Citrus Sinensis ID: 035291

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------
Protein Sequence
MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSYQ
Secondary Structure (PSIPRED)
cEEEEEEEcccEEEEEEEccccccccccccEEEEEEEccEEEEEEEEEEcEEcEEEEcccHHHHEccc
Secondary Structure Prediction (SSPRO)
cEEEEEEEccccEEccccccccEccccccccEEccccccccEcEccEEHHHHHHHEHHHHHHHHHccc
Coil and Loop (DISEMBL)
mvcfcflvdqtrkvhkckpaagicsrcgggasvadmktatrfchvpfyWKSWRAIICTFCGAVLKSYQ
Flexible Loop (DISEMBL)
mvcfcflvdqtrkvhkckpaagicsrcggGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSYQ
Low Complexity Region (SEG)
MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSYQ
Disordered region (IsUnstruct)
*VCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK***
Disordered Region (DISOPRED)
MVCFCFLVDQT***********ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY*
Disordered Region (DISEMBL)
MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSYQ
Disordered Region (DISPRO)
MVCFCFLVDQTRKVHKCKPAAGICSRC*GGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSYQ
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSYQ
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
225447245	68	PREDICTED: uncharacterized protein LOC10	1.0	1.0	0.867	5e-28
224110306	68	predicted protein [Populus trichocarpa]	1.0	1.0	0.897	8e-28
356543799	69	PREDICTED: uncharacterized protein LOC10	1.0	0.985	0.867	2e-27
297739264	215	unnamed protein product [Vitis vinifera]	0.985	0.311	0.850	3e-27
225461345	68	PREDICTED: uncharacterized protein LOC10	1.0	1.0	0.852	3e-27
449438070	68	PREDICTED: uncharacterized protein LOC10	1.0	1.0	0.838	5e-27
356549948	69	PREDICTED: uncharacterized protein LOC10	1.0	0.985	0.852	6e-27
255553865	68	conserved hypothetical protein [Ricinus	1.0	1.0	0.852	3e-26
449444390	68	PREDICTED: uncharacterized protein LOC10	1.0	1.0	0.794	2e-25
224115042	68	predicted protein [Populus trichocarpa]	1.0	1.0	0.808	2e-25

>gi|225447245|ref|XP_002272845.1| PREDICTED: uncharacterized protein LOC100261846 [Vitis vinifera]

 Score =  128 bits (321), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 59/68 (86%), Positives = 65/68 (95%)

Query: 1  MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
          MVCFCFLVDQTR+V   KPAAGICSRCGGGASVADMKTATRFC+VPFYWKSWRAIICTFC
Sbjct: 1  MVCFCFLVDQTRQVRSSKPAAGICSRCGGGASVADMKTATRFCYVPFYWKSWRAIICTFC 60

Query: 61 GAVLKSYQ 68
          G++L+SY+
Sbjct: 61 GSILRSYR 68

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224110306|ref|XP_002333114.1| predicted protein [Populus trichocarpa] gi|224127116|ref|XP_002329403.1| predicted protein [Populus trichocarpa] gi|224127118|ref|XP_002329404.1| predicted protein [Populus trichocarpa] gi|222834905|gb|EEE73354.1| predicted protein [Populus trichocarpa] gi|222870453|gb|EEF07584.1| predicted protein [Populus trichocarpa] gi|222870454|gb|EEF07585.1| predicted protein [Populus trichocarpa]

 Score =  127 bits (319), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 61/68 (89%), Positives = 64/68 (94%)

Query: 1  MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
          MVCFCFLVDQTRKV + KPAAGICSRCGGGASVADMKT TRFC+VPFYWKSWRAI+CTFC
Sbjct: 1  MVCFCFLVDQTRKVRRSKPAAGICSRCGGGASVADMKTCTRFCYVPFYWKSWRAIMCTFC 60

Query: 61 GAVLKSYQ 68
          GAVLKSY 
Sbjct: 61 GAVLKSYH 68

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543799|ref|XP_003540347.1| PREDICTED: uncharacterized protein LOC100819670 [Glycine max]

 Score =  126 bits (317), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 59/68 (86%), Positives = 64/68 (94%)

Query: 1  MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
          MV FCFLVDQ R+V + KPAAGICSRCGGGASVADMKTATRFC+VPFYWKSWRAI+CTFC
Sbjct: 1  MVFFCFLVDQQRQVQRSKPAAGICSRCGGGASVADMKTATRFCYVPFYWKSWRAIVCTFC 60

Query: 61 GAVLKSYQ 68
          GAVL+SYQ
Sbjct: 61 GAVLRSYQ 68

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297739264|emb|CBI28915.3| unnamed protein product [Vitis vinifera]

 Score =  125 bits (315), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 57/67 (85%), Positives = 62/67 (92%)

Query: 1   MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
           MVCFCFLVDQTR+V   KPAAGICSRCGGGASVADMKTATRFC+VPFYWKSWRAIICTFC
Sbjct: 135 MVCFCFLVDQTRQVRSSKPAAGICSRCGGGASVADMKTATRFCYVPFYWKSWRAIICTFC 194

Query: 61  GAVLKSY 67
           G++L  +
Sbjct: 195 GSILSFF 201

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461345|ref|XP_002284622.1| PREDICTED: uncharacterized protein LOC100241874 [Vitis vinifera]

 Score =  125 bits (314), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 58/68 (85%), Positives = 64/68 (94%)

Query: 1  MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
          MVCFCFLVDQTRKV + KPAAG CSRCG GASVADM+TATRFCHVPFYWKSW+AI+CTFC
Sbjct: 1  MVCFCFLVDQTRKVRRSKPAAGTCSRCGRGASVADMRTATRFCHVPFYWKSWKAIMCTFC 60

Query: 61 GAVLKSYQ 68
          GA+LKSY+
Sbjct: 61 GAILKSYR 68

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438070|ref|XP_004136813.1| PREDICTED: uncharacterized protein LOC101203862 [Cucumis sativus] gi|449493086|ref|XP_004159189.1| PREDICTED: uncharacterized LOC101203862 [Cucumis sativus]

 Score =  125 bits (313), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 57/68 (83%), Positives = 64/68 (94%)

Query: 1  MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
          MVCFCFLVDQTR+V + KPAAG CSRCGGGASVADMKTATRFC VPFYW+SWRAIICTFC
Sbjct: 1  MVCFCFLVDQTRQVRRSKPAAGFCSRCGGGASVADMKTATRFCFVPFYWRSWRAIICTFC 60

Query: 61 GAVLKSYQ 68
          GA+++SY+
Sbjct: 61 GAIIRSYR 68

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356549948|ref|XP_003543352.1| PREDICTED: uncharacterized protein LOC100790961 [Glycine max]

 Score =  124 bits (312), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 58/68 (85%), Positives = 64/68 (94%)

Query: 1  MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
          MV FCFLVDQ R+V + KPAAGICSRCGGGASVAD+KTATRFC+VPFYWKSWRAI+CTFC
Sbjct: 1  MVFFCFLVDQRREVQRSKPAAGICSRCGGGASVADIKTATRFCYVPFYWKSWRAIVCTFC 60

Query: 61 GAVLKSYQ 68
          GAVL+SYQ
Sbjct: 61 GAVLRSYQ 68

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553865|ref|XP_002517973.1| conserved hypothetical protein [Ricinus communis] gi|223542955|gb|EEF44491.1| conserved hypothetical protein [Ricinus communis]

 Score =  122 bits (306), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 58/68 (85%), Positives = 64/68 (94%)

Query: 1  MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
          MVCFCFLVDQTR+V K KPAAGICSRCGGGASVADMKT TRFC+VPFY KSWRAIICTFC
Sbjct: 1  MVCFCFLVDQTREVRKSKPAAGICSRCGGGASVADMKTFTRFCYVPFYCKSWRAIICTFC 60

Query: 61 GAVLKSYQ 68
          G++L+SY+
Sbjct: 61 GSILRSYR 68

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449444390|ref|XP_004139958.1| PREDICTED: uncharacterized protein LOC101208066 [Cucumis sativus] gi|449475737|ref|XP_004154538.1| PREDICTED: uncharacterized LOC101208066 [Cucumis sativus]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 54/68 (79%), Positives = 62/68 (91%)

Query: 1  MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
          MV FCF+VDQ RKV + +PA GIC+RCGGGASVADMKTA RFCHVPFYWKSWRA+ICTFC
Sbjct: 1  MVFFCFMVDQKRKVRRSRPAPGICARCGGGASVADMKTAVRFCHVPFYWKSWRALICTFC 60

Query: 61 GAVLKSYQ 68
          G+VL+SY+
Sbjct: 61 GSVLRSYR 68

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115042|ref|XP_002316925.1| predicted protein [Populus trichocarpa] gi|222859990|gb|EEE97537.1| predicted protein [Populus trichocarpa]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 55/68 (80%), Positives = 62/68 (91%)

Query: 1  MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
          MVCFCFLVDQTRKV + KP AG CSRCG GASVADM+T+TRFC+VPFYW SWRA+ICTFC
Sbjct: 1  MVCFCFLVDQTRKVRRFKPVAGSCSRCGHGASVADMRTSTRFCYVPFYWDSWRAVICTFC 60

Query: 61 GAVLKSYQ 68
          GA+LKSY+
Sbjct: 61 GAILKSYR 68

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:1006230684	68	AT1G52855 "AT1G52855" [Arabido	1.0	1.0	0.75	1.7e-27
TAIR|locus:4515103075	68	AT3G15534 "AT3G15534" [Arabido	1.0	1.0	0.75	1.8e-25
TAIR|locus:2827497	68	AT2G20835 "AT2G20835" [Arabido	0.985	0.985	0.731	5.3e-24
TAIR|locus:505006594	67	AT5G10695 [Arabidopsis thalian	0.882	0.895	0.4	1.4e-07
TAIR|locus:504955497	67	AT4G29905 "AT4G29905" [Arabido	0.705	0.716	0.375	0.00045
TAIR|locus:504954859	67	AT5G57123 "AT5G57123" [Arabido	0.941	0.955	0.313	0.00057

TAIR|locus:1006230684 AT1G52855 "AT1G52855" [Arabidopsis thaliana (taxid:3702)]

 Score = 308 (113.5 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 51/68 (75%), Positives = 61/68 (89%)

Query:     1 MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
             MVCFCFLVDQTRKV + KPAAG CSRCG  AS+ADMKT+TRFC +P YW+SWRA++C+FC
Sbjct:     1 MVCFCFLVDQTRKVKRSKPAAGTCSRCGHCASIADMKTSTRFCFIPIYWRSWRAVVCSFC 60

Query:    61 GAVLKSYQ 68
             G+VLKSY+
Sbjct:    61 GSVLKSYR 68

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:4515103075 AT3G15534 "AT3G15534" [Arabidopsis thaliana (taxid:3702)]

 Score = 289 (106.8 bits), Expect = 1.8e-25, P = 1.8e-25
 Identities = 51/68 (75%), Positives = 58/68 (85%)

Query:     1 MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
             MVCFCFLVDQ RKV   KPAAG CSRCG GA VADMKT+TRFC +P Y +SWRAI+C+FC
Sbjct:     1 MVCFCFLVDQKRKVKGSKPAAGTCSRCGRGARVADMKTSTRFCLIPIYCRSWRAIVCSFC 60

Query:    61 GAVLKSYQ 68
             G+VLKSY+
Sbjct:    61 GSVLKSYR 68

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 49/67 (73%), Positives = 56/67 (83%)

Query:     1 MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
             M  FCFLVDQ +KV   KPAAG+CSRCGGGA VADM+T+TRFC VPFY K+W+AI+C  C
Sbjct:     1 MAIFCFLVDQRKKVRGRKPAAGLCSRCGGGAVVADMRTSTRFCGVPFYRKAWKAIVCHIC 60

Query:    61 GAVLKSY 67
             GAVLKSY
Sbjct:    61 GAVLKSY 67

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 120 (47.3 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 24/60 (40%), Positives = 31/60 (51%)

Query:     2 VCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCG 61
             +C  F+ DQ  +V     A G C  CGG   V D+ +  RFC VP   KS R  +C+ CG
Sbjct:     1 MCLVFVCDQDERVIGRYAAPGACPYCGGAVQVVDVNSQWRFCFVPLSNKSKRRHLCSTCG 60

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

 Score = 87 (35.7 bits), Expect = 0.00045, P = 0.00045
 Identities = 18/48 (37%), Positives = 24/48 (50%)

Query:    20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY 67
             A G+C  CGG  S  D++T   FC +P  +K  R   C+ C   L  Y
Sbjct:    19 APGMCPYCGGKVSAVDIETKWLFCFLPLCFKVKRKYSCSSCERHLVLY 66

GO:0005575 "cellular_component" evidence=ND

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

 Score = 86 (35.3 bits), Expect = 0.00057, P = 0.00057
 Identities = 21/67 (31%), Positives = 29/67 (43%)

Query:     1 MVCFCFLVDQTRKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFC 60
             +VC C   D+       + A G C  CGG   + D++    FC VP  +K  R   C+ C
Sbjct:     3 LVCLC---DEEETELGRQQAPGSCPYCGGKVQMLDVERKWMFCFVPLCFKIKRKYSCSSC 59

Query:    61 GAVLKSY 67
                L  Y
Sbjct:    60 DRRLVLY 66


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        0.334   0.139   0.520    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  0.49    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:  6
  No. of states in DFA:  571 (61 KB)
  Total size of DFA:  122 KB (2078 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.92u 0.12s 9.04t   Elapsed:  00:00:01
  Total cpu time:  8.92u 0.12s 9.04t   Elapsed:  00:00:01
  Start:  Fri May 10 07:11:58 2013   End:  Fri May 10 07:11:59 2013

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

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
PF10601	73	zf-LITAF-like: LITAF-like zinc ribbon domain; Inte	97.13
smart00714	67	LITAF Possible membrane-associated motif in LPS-in	95.93
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	93.43
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	93.21
COG3813	84	Uncharacterized protein conserved in bacteria [Fun	92.73
PF14690	47	zf-ISL3: zinc-finger of transposase IS204/IS1001/I	92.45
smart00661	52	RPOL9 RNA polymerase subunit 9.	92.16
PF13248	26	zf-ribbon_3: zinc-ribbon domain	92.15
PF13005	47	zf-IS66: zinc-finger binding domain of transposase	91.85
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	91.25
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	90.98
TIGR03831	46	YgiT_finger YgiT-type zinc finger domain. This dom	89.41
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	88.93
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	88.85
PF06827	30	zf-FPG_IleRS: Zinc finger found in FPG and IleRS;	87.7
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	86.6
PRK00420	112	hypothetical protein; Validated	86.56
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	83.89
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	83.16
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	83.11
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	81.18
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	80.96
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	80.85
PF11672	102	DUF3268: Protein of unknown function (DUF3268); In	80.6
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	80.35

>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=97.13  E-value=0.00033  Score=41.92  Aligned_cols=52  Identities=25%  Similarity=0.485  Sum_probs=40.4

Q ss_pred             eeccCceeCCCCCCceeEEEeeee-----------------eEEEEEeeeecee--eeEEeecccceeeeeC
Q 035291           16 KCKPAAGICSRCGGGASVADMKTA-----------------TRFCHVPFYWKSW--RAIICTFCGAVLKSYQ   68 (68)
Q Consensus        16 g~~~a~g~Cp~CGg~v~a~dv~s~-----------------~rfCflPl~~k~k--r~~~Ct~C~r~L~~~~   68 (68)
                      |.+|+.-.||+||..+ -+.++..                 |-+|+||++++.-  ..+.|+.|++.|-.|+
T Consensus         2 ~~~p~~~~CP~C~~~~-~T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~~   72 (73)
T PF10601_consen    2 GPEPVRIYCPYCQQQV-QTRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCGAFLGTYK   72 (73)
T ss_pred             CCCceeeECCCCCCEE-EEEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEECCCCCCEeEEEe
Confidence            5688889999999999 5666641                 3357889998654  4679999999998764

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 [].

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

Probab=95.93  E-value=0.0042  Score=36.61  Aligned_cols=48  Identities=31%  Similarity=0.652  Sum_probs=35.0

Q ss_pred             cCceeCCCCCCceeEEEeeeee---------------EEEEEeeeecee--eeEEeecccceeeee
Q 035291           19 PAAGICSRCGGGASVADMKTAT---------------RFCHVPFYWKSW--RAIICTFCGAVLKSY   67 (68)
Q Consensus        19 ~a~g~Cp~CGg~v~a~dv~s~~---------------rfCflPl~~k~k--r~~~Ct~C~r~L~~~   67 (68)
                      |+.-.||+||.-+ .+.||...               -+|+||++++.-  ..++|+.|++.|-.|
T Consensus         1 p~~i~Cp~C~~~~-~T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~   65 (67)
T smart00714        1 PYQLFCPRCQNNV-TTRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHYCPNCGAFLGTY   65 (67)
T ss_pred             CcceECCCCCCEE-EEEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEECCCCCCEeEEe
Confidence            4566899999998 77777521               245679865543  457999999999876

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=93.43  E-value=0.076  Score=36.73  Aligned_cols=40  Identities=18%  Similarity=0.306  Sum_probs=26.3

Q ss_pred             eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeeee
Q 035291           23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY   67 (68)
Q Consensus        23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~~   67 (68)
                      .||+||++. ...++|+.    ++=-...+|.+.|..||++...|
T Consensus         2 ~cp~c~~~~-~~~~~s~~----~~~~~~~~~~~~c~~c~~~f~~~   41 (154)
T PRK00464          2 RCPFCGHPD-TRVIDSRP----AEDGNAIRRRRECLACGKRFTTF   41 (154)
T ss_pred             cCCCCCCCC-CEeEeccc----cCCCCceeeeeeccccCCcceEe
Confidence            599999977 23333431    21122456779999999988766

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=93.21  E-value=0.03  Score=27.77  Aligned_cols=9  Identities=33%  Similarity=1.088  Sum_probs=7.1

Q ss_pred             CCCCCCcee
Q 035291           24 CSRCGGGAS   32 (68)
Q Consensus        24 Cp~CGg~v~   32 (68)
                      ||+||..++
T Consensus         2 Cp~CG~~~~   10 (23)
T PF13240_consen    2 CPNCGAEIE   10 (23)
T ss_pred             CcccCCCCC
Confidence            888888873

>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.73  E-value=0.034  Score=35.71  Aligned_cols=19  Identities=26%  Similarity=0.796  Sum_probs=15.5

Q ss_pred             CceeCCCCCCceeEEEeee
Q 035291           20 AAGICSRCGGGASVADMKT   38 (68)
Q Consensus        20 a~g~Cp~CGg~v~a~dv~s   38 (68)
                      .-|+||||||..++..++-
T Consensus        40 l~g~CPnCGGelv~RP~RP   58 (84)
T COG3813          40 LHGLCPNCGGELVARPIRP   58 (84)
T ss_pred             hcCcCCCCCchhhcCcCCh
Confidence            4689999999998877653

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

Probab=92.45  E-value=0.23  Score=26.74  Aligned_cols=39  Identities=28%  Similarity=0.609  Sum_probs=22.0

Q ss_pred             ceeCCCCCCceeEE-EeeeeeEEEEE-----eeeece-eeeEEeecc
Q 035291           21 AGICSRCGGGASVA-DMKTATRFCHV-----PFYWKS-WRAIICTFC   60 (68)
Q Consensus        21 ~g~Cp~CGg~v~a~-dv~s~~rfCfl-----Pl~~k~-kr~~~Ct~C   60 (68)
                      |-.||+||...... +.+ +.++=.+     |+..+. +++|.|..|
T Consensus         2 ~~~Cp~Cg~~~~~~~g~~-~r~i~~l~~~~~~~~L~i~~~R~~C~~C   47 (47)
T PF14690_consen    2 PPRCPHCGSPSVHRHGYK-TRRIRHLPIGGRPVYLRIRKRRYRCKNC   47 (47)
T ss_pred             CccCCCcCCCceECCceE-EEEEeecccCCEEEEEEEEeEEEECcCC
Confidence            56899999776221 221 2223344     444443 577888766

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=92.16  E-value=0.094  Score=28.80  Aligned_cols=29  Identities=28%  Similarity=0.597  Sum_probs=16.9

Q ss_pred             eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccccee
Q 035291           23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVL   64 (68)
Q Consensus        23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L   64 (68)
                      -||.||+.+...+.             +....+.|+.|+...
T Consensus         2 FCp~Cg~~l~~~~~-------------~~~~~~vC~~Cg~~~   30 (52)
T smart00661        2 FCPKCGNMLIPKEG-------------KEKRRFVCRKCGYEE   30 (52)
T ss_pred             CCCCCCCccccccC-------------CCCCEEECCcCCCeE
Confidence            38899987732221             122367788887543

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=92.15  E-value=0.05  Score=27.27  Aligned_cols=9  Identities=33%  Similarity=1.117  Sum_probs=7.1

Q ss_pred             eCCCCCCce
Q 035291           23 ICSRCGGGA   31 (68)
Q Consensus        23 ~Cp~CGg~v   31 (68)
                      .||+||..+
T Consensus         4 ~Cp~Cg~~~   12 (26)
T PF13248_consen    4 FCPNCGAEI   12 (26)
T ss_pred             CCcccCCcC
Confidence            589999855

>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=91.85  E-value=0.38  Score=26.09  Aligned_cols=41  Identities=20%  Similarity=0.361  Sum_probs=25.2

Q ss_pred             ceeCCCCCCceeEEEee-eeeEEEEEeeeeceee----eEEeeccc
Q 035291           21 AGICSRCGGGASVADMK-TATRFCHVPFYWKSWR----AIICTFCG   61 (68)
Q Consensus        21 ~g~Cp~CGg~v~a~dv~-s~~rfCflPl~~k~kr----~~~Ct~C~   61 (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            46899999988533333 2444556776665433    56677664

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

Probab=91.25  E-value=0.065  Score=32.43  Aligned_cols=14  Identities=36%  Similarity=0.968  Sum_probs=11.6

Q ss_pred             ceeCCCCCCceeEE
Q 035291           21 AGICSRCGGGASVA   34 (68)
Q Consensus        21 ~g~Cp~CGg~v~a~   34 (68)
                      .+.||||||..+..
T Consensus        41 ~~~CPNCgGelv~R   54 (57)
T PF06906_consen   41 NGVCPNCGGELVRR   54 (57)
T ss_pred             cCcCcCCCCccccC
Confidence            68999999988543

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

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

Probab=90.98  E-value=0.57  Score=29.27  Aligned_cols=41  Identities=27%  Similarity=0.505  Sum_probs=31.7

Q ss_pred             CCCCCCceeEEEeee-eeEEEEEeeeeceeeeEEeecccceee
Q 035291           24 CSRCGGGASVADMKT-ATRFCHVPFYWKSWRAIICTFCGAVLK   65 (68)
Q Consensus        24 Cp~CGg~v~a~dv~s-~~rfCflPl~~k~kr~~~Ct~C~r~L~   65 (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            899997655677776 66788777777 778889999998654

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.

>TIGR03831 YgiT_finger YgiT-type zinc finger domain

Probab=89.41  E-value=0.75  Score=24.20  Aligned_cols=42  Identities=21%  Similarity=0.454  Sum_probs=22.6

Q ss_pred             CCCCCCceeEEEeee-eeEEEEEeeeeceeeeEEeecccceee
Q 035291           24 CSRCGGGASVADMKT-ATRFCHVPFYWKSWRAIICTFCGAVLK   65 (68)
Q Consensus        24 Cp~CGg~v~a~dv~s-~~rfCflPl~~k~kr~~~Ct~C~r~L~   65 (68)
                      ||.|||.....++++ ++..=--=+-.+.-....|+.||..+-
T Consensus         1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE~~~   43 (46)
T TIGR03831         1 CPICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGEEYL   43 (46)
T ss_pred             CCCCCCceecceEEEEEEEeCCEEEEEeCCCccccccCCCEee
Confidence            788977765555543 222200122333444556888887654

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.

>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=88.93  E-value=0.2  Score=36.43  Aligned_cols=43  Identities=28%  Similarity=0.801  Sum_probs=21.6

Q ss_pred             CceeCCCCCCceeEEEeeee----eEEEEEeeeeceee--eEEeecccc
Q 035291           20 AAGICSRCGGGASVADMKTA----TRFCHVPFYWKSWR--AIICTFCGA   62 (68)
Q Consensus        20 a~g~Cp~CGg~v~a~dv~s~----~rfCflPl~~k~kr--~~~Ct~C~r   62 (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            35899999999888888874    46666566654443  456666664

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.

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

Probab=88.85  E-value=0.52  Score=25.20  Aligned_cols=28  Identities=32%  Similarity=0.545  Sum_probs=18.8

Q ss_pred             eCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccccee
Q 035291           23 ICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVL   64 (68)
Q Consensus        23 ~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L   64 (68)
                      -||.|||..             +|---+..+. .|+.|+..-
T Consensus         3 FCp~C~nlL-------------~p~~~~~~~~-~C~~C~Y~~   30 (35)
T PF02150_consen    3 FCPECGNLL-------------YPKEDKEKRV-ACRTCGYEE   30 (35)
T ss_dssp             BETTTTSBE-------------EEEEETTTTE-EESSSS-EE
T ss_pred             eCCCCCccc-------------eEcCCCccCc-CCCCCCCcc
Confidence            389999998             4555555544 788887654

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

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

Probab=87.70  E-value=0.7  Score=23.32  Aligned_cols=14  Identities=21%  Similarity=0.399  Sum_probs=7.3

Q ss_pred             eCCCCCCceeEEEe
Q 035291           23 ICSRCGGGASVADM   36 (68)
Q Consensus        23 ~Cp~CGg~v~a~dv   36 (68)
                      .|++||+.+....+
T Consensus         3 ~C~rC~~~~~~~~~   16 (30)
T PF06827_consen    3 KCPRCWNYIEDIGI   16 (30)
T ss_dssp             B-TTT--BBEEEEE
T ss_pred             cCccCCCcceEeEe
Confidence            59999999844433

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

>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=86.60  E-value=0.73  Score=25.40  Aligned_cols=28  Identities=25%  Similarity=0.513  Sum_probs=18.8

Q ss_pred             eeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291           22 GICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV   63 (68)
Q Consensus        22 g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~   63 (68)
                      -.||+||+.- +.-+++             ...+-|..|+++
T Consensus        19 ~~CP~Cg~~~-~~~~~~-------------~~~~~C~~C~~q   46 (46)
T PF12760_consen   19 FVCPHCGSTK-HYRLKT-------------RGRYRCKACRKQ   46 (46)
T ss_pred             CCCCCCCCee-eEEeCC-------------CCeEECCCCCCc
Confidence            3499999973 444444             556778877753

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

>PRK00420 hypothetical protein; Validated

Probab=86.56  E-value=0.35  Score=32.18  Aligned_cols=34  Identities=21%  Similarity=0.338  Sum_probs=23.9

Q ss_pred             eeccCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291           16 KCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK   65 (68)
Q Consensus        16 g~~~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~   65 (68)
                      |..-....||.||.+.                .--...+++|+.||..+.
T Consensus        18 Ga~ml~~~CP~Cg~pL----------------f~lk~g~~~Cp~Cg~~~~   51 (112)
T PRK00420         18 GAKMLSKHCPVCGLPL----------------FELKDGEVVCPVHGKVYI   51 (112)
T ss_pred             HHHHccCCCCCCCCcc----------------eecCCCceECCCCCCeee
Confidence            5555678899999776                211456888999988664

>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines

Probab=83.89  E-value=1.8  Score=26.96  Aligned_cols=37  Identities=16%  Similarity=0.455  Sum_probs=20.0

Q ss_pred             cCceeCCCCC-CceeEEEeeeeeEEEEEeeeeceeeeEEeecccceee
Q 035291           19 PAAGICSRCG-GGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLK   65 (68)
Q Consensus        19 ~a~g~Cp~CG-g~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~   65 (68)
                      +..=.||.|| ..++..+|+..          ...-.+.|..|+....
T Consensus        20 ~~~F~CPfC~~~~sV~v~idkk----------~~~~~~~C~~Cg~~~~   57 (81)
T PF05129_consen   20 PKVFDCPFCNHEKSVSVKIDKK----------EGIGILSCRVCGESFQ   57 (81)
T ss_dssp             SS----TTT--SS-EEEEEETT----------TTEEEEEESSS--EEE
T ss_pred             CceEcCCcCCCCCeEEEEEEcc----------CCEEEEEecCCCCeEE
Confidence            3456899999 55656666554          4566788999987654

; PDB: 1WII_A.

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

Probab=83.16  E-value=1.3  Score=24.23  Aligned_cols=11  Identities=27%  Similarity=0.522  Sum_probs=7.7

Q ss_pred             ceeCCCCCCce
Q 035291           21 AGICSRCGGGA   31 (68)
Q Consensus        21 ~g~Cp~CGg~v   31 (68)
                      ...||+||+.+
T Consensus        21 ~~~Cp~CG~~~   31 (46)
T PRK00398         21 GVRCPYCGYRI   31 (46)
T ss_pred             ceECCCCCCeE
Confidence            56777777766

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

Probab=83.11  E-value=0.62  Score=27.65  Aligned_cols=34  Identities=35%  Similarity=0.675  Sum_probs=21.0

Q ss_pred             eeeeeeccCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291           12 RKVHKCKPAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV   63 (68)
Q Consensus        12 ~kv~g~~~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~   63 (68)
                      ++|+...+   -|||||.++--+|=               +.++.|-.||-.
T Consensus        13 ~kv~rk~~---~CPrCG~gvfmA~H---------------~dR~~CGkCgyT   46 (51)
T COG1998          13 EKVKRKNR---FCPRCGPGVFMADH---------------KDRWACGKCGYT   46 (51)
T ss_pred             CcEEEccc---cCCCCCCcchhhhc---------------CceeEeccccce
Confidence            34555443   69999988743332               336777777643

>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=81.18  E-value=1.3  Score=25.60  Aligned_cols=29  Identities=31%  Similarity=0.660  Sum_probs=20.8

Q ss_pred             CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291           20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV   63 (68)
Q Consensus        20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~   63 (68)
                      -.-.||.||.....               ..+.|.+.|+.||..
T Consensus        27 TSq~C~~CG~~~~~---------------~~~~r~~~C~~Cg~~   55 (69)
T PF07282_consen   27 TSQTCPRCGHRNKK---------------RRSGRVFTCPNCGFE   55 (69)
T ss_pred             CccCccCccccccc---------------ccccceEEcCCCCCE
Confidence            34569999988733               445778888888865

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

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

Probab=80.96  E-value=0.9  Score=23.05  Aligned_cols=15  Identities=20%  Similarity=0.532  Sum_probs=11.0

Q ss_pred             eeeec-cCceeCCCCC
Q 035291           14 VHKCK-PAAGICSRCG   28 (68)
Q Consensus        14 v~g~~-~a~g~Cp~CG   28 (68)
                      +.+++ .++=.|||||
T Consensus         8 i~~r~~~v~f~CPnCG   23 (24)
T PF07754_consen    8 IAPREQAVPFPCPNCG   23 (24)
T ss_pred             ccCcccCceEeCCCCC
Confidence            44454 7778899998

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

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=80.85  E-value=0.36  Score=32.91  Aligned_cols=35  Identities=20%  Similarity=0.291  Sum_probs=22.8

Q ss_pred             cCceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccceeeee
Q 035291           19 PAAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVLKSY   67 (68)
Q Consensus        19 ~a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L~~~   67 (68)
                      +.-=.||+||-..+..|.-+              ..|.|+.||..|+-+
T Consensus       107 ~~~Y~Cp~c~~r~tf~eA~~--------------~~F~Cp~Cg~~L~~~  141 (158)
T TIGR00373       107 NMFFICPNMCVRFTFNEAME--------------LNFTCPRCGAMLDYL  141 (158)
T ss_pred             CCeEECCCCCcEeeHHHHHH--------------cCCcCCCCCCEeeec
Confidence            34446888886665444433              268888888888754

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.

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

Probab=80.60  E-value=0.94  Score=29.71  Aligned_cols=39  Identities=28%  Similarity=0.525  Sum_probs=22.7

Q ss_pred             ceeCCCCCCceeEEEeeeeeEEEEEeeeeceee-eEEeeccccee
Q 035291           21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWR-AIICTFCGAVL   64 (68)
Q Consensus        21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr-~~~Ct~C~r~L   64 (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            4579999999865552 111    131111122 38999998753

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

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=80.35  E-value=1.3  Score=25.02  Aligned_cols=10  Identities=40%  Similarity=0.999  Sum_probs=8.1

Q ss_pred             eCCCCCCcee
Q 035291           23 ICSRCGGGAS   32 (68)
Q Consensus        23 ~Cp~CGg~v~   32 (68)
                      .||.|||...
T Consensus         3 PCPfCGg~~~   12 (53)
T TIGR03655         3 PCPFCGGADV   12 (53)
T ss_pred             CCCCCCCcce
Confidence            4999999774

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.

---

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
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	89.29
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	88.78
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	87.02
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	86.14
3ga8_A	78	HTH-type transcriptional regulator MQSA (YGIT/B30;	80.08

>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=89.29  E-value=0.73  Score=28.00  Aligned_cols=43  Identities=21%  Similarity=0.427  Sum_probs=26.3

Q ss_pred             eCCCCCCceeEEEeee-eeEEEEEeeeeceeeeEEeecccceee
Q 035291           23 ICSRCGGGASVADMKT-ATRFCHVPFYWKSWRAIICTFCGAVLK   65 (68)
Q Consensus        23 ~Cp~CGg~v~a~dv~s-~~rfCflPl~~k~kr~~~Ct~C~r~L~   65 (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            6999999864444333 222222344444446789999997653

>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=88.78  E-value=0.19  Score=28.52  Aligned_cols=29  Identities=28%  Similarity=0.605  Sum_probs=20.3

Q ss_pred             ceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeeccccee
Q 035291           21 AGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAVL   64 (68)
Q Consensus        21 ~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~L   64 (68)
                      .-.||.||+.+.            +.   +...++.|..|+-..
T Consensus        18 ~~fCPkCG~~~~------------ma---~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           18 HRFCPRCGPGVF------------LA---EHADRYSCGRCGYTE   46 (55)
T ss_dssp             SCCCTTTTTTCC------------CE---ECSSEEECTTTCCCE
T ss_pred             cccCcCCCCcee------------Ee---ccCCEEECCCCCCEE
Confidence            467999999872            11   224589999998653

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

Probab=87.02  E-value=0.37  Score=26.83  Aligned_cols=29  Identities=34%  Similarity=0.692  Sum_probs=19.5

Q ss_pred             CceeCCCCCCceeEEEeeeeeEEEEEeeeeceeeeEEeecccce
Q 035291           20 AAGICSRCGGGASVADMKTATRFCHVPFYWKSWRAIICTFCGAV   63 (68)
Q Consensus        20 a~g~Cp~CGg~v~a~dv~s~~rfCflPl~~k~kr~~~Ct~C~r~   63 (68)
                      ..--||+||.++.-++               ...+..|..||-.
T Consensus        18 ~~k~CP~CG~~~fm~~---------------~~~R~~C~kCG~t   46 (50)
T 3j20_Y           18 KNKFCPRCGPGVFMAD---------------HGDRWACGKCGYT   46 (50)
T ss_dssp             SSEECSSSCSSCEEEE---------------CSSEEECSSSCCE
T ss_pred             ecccCCCCCCceEEec---------------CCCeEECCCCCCE
Confidence            3557999999872221               2367889888853

>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=86.14  E-value=0.31  Score=35.60  Aligned_cols=44  Identities=20%  Similarity=0.563  Sum_probs=28.9

Q ss_pred             cCceeCCCCCCceeEEEee-----eeeEEEEEeeeecee--eeEEeecccc
Q 035291           19 PAAGICSRCGGGASVADMK-----TATRFCHVPFYWKSW--RAIICTFCGA   62 (68)
Q Consensus        19 ~a~g~Cp~CGg~v~a~dv~-----s~~rfCflPl~~k~k--r~~~Ct~C~r   62 (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            4579999999999888776     244555545554433  3456666654

>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=80.08  E-value=3.7  Score=23.61  Aligned_cols=41  Identities=22%  Similarity=0.416  Sum_probs=23.2

Q ss_pred             eCCCCCCceeEEEeee---eeEEEEEeeeeceeeeEEeecccceee
Q 035291           23 ICSRCGGGASVADMKT---ATRFCHVPFYWKSWRAIICTFCGAVLK   65 (68)
Q Consensus        23 ~Cp~CGg~v~a~dv~s---~~rfCflPl~~k~kr~~~Ct~C~r~L~   65 (68)
                      .||.||++-...++.+   ++.=.  =+-.+.-....|..||..+-
T Consensus         4 ~Cp~Cg~~~l~~~~~~~~~~~~G~--~~~I~~Vp~~~C~~CGE~~~   47 (78)
T 3ga8_A            4 KCPVCHQGEMVSGIKDIPYTFRGR--KTVLKGIHGLYCVHCEESIM   47 (78)
T ss_dssp             BCTTTSSSBEEEEEEEEEEEETTE--EEEEEEEEEEEETTTCCEEC
T ss_pred             ECCCCCCCeeEeEEEEEEEEECCE--EEEEcCceeEECCCCCCEEE
Confidence            5999998732333332   11111  12234456788999997654

---

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
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	83.48

>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=83.48  E-value=0.2  Score=34.67  Aligned_cols=44  Identities=18%  Similarity=0.544  Sum_probs=29.8

Q ss_pred             cCceeCCCCCCceeEEEeee-----eeEEEEEeeeecee--eeEEeecccc
Q 035291           19 PAAGICSRCGGGASVADMKT-----ATRFCHVPFYWKSW--RAIICTFCGA   62 (68)
Q Consensus        19 ~a~g~Cp~CGg~v~a~dv~s-----~~rfCflPl~~k~k--r~~~Ct~C~r   62 (68)
                      ...|.||-||+.-++..++.     -.|++.=.+|.--|  .++.|+.|+.
T Consensus       162 ~~~~~CPvCGs~P~~s~l~~~~~~~G~R~l~C~~C~teW~~~R~~C~~Cg~  212 (290)
T d2fiya1         162 ESRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEE  212 (290)
T ss_dssp             TTCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECCTTSCSSSCC
T ss_pred             ccCCcCCCCCCcchhheeeccCCCCCceEEECCCCCCccccccccCCCCCC
Confidence            35688999999998888853     34666556655444  3556666654