Citrus Sinensis ID: 035300

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------
Protein Sequence
MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPATS
Secondary Structure (PSIPRED)
cEEEEEEcccEEEEEEcccccccccccccEEEEEEccEEEEEEEEEEEEEEEEEEEEccccEEEEEcc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccEEEccccccccccccccEEEEEEEcccEEEEEcHHHHHcccEEHHHHHHcccccccc
Coil and Loop (DISEMBL)
MSVLSIFDLREKVIRrngadaacpycggpvlaidfdahlrfcflpishkvkkkfycticsrrlvpats
Flexible Loop (DISEMBL)
MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPATS
Low Complexity Region (SEG)
MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPATS
Disordered region (IsUnstruct)
***LSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV****
Disordered Region (DISOPRED)
MSVLS**DLR************CPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPA**
Disordered Region (DISEMBL)
MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPATS
Disordered Region (DISPRO)
MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVP***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPATS
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

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	68
224097456	67	predicted protein [Populus trichocarpa]	0.941	0.955	0.593	3e-16
359483243	67	PREDICTED: uncharacterized protein LOC10	0.941	0.955	0.546	2e-14
297735801	68	unnamed protein product [Vitis vinifera]	0.985	0.985	0.522	2e-13
356554423	68	PREDICTED: uncharacterized protein LOC10	0.985	0.985	0.507	7e-13
255582685	67	conserved hypothetical protein [Ricinus	0.941	0.955	0.515	1e-12
224090505	67	predicted protein [Populus trichocarpa]	0.926	0.940	0.507	3e-12
224143427	67	predicted protein [Populus trichocarpa]	0.926	0.940	0.492	4e-12
356561869	66	PREDICTED: uncharacterized protein LOC10	0.926	0.954	0.492	8e-12
357449639	104	hypothetical protein MTR_2g038220 [Medic	0.926	0.605	0.507	1e-11
224144308	68	predicted protein [Populus trichocarpa]	0.926	0.926	0.492	3e-11

>gi|224097456|ref|XP_002310942.1| predicted protein [Populus trichocarpa] gi|222850762|gb|EEE88309.1| predicted protein [Populus trichocarpa]

 Score = 89.0 bits (219), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 38/64 (59%), Positives = 50/64 (78%)

Query: 1  MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
          M  + IFD R+K+ R+  A + CP  GGPV+A+D+D+HL FCF+PISHKVK+KF C +CS
Sbjct: 1  MGAMQIFDFRDKLTRKEEARSLCPCSGGPVMAMDYDSHLYFCFIPISHKVKRKFSCVVCS 60

Query: 61 RRLV 64
          RRLV
Sbjct: 61 RRLV 64

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359483243|ref|XP_003632928.1| PREDICTED: uncharacterized protein LOC100852964 [Vitis vinifera]

 Score = 82.8 bits (203), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/64 (54%), Positives = 46/64 (71%)

Query: 1  MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
          MS+  +FD+REKVI+R GA A CP CGGPV+A   D +L  C +P+S K K K++C ICS
Sbjct: 1  MSIFQVFDMREKVIKREGAGAVCPCCGGPVVATHLDCNLHVCCVPVSRKTKTKYFCAICS 60

Query: 61 RRLV 64
          R L+
Sbjct: 61 RSLI 64

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297735801|emb|CBI18488.3| unnamed protein product [Vitis vinifera]

 Score = 80.1 bits (196), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 46/67 (68%)

Query: 1  MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
          MS+  +FD+R+KVI+R GA A CP CGGPV+A   D +L  C +P+S K K K++C ICS
Sbjct: 1  MSIFQVFDMRKKVIKREGAGAVCPCCGGPVVATLLDCNLHVCCIPVSSKTKTKYFCAICS 60

Query: 61 RRLVPAT 67
          R L   T
Sbjct: 61 RPLTLTT 67

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356554423|ref|XP_003545546.1| PREDICTED: uncharacterized protein LOC100813676 [Glycine max]

 Score = 77.8 bits (190), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 34/67 (50%), Positives = 46/67 (68%)

Query: 1  MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
          M ++ + D  E+V+ R  A  ACPYCGG V AID ++  RFCFLP+  K K+K+YCT+C+
Sbjct: 1  MCLVFVCDEEERVLGRQTAPGACPYCGGMVQAIDVESQWRFCFLPLCFKTKRKYYCTMCT 60

Query: 61 RRLVPAT 67
          RRL   T
Sbjct: 61 RRLETNT 67

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255582685|ref|XP_002532121.1| conserved hypothetical protein [Ricinus communis] gi|223528201|gb|EEF30261.1| conserved hypothetical protein [Ricinus communis]

 Score = 77.4 bits (189), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/64 (51%), Positives = 46/64 (71%)

Query: 1  MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
          M ++ + D  E+V+ R  A  ACPYCGG V A+D ++  RFCFLP+  K KK+FYC++C+
Sbjct: 1  MCLVFVCDEEERVVARQPAPGACPYCGGMVQAMDVESQWRFCFLPLYFKTKKRFYCSVCA 60

Query: 61 RRLV 64
          RRLV
Sbjct: 61 RRLV 64

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224090505|ref|XP_002309004.1| predicted protein [Populus trichocarpa] gi|222854980|gb|EEE92527.1| predicted protein [Populus trichocarpa]

 Score = 75.9 bits (185), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/63 (50%), Positives = 45/63 (71%)

Query: 1  MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
          M  + + D  EK + R  A  +CP+CGG V A+DF+   RFCFLPI +K+K+K++CT+CS
Sbjct: 1  MCFVFLCDEEEKELGRQQASGSCPHCGGKVQAVDFEGRWRFCFLPICYKMKRKYFCTLCS 60

Query: 61 RRL 63
          RRL
Sbjct: 61 RRL 63

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224143427|ref|XP_002324952.1| predicted protein [Populus trichocarpa] gi|222866386|gb|EEF03517.1| predicted protein [Populus trichocarpa]

 Score = 75.5 bits (184), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 31/63 (49%), Positives = 45/63 (71%)

Query: 1  MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
          M ++ + D  EKV+ R  A  ACPYCGG + A+D ++  RFCFLP+  K KK++YCT+C+
Sbjct: 1  MCLVFVCDEDEKVVARQTAPGACPYCGGAIQAMDVESQWRFCFLPLYFKTKKRYYCTLCA 60

Query: 61 RRL 63
          R+L
Sbjct: 61 RKL 63

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356561869|ref|XP_003549199.1| PREDICTED: uncharacterized protein LOC100800541 [Glycine max]

 Score = 74.3 bits (181), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 31/63 (49%), Positives = 45/63 (71%)

Query: 1  MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
          M ++ + +  E+V+ R  A  ACPYCGG V AI+ ++  RFCFLP+  K K+K+YCT+C+
Sbjct: 1  MCLVFVCNEEERVLGRQTAPGACPYCGGMVQAINVESQWRFCFLPLCFKTKRKYYCTMCT 60

Query: 61 RRL 63
          RRL
Sbjct: 61 RRL 63

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357449639|ref|XP_003595096.1| hypothetical protein MTR_2g038220 [Medicago truncatula] gi|87162672|gb|ABD28467.1| hypothetical protein MtrDRAFT_AC148819g4v2 [Medicago truncatula] gi|355484144|gb|AES65347.1| hypothetical protein MTR_2g038220 [Medicago truncatula]

 Score = 73.9 bits (180), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/63 (50%), Positives = 42/63 (66%)

Query: 1  MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
          M  + I D  EK + R  A   CPYCGG V A+D +   RFCFLP+  K+K+KF+CT+C+
Sbjct: 37 MWFVYICDEEEKELGRQKASGCCPYCGGKVEAMDVEMQWRFCFLPMCFKIKRKFFCTLCA 96

Query: 61 RRL 63
          RRL
Sbjct: 97 RRL 99

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144308|ref|XP_002325255.1| predicted protein [Populus trichocarpa] gi|222866689|gb|EEF03820.1| predicted protein [Populus trichocarpa]

 Score = 72.4 bits (176), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 31/63 (49%), Positives = 44/63 (69%)

Query: 1  MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
          M  + + D  E+ + R  A  +CP+CGG V A+DF++  RFCFLPI +K K+K+ CT+CS
Sbjct: 1  MCFVFLCDEEERELGRQQASGSCPHCGGKVQAVDFESRWRFCFLPICYKNKRKYLCTLCS 60

Query: 61 RRL 63
          RRL
Sbjct: 61 RRL 63

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	68
TAIR|locus:505006594	67	AT5G10695 [Arabidopsis thalian	0.941	0.955	0.437	1.9e-12
TAIR|locus:504954859	67	AT5G57123 "AT5G57123" [Arabido	0.941	0.955	0.406	9.4e-11
TAIR|locus:504955497	67	AT4G29905 "AT4G29905" [Arabido	0.794	0.805	0.490	3.2e-10
TAIR|locus:2827497	68	AT2G20835 "AT2G20835" [Arabido	0.794	0.794	0.370	8.1e-05

TAIR|locus:505006594 AT5G10695 [Arabidopsis thaliana (taxid:3702)]

 Score = 166 (63.5 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 28/64 (43%), Positives = 43/64 (67%)

Query:     1 MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
             M ++ + D  E+VI R  A  ACPYCGG V  +D ++  RFCF+P+S+K K++  C+ C 
Sbjct:     1 MCLVFVCDQDERVIGRYAAPGACPYCGGAVQVVDVNSQWRFCFVPLSNKSKRRHLCSTCG 60

Query:    61 RRLV 64
             +RL+
Sbjct:    61 KRLI 64

GO:0005576 "extracellular region" evidence=ISM

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0006944 "cellular membrane fusion" evidence=RCA

GO:0010286 "heat acclimation" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0030968 "endoplasmic reticulum unfolded protein response" evidence=RCA

GO:0043069 "negative regulation of programmed cell death" evidence=RCA

TAIR|locus:504954859 AT5G57123 "AT5G57123" [Arabidopsis thaliana (taxid:3702)]

 Score = 150 (57.9 bits), Expect = 9.4e-11, P = 9.4e-11
 Identities = 26/64 (40%), Positives = 39/64 (60%)

Query:     1 MSVLSIFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS 60
             M ++ + D  E  + R  A  +CPYCGG V  +D +    FCF+P+  K+K+K+ C+ C 
Sbjct:     1 MCLVCLCDEEETELGRQQAPGSCPYCGGKVQMLDVERKWMFCFVPLCFKIKRKYSCSSCD 60

Query:    61 RRLV 64
             RRLV
Sbjct:    61 RRLV 64

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:504955497 AT4G29905 "AT4G29905" [Arabidopsis thaliana (taxid:3702)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 27/55 (49%), Positives = 34/55 (61%)

Query:    11 EKV-IRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV 64
             EK  + R  A   CPYCGG V A+D +    FCFLP+  KVK+K+ C+ C R LV
Sbjct:    10 EKTELGRQQAPGMCPYCGGKVSAVDIETKWLFCFLPLCFKVKRKYSCSSCERHLV 64

GO:0005575 "cellular_component" evidence=ND

TAIR|locus:2827497 AT2G20835 "AT2G20835" [Arabidopsis thaliana (taxid:3702)]

 Score = 94 (38.1 bits), Expect = 8.1e-05, P = 8.1e-05
 Identities = 20/54 (37%), Positives = 24/54 (44%)

Query:     6 IFDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTIC 59
             + D R+KV  R  A   C  CGG  +  D     RFC +P   K  K   C IC
Sbjct:     7 LVDQRKKVRGRKPAAGLCSRCGGGAVVADMRTSTRFCGVPFYRKAWKAIVCHIC 60


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        0.333   0.144   0.471    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       68        68   0.00091  102 3  11 21  0.50    27
                                                     29  0.38    29


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:  497 (53 KB)
  Total size of DFA:  94 KB (2069 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:  9.08u 0.16s 9.24t   Elapsed:  00:00:01
  Total cpu time:  9.08u 0.16s 9.24t   Elapsed:  00:00:01
  Start:  Fri May 10 07:14:53 2013   End:  Fri May 10 07:14:54 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	68
PF13005	47	zf-IS66: zinc-finger binding domain of transposase	94.88
PF10601	73	zf-LITAF-like: LITAF-like zinc ribbon domain; Inte	94.48
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	94.44
PF14690	47	zf-ISL3: zinc-finger of transposase IS204/IS1001/I	93.92
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	93.65
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	93.29
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	91.43
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	90.86
COG3813	84	Uncharacterized protein conserved in bacteria [Fun	90.83
PF11672	102	DUF3268: Protein of unknown function (DUF3268); In	89.96
PF13248	26	zf-ribbon_3: zinc-ribbon domain	89.77
PRK10445	263	endonuclease VIII; Provisional	89.7
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	89.69
PRK14810	272	formamidopyrimidine-DNA glycosylase; Provisional	89.65
PRK13945	282	formamidopyrimidine-DNA glycosylase; Provisional	89.13
TIGR03831	46	YgiT_finger YgiT-type zinc finger domain. This dom	89.07
PRK12775	1006	putative trifunctional 2-polyprenylphenol hydroxyl	88.9
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	88.85
PF01599	47	Ribosomal_S27: Ribosomal protein S27a; InterPro: I	88.58
PRK00432	50	30S ribosomal protein S27ae; Validated	88.47
smart00714	67	LITAF Possible membrane-associated motif in LPS-in	88.45
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	88.13
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	87.75
TIGR00577	272	fpg formamidopyrimidine-DNA glycosylase (fpg). All	87.52
smart00661	52	RPOL9 RNA polymerase subunit 9.	87.41
PF01927	147	Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T	87.3
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	86.85
PRK09678	72	DNA-binding transcriptional regulator; Provisional	86.81
PRK01103	274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	86.55
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	85.84
COG0675	364	Transposase and inactivated derivatives [DNA repli	85.53
PRK14811	269	formamidopyrimidine-DNA glycosylase; Provisional	85.26
PF14369	35	zf-RING_3: zinc-finger	85.04
smart00531	147	TFIIE Transcription initiation factor IIE.	84.68
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	84.65
PRK00420	112	hypothetical protein; Validated	84.28
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	82.93
PF12773	50	DZR: Double zinc ribbon	82.06
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	81.9
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	81.73
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	81.49
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	81.16
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	80.96
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	80.13

>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases []

Probab=94.88  E-value=0.053  Score=29.66  Aligned_cols=41  Identities=29%  Similarity=0.646  Sum_probs=29.1

Q ss_pred             CCcCCCCCCceEEEEec-ceeeeEEeeeeeeec----ceEEeeccc
Q 035300           20 DAACPYCGGPVLAIDFD-AHLRFCFLPISHKVK----KKFYCTICS   60 (68)
Q Consensus        20 ~G~Cp~CGG~v~a~Dve-s~~rfCflP~~~k~k----rk~~Ct~C~   60 (68)
                      +.+||.||+.+.-+-.+ .+-.|=++|.-++..    -+|.|+-|+
T Consensus         2 ~~~C~~Cg~~l~~ig~~~~~q~l~~~p~~~~V~e~~~~~y~C~~C~   47 (47)
T PF13005_consen    2 PRACPDCGGELKEIGEEKVRQVLDLPPAKPEVTEHVRHKYACPCCG   47 (47)
T ss_pred             CCcCCCCCceeeECCceeeEEEEeecccceEEEEEEeceEECCCCC
Confidence            56899999998866555 556666788766544    366777774

>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues

Probab=94.48  E-value=0.024  Score=33.92  Aligned_cols=51  Identities=22%  Similarity=0.461  Sum_probs=37.9

Q ss_pred             eecCCCCcCCCCCCceEEEEecce-----------------eeeEEeeeeeee--cceEEeecccceeeec
Q 035300           15 RRNGADAACPYCGGPVLAIDFDAH-----------------LRFCFLPISHKV--KKKFYCTICSRRLVPA   66 (68)
Q Consensus        15 ~~~~A~G~Cp~CGG~v~a~Dves~-----------------~rfCflP~~~k~--krk~~Ct~C~r~L~~~   66 (68)
                      +++|..-.||+||-.+. +.++.+                 |-+|+||++.+.  ...++|+.|++.|-.|
T Consensus         2 ~~~p~~~~CP~C~~~~~-T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~   71 (73)
T PF10601_consen    2 GPEPVRIYCPYCQQQVQ-TRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCGAFLGTY   71 (73)
T ss_pred             CCCceeeECCCCCCEEE-EEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEECCCCCCEeEEE
Confidence            46788889999998764 334422                 345789999854  4579999999998776

Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=94.44  E-value=0.033  Score=38.75  Aligned_cols=40  Identities=25%  Similarity=0.652  Sum_probs=27.4

Q ss_pred             cCCCCCCce-EEEEecceeeeEEeeeeeeecceEEeecccceeeecc
Q 035300           22 ACPYCGGPV-LAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPAT   67 (68)
Q Consensus        22 ~Cp~CGG~v-~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~~   67 (68)
                      .|||||++. .|.|=+.      ++==.-.+|++.|..||++...|-
T Consensus         2 ~cp~c~~~~~~~~~s~~------~~~~~~~~~~~~c~~c~~~f~~~e   42 (154)
T PRK00464          2 RCPFCGHPDTRVIDSRP------AEDGNAIRRRRECLACGKRFTTFE   42 (154)
T ss_pred             cCCCCCCCCCEeEeccc------cCCCCceeeeeeccccCCcceEeE
Confidence            499999976 6655431      111123677799999999987764

>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165

Probab=93.92  E-value=0.094  Score=28.41  Aligned_cols=38  Identities=32%  Similarity=0.751  Sum_probs=23.2

Q ss_pred             CCcCCCCCCceEEE--EecceeeeEEeee-----eee-ecceEEeecc
Q 035300           20 DAACPYCGGPVLAI--DFDAHLRFCFLPI-----SHK-VKKKFYCTIC   59 (68)
Q Consensus        20 ~G~Cp~CGG~v~a~--Dves~~rfCflP~-----~~k-~krk~~Ct~C   59 (68)
                      |-.||+||..-..-  -.+..|+  .+|+     +.+ .+++|.|..|
T Consensus         2 ~~~Cp~Cg~~~~~~~g~~~r~i~--~l~~~~~~~~L~i~~~R~~C~~C   47 (47)
T PF14690_consen    2 PPRCPHCGSPSVHRHGYKTRRIR--HLPIGGRPVYLRIRKRRYRCKNC   47 (47)
T ss_pred             CccCCCcCCCceECCceEEEEEe--ecccCCEEEEEEEEeEEEECcCC
Confidence            56899999776332  2333444  4444     433 3678888876

>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]

Probab=93.65  E-value=0.054  Score=32.57  Aligned_cols=36  Identities=39%  Similarity=0.708  Sum_probs=25.7

Q ss_pred             CceeeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300            9 LREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR   62 (68)
Q Consensus         9 e~~kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~   62 (68)
                      +.+||++.++   -||+||-++-.+|               ++.++.|-.||-.
T Consensus        11 ~~~kv~rk~~---~CPrCG~gvfmA~---------------H~dR~~CGkCgyT   46 (51)
T COG1998          11 DDEKVKRKNR---FCPRCGPGVFMAD---------------HKDRWACGKCGYT   46 (51)
T ss_pred             cCCcEEEccc---cCCCCCCcchhhh---------------cCceeEeccccce
Confidence            4456776655   6999998877666               4457888888743

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

Probab=93.29  E-value=0.039  Score=40.24  Aligned_cols=43  Identities=19%  Similarity=0.508  Sum_probs=24.5

Q ss_pred             CCCcCCCCCCceEEEEecce----eeeEEeeeeeeecc--eEEeecccc
Q 035300           19 ADAACPYCGGPVLAIDFDAH----LRFCFLPISHKVKK--KFYCTICSR   61 (68)
Q Consensus        19 A~G~Cp~CGG~v~a~Dves~----~rfCflP~~~k~kr--k~~Ct~C~r   61 (68)
                      ..|.||-||+.-++.-++..    .|+.+=.+|.-.|+  +..|+.||.
T Consensus       171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~  219 (290)
T PF04216_consen  171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN  219 (290)
T ss_dssp             T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred             cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence            35999999999888877764    58888788866653  568999985

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

>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length

Probab=91.43  E-value=0.092  Score=32.14  Aligned_cols=13  Identities=38%  Similarity=1.221  Sum_probs=11.1

Q ss_pred             CCcCCCCCCceEE
Q 035300           20 DAACPYCGGPVLA   32 (68)
Q Consensus        20 ~G~Cp~CGG~v~a   32 (68)
                      .|.||+|||.++.
T Consensus        41 ~~~CPNCgGelv~   53 (57)
T PF06906_consen   41 NGVCPNCGGELVR   53 (57)
T ss_pred             cCcCcCCCCcccc
Confidence            6899999998753

This family contains a number of conserved cysteine residues and its function is unknown.

>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc

Probab=90.86  E-value=0.4  Score=26.63  Aligned_cols=28  Identities=21%  Similarity=0.790  Sum_probs=20.6

Q ss_pred             CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300           21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR   62 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~   62 (68)
                      -.||+||.. .+.-+.+             ...|.|..|+++
T Consensus        19 ~~CP~Cg~~-~~~~~~~-------------~~~~~C~~C~~q   46 (46)
T PF12760_consen   19 FVCPHCGST-KHYRLKT-------------RGRYRCKACRKQ   46 (46)
T ss_pred             CCCCCCCCe-eeEEeCC-------------CCeEECCCCCCc
Confidence            459999997 5555555             677888888764

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

>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.83  E-value=0.096  Score=34.11  Aligned_cols=18  Identities=33%  Similarity=0.815  Sum_probs=14.5

Q ss_pred             CCCcCCCCCCceEEEEec
Q 035300           19 ADAACPYCGGPVLAIDFD   36 (68)
Q Consensus        19 A~G~Cp~CGG~v~a~Dve   36 (68)
                      -.|.||+|||.+++--++
T Consensus        40 l~g~CPnCGGelv~RP~R   57 (84)
T COG3813          40 LHGLCPNCGGELVARPIR   57 (84)
T ss_pred             hcCcCCCCCchhhcCcCC
Confidence            469999999999876554

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

Probab=89.96  E-value=0.18  Score=33.29  Aligned_cols=39  Identities=28%  Similarity=0.635  Sum_probs=24.3

Q ss_pred             CCcCCCCCCceEEEEecceeeeEEeeeeeeecc-eEEeeccccee
Q 035300           20 DAACPYCGGPVLAIDFDAHLRFCFLPISHKVKK-KFYCTICSRRL   63 (68)
Q Consensus        20 ~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr-k~~Ct~C~r~L   63 (68)
                      |-.||||||++.-+|= +..    -|=-...+. -|.|+.|++-.
T Consensus         2 p~~CpYCg~~~~l~~~-~~i----Yg~~~~~~~~~y~C~~C~AyV   41 (102)
T PF11672_consen    2 PIICPYCGGPAELVDG-SEI----YGHRYDDGPYLYVCTPCDAYV   41 (102)
T ss_pred             CcccCCCCCeeEEccc-chh----cCccCCCCceeEECCCCCcee
Confidence            5689999999998772 221    131111123 38999998753

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

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=89.77  E-value=0.1  Score=26.30  Aligned_cols=9  Identities=44%  Similarity=1.353  Sum_probs=6.7

Q ss_pred             cCCCCCCce
Q 035300           22 ACPYCGGPV   30 (68)
Q Consensus        22 ~Cp~CGG~v   30 (68)
                      .||+||-.+
T Consensus         4 ~Cp~Cg~~~   12 (26)
T PF13248_consen    4 FCPNCGAEI   12 (26)
T ss_pred             CCcccCCcC
Confidence            588888743

>PRK10445 endonuclease VIII; Provisional

Probab=89.70  E-value=0.43  Score=34.78  Aligned_cols=34  Identities=29%  Similarity=0.746  Sum_probs=23.4

Q ss_pred             eeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300           12 KVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS   60 (68)
Q Consensus        12 kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (68)
                      +|-++  +...||+||+.+.-+.+-.             ...|+|+.|-
T Consensus       229 ~Vy~r--~g~~Cp~Cg~~I~~~~~~g-------------R~t~~CP~CQ  262 (263)
T PRK10445        229 KVFHR--DGEACERCGGIIEKTTLSS-------------RPFYWCPGCQ  262 (263)
T ss_pred             EEeCC--CCCCCCCCCCEeEEEEECC-------------CCcEECCCCc
Confidence            44443  3456999999999887763             5566777663

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=89.69  E-value=0.098  Score=26.17  Aligned_cols=9  Identities=44%  Similarity=1.335  Sum_probs=6.5

Q ss_pred             CCCCCCceE
Q 035300           23 CPYCGGPVL   31 (68)
Q Consensus        23 Cp~CGG~v~   31 (68)
                      ||+||-.+.
T Consensus         2 Cp~CG~~~~   10 (23)
T PF13240_consen    2 CPNCGAEIE   10 (23)
T ss_pred             CcccCCCCC
Confidence            777877664

>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional

Probab=89.65  E-value=0.39  Score=35.15  Aligned_cols=26  Identities=23%  Similarity=0.737  Sum_probs=20.1

Q ss_pred             cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300           22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS   60 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (68)
                      .||+||+++.-..+..             ...|+|+.|-
T Consensus       246 pCprCG~~I~~~~~~g-------------R~t~~CP~CQ  271 (272)
T PRK14810        246 PCLNCKTPIRRVVVAG-------------RSSHYCPHCQ  271 (272)
T ss_pred             cCCCCCCeeEEEEECC-------------CccEECcCCc
Confidence            5999999998777753             5667777774

>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional

Probab=89.13  E-value=0.49  Score=34.75  Aligned_cols=34  Identities=29%  Similarity=0.745  Sum_probs=23.4

Q ss_pred             eeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300           12 KVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS   60 (68)
Q Consensus        12 kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (68)
                      +|-++.  ...||+||+.+.-.-+..             ...|+|+.|-
T Consensus       248 ~Vy~R~--g~pC~~Cg~~I~~~~~~g-------------R~t~~CP~CQ  281 (282)
T PRK13945        248 WVYRRT--GKPCRKCGTPIERIKLAG-------------RSTHWCPNCQ  281 (282)
T ss_pred             EEeCCC--cCCCCcCCCeeEEEEECC-------------CccEECCCCc
Confidence            354443  346999999998877754             5667777763

>TIGR03831 YgiT_finger YgiT-type zinc finger domain

Probab=89.07  E-value=0.87  Score=24.02  Aligned_cols=43  Identities=21%  Similarity=0.336  Sum_probs=25.2

Q ss_pred             CCCCCCceEEEEecceeeeEE-eeeeeeecceEEeecccceeee
Q 035300           23 CPYCGGPVLAIDFDAHLRFCF-LPISHKVKKKFYCTICSRRLVP   65 (68)
Q Consensus        23 Cp~CGG~v~a~Dves~~rfCf-lP~~~k~krk~~Ct~C~r~L~~   65 (68)
                      ||-|||....-++++.+.--- -=+..+.=..+.|+.||..+-+
T Consensus         1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE~~~~   44 (46)
T TIGR03831         1 CPICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGEEYLD   44 (46)
T ss_pred             CCCCCCceecceEEEEEEEeCCEEEEEeCCCccccccCCCEeeC
Confidence            888988877777654432111 1122334456678988877643

This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.

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

Probab=88.90  E-value=0.13  Score=43.74  Aligned_cols=29  Identities=34%  Similarity=0.507  Sum_probs=22.1

Q ss_pred             EeCCceeeeeecCCC-CcCCCCCCceEEEE
Q 035300            6 IFDLREKVIRRNGAD-AACPYCGGPVLAID   34 (68)
Q Consensus         6 vcde~~kv~~~~~A~-G~Cp~CGG~v~a~D   34 (68)
                      =||.-+||----.+| |.||+|||.+++.|
T Consensus       823 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  852 (1006)
T PRK12775        823 RCDDCGKVSEGFAFPYGMCPACGGKLQALD  852 (1006)
T ss_pred             ehhhhccccccccCCcCcCcccccchhhhh
Confidence            456666665555666 99999999998876

>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family

Probab=88.85  E-value=0.99  Score=28.17  Aligned_cols=41  Identities=27%  Similarity=0.576  Sum_probs=31.1

Q ss_pred             CCCCCCceEEEEecc-eeeeEEeeeeeeecceEEeecccceee
Q 035300           23 CPYCGGPVLAIDFDA-HLRFCFLPISHKVKKKFYCTICSRRLV   64 (68)
Q Consensus        23 Cp~CGG~v~a~Dves-~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (68)
                      ||.||++....+++. .+.+.-.-+-+ .-..+.|+.||..+.
T Consensus         1 C~~C~~~~~~~~~~~~~~~~~G~~~~v-~~~~~~C~~CGe~~~   42 (127)
T TIGR03830         1 CPICGSGELVRDVKDEPYTYKGESITI-GVPGWYCPACGEELL   42 (127)
T ss_pred             CCCCCCccceeeeecceEEEcCEEEEE-eeeeeECCCCCCEEE
Confidence            899997666677776 44677777777 667788999998654

This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.

>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=88.58  E-value=0.7  Score=27.05  Aligned_cols=38  Identities=34%  Similarity=0.697  Sum_probs=25.8

Q ss_pred             EEeCCceeeeeecCCCCcCC--CCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300            5 SIFDLREKVIRRNGADAACP--YCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS   60 (68)
Q Consensus         5 ~vcde~~kv~~~~~A~G~Cp--~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (68)
                      +=+|+++||.+.+   -.||  +||.+|-.++-               +.+++|-.||
T Consensus         6 Ykvd~~Gkv~r~r---k~CP~~~CG~GvFMA~H---------------~dR~~CGKCg   45 (47)
T PF01599_consen    6 YKVDENGKVKRLR---KECPSPRCGAGVFMAEH---------------KDRHYCGKCG   45 (47)
T ss_dssp             CEEETTTEEEESS---EE-TSTTTTSSSEEEE----------------SSEEEETTTS
T ss_pred             EEECCCCcEEEhh---hcCCCcccCCceEeeec---------------CCCccCCCcc
Confidence            3468888887654   4699  99999865543               4577777776

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=88.47  E-value=0.65  Score=26.89  Aligned_cols=36  Identities=33%  Similarity=0.623  Sum_probs=23.3

Q ss_pred             eCCceeeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300            7 FDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR   62 (68)
Q Consensus         7 cde~~kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~   62 (68)
                      +|.+ +|....+   -||+||..+.+.                ++.++.|..||..
T Consensus        11 v~~~-~v~~~~~---fCP~Cg~~~m~~----------------~~~r~~C~~Cgyt   46 (50)
T PRK00432         11 VDGG-KVKRKNK---FCPRCGSGFMAE----------------HLDRWHCGKCGYT   46 (50)
T ss_pred             ECCC-EEEEccC---cCcCCCcchhec----------------cCCcEECCCcCCE
Confidence            4544 6665444   899999752222                2368889999864

>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins

Probab=88.45  E-value=0.26  Score=28.99  Aligned_cols=49  Identities=22%  Similarity=0.428  Sum_probs=32.2

Q ss_pred             CCCCcCCCCCCceEEEEeccee---------------eeEEeeeeeee--cceEEeecccceeeecc
Q 035300           18 GADAACPYCGGPVLAIDFDAHL---------------RFCFLPISHKV--KKKFYCTICSRRLVPAT   67 (68)
Q Consensus        18 ~A~G~Cp~CGG~v~a~Dves~~---------------rfCflP~~~k~--krk~~Ct~C~r~L~~~~   67 (68)
                      |+.-.||+||.-++ +.+|.+.               =+|+||++.+.  ...++|+.|++.|-.|.
T Consensus         1 p~~i~Cp~C~~~~~-T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~~   66 (67)
T smart00714        1 PYQLFCPRCQNNVT-TRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHYCPNCGAFLGTYN   66 (67)
T ss_pred             CcceECCCCCCEEE-EEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEECCCCCCEeEEec
Confidence            45567999987543 4444222               24568985443  45689999999988764

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

Probab=88.13  E-value=0.39  Score=27.86  Aligned_cols=30  Identities=23%  Similarity=0.644  Sum_probs=23.0

Q ss_pred             CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300           19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL   63 (68)
Q Consensus        19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L   63 (68)
                      ..-.||.||.....               ..+.|.|.|+.||...
T Consensus        27 TSq~C~~CG~~~~~---------------~~~~r~~~C~~Cg~~~   56 (69)
T PF07282_consen   27 TSQTCPRCGHRNKK---------------RRSGRVFTCPNCGFEM   56 (69)
T ss_pred             CccCccCccccccc---------------ccccceEEcCCCCCEE
Confidence            35579999987765               4577889999998753

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

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

Probab=87.75  E-value=0.92  Score=25.02  Aligned_cols=13  Identities=46%  Similarity=1.140  Sum_probs=8.1

Q ss_pred             CCcCCCCCCceEE
Q 035300           20 DAACPYCGGPVLA   32 (68)
Q Consensus        20 ~G~Cp~CGG~v~a   32 (68)
                      +..||+||+.+..
T Consensus        21 ~~~Cp~CG~~~~~   33 (46)
T PRK00398         21 GVRCPYCGYRILF   33 (46)
T ss_pred             ceECCCCCCeEEE
Confidence            4567777766553

>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg)

Probab=87.52  E-value=0.73  Score=33.69  Aligned_cols=26  Identities=27%  Similarity=0.855  Sum_probs=19.8

Q ss_pred             CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecc
Q 035300           21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTIC   59 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C   59 (68)
                      -.||+||+.+.-.-+..             ...|+|+.|
T Consensus       246 ~pC~~Cg~~I~~~~~~g-------------R~t~~CP~C  271 (272)
T TIGR00577       246 EPCRRCGTPIEKIKVGG-------------RGTHFCPQC  271 (272)
T ss_pred             CCCCCCCCeeEEEEECC-------------CCCEECCCC
Confidence            36999999998877763             566777766

All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=87.41  E-value=0.38  Score=26.41  Aligned_cols=29  Identities=28%  Similarity=0.724  Sum_probs=18.3

Q ss_pred             cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300           22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL   63 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L   63 (68)
                      -||.||..+..-+.+.             ...+.|+.||...
T Consensus         2 FCp~Cg~~l~~~~~~~-------------~~~~vC~~Cg~~~   30 (52)
T smart00661        2 FCPKCGNMLIPKEGKE-------------KRRFVCRKCGYEE   30 (52)
T ss_pred             CCCCCCCccccccCCC-------------CCEEECCcCCCeE
Confidence            4899998665443331             2367788887543

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

Probab=87.30  E-value=0.6  Score=31.17  Aligned_cols=45  Identities=16%  Similarity=0.331  Sum_probs=31.0

Q ss_pred             CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300           19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL   63 (68)
Q Consensus        19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L   63 (68)
                      ....||.|+|.++.++-|....----.++..+..=+.|+.||+.+
T Consensus        90 ~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy  134 (147)
T PF01927_consen   90 IFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY  134 (147)
T ss_pred             CCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence            348999999999888766544432222333445667899999864

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

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=86.85  E-value=0.52  Score=26.88  Aligned_cols=35  Identities=26%  Similarity=0.663  Sum_probs=19.3

Q ss_pred             cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300           22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV   64 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (68)
                      -||.|||....+.-.    +  -  -...+.-|.|+-||....
T Consensus         3 PCPfCGg~~~~~~~~----~--~--~~~~~~~~~C~~Cga~~~   37 (53)
T TIGR03655         3 PCPFCGGADVYLRRG----F--D--PLDLSHYFECSTCGASGP   37 (53)
T ss_pred             CCCCCCCcceeeEec----c--C--CCCCEEEEECCCCCCCcc
Confidence            499999987743210    0  0  011122346889987654

Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=86.81  E-value=0.57  Score=29.24  Aligned_cols=40  Identities=20%  Similarity=0.342  Sum_probs=28.0

Q ss_pred             cCCCCCCceEEEEecceeeeEEeeeeeeecceEEee--cccceeeeccC
Q 035300           22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCT--ICSRRLVPATS   68 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct--~C~r~L~~~~~   68 (68)
                      -||.||..+.+.|=+-..     +.  -..+.+.|+  .||.+.+++.+
T Consensus         3 ~CP~Cg~~a~irtSr~~s-----~~--~~~~Y~qC~N~eCg~tF~t~es   44 (72)
T PRK09678          3 HCPLCQHAAHARTSRYIT-----DT--TKERYHQCQNVNCSATFITYES   44 (72)
T ss_pred             cCCCCCCccEEEEChhcC-----hh--hheeeeecCCCCCCCEEEEEEE
Confidence            499999999666544222     22  245677899  99999988753

>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated

Probab=86.55  E-value=0.88  Score=33.15  Aligned_cols=28  Identities=29%  Similarity=0.889  Sum_probs=20.6

Q ss_pred             CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300           21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR   61 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (68)
                      -.||+||+.+.-..+-.             ...|+|+.|-+
T Consensus       246 ~pC~~Cg~~I~~~~~~g-------------R~t~~CP~CQ~  273 (274)
T PRK01103        246 EPCRRCGTPIEKIKQGG-------------RSTFFCPRCQK  273 (274)
T ss_pred             CCCCCCCCeeEEEEECC-------------CCcEECcCCCC
Confidence            35999999998777753             55677777753

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

Probab=85.84  E-value=1.1  Score=23.97  Aligned_cols=20  Identities=30%  Similarity=0.695  Sum_probs=14.2

Q ss_pred             eeeeeecCCCCcCCCCCCce
Q 035300           11 EKVIRRNGADAACPYCGGPV   30 (68)
Q Consensus        11 ~kv~~~~~A~G~Cp~CGG~v   30 (68)
                      +-+.....+|..||-||.+-
T Consensus         9 G~i~~g~~~p~~CP~Cg~~~   28 (34)
T cd00729           9 GYIHEGEEAPEKCPICGAPK   28 (34)
T ss_pred             CCEeECCcCCCcCcCCCCch
Confidence            33444456899999999864

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

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

Probab=85.53  E-value=0.48  Score=32.49  Aligned_cols=24  Identities=29%  Similarity=0.747  Sum_probs=19.2

Q ss_pred             CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300           19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR   62 (68)
Q Consensus        19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~   62 (68)
                      ..-.||.||.                    .+.|.+.|+.||-.
T Consensus       308 tS~~C~~cg~--------------------~~~r~~~C~~cg~~  331 (364)
T COG0675         308 TSKTCPCCGH--------------------LSGRLFKCPRCGFV  331 (364)
T ss_pred             CcccccccCC--------------------ccceeEECCCCCCe
Confidence            3357999999                    45788999999964

>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional

Probab=85.26  E-value=1  Score=33.04  Aligned_cols=28  Identities=29%  Similarity=0.844  Sum_probs=21.2

Q ss_pred             CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300           21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR   61 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (68)
                      -.||+||+.+.-.-+-.             ...|+|+.|-+
T Consensus       236 ~pC~~Cg~~I~~~~~~g-------------R~ty~Cp~CQ~  263 (269)
T PRK14811        236 QPCPRCGTPIEKIVVGG-------------RGTHFCPQCQP  263 (269)
T ss_pred             CCCCcCCCeeEEEEECC-------------CCcEECCCCcC
Confidence            35999999998877753             56677777754

>PF14369 zf-RING_3: zinc-finger

Probab=85.04  E-value=0.86  Score=24.66  Aligned_cols=15  Identities=40%  Similarity=0.884  Sum_probs=10.6

Q ss_pred             ecCCCCcCCCCCCce
Q 035300           16 RNGADAACPYCGGPV   30 (68)
Q Consensus        16 ~~~A~G~Cp~CGG~v   30 (68)
                      .....-+||+|+|+-
T Consensus        17 ~~~~~~~CP~C~~gF   31 (35)
T PF14369_consen   17 SPDSDVACPRCHGGF   31 (35)
T ss_pred             CCCCCcCCcCCCCcE
Confidence            344455699999975

>smart00531 TFIIE Transcription initiation factor IIE

Probab=84.68  E-value=0.34  Score=32.46  Aligned_cols=41  Identities=22%  Similarity=0.433  Sum_probs=27.9

Q ss_pred             CCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeecc
Q 035300           18 GADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPAT   67 (68)
Q Consensus        18 ~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~~   67 (68)
                      .+-=.||+||-...+.|.....-    |     -..|.|+.||..|+.+.
T Consensus        97 ~~~Y~Cp~C~~~y~~~ea~~~~d----~-----~~~f~Cp~Cg~~l~~~d  137 (147)
T smart00531       97 NAYYKCPNCQSKYTFLEANQLLD----M-----DGTFTCPRCGEELEEDD  137 (147)
T ss_pred             CcEEECcCCCCEeeHHHHHHhcC----C-----CCcEECCCCCCEEEEcC
Confidence            44557999998887655432111    1     25599999999998764

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=84.65  E-value=0.38  Score=36.70  Aligned_cols=45  Identities=22%  Similarity=0.528  Sum_probs=34.3

Q ss_pred             CCCCcCCCCCCceEEEEe-----cceeeeEEeeeeeeecc--eEEeecccce
Q 035300           18 GADAACPYCGGPVLAIDF-----DAHLRFCFLPISHKVKK--KFYCTICSRR   62 (68)
Q Consensus        18 ~A~G~Cp~CGG~v~a~Dv-----es~~rfCflP~~~k~kr--k~~Ct~C~r~   62 (68)
                      ...|.||-||+.-.+.-+     +...|+..=++|.--|+  |..|+.||..
T Consensus       182 ~~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~  233 (305)
T TIGR01562       182 ESRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEES  233 (305)
T ss_pred             CCCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCC
Confidence            457799999999766544     34578888888876664  7899999863

The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).

>PRK00420 hypothetical protein; Validated

Probab=84.28  E-value=0.81  Score=30.70  Aligned_cols=30  Identities=20%  Similarity=0.569  Sum_probs=22.0

Q ss_pred             CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300           19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV   64 (68)
Q Consensus        19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (68)
                      ....||.||.                |++.=...+.+|..||..+.
T Consensus        22 l~~~CP~Cg~----------------pLf~lk~g~~~Cp~Cg~~~~   51 (112)
T PRK00420         22 LSKHCPVCGL----------------PLFELKDGEVVCPVHGKVYI   51 (112)
T ss_pred             ccCCCCCCCC----------------cceecCCCceECCCCCCeee
Confidence            4578999986                44443667889999998765

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

Probab=82.93  E-value=0.93  Score=24.62  Aligned_cols=29  Identities=28%  Similarity=0.731  Sum_probs=13.6

Q ss_pred             cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300           22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR   61 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (68)
                      -||.||++++-.=.+-           -...|+.|+.||.
T Consensus         2 fC~~CG~~l~~~ip~g-----------d~r~R~vC~~Cg~   30 (34)
T PF14803_consen    2 FCPQCGGPLERRIPEG-----------DDRERLVCPACGF   30 (34)
T ss_dssp             B-TTT--B-EEE--TT------------SS-EEEETTTTE
T ss_pred             ccccccChhhhhcCCC-----------CCccceECCCCCC
Confidence            3999999987654411           1334567788775

>PF12773 DZR: Double zinc ribbon

Probab=82.06  E-value=0.36  Score=26.50  Aligned_cols=14  Identities=21%  Similarity=0.368  Sum_probs=7.9

Q ss_pred             ecceEEeeccccee
Q 035300           50 VKKKFYCTICSRRL   63 (68)
Q Consensus        50 ~krk~~Ct~C~r~L   63 (68)
                      .....+|+.||+.+
T Consensus        26 ~~~~~~C~~Cg~~~   39 (50)
T PF12773_consen   26 DQSKKICPNCGAEN   39 (50)
T ss_pred             cCCCCCCcCCcCCC
Confidence            34455666666654

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=81.90  E-value=0.86  Score=34.95  Aligned_cols=43  Identities=19%  Similarity=0.529  Sum_probs=32.3

Q ss_pred             CCCcCCCCCCceEE--EEe--cceeeeEEeeeeeeecc--eEEeecccc
Q 035300           19 ADAACPYCGGPVLA--IDF--DAHLRFCFLPISHKVKK--KFYCTICSR   61 (68)
Q Consensus        19 A~G~Cp~CGG~v~a--~Dv--es~~rfCflP~~~k~kr--k~~Ct~C~r   61 (68)
                      ..|.||-||+.-++  ++.  +...|++.=++|.--|+  |..|+.||.
T Consensus       186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~  234 (309)
T PRK03564        186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQ  234 (309)
T ss_pred             CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCC
Confidence            57999999998533  333  34578888888877664  789999985

>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=81.73  E-value=1.6  Score=23.75  Aligned_cols=30  Identities=27%  Similarity=0.696  Sum_probs=20.3

Q ss_pred             cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeee
Q 035300           22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVP   65 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~   65 (68)
                      .||+||..-...|-+              .-.++|+.||..|.-
T Consensus         2 ~Cp~Cg~~~~~~D~~--------------~g~~vC~~CG~Vl~e   31 (43)
T PF08271_consen    2 KCPNCGSKEIVFDPE--------------RGELVCPNCGLVLEE   31 (43)
T ss_dssp             SBTTTSSSEEEEETT--------------TTEEEETTT-BBEE-
T ss_pred             CCcCCcCCceEEcCC--------------CCeEECCCCCCEeec
Confidence            599999987655533              345678899887753

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.

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

Probab=81.49  E-value=0.98  Score=23.38  Aligned_cols=17  Identities=24%  Similarity=0.382  Sum_probs=9.5

Q ss_pred             CcCCCCCCceEEEEecc
Q 035300           21 AACPYCGGPVLAIDFDA   37 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves   37 (68)
                      .-||+||++...++=+.
T Consensus         4 rfC~~CG~~t~~~~~g~   20 (32)
T PF09297_consen    4 RFCGRCGAPTKPAPGGW   20 (32)
T ss_dssp             SB-TTT--BEEE-SSSS
T ss_pred             cccCcCCccccCCCCcC
Confidence            46999999988776543

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

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=81.16  E-value=1.7  Score=24.63  Aligned_cols=33  Identities=27%  Similarity=0.672  Sum_probs=19.6

Q ss_pred             cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300           22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR   61 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (68)
                      -||-||.+....+-+..+.---.       -.+.|+.||.
T Consensus         5 PCPFCG~~~~~~~~~~~~~~~~~-------~~V~C~~Cga   37 (61)
T PF14354_consen    5 PCPFCGSADVLIRQDEGFDYGMY-------YYVECTDCGA   37 (61)
T ss_pred             CCCCCCCcceEeecccCCCCCCE-------EEEEcCCCCC
Confidence            39999877766665433210000       3467899987

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=80.96  E-value=0.44  Score=32.62  Aligned_cols=35  Identities=17%  Similarity=0.124  Sum_probs=23.9

Q ss_pred             CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeecc
Q 035300           19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPAT   67 (68)
Q Consensus        19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~~   67 (68)
                      .-=.||+||-..+..|.-+              .-|.|+.||..|+-+.
T Consensus       108 ~~Y~Cp~c~~r~tf~eA~~--------------~~F~Cp~Cg~~L~~~d  142 (158)
T TIGR00373       108 MFFICPNMCVRFTFNEAME--------------LNFTCPRCGAMLDYLD  142 (158)
T ss_pred             CeEECCCCCcEeeHHHHHH--------------cCCcCCCCCCEeeecc
Confidence            3346888887666655554              1588888888887664

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

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=80.13  E-value=1.8  Score=25.64  Aligned_cols=33  Identities=21%  Similarity=0.470  Sum_probs=22.5

Q ss_pred             CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeec
Q 035300           21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPA   66 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~   66 (68)
                      ..||.||..+..-|....             --+.|..||+.|...
T Consensus         3 ~~CP~CG~~iev~~~~~G-------------eiV~Cp~CGaeleVv   35 (54)
T TIGR01206         3 FECPDCGAEIELENPELG-------------ELVICDECGAELEVV   35 (54)
T ss_pred             cCCCCCCCEEecCCCccC-------------CEEeCCCCCCEEEEE
Confidence            479999998766443211             135899999988764

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

---

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	68
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	93.42
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	92.17
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	91.18
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	89.19
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	88.33
3ga8_A	78	HTH-type transcriptional regulator MQSA (YGIT/B30;	87.46
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	83.46
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	83.19
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	82.1
1k3x_A	262	Endonuclease VIII; hydrolase/DNA, hydrolase-DNA co	80.75
2xzf_A	271	Formamidopyrimidine-DNA glycosylase; hydrolase-DNA	80.32
1vd4_A	62	Transcription initiation factor IIE, alpha subunit	80.01

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

Probab=93.42  E-value=0.037  Score=31.81  Aligned_cols=38  Identities=26%  Similarity=0.624  Sum_probs=25.9

Q ss_pred             eCCceeeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300            7 FDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL   63 (68)
Q Consensus         7 cde~~kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L   63 (68)
                      +|+ +++.+.   --.||.||.++.            +.   ++..+++|..|+-..
T Consensus         9 v~~-gki~~~---~~fCPkCG~~~~------------ma---~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A            9 IAD-GKLVRK---HRFCPRCGPGVF------------LA---EHADRYSCGRCGYTE   46 (55)
T ss_dssp             CCC-CCCCCS---SCCCTTTTTTCC------------CE---ECSSEEECTTTCCCE
T ss_pred             EcC-CEEEEc---cccCcCCCCcee------------Ee---ccCCEEECCCCCCEE
Confidence            455 666542   467999998772            21   445699999998653

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

Probab=92.17  E-value=0.11  Score=29.31  Aligned_cols=37  Identities=32%  Similarity=0.706  Sum_probs=25.1

Q ss_pred             eCCceeeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccce
Q 035300            7 FDLREKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRR   62 (68)
Q Consensus         7 cde~~kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~   62 (68)
                      +| .+||.+.   .--||.||.++..++               +..++.|..||-.
T Consensus        10 v~-~~kv~~~---~k~CP~CG~~~fm~~---------------~~~R~~C~kCG~t   46 (50)
T 3j20_Y           10 IK-DGKVIRK---NKFCPRCGPGVFMAD---------------HGDRWACGKCGYT   46 (50)
T ss_dssp             EC-SSCEECS---SEECSSSCSSCEEEE---------------CSSEEECSSSCCE
T ss_pred             EE-CCEEEEe---cccCCCCCCceEEec---------------CCCeEECCCCCCE
Confidence            35 5666654   346999998875443               2467899999854

>2fiy_A Protein FDHE homolog; FDHE protein, structural genomics, P protein structure initiative, midwest center for structural genomics, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: e.59.1.1

Probab=91.18  E-value=0.083  Score=38.85  Aligned_cols=44  Identities=23%  Similarity=0.498  Sum_probs=34.1

Q ss_pred             CCCCcCCCCCCceEEEEec-----ceeeeEEeeeeeeecc--eEEeecccc
Q 035300           18 GADAACPYCGGPVLAIDFD-----AHLRFCFLPISHKVKK--KFYCTICSR   61 (68)
Q Consensus        18 ~A~G~Cp~CGG~v~a~Dve-----s~~rfCflP~~~k~kr--k~~Ct~C~r   61 (68)
                      ...|.||-||+.-++.-+.     ...|++.=.+|.-.|+  +..|+.||.
T Consensus       180 ~~~~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~t~W~~~R~~C~~Cg~  230 (309)
T 2fiy_A          180 ESRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEE  230 (309)
T ss_dssp             TTCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECCTTSCSSSCC
T ss_pred             ccCCCCCCCCCcCceeEEeecCCCCCcEEEEeCCCCCEEeecCcCCcCCCC
Confidence            4579999999999887664     5678887777765553  668999985

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=89.19  E-value=0.79  Score=27.85  Aligned_cols=43  Identities=19%  Similarity=0.391  Sum_probs=26.6

Q ss_pred             cCCCCCCceEEEEecc-eeeeEEeeeeeeecceEEeecccceee
Q 035300           22 ACPYCGGPVLAIDFDA-HLRFCFLPISHKVKKKFYCTICSRRLV   64 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves-~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (68)
                      .||.||+.....+.++ ...+--.-+-.+.=..++|..||..+.
T Consensus         4 ~Cp~Cg~~~~~~~~~~~~~~~kg~~~~v~~v~~~~C~~CGE~~~   47 (133)
T 3o9x_A            4 KCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIM   47 (133)
T ss_dssp             BCTTTSSSBEEEEEEEEEEEETTEEEEEEEEEEEEESSSSCEEC
T ss_pred             CCCcCCCCceeeceEEEEEEECCEEEEECCCceeECCCCCCEee
Confidence            5999999865544433 223333334444446789999998653

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f

Probab=88.33  E-value=0.48  Score=31.26  Aligned_cols=41  Identities=27%  Similarity=0.584  Sum_probs=29.7

Q ss_pred             EeCCceeeeeecCCCCcCCC--CCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300            6 IFDLREKVIRRNGADAACPY--CGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV   64 (68)
Q Consensus         6 vcde~~kv~~~~~A~G~Cp~--CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (68)
                      =+|+++||.+.+.   .||+  ||.+|-.++-               +.|++|-.|+-.+.
T Consensus       107 ~~~~~~~~~~~~~---~c~~~~cg~g~fma~h---------------~~r~~cgkc~~t~~  149 (152)
T 3u5c_f          107 KVDAEGKVTKLRR---ECSNPTCGAGVFLANH---------------KDRLYCGKCHSVYK  149 (152)
T ss_dssp             EECSSSCEECCSC---BCCSTTSCSSSBEEEC---------------SSCEEESSSSSCCE
T ss_pred             EEccCCeEEECcC---cCCCccCCCceEeccc---------------CCCcccCCCceEEE
Confidence            3688888876644   5999  9988766543               35788888886553

>3ga8_A HTH-type transcriptional regulator MQSA (YGIT/B30; helix-turn-helix, Zn-binding protein, DNA-binding, transcrip transcription regulation; HET: PE4; 1.70A {Escherichia coli k-12} PDB: 3hi2_A

Probab=87.46  E-value=1.2  Score=25.98  Aligned_cols=41  Identities=22%  Similarity=0.408  Sum_probs=24.6

Q ss_pred             cCCCCCCceE---EEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300           22 ACPYCGGPVL---AIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV   64 (68)
Q Consensus        22 ~Cp~CGG~v~---a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (68)
                      .||.||++-.   ..|+.-.+.=.-+  -.+.=...+|+.||..+-
T Consensus         4 ~Cp~Cg~~~l~~~~~~~~~~~~G~~~--~I~~Vp~~~C~~CGE~~~   47 (78)
T 3ga8_A            4 KCPVCHQGEMVSGIKDIPYTFRGRKT--VLKGIHGLYCVHCEESIM   47 (78)
T ss_dssp             BCTTTSSSBEEEEEEEEEEEETTEEE--EEEEEEEEEETTTCCEEC
T ss_pred             ECCCCCCCeeEeEEEEEEEEECCEEE--EEcCceeEECCCCCCEEE
Confidence            5999998633   2333333333322  224556889999998764

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

Probab=83.46  E-value=0.83  Score=27.21  Aligned_cols=29  Identities=17%  Similarity=0.387  Sum_probs=20.8

Q ss_pred             CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300           21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV   64 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (68)
                      -+||.|+|++...+.               .....|+.|++.+-
T Consensus         9 L~CP~ck~~L~~~~~---------------~~~LiC~~cg~~YP   37 (70)
T 2js4_A            9 LVCPVCKGRLEFQRA---------------QAELVCNADRLAFP   37 (70)
T ss_dssp             CBCTTTCCBEEEETT---------------TTEEEETTTTEEEE
T ss_pred             eECCCCCCcCEEeCC---------------CCEEEcCCCCceec
Confidence            379999998875432               35667888887654

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

Probab=83.19  E-value=0.89  Score=26.93  Aligned_cols=29  Identities=14%  Similarity=0.209  Sum_probs=21.0

Q ss_pred             CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300           21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV   64 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (68)
                      -+||.|+|++...+.               +....|+.|++.+-
T Consensus         9 L~CP~ck~~L~~~~~---------------~~~LiC~~cg~~YP   37 (68)
T 2jr6_A            9 LVCPVTKGRLEYHQD---------------KQELWSRQAKLAYP   37 (68)
T ss_dssp             CBCSSSCCBCEEETT---------------TTEEEETTTTEEEE
T ss_pred             eECCCCCCcCeEeCC---------------CCEEEcCCCCcEec
Confidence            379999999876432               35667888887664

>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=82.10  E-value=1.1  Score=26.55  Aligned_cols=28  Identities=25%  Similarity=0.552  Sum_probs=20.5

Q ss_pred             cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300           22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV   64 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (68)
                      +||.|+|++...+.               +....|+.|++.+-
T Consensus        10 ~CP~ck~~L~~~~~---------------~~~LiC~~cg~~YP   37 (68)
T 2hf1_A           10 VCPLCKGPLVFDKS---------------KDELICKGDRLAFP   37 (68)
T ss_dssp             BCTTTCCBCEEETT---------------TTEEEETTTTEEEE
T ss_pred             ECCCCCCcCeEeCC---------------CCEEEcCCCCcEec
Confidence            79999999876432               35667888887654

>1k3x_A Endonuclease VIII; hydrolase/DNA, hydrolase-DNA complex; HET: BRU PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A*

Probab=80.75  E-value=0.98  Score=31.83  Aligned_cols=26  Identities=19%  Similarity=0.680  Sum_probs=19.3

Q ss_pred             cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300           22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS   60 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (68)
                      .||+||+++.-..+-             ...-|+|+.|-
T Consensus       236 pC~~CG~~I~~~~~~-------------gR~t~~CP~CQ  261 (262)
T 1k3x_A          236 PCERCGSIIEKTTLS-------------SRPFYWCPGCQ  261 (262)
T ss_dssp             BCTTTCCBCEEEEET-------------TEEEEECTTTC
T ss_pred             CCCCCCCEeEEEEEC-------------CCCeEECCCCC
Confidence            499999999887775             34556676663

>2xzf_A Formamidopyrimidine-DNA glycosylase; hydrolase-DNA complex; HET: VET; 1.80A {Lactococcus lactis subsp} PDB: 1pm5_A* 1xc8_A* 1pji_A* 2xzu_A* 3c58_A* 1tdz_A* 1nnj_A 1kfv_A 1pjj_A*

Probab=80.32  E-value=1.1  Score=31.70  Aligned_cols=27  Identities=22%  Similarity=0.796  Sum_probs=20.7

Q ss_pred             cCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300           22 ACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR   61 (68)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (68)
                      .||+||+++.-..+-             ...-|+|+.|-+
T Consensus       244 pC~~CG~~I~~~~~~-------------gR~t~~CP~CQ~  270 (271)
T 2xzf_A          244 KCSRCGAEIQKIKVA-------------GRGTHFCPVCQQ  270 (271)
T ss_dssp             BCTTTCCBCEEEEET-------------TEEEEECTTTSC
T ss_pred             CCCCCCCEeeEEEEC-------------CCceEECCCCCC
Confidence            499999999887775             355677777754

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

Probab=80.01  E-value=0.35  Score=25.78  Aligned_cols=41  Identities=20%  Similarity=0.488  Sum_probs=27.2

Q ss_pred             CCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceeeec
Q 035300           18 GADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLVPA   66 (68)
Q Consensus        18 ~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~~   66 (68)
                      .-|=.|+.||-...-.   +.+.     ..+...+.|.|..||+.....
T Consensus        12 ~k~~~C~~C~k~F~~~---~~l~-----~~H~~~k~~~C~~C~k~f~~~   52 (62)
T 1vd4_A           12 RASFKCPVCSSTFTDL---EANQ-----LFDPMTGTFRCTFCHTEVEED   52 (62)
T ss_dssp             SSEEECSSSCCEEEHH---HHHH-----HEETTTTEEBCSSSCCBCEEC
T ss_pred             CCCccCCCCCchhccH---HHhH-----hhcCCCCCEECCCCCCccccC
Confidence            3456799999765432   2222     334556889999999987654

---

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	68
d1k3xa3	40	Endonuclease VIII {Escherichia coli [TaxId: 562]}	90.95
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	90.7
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	89.81
d1k82a3	44	DNA repair protein MutM (Fpg) {Escherichia coli [T	86.16
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	85.99
d1tdza3	47	DNA repair protein MutM (Fpg) {Lactococcus lactis	84.85
d1r2za3	46	DNA repair protein MutM (Fpg) {Bacillus stearother	84.15
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	80.56
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	80.15

>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: Endonuclease VIII
species: Escherichia coli [TaxId: 562]

Probab=90.95  E-value=0.09  Score=27.29  Aligned_cols=18  Identities=17%  Similarity=0.527  Sum_probs=14.9

Q ss_pred             CCcCCCCCCceEEEEecc
Q 035300           20 DAACPYCGGPVLAIDFDA   37 (68)
Q Consensus        20 ~G~Cp~CGG~v~a~Dves   37 (68)
                      .-.|++||+.|.-+.+..
T Consensus        12 g~pC~~C~~~I~~~~~~g   29 (40)
T d1k3xa3          12 GEPCERCGSIIEKTTLSS   29 (40)
T ss_dssp             TSBCTTTCCBCEEEEETT
T ss_pred             CCccCcCCCEEEEEEECC
Confidence            345999999999998874

>d2fiya1 e.59.1.1 (A:19-308) FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId: 287]}

class: Multi-domain proteins (alpha and beta)
fold: FdhE-like
superfamily: FdhE-like
family: FdhE-like
domain: FdhE homolog PA4809
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=90.70  E-value=0.051  Score=37.98  Aligned_cols=45  Identities=22%  Similarity=0.468  Sum_probs=34.6

Q ss_pred             CCCCcCCCCCCceEEEEec-----ceeeeEEeeeeeeec--ceEEeecccce
Q 035300           18 GADAACPYCGGPVLAIDFD-----AHLRFCFLPISHKVK--KKFYCTICSRR   62 (68)
Q Consensus        18 ~A~G~Cp~CGG~v~a~Dve-----s~~rfCflP~~~k~k--rk~~Ct~C~r~   62 (68)
                      ...|.||-||+.-++.-++     ...|++.=.+|.--|  .+..|+.||..
T Consensus       162 ~~~~~CPvCGs~P~~s~l~~~~~~~G~R~l~C~~C~teW~~~R~~C~~Cg~~  213 (290)
T d2fiya1         162 ESRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEES  213 (290)
T ss_dssp             TTCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECCTTSCSSSCCC
T ss_pred             ccCCcCCCCCCcchhheeeccCCCCCceEEECCCCCCccccccccCCCCCCC
Confidence            4578999999998888774     346888778887666  46688888854

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=89.81  E-value=0.021  Score=28.68  Aligned_cols=13  Identities=38%  Similarity=0.922  Sum_probs=11.1

Q ss_pred             cCCCCCCceEEEE
Q 035300           22 ACPYCGGPVLAID   34 (68)
Q Consensus        22 ~Cp~CGG~v~a~D   34 (68)
                      .|||||+.|-|++
T Consensus         3 ~CpRC~~~VyaAE   15 (28)
T d1ibia1           3 KCSRCGDSVYAAE   15 (28)
T ss_dssp             ECTTTSSEESSSS
T ss_pred             cCcccchhHHHHH
Confidence            5999999998764

>d1k82a3 g.39.1.8 (A:225-268) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Escherichia coli [TaxId: 562]

Probab=86.16  E-value=0.46  Score=24.70  Aligned_cols=17  Identities=29%  Similarity=0.804  Sum_probs=14.2

Q ss_pred             CcCCCCCCceEEEEecc
Q 035300           21 AACPYCGGPVLAIDFDA   37 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves   37 (68)
                      -.||+||+.|..+.+..
T Consensus        17 ~~C~~C~~~I~~~~~~~   33 (44)
T d1k82a3          17 EPCRVCGTPIVATKHAQ   33 (44)
T ss_dssp             SBCTTTCCBCEEEEETT
T ss_pred             CCcCCCCCEEEEEEECC
Confidence            36999999999887764

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=85.99  E-value=0.15  Score=28.69  Aligned_cols=34  Identities=26%  Similarity=0.717  Sum_probs=23.9

Q ss_pred             ceeeeeecCCCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300           10 REKVIRRNGADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR   61 (68)
Q Consensus        10 ~~kv~~~~~A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (68)
                      ++||.+.+   -.||+||-+|-.++               ++.|++|-.||-
T Consensus        11 ~gkv~r~~---k~CP~CG~GvFmA~---------------H~dR~~CGKCgy   44 (55)
T d2k4xa1          11 DGKLVRKH---RFCPRCGPGVFLAE---------------HADRYSCGRCGY   44 (55)
T ss_dssp             CCCCCCSS---CCCTTTTTTCCCEE---------------CSSEEECTTTCC
T ss_pred             CCEEEEec---CcCcCCCCcEEeee---------------cCCCccccCCcc
Confidence            46666544   46999999886554               567788888874

>d1tdza3 g.39.1.8 (A:225-271) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Lactococcus lactis [TaxId: 1358]

Probab=84.85  E-value=0.37  Score=25.37  Aligned_cols=29  Identities=21%  Similarity=0.786  Sum_probs=21.0

Q ss_pred             CCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccc
Q 035300           20 DAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSR   61 (68)
Q Consensus        20 ~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (68)
                      .-.||+||..|.-+.+..             ...|+|+.|-+
T Consensus        18 g~~C~~C~~~I~~~~~~g-------------R~t~~Cp~CQk   46 (47)
T d1tdza3          18 GEKCSRCGAEIQKIKVAG-------------RGTHFCPVCQQ   46 (47)
T ss_dssp             TSBCTTTCCBCEEEEETT-------------EEEEECTTTSC
T ss_pred             CCCcCCCCcEEEEEEECC-------------cccEECccccC
Confidence            346999999999888753             34566776654

>d1r2za3 g.39.1.8 (A:229-274) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=84.15  E-value=0.64  Score=24.20  Aligned_cols=29  Identities=24%  Similarity=0.697  Sum_probs=20.8

Q ss_pred             CCCcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccc
Q 035300           19 ADAACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICS   60 (68)
Q Consensus        19 A~G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (68)
                      +.-.||+||.+|.-+.+..             .+.|+|+.|-
T Consensus        17 ~g~~C~~C~~~I~~~~~~g-------------R~t~~Cp~CQ   45 (46)
T d1r2za3          17 QGNPCKRCGTPIEKTVVAG-------------RGTHYCPRCQ   45 (46)
T ss_dssp             TTSBCTTTCCBCEEEEETT-------------EEEEECTTTC
T ss_pred             CCCccCCCCCeEEEEEECC-------------CcCEEChhhC
Confidence            3446999999999877753             4556777663

>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=80.56  E-value=0.54  Score=25.01  Aligned_cols=29  Identities=24%  Similarity=0.555  Sum_probs=21.3

Q ss_pred             CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeeccccee
Q 035300           21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRL   63 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L   63 (68)
                      ..||+||..--..|.++--              ++|+.||..+
T Consensus         6 ~~Cp~Cgs~~iv~D~~~Ge--------------~vC~~CG~Vi   34 (50)
T d1pfta_           6 KVCPACESAELIYDPERGE--------------IVCAKCGYVI   34 (50)
T ss_dssp             CSCTTTSCCCEEEETTTTE--------------EEESSSCCBC
T ss_pred             ccCcCCCCCcEEEECCCCe--------------EecccCCcEe
Confidence            3699999987778866544              5567887655

>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=80.15  E-value=0.69  Score=25.42  Aligned_cols=29  Identities=17%  Similarity=0.252  Sum_probs=21.1

Q ss_pred             CcCCCCCCceEEEEecceeeeEEeeeeeeecceEEeecccceee
Q 035300           21 AACPYCGGPVLAIDFDAHLRFCFLPISHKVKKKFYCTICSRRLV   64 (68)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (68)
                      -+||.|+|++...+               .+....|+.|++.+.
T Consensus        11 L~CP~ck~~L~~~~---------------~~~~Lvc~~~~~~YP   39 (59)
T d2jnya1          11 LACPKDKGPLRYLE---------------SEQLLVNERLNLAYR   39 (59)
T ss_dssp             CBCTTTCCBCEEET---------------TTTEEEETTTTEEEE
T ss_pred             hcCCCCCCEeEEeC---------------CCCEEEcCccCcccc
Confidence            37999999998743               234567888887664