCCSSCCEECCCC
T ss_pred             eCCCCEEEcCccCccccccCCccccCHHHhccCCCC
Confidence            457789999999999999999999999999999875

>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]}

class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Hypothetical protein CV3345
species: Chromobacterium violaceum [TaxId: 536]

Probab=99.65  E-value=9.1e-18  Score=92.62  Aligned_cols=39  Identities=28%  Similarity=0.594  Sum_probs=35.1

Q ss_pred             CcccCCeEEcCCCCeeeeeeCCccccCCCCCccCCCCcc
Q 036116            1 VCEETNSLISDSIGVSFPIKDGIPSLVPKDGKILGVDDD   39 (53)
Q Consensus         1 ~~~~~g~LiC~~c~~~YPI~dGIPvLL~~ear~l~~~e~   39 (53)
                      |+..+++|+|+.|+++|||+|||||||+++||.++.+++
T Consensus        19 ~~~~~~~Lvc~~~~l~YPI~dGIPvlL~~eAr~l~~~e~   57 (59)
T d2hf1a1          19 FDKSKDELICKGDRLAFPIKDGIPMMLESEARELAPEEE   57 (59)
T ss_dssp             EETTTTEEEETTTTEEEEEETTEECCCGGGCEECCHHHH
T ss_pred             EeCCCCEEecCCcCccccccCCccccCHHHhccCchhhh
Confidence            356788999999999999999999999999999987664

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=90.25  E-value=0.065  Score=26.16  Aligned_cols=17  Identities=6%  Similarity=0.114  Sum_probs=14.1

Q ss_pred             cCCeEEcCCCCeeeeee
Q 036116            4 ETNSLISDSIGVSFPIK   20 (53)
Q Consensus         4 ~~g~LiC~~c~~~YPI~   20 (53)
                      +.+.|+||.|++.|.-.
T Consensus        17 dg~l~vCPeC~hEW~~~   33 (38)
T d2akla2          17 DGALLVCPECAHEWSPN   33 (38)
T ss_dssp             CSSSEEETTTTEEECTT
T ss_pred             CCCEEECCcccCcCCcc
Confidence            56789999999998754

>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.37  E-value=0.091  Score=25.27  Aligned_cols=17  Identities=24%  Similarity=0.180  Sum_probs=14.0

Q ss_pred             CeEEcCCCCeeeeeeCC
Q 036116            6 NSLISDSIGVSFPIKDG   22 (53)
Q Consensus         6 g~LiC~~c~~~YPI~dG   22 (53)
                      |..+|+.||+.|-|.--
T Consensus         1 GRr~C~~cG~~Yh~~~~   17 (38)
T d1akya2           1 GRLIHPASGRSYHKIFN   17 (38)
T ss_dssp             TEEECTTTCCEEETTTB
T ss_pred             CccCCcCccchhhhhcc
Confidence            67899999999977543

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

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Escherichia coli [TaxId: 562]

Probab=89.32  E-value=0.093  Score=24.78  Aligned_cols=17  Identities=12%  Similarity=0.178  Sum_probs=14.3

Q ss_pred             CeEEcCCCCeeeeeeCC
Q 036116            6 NSLISDSIGVSFPIKDG   22 (53)
Q Consensus         6 g~LiC~~c~~~YPI~dG   22 (53)
                      |..+|+.||+.|-|.--
T Consensus         1 GRr~c~~cG~~Yh~~~~   17 (35)
T d1e4va2           1 GRRVHAPSGRVYHVKFN   17 (35)
T ss_dssp             TEEEETTTTEEEETTTB
T ss_pred             CccCCcCcCChhhhccC
Confidence            67899999999988643

>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus globisporus [TaxId: 1459]

Probab=87.92  E-value=0.13  Score=24.27  Aligned_cols=16  Identities=19%  Similarity=0.200  Sum_probs=13.5

Q ss_pred             CeEEcCCCCeeeeeeC
Q 036116            6 NSLISDSIGVSFPIKD   21 (53)
Q Consensus         6 g~LiC~~c~~~YPI~d   21 (53)
                      |.++|+.||+.|-|.-
T Consensus         1 GR~~C~~CG~~Yh~~~   16 (35)
T d1s3ga2           1 GRRICKVCGTSYHLLF   16 (35)
T ss_dssp             SEEEETTTCCEEETTT
T ss_pred             CccCCcCcCchhcccc
Confidence            6799999999997743

>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=86.69  E-value=0.16  Score=23.90  Aligned_cols=16  Identities=13%  Similarity=0.210  Sum_probs=13.8

Q ss_pred             CeEEcCCCCeeeeeeC
Q 036116            6 NSLISDSIGVSFPIKD   21 (53)
Q Consensus         6 g~LiC~~c~~~YPI~d   21 (53)
                      |..+|+.||..|-|.-
T Consensus         1 GRr~C~~CG~~Yh~~~   16 (35)
T d1zina2           1 GRRICRNCGATYHLIF   16 (35)
T ss_dssp             TEEEETTTCCEEETTT
T ss_pred             CccCCcCcCchhcccc
Confidence            6789999999998754

>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=83.78  E-value=0.18  Score=25.18  Aligned_cols=15  Identities=13%  Similarity=0.213  Sum_probs=12.3

Q ss_pred             cccCCeEEcCCCCee
Q 036116            2 CEETNSLISDSIGVS   16 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~   16 (53)
                      |..+|+++|..||+.
T Consensus        19 D~~~Ge~vC~~CG~V   33 (50)
T d1pfta_          19 DPERGEIVCAKCGYV   33 (50)
T ss_dssp             ETTTTEEEESSSCCB
T ss_pred             ECCCCeEecccCCcE
Confidence            456799999999963

>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=82.56  E-value=0.33  Score=23.03  Aligned_cols=16  Identities=19%  Similarity=0.204  Sum_probs=13.4

Q ss_pred             eEEcCCCCeeeeeeCC
Q 036116            7 SLISDSIGVSFPIKDG   22 (53)
Q Consensus         7 ~LiC~~c~~~YPI~dG   22 (53)
                      .++|+.||+.|-|.--
T Consensus         2 R~vc~~cG~~Yh~~~~   17 (37)
T d2ak3a2           2 RWIHPGSGRVYNIEFN   17 (37)
T ss_dssp             EEEETTTTEEEETTTB
T ss_pred             ceeeCCcCChhhhccC
Confidence            6899999999987643

>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.34  E-value=0.27  Score=25.19  Aligned_cols=15  Identities=13%  Similarity=0.195  Sum_probs=12.3

Q ss_pred             cccCCeEEcCCCCee
Q 036116            2 CEETNSLISDSIGVS   16 (53)
Q Consensus         2 ~~~~g~LiC~~c~~~   16 (53)
                      +...|.++|..||+.
T Consensus        25 D~~~Ge~vC~~CG~V   39 (58)
T d1dl6a_          25 DYRAGDMICPECGLV   39 (58)
T ss_dssp             CSSSCCEECTTTCCE
T ss_pred             ECCCCcEecccCCCE
Confidence            456799999999974