Citrus Sinensis ID: 046214

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60------
Protein Sequence
MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVVQ
Secondary Structure (PSIPRED)
cEEEEEEcccEEEEEEcccccccccccccEEEEEccEEEEEEEEEEEEEEccEEEEcccccEEEEc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccEEEEEccccccccccccEEEEEEEcccEEEEEccEEHHcccEEEHHHHHcEEEEc
Coil and Loop (DISEMBL)
mclvcvcdedervlgtqtapgacpfcggmiraMDVQsewrfcflplyfktkRKFYCTVCARRLVVQ
Flexible Loop (DISEMBL)
MCLVCVCDedervlgtqtapgacpFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVVQ
Low Complexity Region (SEG)
MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVVQ
Disordered region (IsUnstruct)
*CLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV**
Disordered Region (DISOPRED)
MCLVCV*DEDER********GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVV*
Disordered Region (DISEMBL)
MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVVQ
Disordered Region (DISPRO)
MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVVQ
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVVQ
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	66
255582685	67	conserved hypothetical protein [Ricinus	1.0	0.985	0.772	4e-24
224143427	67	predicted protein [Populus trichocarpa]	1.0	0.985	0.757	6e-24
356554423	68	PREDICTED: uncharacterized protein LOC10	0.954	0.926	0.793	1e-22
449441998	66	PREDICTED: uncharacterized protein LOC10	1.0	1.0	0.757	1e-22
356561869	66	PREDICTED: uncharacterized protein LOC10	0.984	0.984	0.753	3e-22
356507827	66	PREDICTED: uncharacterized protein LOC10	1.0	1.0	0.712	6e-21
357466511	66	hypothetical protein MTR_3g108890 [Medic	1.0	1.0	0.681	3e-20
116782851	67	unknown [Picea sitchensis]	0.984	0.970	0.630	3e-18
18416352	67	uncharacterized protein [Arabidopsis tha	1.0	0.985	0.590	8e-18
297807101	67	hypothetical protein ARALYDRAFT_909027 [	1.0	0.985	0.590	1e-17

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

 Score =  115 bits (287), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 51/66 (77%), Positives = 62/66 (93%)

Query: 1  MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
          MCLV VCDE+ERV+  Q APGACP+CGGM++AMDV+S+WRFCFLPLYFKTK++FYC+VCA
Sbjct: 1  MCLVFVCDEEERVVARQPAPGACPYCGGMVQAMDVESQWRFCFLPLYFKTKKRFYCSVCA 60

Query: 61 RRLVVQ 66
          RRLV+Q
Sbjct: 61 RRLVMQ 66

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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 =  114 bits (286), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 50/66 (75%), Positives = 61/66 (92%)

Query: 1  MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
          MCLV VCDEDE+V+  QTAPGACP+CGG I+AMDV+S+WRFCFLPLYFKTK+++YCT+CA
Sbjct: 1  MCLVFVCDEDEKVVARQTAPGACPYCGGAIQAMDVESQWRFCFLPLYFKTKKRYYCTLCA 60

Query: 61 RRLVVQ 66
          R+L VQ
Sbjct: 61 RKLAVQ 66

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  110 bits (275), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 50/63 (79%), Positives = 59/63 (93%)

Query: 1  MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
          MCLV VCDE+ERVLG QTAPGACP+CGGM++A+DV+S+WRFCFLPL FKTKRK+YCT+C 
Sbjct: 1  MCLVFVCDEEERVLGRQTAPGACPYCGGMVQAIDVESQWRFCFLPLCFKTKRKYYCTMCT 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|449441998|ref|XP_004138769.1| PREDICTED: uncharacterized protein LOC101206986 [Cucumis sativus] gi|449499286|ref|XP_004160776.1| PREDICTED: uncharacterized protein LOC101228264 [Cucumis sativus]

 Score =  110 bits (274), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 50/66 (75%), Positives = 59/66 (89%)

Query: 1  MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
          MCLV VCDED+RVL  Q APG CPFCGGMI+A DV+S+WRFCF+PLY+KTKRKFYCT+C 
Sbjct: 1  MCLVFVCDEDQRVLSRQPAPGVCPFCGGMIQATDVESQWRFCFVPLYWKTKRKFYCTMCT 60

Query: 61 RRLVVQ 66
          R+LV+Q
Sbjct: 61 RQLVMQ 66

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  108 bits (271), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 49/65 (75%), Positives = 60/65 (92%)

Query: 1  MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
          MCLV VC+E+ERVLG QTAPGACP+CGGM++A++V+S+WRFCFLPL FKTKRK+YCT+C 
Sbjct: 1  MCLVFVCNEEERVLGRQTAPGACPYCGGMVQAINVESQWRFCFLPLCFKTKRKYYCTMCT 60

Query: 61 RRLVV 65
          RRL V
Sbjct: 61 RRLEV 65

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356507827|ref|XP_003522665.1| PREDICTED: uncharacterized protein LOC100787739 [Glycine max]

 Score =  104 bits (260), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 47/66 (71%), Positives = 57/66 (86%)

Query: 1  MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
          MCLV VC EDERV+  Q APGACP+C GMI+AMDV+S+W FCFLPLY KTKR++YCT+C 
Sbjct: 1  MCLVFVCGEDERVVSRQPAPGACPYCRGMIQAMDVESQWNFCFLPLYSKTKRRYYCTMCT 60

Query: 61 RRLVVQ 66
          R+LV+Q
Sbjct: 61 RKLVLQ 66

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357466511|ref|XP_003603540.1| hypothetical protein MTR_3g108890 [Medicago truncatula] gi|355492588|gb|AES73791.1| hypothetical protein MTR_3g108890 [Medicago truncatula]

 Score =  102 bits (254), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 45/66 (68%), Positives = 56/66 (84%)

Query: 1  MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
          MCLV VC EDERV+  Q APG+CP+CGGMI+A+DV S W FCF+PLY KTKR+ YCT+C+
Sbjct: 1  MCLVFVCGEDERVVSRQQAPGSCPYCGGMIQAVDVDSRWNFCFVPLYHKTKRRHYCTMCS 60

Query: 61 RRLVVQ 66
          R+LVV+
Sbjct: 61 RKLVVK 66

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116782851|gb|ABK22689.1| unknown [Picea sitchensis]

 Score = 95.5 bits (236), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 41/65 (63%), Positives = 49/65 (75%)

Query: 1  MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
          MCLVC CDE  ++L TQ APGACP CGG I A DVQSEWRFCF+P++FK +R   CT C 
Sbjct: 1  MCLVCTCDEKRKILNTQVAPGACPHCGGAIAASDVQSEWRFCFVPVFFKKRRTHTCTRCG 60

Query: 61 RRLVV 65
          + LV+
Sbjct: 61 KNLVI 65

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18416352|ref|NP_568234.1| uncharacterized protein [Arabidopsis thaliana] gi|19347741|gb|AAL86296.1| unknown protein [Arabidopsis thaliana] gi|24030282|gb|AAN41313.1| unknown protein [Arabidopsis thaliana] gi|332004199|gb|AED91582.1| uncharacterized protein [Arabidopsis thaliana]

 Score = 94.4 bits (233), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 39/66 (59%), Positives = 52/66 (78%)

Query: 1  MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
          MCLV VCD+DERV+G   APGACP+CGG ++ +DV S+WRFCF+PL  K+KR+  C+ C 
Sbjct: 1  MCLVFVCDQDERVIGRYAAPGACPYCGGAVQVVDVNSQWRFCFVPLSNKSKRRHLCSTCG 60

Query: 61 RRLVVQ 66
          +RL+V 
Sbjct: 61 KRLIVH 66

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297807101|ref|XP_002871434.1| hypothetical protein ARALYDRAFT_909027 [Arabidopsis lyrata subsp. lyrata] gi|297317271|gb|EFH47693.1| hypothetical protein ARALYDRAFT_909027 [Arabidopsis lyrata subsp. lyrata]

 Score = 94.0 bits (232), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 39/66 (59%), Positives = 52/66 (78%)

Query: 1  MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
          MCLV VCD+DERV+G   APGACP+CGG ++ +DV S+WRFCF+PL  K+KR+  C+ C 
Sbjct: 1  MCLVFVCDKDERVIGRYAAPGACPYCGGAVQVVDVNSQWRFCFVPLSNKSKRRHICSTCG 60

Query: 61 RRLVVQ 66
          +RL+V 
Sbjct: 61 KRLIVH 66

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	66
TAIR|locus:505006594	67	AT5G10695 [Arabidopsis thalian	0.984	0.970	0.6	8e-21
TAIR|locus:504954859	67	AT5G57123 "AT5G57123" [Arabido	0.984	0.970	0.6	1e-20
TAIR|locus:504955497	67	AT4G29905 "AT4G29905" [Arabido	0.984	0.970	0.538	5.3e-17
TAIR|locus:4515103075	68	AT3G15534 "AT3G15534" [Arabido	0.863	0.838	0.35	1.8e-07
TAIR|locus:1006230684	68	AT1G52855 "AT1G52855" [Arabido	0.863	0.838	0.333	6.1e-07
TAIR|locus:2827497	68	AT2G20835 "AT2G20835" [Arabido	0.893	0.867	0.333	5.5e-06

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

 Score = 245 (91.3 bits), Expect = 8.0e-21, P = 8.0e-21
 Identities = 39/65 (60%), Positives = 52/65 (80%)

Query:     1 MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
             MCLV VCD+DERV+G   APGACP+CGG ++ +DV S+WRFCF+PL  K+KR+  C+ C 
Sbjct:     1 MCLVFVCDQDERVIGRYAAPGACPYCGGAVQVVDVNSQWRFCFVPLSNKSKRRHLCSTCG 60

Query:    61 RRLVV 65
             +RL+V
Sbjct:    61 KRLIV 65

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 = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 39/65 (60%), Positives = 52/65 (80%)

Query:     1 MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
             MCLVC+CDE+E  LG Q APG+CP+CGG ++ +DV+ +W FCF+PL FK KRK+ C+ C 
Sbjct:     1 MCLVCLCDEEETELGRQQAPGSCPYCGGKVQMLDVERKWMFCFVPLCFKIKRKYSCSSCD 60

Query:    61 RRLVV 65
             RRLV+
Sbjct:    61 RRLVL 65

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 = 209 (78.6 bits), Expect = 5.3e-17, P = 5.3e-17
 Identities = 35/65 (53%), Positives = 47/65 (72%)

Query:     1 MCLVCVCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA 60
             MCL  V  E++  LG Q APG CP+CGG + A+D++++W FCFLPL FK KRK+ C+ C 
Sbjct:     1 MCLEVVYHEEKTELGRQQAPGMCPYCGGKVSAVDIETKWLFCFLPLCFKVKRKYSCSSCE 60

Query:    61 RRLVV 65
             R LV+
Sbjct:    61 RHLVL 65

GO:0005575 "cellular_component" evidence=ND

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

 Score = 119 (46.9 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 21/60 (35%), Positives = 34/60 (56%)

Query:     3 LVCVC---DEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVC 59
             +VC C   D+  +V G++ A G C  CG   R  D+++  RFC +P+Y ++ R   C+ C
Sbjct:     1 MVCFCFLVDQKRKVKGSKPAAGTCSRCGRGARVADMKTSTRFCLIPIYCRSWRAIVCSFC 60

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 114 (45.2 bits), Expect = 6.1e-07, P = 6.1e-07
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query:     3 LVCVC---DEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVC 59
             +VC C   D+  +V  ++ A G C  CG      D+++  RFCF+P+Y+++ R   C+ C
Sbjct:     1 MVCFCFLVDQTRKVKRSKPAAGTCSRCGHCASIADMKTSTRFCFIPIYWRSWRAVVCSFC 60

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 = 105 (42.0 bits), Expect = 5.5e-06, P = 5.5e-06
 Identities = 20/60 (33%), Positives = 32/60 (53%)

Query:     1 MCLVC-VCDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVC 59
             M + C + D+ ++V G + A G C  CGG     D+++  RFC +P Y K  +   C +C
Sbjct:     1 MAIFCFLVDQRKKVRGRKPAAGLCSRCGGGAVVADMRTSTRFCGVPFYRKAWKAIVCHIC 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        0.336   0.145   0.522    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       66        66   0.00091  102 3  11 21  0.46    27
                                                     29  0.48    28


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:  544 (58 KB)
  Total size of DFA:  112 KB (2075 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:  8.30u 0.14s 8.44t   Elapsed:  00:00:00
  Total cpu time:  8.30u 0.14s 8.44t   Elapsed:  00:00:00
  Start:  Sat May 11 01:40:48 2013   End:  Sat May 11 01:40:48 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	66
PF13005	47	zf-IS66: zinc-finger binding domain of transposase	95.15
PF14690	47	zf-ISL3: zinc-finger of transposase IS204/IS1001/I	93.9
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	93.3
PF10601	73	zf-LITAF-like: LITAF-like zinc ribbon domain; Inte	93.29
PF11672	102	DUF3268: Protein of unknown function (DUF3268); In	93.29
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	92.72
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	92.58
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	91.41
COG3813	84	Uncharacterized protein conserved in bacteria [Fun	90.86
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	90.83
TIGR03831	46	YgiT_finger YgiT-type zinc finger domain. This dom	89.68
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	89.48
PF13248	26	zf-ribbon_3: zinc-ribbon domain	89.41
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	88.63
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	88.57
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	88.25
PF01927	147	Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T	87.87
smart00661	52	RPOL9 RNA polymerase subunit 9.	87.7
PRK12775	1006	putative trifunctional 2-polyprenylphenol hydroxyl	87.07
PRK00432	50	30S ribosomal protein S27ae; Validated	86.92
COG0675	364	Transposase and inactivated derivatives [DNA repli	86.06
PRK10445	263	endonuclease VIII; Provisional	85.67
PRK14810	272	formamidopyrimidine-DNA glycosylase; Provisional	85.6
PRK13945	282	formamidopyrimidine-DNA glycosylase; Provisional	84.66
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	84.6
PRK00420	112	hypothetical protein; Validated	84.4
smart00714	67	LITAF Possible membrane-associated motif in LPS-in	83.4
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	83.33
PF12773	50	DZR: Double zinc ribbon	83.02
TIGR00577	272	fpg formamidopyrimidine-DNA glycosylase (fpg). All	82.13
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	81.87
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	81.84
PF14369	35	zf-RING_3: zinc-finger	81.52
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	81.21
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	80.94
PRK01103	274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	80.91
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	80.54
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	80.39
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	80.13
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	80.05

>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=95.15  E-value=0.044  Score=29.84  Aligned_cols=41  Identities=27%  Similarity=0.647  Sum_probs=29.3

Q ss_pred             CCcCCCCCCceEEEEec-eeeEEEEEeeeeeec----cEEEeeccc
Q 046214           20 PGACPFCGGMIRAMDVQ-SEWRFCFLPLYFKTK----RKFYCTVCA   60 (66)
Q Consensus        20 pG~Cp~CGG~v~a~Dve-s~~rfCflP~~~k~k----rk~~Ct~C~   60 (66)
                      +.+||.||+.+.-+-.+ .+-.|=++|.-++..    -+|.|+-|+
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            56899999999866555 556666788766543    367777775

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

Probab=93.90  E-value=0.1  Score=28.11  Aligned_cols=38  Identities=34%  Similarity=0.826  Sum_probs=23.3

Q ss_pred             CCcCCCCCCceEEE--EeceeeEEEEEee-----eee-eccEEEeecc
Q 046214           20 PGACPFCGGMIRAM--DVQSEWRFCFLPL-----YFK-TKRKFYCTVC   59 (66)
Q Consensus        20 pG~Cp~CGG~v~a~--Dves~~rfCflP~-----~~k-~krk~~Ct~C   59 (66)
                      |-.||+||..-..-  -.+..|+  .+|+     +.+ .+++|.|..|
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  2334444  4444     433 3678988876

>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=93.30  E-value=0.037  Score=40.12  Aligned_cols=43  Identities=23%  Similarity=0.458  Sum_probs=24.2

Q ss_pred             CCCcCCCCCCceEEEEecee----eEEEEEeeeeeecc--EEEeecccc
Q 046214           19 APGACPFCGGMIRAMDVQSE----WRFCFLPLYFKTKR--KFYCTVCAR   61 (66)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~----~rfCflP~~~k~kr--k~~Ct~C~r   61 (66)
                      ..|.||-||+.-++.-+...    .|+.+=.+|.-.|+  +..|+.||.
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            35999999999888887764    58888788765553  457888885

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.

>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=93.29  E-value=0.05  Score=32.33  Aligned_cols=50  Identities=24%  Similarity=0.670  Sum_probs=36.6

Q ss_pred             eeccCCCcCCCCCCceEEEEecee-----------------eEEEEEeeeeee--ccEEEeecccceeee
Q 046214           15 GTQTAPGACPFCGGMIRAMDVQSE-----------------WRFCFLPLYFKT--KRKFYCTVCARRLVV   65 (66)
Q Consensus        15 ~~~~ApG~Cp~CGG~v~a~Dves~-----------------~rfCflP~~~k~--krk~~Ct~C~r~L~~   65 (66)
                      +++|..-.||+||-.+. +.++.+                 |-+|+||++.+.  ...++|+.|++.|-.
T Consensus         2 ~~~p~~~~CP~C~~~~~-T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~   70 (73)
T PF10601_consen    2 GPEPVRIYCPYCQQQVQ-TRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCGAFLGT   70 (73)
T ss_pred             CCCceeeECCCCCCEEE-EEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEECCCCCCEeEE
Confidence            56788889999998764 334422                 345789999854  457899999998854

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 [].

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

Probab=93.29  E-value=0.077  Score=34.90  Aligned_cols=39  Identities=31%  Similarity=0.660  Sum_probs=24.6

Q ss_pred             CCcCCCCCCceEEEEeceeeEEEEEeeeeeecc-EEEeeccccee
Q 046214           20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKR-KFYCTVCARRL   63 (66)
Q Consensus        20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr-k~~Ct~C~r~L   63 (66)
                      |-.||||||.+.-+|= +..    -|--...+. -|.|+.|++-.
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 39999998754

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

>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=92.72  E-value=0.15  Score=28.26  Aligned_cols=28  Identities=21%  Similarity=0.863  Sum_probs=20.6

Q ss_pred             CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214           21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR   62 (66)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~   62 (66)
                      -.||+||.. .+.-+.+             ...|.|..|+++
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 5555554             677888888764

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

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=92.58  E-value=0.1  Score=36.09  Aligned_cols=37  Identities=30%  Similarity=0.640  Sum_probs=24.3

Q ss_pred             cCCCCCCce-EEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214           22 ACPFCGGMI-RAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        22 ~Cp~CGG~v-~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      .|||||++. .|.|=+.      ++==.-.+|++.|..||++..
T Consensus         2 ~cp~c~~~~~~~~~s~~------~~~~~~~~~~~~c~~c~~~f~   39 (154)
T PRK00464          2 RCPFCGHPDTRVIDSRP------AEDGNAIRRRRECLACGKRFT   39 (154)
T ss_pred             cCCCCCCCCCEeEeccc------cCCCCceeeeeeccccCCcce
Confidence            499999976 5555331      111123667799999998754

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

Probab=91.41  E-value=0.093  Score=31.95  Aligned_cols=13  Identities=46%  Similarity=1.145  Sum_probs=11.1

Q ss_pred             CCcCCCCCCceEE
Q 046214           20 PGACPFCGGMIRA   32 (66)
Q Consensus        20 pG~Cp~CGG~v~a   32 (66)
                      .|.||+|||.++.
T Consensus        41 ~~~CPNCgGelv~   53 (57)
T PF06906_consen   41 NGVCPNCGGELVR   53 (57)
T ss_pred             cCcCcCCCCcccc
Confidence            6999999998753

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

>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.86  E-value=0.094  Score=33.95  Aligned_cols=18  Identities=39%  Similarity=0.874  Sum_probs=14.5

Q ss_pred             CCCcCCCCCCceEEEEec
Q 046214           19 APGACPFCGGMIRAMDVQ   36 (66)
Q Consensus        19 ApG~Cp~CGG~v~a~Dve   36 (66)
                      -.|.||+|||.+++--++
T Consensus        40 l~g~CPnCGGelv~RP~R   57 (84)
T COG3813          40 LHGLCPNCGGELVARPIR   57 (84)
T ss_pred             hcCcCCCCCchhhcCcCC
Confidence            469999999999876554

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

Probab=90.83  E-value=0.12  Score=30.84  Aligned_cols=36  Identities=31%  Similarity=0.647  Sum_probs=25.4

Q ss_pred             CcceeeeeccCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214            9 EDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR   62 (66)
Q Consensus         9 e~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~   62 (66)
                      +.+||+...+   .||+||-++-.+|               ++.++.|-.||-.
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            4455666554   6999998877666               4457888888754

>TIGR03831 YgiT_finger YgiT-type zinc finger domain

Probab=89.68  E-value=0.82  Score=23.98  Aligned_cols=43  Identities=19%  Similarity=0.343  Sum_probs=25.7

Q ss_pred             CCCCCCceEEEEeceeeEEEE-EeeeeeeccEEEeecccceeee
Q 046214           23 CPFCGGMIRAMDVQSEWRFCF-LPLYFKTKRKFYCTVCARRLVV   65 (66)
Q Consensus        23 Cp~CGG~v~a~Dves~~rfCf-lP~~~k~krk~~Ct~C~r~L~~   65 (66)
                      ||-|||....-++++.+.--- -=+..+.=..+.|+.||..+-+
T Consensus         1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE~~~~   44 (46)
T TIGR03831         1 CPICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGEEYLD   44 (46)
T ss_pred             CCCCCCceecceEEEEEEEeCCEEEEEeCCCccccccCCCEeeC
Confidence            889988877777654432111 1223344456679999877643

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.

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=89.48  E-value=0.098  Score=26.03  Aligned_cols=9  Identities=56%  Similarity=1.368  Sum_probs=6.5

Q ss_pred             CCCCCCceE
Q 046214           23 CPFCGGMIR   31 (66)
Q Consensus        23 Cp~CGG~v~   31 (66)
                      ||+||-.+.
T Consensus         2 Cp~CG~~~~   10 (23)
T PF13240_consen    2 CPNCGAEIE   10 (23)
T ss_pred             CcccCCCCC
Confidence            778877664

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=89.41  E-value=0.11  Score=26.08  Aligned_cols=9  Identities=56%  Similarity=1.269  Sum_probs=6.7

Q ss_pred             cCCCCCCce
Q 046214           22 ACPFCGGMI   30 (66)
Q Consensus        22 ~Cp~CGG~v   30 (66)
                      .||+||-.+
T Consensus         4 ~Cp~Cg~~~   12 (26)
T PF13248_consen    4 FCPNCGAEI   12 (26)
T ss_pred             CCcccCCcC
Confidence            588898743

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

Probab=88.63  E-value=1.1  Score=27.88  Aligned_cols=41  Identities=27%  Similarity=0.648  Sum_probs=30.8

Q ss_pred             CCCCCCceEEEEecee-eEEEEEeeeeeeccEEEeecccceee
Q 046214           23 CPFCGGMIRAMDVQSE-WRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        23 Cp~CGG~v~a~Dves~-~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      ||.||++....++++. +.+.-.-+-+ .-..+.|+.||..+.
T Consensus         1 C~~C~~~~~~~~~~~~~~~~~G~~~~v-~~~~~~C~~CGe~~~   42 (127)
T TIGR03830         1 CPICGSGELVRDVKDEPYTYKGESITI-GVPGWYCPACGEELL   42 (127)
T ss_pred             CCCCCCccceeeeecceEEEcCEEEEE-eeeeeECCCCCCEEE
Confidence            8999976666777764 4677777777 667788999998764

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.

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=88.57  E-value=0.35  Score=27.45  Aligned_cols=35  Identities=29%  Similarity=0.609  Sum_probs=19.1

Q ss_pred             cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214           22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      -||.|||......-.    +  -  -...+.-|.|+.||....
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            499999987733200    0  0  011122336888987643

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.

>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=88.25  E-value=0.39  Score=27.69  Aligned_cols=30  Identities=27%  Similarity=0.671  Sum_probs=23.0

Q ss_pred             CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214           19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL   63 (66)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L   63 (66)
                      ..-.||.||.....               ..+.|.|.|+.||...
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            34579999987765               4577889999998753

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

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

Probab=87.87  E-value=0.55  Score=31.18  Aligned_cols=44  Identities=18%  Similarity=0.333  Sum_probs=30.9

Q ss_pred             CCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214           20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL   63 (66)
Q Consensus        20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L   63 (66)
                      ...|+.|+|.++.++-|....----.++..+..=+.|+.||+.+
T Consensus        91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy  134 (147)
T PF01927_consen   91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY  134 (147)
T ss_pred             CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence            48999999999888766544442223334455678899999865

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

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=87.70  E-value=0.37  Score=26.28  Aligned_cols=29  Identities=34%  Similarity=0.811  Sum_probs=17.9

Q ss_pred             cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214           22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL   63 (66)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L   63 (66)
                      -||.||..+..-+.+.             ...+.|+.||...
T Consensus         2 FCp~Cg~~l~~~~~~~-------------~~~~vC~~Cg~~~   30 (52)
T smart00661        2 FCPKCGNMLIPKEGKE-------------KRRFVCRKCGYEE   30 (52)
T ss_pred             CCCCCCCccccccCCC-------------CCEEECCcCCCeE
Confidence            4899998664443331             2367788887543

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

Probab=87.07  E-value=0.2  Score=42.47  Aligned_cols=28  Identities=43%  Similarity=0.958  Sum_probs=20.3

Q ss_pred             ecCcceeeeeccCC-CcCCCCCCceEEEE
Q 046214            7 CDEDERVLGTQTAP-GACPFCGGMIRAMD   34 (66)
Q Consensus         7 cde~~kv~~~~~Ap-G~Cp~CGG~v~a~D   34 (66)
                      ||.=+||----.+| |.||+|||.+++.|
T Consensus       824 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  852 (1006)
T PRK12775        824 CDDCGKVSEGFAFPYGMCPACGGKLQALD  852 (1006)
T ss_pred             hhhhccccccccCCcCcCcccccchhhhh
Confidence            55445554444566 99999999998876

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=86.92  E-value=0.87  Score=26.20  Aligned_cols=37  Identities=24%  Similarity=0.483  Sum_probs=23.4

Q ss_pred             ecCcceeeeeccCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214            7 CDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL   63 (66)
Q Consensus         7 cde~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L   63 (66)
                      +|.+ +|....+   -||+||..+.+.                ++.++.|..||...
T Consensus        11 v~~~-~v~~~~~---fCP~Cg~~~m~~----------------~~~r~~C~~Cgyt~   47 (50)
T PRK00432         11 VDGG-KVKRKNK---FCPRCGSGFMAE----------------HLDRWHCGKCGYTE   47 (50)
T ss_pred             ECCC-EEEEccC---cCcCCCcchhec----------------cCCcEECCCcCCEE
Confidence            3543 6664443   899999752222                23688899998654

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

Probab=86.06  E-value=0.46  Score=32.42  Aligned_cols=24  Identities=33%  Similarity=0.801  Sum_probs=19.2

Q ss_pred             CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214           19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR   62 (66)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~   62 (66)
                      ..-.||.||.                    .+.|.|.|+.||-.
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                    45789999999964

>PRK10445 endonuclease VIII; Provisional

Probab=85.67  E-value=0.94  Score=32.84  Aligned_cols=29  Identities=31%  Similarity=0.800  Sum_probs=21.3

Q ss_pred             CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214           19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA   60 (66)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (66)
                      +...||+||+.+.-..+-.             ...|+|+.|-
T Consensus       234 ~g~~Cp~Cg~~I~~~~~~g-------------R~t~~CP~CQ  262 (263)
T PRK10445        234 DGEACERCGGIIEKTTLSS-------------RPFYWCPGCQ  262 (263)
T ss_pred             CCCCCCCCCCEeEEEEECC-------------CCcEECCCCc
Confidence            3456999999999887763             5567777663

>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional

Probab=85.60  E-value=0.75  Score=33.50  Aligned_cols=26  Identities=31%  Similarity=0.704  Sum_probs=20.1

Q ss_pred             cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214           22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA   60 (66)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (66)
                      .||+||+.+.-..+..             ...|+|+.|-
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=84.66  E-value=0.86  Score=33.30  Aligned_cols=27  Identities=22%  Similarity=0.706  Sum_probs=20.5

Q ss_pred             CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214           21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA   60 (66)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (66)
                      ..||+||+.+.-.-|..             ...|+|+.|-
T Consensus       255 ~pC~~Cg~~I~~~~~~g-------------R~t~~CP~CQ  281 (282)
T PRK13945        255 KPCRKCGTPIERIKLAG-------------RSTHWCPNCQ  281 (282)
T ss_pred             CCCCcCCCeeEEEEECC-------------CccEECCCCc
Confidence            46999999998877754             5667777773

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=84.60  E-value=0.41  Score=36.33  Aligned_cols=45  Identities=22%  Similarity=0.411  Sum_probs=34.1

Q ss_pred             cCCCcCCCCCCceEEEEe-----ceeeEEEEEeeeeeecc--EEEeecccce
Q 046214           18 TAPGACPFCGGMIRAMDV-----QSEWRFCFLPLYFKTKR--KFYCTVCARR   62 (66)
Q Consensus        18 ~ApG~Cp~CGG~v~a~Dv-----es~~rfCflP~~~k~kr--k~~Ct~C~r~   62 (66)
                      ...|.||-||+.-++.-+     +...|+..=++|.--|+  +..|+.||..
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            457799999999766555     34578888888876664  7889999853

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=84.40  E-value=0.83  Score=30.47  Aligned_cols=30  Identities=27%  Similarity=0.652  Sum_probs=22.3

Q ss_pred             CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214           19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      ....||.||.                |++.=...+.+|..||..+.
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            4578999985                44443667889999998764

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

Probab=83.40  E-value=0.63  Score=27.20  Aligned_cols=47  Identities=26%  Similarity=0.496  Sum_probs=30.1

Q ss_pred             cCCCcCCCCCCceEEEEeceee---------------EEEEEeeeeee--ccEEEeecccceeee
Q 046214           18 TAPGACPFCGGMIRAMDVQSEW---------------RFCFLPLYFKT--KRKFYCTVCARRLVV   65 (66)
Q Consensus        18 ~ApG~Cp~CGG~v~a~Dves~~---------------rfCflP~~~k~--krk~~Ct~C~r~L~~   65 (66)
                      |+.-.||+||.-+. +.||.+.               =+|+||++.+.  ...++|+.|++.|-.
T Consensus         1 p~~i~Cp~C~~~~~-T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~   64 (67)
T smart00714        1 PYQLFCPRCQNNVT-TRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHYCPNCGAFLGT   64 (67)
T ss_pred             CcceECCCCCCEEE-EEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEECCCCCCEeEE
Confidence            34557999987543 4454322               24568985443  346899999998754

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=83.33  E-value=1.2  Score=25.15  Aligned_cols=33  Identities=24%  Similarity=0.629  Sum_probs=19.2

Q ss_pred             cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214           22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR   61 (66)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (66)
                      -||.||.+....+-+..+.---.       -.+.|+.||.
T Consensus         5 PCPFCG~~~~~~~~~~~~~~~~~-------~~V~C~~Cga   37 (61)
T PF14354_consen    5 PCPFCGSADVLIRQDEGFDYGMY-------YYVECTDCGA   37 (61)
T ss_pred             CCCCCCCcceEeecccCCCCCCE-------EEEEcCCCCC
Confidence            39999777766665433210000       3466888886

>PF12773 DZR: Double zinc ribbon

Probab=83.02  E-value=0.32  Score=26.57  Aligned_cols=14  Identities=21%  Similarity=0.446  Sum_probs=7.4

Q ss_pred             eccEEEeeccccee
Q 046214           50 TKRKFYCTVCARRL   63 (66)
Q Consensus        50 ~krk~~Ct~C~r~L   63 (66)
                      .....+|+.||+.+
T Consensus        26 ~~~~~~C~~Cg~~~   39 (50)
T PF12773_consen   26 DQSKKICPNCGAEN   39 (50)
T ss_pred             cCCCCCCcCCcCCC
Confidence            33445566666543

>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg)

Probab=82.13  E-value=1.3  Score=32.27  Aligned_cols=26  Identities=27%  Similarity=0.765  Sum_probs=19.8

Q ss_pred             CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecc
Q 046214           21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVC   59 (66)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C   59 (66)
                      -.||+||+.+.-.-+..             ...|+|+.|
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            36999999998877753             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).

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

Probab=81.87  E-value=1.1  Score=24.27  Aligned_cols=29  Identities=24%  Similarity=0.708  Sum_probs=13.6

Q ss_pred             cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214           22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR   61 (66)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (66)
                      -||.||++++-.=.+-           -...++.|+.||.
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            3999999987653311           1334567787775

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=81.84  E-value=0.86  Score=34.74  Aligned_cols=43  Identities=21%  Similarity=0.485  Sum_probs=32.1

Q ss_pred             CCCcCCCCCCceEEE--Ee--ceeeEEEEEeeeeeecc--EEEeecccc
Q 046214           19 APGACPFCGGMIRAM--DV--QSEWRFCFLPLYFKTKR--KFYCTVCAR   61 (66)
Q Consensus        19 ApG~Cp~CGG~v~a~--Dv--es~~rfCflP~~~k~kr--k~~Ct~C~r   61 (66)
                      ..|.||-||+.-++.  +.  +...|++.=++|.--|+  +..|+.||.
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            579999999985433  33  34578888888877664  788999985

>PF14369 zf-RING_3: zinc-finger

Probab=81.52  E-value=1.1  Score=24.12  Aligned_cols=14  Identities=36%  Similarity=0.700  Sum_probs=10.1

Q ss_pred             ccCCCcCCCCCCce
Q 046214           17 QTAPGACPFCGGMI   30 (66)
Q Consensus        17 ~~ApG~Cp~CGG~v   30 (66)
                      ....-+||+|+|+-
T Consensus        18 ~~~~~~CP~C~~gF   31 (35)
T PF14369_consen   18 PDSDVACPRCHGGF   31 (35)
T ss_pred             CCCCcCCcCCCCcE
Confidence            34444699999975

>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=81.21  E-value=1.7  Score=23.56  Aligned_cols=29  Identities=28%  Similarity=0.655  Sum_probs=20.1

Q ss_pred             cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214           22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      .||+||..-...|-+              .-.++|+.||..|.
T Consensus         2 ~Cp~Cg~~~~~~D~~--------------~g~~vC~~CG~Vl~   30 (43)
T PF08271_consen    2 KCPNCGSKEIVFDPE--------------RGELVCPNCGLVLE   30 (43)
T ss_dssp             SBTTTSSSEEEEETT--------------TTEEEETTT-BBEE
T ss_pred             CCcCCcCCceEEcCC--------------CCeEECCCCCCEee
Confidence            599999987655533              34677889988775

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.

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

Probab=80.94  E-value=2.7  Score=22.98  Aligned_cols=13  Identities=38%  Similarity=0.784  Sum_probs=8.3

Q ss_pred             CCcCCCCCCceEE
Q 046214           20 PGACPFCGGMIRA   32 (66)
Q Consensus        20 pG~Cp~CGG~v~a   32 (66)
                      +..||+||+.+..
T Consensus        21 ~~~Cp~CG~~~~~   33 (46)
T PRK00398         21 GVRCPYCGYRILF   33 (46)
T ss_pred             ceECCCCCCeEEE
Confidence            5667777766553

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

Probab=80.91  E-value=1.6  Score=31.59  Aligned_cols=28  Identities=25%  Similarity=0.770  Sum_probs=20.6

Q ss_pred             CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214           21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR   61 (66)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (66)
                      -.||+||+.+.-..+..             ...|+|+.|-+
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            36999999998777653             56677777753

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=80.54  E-value=1.8  Score=25.50  Aligned_cols=32  Identities=28%  Similarity=0.532  Sum_probs=20.9

Q ss_pred             CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceeee
Q 046214           21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLVV   65 (66)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~~   65 (66)
                      ..||.||..+..-|....             --+.|..||+.|..
T Consensus         3 ~~CP~CG~~iev~~~~~G-------------eiV~Cp~CGaeleV   34 (54)
T TIGR01206         3 FECPDCGAEIELENPELG-------------ELVICDECGAELEV   34 (54)
T ss_pred             cCCCCCCCEEecCCCccC-------------CEEeCCCCCCEEEE
Confidence            479999987766443211             13478888888753

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.

>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=80.39  E-value=1.1  Score=23.02  Aligned_cols=16  Identities=19%  Similarity=0.341  Sum_probs=9.1

Q ss_pred             CcCCCCCCceEEEEec
Q 046214           21 GACPFCGGMIRAMDVQ   36 (66)
Q Consensus        21 G~Cp~CGG~v~a~Dve   36 (66)
                      .-||+||++...++=+
T Consensus         4 rfC~~CG~~t~~~~~g   19 (32)
T PF09297_consen    4 RFCGRCGAPTKPAPGG   19 (32)
T ss_dssp             SB-TTT--BEEE-SSS
T ss_pred             cccCcCCccccCCCCc
Confidence            5699999998876654

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

>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=80.13  E-value=2.5  Score=22.43  Aligned_cols=16  Identities=38%  Similarity=0.889  Sum_probs=12.3

Q ss_pred             eeccCCCcCCCCCCce
Q 046214           15 GTQTAPGACPFCGGMI   30 (66)
Q Consensus        15 ~~~~ApG~Cp~CGG~v   30 (66)
                      ....+|..||-||.+-
T Consensus        13 ~g~~~p~~CP~Cg~~~   28 (34)
T cd00729          13 EGEEAPEKCPICGAPK   28 (34)
T ss_pred             ECCcCCCcCcCCCCch
Confidence            3345899999999864

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.

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=80.05  E-value=1.5  Score=30.11  Aligned_cols=28  Identities=39%  Similarity=0.963  Sum_probs=21.2

Q ss_pred             CCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214           20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      .-.||.||                .||+. .--.++|+.|+.+-+
T Consensus        28 ~~hCp~Cg----------------~PLF~-KdG~v~CPvC~~~~~   55 (131)
T COG1645          28 AKHCPKCG----------------TPLFR-KDGEVFCPVCGYREV   55 (131)
T ss_pred             HhhCcccC----------------Cccee-eCCeEECCCCCceEE
Confidence            34688888                67877 667899999996543

---

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	66
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	93.33
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	91.82
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	91.05
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	89.46
3ga8_A	78	HTH-type transcriptional regulator MQSA (YGIT/B30;	87.04
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	86.21
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	84.15
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	84.04
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	83.15
1k3x_A	262	Endonuclease VIII; hydrolase/DNA, hydrolase-DNA co	80.2

>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=93.33  E-value=0.042  Score=31.40  Aligned_cols=38  Identities=18%  Similarity=0.495  Sum_probs=25.6

Q ss_pred             ecCcceeeeeccCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccccee
Q 046214            7 CDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRL   63 (66)
Q Consensus         7 cde~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L   63 (66)
                      +|+ +++...   --.||.||.++.            +.   ++..++.|..|+-..
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 665442   467999998772            11   445699999998653

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

Probab=91.82  E-value=0.13  Score=28.74  Aligned_cols=37  Identities=24%  Similarity=0.543  Sum_probs=25.0

Q ss_pred             ecCcceeeeeccCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccce
Q 046214            7 CDEDERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARR   62 (66)
Q Consensus         7 cde~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~   62 (66)
                      +| ++||...   .--||.||.++..++               +..++.|..||-.
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   345999998875443               2467889999854

>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=91.05  E-value=0.086  Score=38.52  Aligned_cols=45  Identities=20%  Similarity=0.379  Sum_probs=33.8

Q ss_pred             cCCCcCCCCCCceEEEEec-----eeeEEEEEeeeeeecc--EEEeecccce
Q 046214           18 TAPGACPFCGGMIRAMDVQ-----SEWRFCFLPLYFKTKR--KFYCTVCARR   62 (66)
Q Consensus        18 ~ApG~Cp~CGG~v~a~Dve-----s~~rfCflP~~~k~kr--k~~Ct~C~r~   62 (66)
                      ...|.||-||+.-++.-|.     ...|+++=.+|--.|+  +..|+.||..
T Consensus       180 ~~~~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~t~W~~~R~~C~~Cg~~  231 (309)
T 2fiy_A          180 ESRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHYVRIKCSHCEES  231 (309)
T ss_dssp             TTCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEECCTTSCSSSCCC
T ss_pred             ccCCCCCCCCCcCceeEEeecCCCCCcEEEEeCCCCCEEeecCcCCcCCCCC
Confidence            4579999999999887664     5668887777755553  5688888853

>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=89.46  E-value=0.76  Score=27.76  Aligned_cols=43  Identities=19%  Similarity=0.455  Sum_probs=26.6

Q ss_pred             cCCCCCCceEEEEece-eeEEEEEeeeeeeccEEEeecccceee
Q 046214           22 ACPFCGGMIRAMDVQS-EWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        22 ~Cp~CGG~v~a~Dves-~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      .||.||+.....+.++ ...+--.-+-.+.=..++|..||..+-
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 223333344444445789999997653

>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=87.04  E-value=1.1  Score=25.97  Aligned_cols=41  Identities=22%  Similarity=0.500  Sum_probs=24.1

Q ss_pred             cCCCCCCc-e--EEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214           22 ACPFCGGM-I--RAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        22 ~Cp~CGG~-v--~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      .||.||++ +  ...|+.-.+.=.-+  -.+.=...+|+.||..+-
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            59999976 3  22333333332222  224456789999998764

>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=86.21  E-value=0.66  Score=30.42  Aligned_cols=41  Identities=22%  Similarity=0.495  Sum_probs=29.4

Q ss_pred             EecCcceeeeeccCCCcCCC--CCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214            6 VCDEDERVLGTQTAPGACPF--CGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus         6 vcde~~kv~~~~~ApG~Cp~--CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      =+|+++||.+.+   -.||+  ||.+|-.++-               +.+++|-.|+-.+.
T Consensus       107 ~~~~~~~~~~~~---~~c~~~~cg~g~fma~h---------------~~r~~cgkc~~t~~  149 (152)
T 3u5c_f          107 KVDAEGKVTKLR---RECSNPTCGAGVFLANH---------------KDRLYCGKCHSVYK  149 (152)
T ss_dssp             EECSSSCEECCS---CBCCSTTSCSSSBEEEC---------------SSCEEESSSSSCCE
T ss_pred             EEccCCeEEECc---CcCCCccCCCceEeccc---------------CCCcccCCCceEEE
Confidence            368888887654   35999  9988766544               35788888886553

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

Probab=84.15  E-value=0.7  Score=27.24  Aligned_cols=29  Identities=14%  Similarity=0.252  Sum_probs=20.9

Q ss_pred             CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214           21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      -+||.|+|++...+.               +....|+.|++.+-
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               35667888887653

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

Probab=84.04  E-value=0.84  Score=27.02  Aligned_cols=29  Identities=17%  Similarity=0.445  Sum_probs=20.7

Q ss_pred             CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214           21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      -+||.|+|++...+.               .....|+.|++.+-
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               35667888887653

>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=83.15  E-value=0.85  Score=26.87  Aligned_cols=28  Identities=21%  Similarity=0.454  Sum_probs=20.5

Q ss_pred             cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214           22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      +||.|+|++...+.               +....|+.|++.+-
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               45667888887653

>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=80.20  E-value=1  Score=31.58  Aligned_cols=26  Identities=23%  Similarity=0.811  Sum_probs=19.0

Q ss_pred             cCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214           22 ACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA   60 (66)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (66)
                      .||+||+++.-..+-             ....|+|+.|-
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             34456666663

---

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	66
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	90.66
d1k3xa3	40	Endonuclease VIII {Escherichia coli [TaxId: 562]}	90.52
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	89.73
d1k82a3	44	DNA repair protein MutM (Fpg) {Escherichia coli [T	86.76
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	84.88
d1tdza3	47	DNA repair protein MutM (Fpg) {Lactococcus lactis	84.44
d1r2za3	46	DNA repair protein MutM (Fpg) {Bacillus stearother	82.54
d2jnya1	59	Uncharacterized protein Cgl1405/cg1592 {Corynebact	80.13

>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=90.66  E-value=0.05  Score=37.79  Aligned_cols=45  Identities=20%  Similarity=0.360  Sum_probs=34.1

Q ss_pred             cCCCcCCCCCCceEEEEec-----eeeEEEEEeeeeeec--cEEEeecccce
Q 046214           18 TAPGACPFCGGMIRAMDVQ-----SEWRFCFLPLYFKTK--RKFYCTVCARR   62 (66)
Q Consensus        18 ~ApG~Cp~CGG~v~a~Dve-----s~~rfCflP~~~k~k--rk~~Ct~C~r~   62 (66)
                      ...|.||-||+.-++.-++     ...|++.=.+|.--|  .+..|+.||..
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     345888778886666  35688888753

>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=90.52  E-value=0.09  Score=27.14  Aligned_cols=18  Identities=28%  Similarity=0.635  Sum_probs=14.8

Q ss_pred             CCcCCCCCCceEEEEece
Q 046214           20 PGACPFCGGMIRAMDVQS   37 (66)
Q Consensus        20 pG~Cp~CGG~v~a~Dves   37 (66)
                      .-.|++||+.|.-+.+..
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            345999999999988864

>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=89.73  E-value=0.021  Score=28.53  Aligned_cols=13  Identities=31%  Similarity=0.790  Sum_probs=11.1

Q ss_pred             cCCCCCCceEEEE
Q 046214           22 ACPFCGGMIRAMD   34 (66)
Q Consensus        22 ~Cp~CGG~v~a~D   34 (66)
                      .|||||+.|-|++
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=86.76  E-value=0.24  Score=25.69  Aligned_cols=17  Identities=29%  Similarity=0.532  Sum_probs=14.2

Q ss_pred             CcCCCCCCceEEEEece
Q 046214           21 GACPFCGGMIRAMDVQS   37 (66)
Q Consensus        21 G~Cp~CGG~v~a~Dves   37 (66)
                      -.|++||+.|..+.+..
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=84.88  E-value=0.19  Score=28.06  Aligned_cols=34  Identities=21%  Similarity=0.592  Sum_probs=23.6

Q ss_pred             cceeeeeccCCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214           10 DERVLGTQTAPGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR   61 (66)
Q Consensus        10 ~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (66)
                      ++|+.+.+   -.||+||-+|-.++               ++.+++|-.||-
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            45665543   46999999886554               567778877764

>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=84.44  E-value=0.37  Score=25.22  Aligned_cols=29  Identities=28%  Similarity=0.791  Sum_probs=20.8

Q ss_pred             CCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccc
Q 046214           20 PGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCAR   61 (66)
Q Consensus        20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r   61 (66)
                      .-.||+||..|.-+.+..             ...|+|+.|-+
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             34566666654

>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=82.54  E-value=0.67  Score=23.99  Aligned_cols=29  Identities=28%  Similarity=0.640  Sum_probs=20.7

Q ss_pred             CCCcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeeccc
Q 046214           19 APGACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCA   60 (66)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~   60 (66)
                      +.-.||+||..|.-+.+..             .+.|+|+.|-
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             4556676663

>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=80.13  E-value=0.62  Score=25.48  Aligned_cols=29  Identities=17%  Similarity=0.197  Sum_probs=20.9

Q ss_pred             CcCCCCCCceEEEEeceeeEEEEEeeeeeeccEEEeecccceee
Q 046214           21 GACPFCGGMIRAMDVQSEWRFCFLPLYFKTKRKFYCTVCARRLV   64 (66)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~krk~~Ct~C~r~L~   64 (66)
                      -+||.|+|.+...+               .+....|+.|++.+.
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            37999999998753               234567888887654