Citrus Sinensis ID: 038108

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60-------
Protein Sequence
MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLELYH
Secondary Structure (PSIPRED)
cEEEEEccccEEEEEEEcccccccccccEEEEEEEccEEEEEEEEEEEEEEEEEEEEccccEEEEcc
Secondary Structure Prediction (SSPRO)
cEEEEEEccccEEEccccccccccccccEEEEEEcccHHEEEEcHHHHHcccEEHHHHHHHHEEEcc
Coil and Loop (DISEMBL)
MCLVYVCSEEERelgrqqapgscpycggkvlaidfesqcrfcflpicyniKKKYFCSLCSRRLELYH
Flexible Loop (DISEMBL)
MCLVYVCSEEErelgrqqapgscpYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLELYH
Low Complexity Region (SEG)
MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLELYH
Disordered region (IsUnstruct)
**LVYVC*************GSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLE***
Disordered Region (DISOPRED)
MCLVYV*SEEE***********CPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLELYH
Disordered Region (DISEMBL)
MCLVYVCSE*********APGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLELYH
Disordered Region (DISPRO)
MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLELYH
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLELYH
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	67
255602084	67	conserved hypothetical protein [Ricinus	1.0	1.0	0.776	2e-22
224144308	68	predicted protein [Populus trichocarpa]	1.0	0.985	0.761	2e-22
224090505	67	predicted protein [Populus trichocarpa]	0.970	0.970	0.753	7e-22
388505372	67	unknown [Lotus japonicus]	1.0	1.0	0.701	4e-21
356548321	69	PREDICTED: uncharacterized protein LOC10	0.985	0.956	0.727	8e-21
356554423	68	PREDICTED: uncharacterized protein LOC10	0.955	0.941	0.718	9e-21
356561869	66	PREDICTED: uncharacterized protein LOC10	0.970	0.984	0.692	2e-20
357449639	104	hypothetical protein MTR_2g038220 [Medic	1.0	0.644	0.671	7e-20
388510416	69	unknown [Lotus japonicus]	1.0	0.971	0.656	2e-19
357479499	68	hypothetical protein MTR_4g127190 [Medic	1.0	0.985	0.671	2e-19

>gi|255602084|ref|XP_002537812.1| conserved hypothetical protein [Ricinus communis] gi|223514986|gb|EEF24571.1| conserved hypothetical protein [Ricinus communis]

 Score =  109 bits (273), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 52/67 (77%), Positives = 59/67 (88%)

Query: 1  MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
          MCLV++C EEERELGRQQAPGSCPYCGGKV A+D E +  FCFLPICY IK+K+FCSLC+
Sbjct: 1  MCLVFLCEEEERELGRQQAPGSCPYCGGKVEAMDVERKWSFCFLPICYKIKRKFFCSLCA 60

Query: 61 RRLELYH 67
          RRLEL H
Sbjct: 61 RRLELCH 67

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  109 bits (273), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 51/67 (76%), Positives = 58/67 (86%)

Query: 1  MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
          MC V++C EEERELGRQQA GSCP+CGGKV A+DFES+ RFCFLPICY  K+KY C+LCS
Sbjct: 1  MCFVFLCDEEERELGRQQASGSCPHCGGKVQAVDFESRWRFCFLPICYKNKRKYLCTLCS 60

Query: 61 RRLELYH 67
          RRLELY 
Sbjct: 61 RRLELYQ 67

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  107 bits (268), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 49/65 (75%), Positives = 58/65 (89%)

Query: 1  MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
          MC V++C EEE+ELGRQQA GSCP+CGGKV A+DFE + RFCFLPICY +K+KYFC+LCS
Sbjct: 1  MCFVFLCDEEEKELGRQQASGSCPHCGGKVQAVDFEGRWRFCFLPICYKMKRKYFCTLCS 60

Query: 61 RRLEL 65
          RRLEL
Sbjct: 61 RRLEL 65

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388505372|gb|AFK40752.1| unknown [Lotus japonicus]

 Score =  105 bits (262), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 47/67 (70%), Positives = 59/67 (88%)

Query: 1  MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
          M  VYVC E E+ELGRQQAPGSCP+CGGKV A+D E + RFCFLP+C+NIK+K+FC+LC+
Sbjct: 1  MWFVYVCDEGEKELGRQQAPGSCPHCGGKVEAMDVEIRWRFCFLPMCFNIKRKFFCTLCA 60

Query: 61 RRLELYH 67
          RRLEL++
Sbjct: 61 RRLELFY 67

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356548321|ref|XP_003542551.1| PREDICTED: uncharacterized protein LOC100527565 [Glycine max] gi|356562056|ref|XP_003549291.1| PREDICTED: uncharacterized protein LOC100795948 [Glycine max] gi|255632626|gb|ACU16663.1| unknown [Glycine max]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 48/66 (72%), Positives = 55/66 (83%)

Query: 1  MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
          M  VYVC EEE+ELGRQQAPGSCPYCG KV A+D E Q R CFLP+C+ IK+KYFC+ C+
Sbjct: 1  MWFVYVCDEEEKELGRQQAPGSCPYCGAKVEAMDVEIQSRLCFLPLCFKIKRKYFCTHCA 60

Query: 61 RRLELY 66
          RRLELY
Sbjct: 61 RRLELY 66

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  103 bits (258), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 46/64 (71%), Positives = 55/64 (85%)

Query: 1  MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
          MCLV+VC EEER LGRQ APG+CPYCGG V AID ESQ RFCFLP+C+  K+KY+C++C+
Sbjct: 1  MCLVFVCDEEERVLGRQTAPGACPYCGGMVQAIDVESQWRFCFLPLCFKTKRKYYCTMCT 60

Query: 61 RRLE 64
          RRLE
Sbjct: 61 RRLE 64

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  102 bits (255), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/65 (69%), Positives = 57/65 (87%)

Query: 1  MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
          MCLV+VC+EEER LGRQ APG+CPYCGG V AI+ ESQ RFCFLP+C+  K+KY+C++C+
Sbjct: 1  MCLVFVCNEEERVLGRQTAPGACPYCGGMVQAINVESQWRFCFLPLCFKTKRKYYCTMCT 60

Query: 61 RRLEL 65
          RRLE+
Sbjct: 61 RRLEV 65

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  101 bits (251), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 45/67 (67%), Positives = 56/67 (83%)

Query: 1   MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
           M  VY+C EEE+ELGRQ+A G CPYCGGKV A+D E Q RFCFLP+C+ IK+K+FC+LC+
Sbjct: 37  MWFVYICDEEEKELGRQKASGCCPYCGGKVEAMDVEMQWRFCFLPMCFKIKRKFFCTLCA 96

Query: 61  RRLELYH 67
           RRLEL +
Sbjct: 97  RRLELQY 103

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388510416|gb|AFK43274.1| unknown [Lotus japonicus]

 Score = 99.4 bits (246), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/67 (65%), Positives = 58/67 (86%)

Query: 1  MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
          M LV VC ++E++LG+QQAPGSCP+CGGKV A+D E Q R CFLP+C+ IK+KYFC+LC+
Sbjct: 1  MWLVCVCEDQEKQLGKQQAPGSCPHCGGKVEAMDVEVQSRLCFLPVCFKIKRKYFCTLCA 60

Query: 61 RRLELYH 67
          RRLEL++
Sbjct: 61 RRLELFY 67

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357479499|ref|XP_003610035.1| hypothetical protein MTR_4g127190 [Medicago truncatula] gi|355511090|gb|AES92232.1| hypothetical protein MTR_4g127190 [Medicago truncatula]

 Score = 99.4 bits (246), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 45/67 (67%), Positives = 56/67 (83%)

Query: 1  MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
          M L YVC  +++ELGRQQAPGSCPYCGGKV A+D E Q + CFLP+C+ IK+KYFC+LCS
Sbjct: 1  MRLSYVCEGQQKELGRQQAPGSCPYCGGKVEAMDVEVQSKLCFLPMCFQIKRKYFCTLCS 60

Query: 61 RRLELYH 67
          RRLE+ +
Sbjct: 61 RRLEILY 67

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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	67
TAIR|locus:504954859	67	AT5G57123 "AT5G57123" [Arabido	1.0	1.0	0.686	2.3e-23
TAIR|locus:504955497	67	AT4G29905 "AT4G29905" [Arabido	1.0	1.0	0.626	8e-21
TAIR|locus:505006594	67	AT5G10695 [Arabidopsis thalian	0.940	0.940	0.539	2e-17
TAIR|locus:2827497	68	AT2G20835 "AT2G20835" [Arabido	0.940	0.926	0.301	5.5e-06
TAIR|locus:4515103075	68	AT3G15534 "AT3G15534" [Arabido	0.985	0.970	0.272	1.9e-05
TAIR|locus:1006230684	68	AT1G52855 "AT1G52855" [Arabido	0.985	0.970	0.272	3e-05

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

 Score = 269 (99.8 bits), Expect = 2.3e-23, P = 2.3e-23
 Identities = 46/67 (68%), Positives = 53/67 (79%)

Query:     1 MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
             MCLV +C EEE ELGRQQAPGSCPYCGGKV  +D E +  FCF+P+C+ IK+KY CS C 
Sbjct:     1 MCLVCLCDEEETELGRQQAPGSCPYCGGKVQMLDVERKWMFCFVPLCFKIKRKYSCSSCD 60

Query:    61 RRLELYH 67
             RRL LYH
Sbjct:    61 RRLVLYH 67

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 = 245 (91.3 bits), Expect = 8.0e-21, P = 8.0e-21
 Identities = 42/67 (62%), Positives = 51/67 (76%)

Query:     1 MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
             MCL  V  EE+ ELGRQQAPG CPYCGGKV A+D E++  FCFLP+C+ +K+KY CS C 
Sbjct:     1 MCLEVVYHEEKTELGRQQAPGMCPYCGGKVSAVDIETKWLFCFLPLCFKVKRKYSCSSCE 60

Query:    61 RRLELYH 67
             R L LY+
Sbjct:    61 RHLVLYY 67

GO:0005575 "cellular_component" evidence=ND

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

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 34/63 (53%), Positives = 46/63 (73%)

Query:     1 MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
             MCLV+VC ++ER +GR  APG+CPYCGG V  +D  SQ RFCF+P+    K+++ CS C 
Sbjct:     1 MCLVFVCDQDERVIGRYAAPGACPYCGGAVQVVDVNSQWRFCFVPLSNKSKRRHLCSTCG 60

Query:    61 RRL 63
             +RL
Sbjct:    61 KRL 63

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

 Score = 105 (42.0 bits), Expect = 5.5e-06, P = 5.5e-06
 Identities = 19/63 (30%), Positives = 30/63 (47%)

Query:     5 YVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLE 64
             ++  + ++  GR+ A G C  CGG  +  D  +  RFC +P      K   C +C   L+
Sbjct:     6 FLVDQRKKVRGRKPAAGLCSRCGGGAVVADMRTSTRFCGVPFYRKAWKAIVCHICGAVLK 65

Query:    65 LYH 67
              YH
Sbjct:    66 SYH 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 = 100 (40.3 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 18/66 (27%), Positives = 31/66 (46%)

Query:     1 MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
             +C  ++  ++ +  G + A G+C  CG      D ++  RFC +PI     +   CS C 
Sbjct:     2 VCFCFLVDQKRKVKGSKPAAGTCSRCGRGARVADMKTSTRFCLIPIYCRSWRAIVCSFCG 61

Query:    61 RRLELY 66
               L+ Y
Sbjct:    62 SVLKSY 67

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 = 98 (39.6 bits), Expect = 3.0e-05, P = 3.0e-05
 Identities = 18/66 (27%), Positives = 31/66 (46%)

Query:     1 MCLVYVCSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS 60
             +C  ++  +  +    + A G+C  CG      D ++  RFCF+PI +   +   CS C 
Sbjct:     2 VCFCFLVDQTRKVKRSKPAAGTCSRCGHCASIADMKTSTRFCFIPIYWRSWRAVVCSFCG 61

Query:    61 RRLELY 66
               L+ Y
Sbjct:    62 SVLKSY 67


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        0.331   0.145   0.507    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       67        67   0.00091  102 3  11 21  0.37    28
                                                     29  0.49    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:  490 (52 KB)
  Total size of DFA:  102 KB (2072 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:  8.76u 0.16s 8.92t   Elapsed:  00:00:01
  Total cpu time:  8.76u 0.16s 8.92t   Elapsed:  00:00:01
  Start:  Fri May 10 15:03:11 2013   End:  Fri May 10 15:03:12 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	67
PF13005	47	zf-IS66: zinc-finger binding domain of transposase	95.07
PF10601	73	zf-LITAF-like: LITAF-like zinc ribbon domain; Inte	94.93
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	94.12
PF14690	47	zf-ISL3: zinc-finger of transposase IS204/IS1001/I	93.9
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	93.58
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	92.87
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	91.66
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	91.15
COG3813	84	Uncharacterized protein conserved in bacteria [Fun	91.12
PF13248	26	zf-ribbon_3: zinc-ribbon domain	90.43
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	90.03
PF11672	102	DUF3268: Protein of unknown function (DUF3268); In	89.97
smart00714	67	LITAF Possible membrane-associated motif in LPS-in	89.4
TIGR03831	46	YgiT_finger YgiT-type zinc finger domain. This dom	89.32
PRK12775	1006	putative trifunctional 2-polyprenylphenol hydroxyl	88.96
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	88.64
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	88.16
smart00661	52	RPOL9 RNA polymerase subunit 9.	87.87
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	87.38
PF01927	147	Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T	87.36
PF14369	35	zf-RING_3: zinc-finger	87.18
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	87.08
PF01599	47	Ribosomal_S27: Ribosomal protein S27a; InterPro: I	86.95
PRK00432	50	30S ribosomal protein S27ae; Validated	86.67
COG0675	364	Transposase and inactivated derivatives [DNA repli	85.96
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	85.75
PRK10445	263	endonuclease VIII; Provisional	85.74
PRK14810	272	formamidopyrimidine-DNA glycosylase; Provisional	85.35
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	84.91
PRK13945	282	formamidopyrimidine-DNA glycosylase; Provisional	84.49
PRK00420	112	hypothetical protein; Validated	84.26
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	82.4
PF12773	50	DZR: Double zinc ribbon	82.22
PRK09678	72	DNA-binding transcriptional regulator; Provisional	82.05
TIGR00577	272	fpg formamidopyrimidine-DNA glycosylase (fpg). All	82.0
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	81.85
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	81.67
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	81.56
PRK01103	274	formamidopyrimidine/5-formyluracil/ 5-hydroxymethy	81.0
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	80.59
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	80.52

>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=95.07  E-value=0.049  Score=29.70  Aligned_cols=41  Identities=32%  Similarity=0.688  Sum_probs=29.2

Q ss_pred             CCCCCCCCcceEEEEec-eeeeEEEeeeEeeec----ceEEecccc
Q 038108           20 PGSCPYCGGKVLAIDFE-SQCRFCFLPICYNIK----KKYFCSLCS   60 (67)
Q Consensus        20 pG~Cp~CGG~v~a~Dve-s~~rfCflP~~~k~k----r~~~Ct~C~   60 (67)
                      +.+||.||+.+.-+-.+ .+-.|=++|.-+...    -+|.|+-|+
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 556666778666543    367777775

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

Probab=94.93  E-value=0.017  Score=34.45  Aligned_cols=52  Identities=27%  Similarity=0.640  Sum_probs=38.4

Q ss_pred             eeecCCCCCCCCCcceEEEEecee-----------------eeEEEeeeEeee--cceEEeccccceeeeeC
Q 038108           15 GRQQAPGSCPYCGGKVLAIDFESQ-----------------CRFCFLPICYNI--KKKYFCSLCSRRLELYH   67 (67)
Q Consensus        15 ~~~~ApG~Cp~CGG~v~a~Dves~-----------------~rfCflP~~~k~--kr~~~Ct~C~r~L~~~~   67 (67)
                      +++|..-.||+||-.+. +.+|.+                 |-+|+||++.+.  ...++|+.|++.|-.|+
T Consensus         2 ~~~p~~~~CP~C~~~~~-T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~~   72 (73)
T PF10601_consen    2 GPEPVRIYCPYCQQQVQ-TRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCGAFLGTYK   72 (73)
T ss_pred             CCCceeeECCCCCCEEE-EEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEECCCCCCEeEEEe
Confidence            46788889999998764 334422                 345789999854  45799999999998763

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

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=94.12  E-value=0.044  Score=38.01  Aligned_cols=39  Identities=26%  Similarity=0.617  Sum_probs=26.4

Q ss_pred             CCCCCCcce-EEEEeceeeeEEEeeeEeeecceEEeccccceeeee
Q 038108           22 SCPYCGGKV-LAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLELY   66 (67)
Q Consensus        22 ~Cp~CGG~v-~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L~~~   66 (67)
                      .|||||++. .|.|=+.      ++==.-.+|++.|..||++..+|
T Consensus         2 ~cp~c~~~~~~~~~s~~------~~~~~~~~~~~~c~~c~~~f~~~   41 (154)
T PRK00464          2 RCPFCGHPDTRVIDSRP------AEDGNAIRRRRECLACGKRFTTF   41 (154)
T ss_pred             cCCCCCCCCCEeEeccc------cCCCCceeeeeeccccCCcceEe
Confidence            499999976 5555331      11112367779999999987765

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

Probab=93.90  E-value=0.099  Score=28.23  Aligned_cols=38  Identities=34%  Similarity=0.729  Sum_probs=23.3

Q ss_pred             CCCCCCCCcceEEE--EeceeeeEEEeee-----Eee-ecceEEeccc
Q 038108           20 PGSCPYCGGKVLAI--DFESQCRFCFLPI-----CYN-IKKKYFCSLC   59 (67)
Q Consensus        20 pG~Cp~CGG~v~a~--Dves~~rfCflP~-----~~k-~kr~~~Ct~C   59 (67)
                      |-.||+||..-..-  -.+..|+  .+|+     +.+ .+++|.|..|
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 3678998876

>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=93.58  E-value=0.035  Score=40.37  Aligned_cols=43  Identities=21%  Similarity=0.542  Sum_probs=24.2

Q ss_pred             CCCCCCCCCcceEEEEecee----eeEEEeeeEeeecc--eEEeccccc
Q 038108           19 APGSCPYCGGKVLAIDFESQ----CRFCFLPICYNIKK--KYFCSLCSR   61 (67)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~----~rfCflP~~~k~kr--~~~Ct~C~r   61 (67)
                      ..|.||-||+.-++.-++..    .|+.+=.+|.-.|+  |..|+.||.
T Consensus       171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~  219 (290)
T PF04216_consen  171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGN  219 (290)
T ss_dssp             T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT--
T ss_pred             cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCC
Confidence            35999999999888877764    58887788765553  567888885

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.

>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=92.87  E-value=0.14  Score=28.40  Aligned_cols=28  Identities=25%  Similarity=0.772  Sum_probs=20.8

Q ss_pred             CCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccce
Q 038108           21 GSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRR   62 (67)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~   62 (67)
                      -.||+||.. .+.-+.+             ...|.|..|+++
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            469999997 5555554             677888888764

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

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

Probab=91.66  E-value=0.084  Score=32.18  Aligned_cols=13  Identities=46%  Similarity=1.313  Sum_probs=11.1

Q ss_pred             CCCCCCCCcceEE
Q 038108           20 PGSCPYCGGKVLA   32 (67)
Q Consensus        20 pG~Cp~CGG~v~a   32 (67)
                      .|.||+|||.++.
T Consensus        41 ~~~CPNCgGelv~   53 (57)
T PF06906_consen   41 NGVCPNCGGELVR   53 (57)
T ss_pred             cCcCcCCCCcccc
Confidence            6999999998763

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

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

Probab=91.15  E-value=0.11  Score=31.16  Aligned_cols=36  Identities=28%  Similarity=0.702  Sum_probs=25.2

Q ss_pred             CceeeeeeecCCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccce
Q 038108            9 EEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRR   62 (67)
Q Consensus         9 e~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~   62 (67)
                      +.+||++.++   -||+||-++-.+|               ++.|+.|-.||-.
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            3455666554   6999998877666               4457888888754

>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.12  E-value=0.087  Score=34.16  Aligned_cols=18  Identities=39%  Similarity=0.927  Sum_probs=14.5

Q ss_pred             CCCCCCCCCcceEEEEec
Q 038108           19 APGSCPYCGGKVLAIDFE   36 (67)
Q Consensus        19 ApG~Cp~CGG~v~a~Dve   36 (67)
                      -.|.||+|||.+++--++
T Consensus        40 l~g~CPnCGGelv~RP~R   57 (84)
T COG3813          40 LHGLCPNCGGELVARPIR   57 (84)
T ss_pred             hcCcCCCCCchhhcCcCC
Confidence            469999999999875554

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=90.43  E-value=0.089  Score=26.46  Aligned_cols=9  Identities=44%  Similarity=1.398  Sum_probs=6.7

Q ss_pred             CCCCCCcce
Q 038108           22 SCPYCGGKV   30 (67)
Q Consensus        22 ~Cp~CGG~v   30 (67)
                      .||+||-.+
T Consensus         4 ~Cp~Cg~~~   12 (26)
T PF13248_consen    4 FCPNCGAEI   12 (26)
T ss_pred             CCcccCCcC
Confidence            588998743

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=90.03  E-value=0.089  Score=26.22  Aligned_cols=9  Identities=44%  Similarity=1.398  Sum_probs=6.5

Q ss_pred             CCCCCcceE
Q 038108           23 CPYCGGKVL   31 (67)
Q Consensus        23 Cp~CGG~v~   31 (67)
                      ||+||-.+.
T Consensus         2 Cp~CG~~~~   10 (23)
T PF13240_consen    2 CPNCGAEIE   10 (23)
T ss_pred             CcccCCCCC
Confidence            778887664

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

Probab=89.97  E-value=0.18  Score=33.18  Aligned_cols=39  Identities=33%  Similarity=0.686  Sum_probs=24.6

Q ss_pred             CCCCCCCCcceEEEEeceeeeEEEeeeEeeecc-eEEecccccee
Q 038108           20 PGSCPYCGGKVLAIDFESQCRFCFLPICYNIKK-KYFCSLCSRRL   63 (67)
Q Consensus        20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr-~~~Ct~C~r~L   63 (67)
                      |-.||||||.+.-+|= +..    -|=-...+. -|.|+.|++-.
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.

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

Probab=89.40  E-value=0.24  Score=29.09  Aligned_cols=48  Identities=27%  Similarity=0.591  Sum_probs=31.7

Q ss_pred             cCCCCCCCCCcceEEEEeceee---------------eEEEeeeEeee--cceEEeccccceeeee
Q 038108           18 QAPGSCPYCGGKVLAIDFESQC---------------RFCFLPICYNI--KKKYFCSLCSRRLELY   66 (67)
Q Consensus        18 ~ApG~Cp~CGG~v~a~Dves~~---------------rfCflP~~~k~--kr~~~Ct~C~r~L~~~   66 (67)
                      |+.-.||+||.-++ +.+|.+.               =+|+||++.+.  ...++|+.|++.|-.|
T Consensus         1 p~~i~Cp~C~~~~~-T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~   65 (67)
T smart00714        1 PYQLFCPRCQNNVT-TRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHYCPNCGAFLGTY   65 (67)
T ss_pred             CcceECCCCCCEEE-EEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEECCCCCCEeEEe
Confidence            34557999987543 4444322               24568986443  4468999999998776

>TIGR03831 YgiT_finger YgiT-type zinc finger domain

Probab=89.32  E-value=0.87  Score=23.95  Aligned_cols=42  Identities=21%  Similarity=0.361  Sum_probs=25.0

Q ss_pred             CCCCCcceEEEEeceeeeEEE-eeeEeeecceEEeccccceee
Q 038108           23 CPYCGGKVLAIDFESQCRFCF-LPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus        23 Cp~CGG~v~a~Dves~~rfCf-lP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      ||-|||....-++++.+.--- -=+..+.=..+.|+.||..+-
T Consensus         1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE~~~   43 (46)
T TIGR03831         1 CPICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGEEYL   43 (46)
T ss_pred             CCCCCCceecceEEEEEEEeCCEEEEEeCCCccccccCCCEee
Confidence            888988877777754432111 112233445667999987664

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

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

Probab=88.96  E-value=0.13  Score=43.66  Aligned_cols=30  Identities=37%  Similarity=0.805  Sum_probs=22.5

Q ss_pred             EEcCCceeeeeeecCC-CCCCCCCcceEEEE
Q 038108            5 YVCSEEERELGRQQAP-GSCPYCGGKVLAID   34 (67)
Q Consensus         5 ~vcde~~kv~~~~~Ap-G~Cp~CGG~v~a~D   34 (67)
                      +=||.-+||----.+| |.||+|||.+++.|
T Consensus       822 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  852 (1006)
T PRK12775        822 WRCDDCGKVSEGFAFPYGMCPACGGKLQALD  852 (1006)
T ss_pred             eehhhhccccccccCCcCcCcccccchhhhh
Confidence            3466666665555667 99999999998876

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

Probab=88.64  E-value=1.1  Score=27.89  Aligned_cols=41  Identities=24%  Similarity=0.541  Sum_probs=30.9

Q ss_pred             CCCCCcceEEEEecee-eeEEEeeeEeeecceEEeccccceee
Q 038108           23 CPYCGGKVLAIDFESQ-CRFCFLPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus        23 Cp~CGG~v~a~Dves~-~rfCflP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      ||.||++....++++. +.+.-.-+-+ .-..+.|+.||..+.
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 667788999998654

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

>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=88.16  E-value=0.4  Score=27.71  Aligned_cols=30  Identities=20%  Similarity=0.598  Sum_probs=23.0

Q ss_pred             CCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccccee
Q 038108           19 APGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRL   63 (67)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L   63 (67)
                      ..-.||.||.....               ..+.|.|.|+.||...
T Consensus        27 TSq~C~~CG~~~~~---------------~~~~r~~~C~~Cg~~~   56 (69)
T PF07282_consen   27 TSQTCPRCGHRNKK---------------RRSGRVFTCPNCGFEM   56 (69)
T ss_pred             CccCccCccccccc---------------ccccceEEcCCCCCEE
Confidence            35579999987765               4577889999998753

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

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=87.87  E-value=0.35  Score=26.48  Aligned_cols=29  Identities=24%  Similarity=0.732  Sum_probs=18.3

Q ss_pred             CCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccccee
Q 038108           22 SCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRL   63 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L   63 (67)
                      -||.||..+..-+.+.             ..++.|+.||...
T Consensus         2 FCp~Cg~~l~~~~~~~-------------~~~~vC~~Cg~~~   30 (52)
T smart00661        2 FCPKCGNMLIPKEGKE-------------KRRFVCRKCGYEE   30 (52)
T ss_pred             CCCCCCCccccccCCC-------------CCEEECCcCCCeE
Confidence            4899998665443331             2367888888543

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=87.38  E-value=0.47  Score=26.97  Aligned_cols=35  Identities=23%  Similarity=0.603  Sum_probs=19.2

Q ss_pred             CCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccceee
Q 038108           22 SCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      -||.|||......-.  ..      -...+.-+.|+.||....
T Consensus         3 PCPfCGg~~~~~~~~--~~------~~~~~~~~~C~~Cga~~~   37 (53)
T TIGR03655         3 PCPFCGGADVYLRRG--FD------PLDLSHYFECSTCGASGP   37 (53)
T ss_pred             CCCCCCCcceeeEec--cC------CCCCEEEEECCCCCCCcc
Confidence            499999987733210  00      011122236899987653

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.

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

Probab=87.36  E-value=0.6  Score=31.08  Aligned_cols=45  Identities=16%  Similarity=0.270  Sum_probs=31.2

Q ss_pred             CCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccccee
Q 038108           19 APGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRL   63 (67)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L   63 (67)
                      ....||.|+|.++.++-|....----.++..+..=+.|+.||+.+
T Consensus        90 ~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy  134 (147)
T PF01927_consen   90 IFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY  134 (147)
T ss_pred             CCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence            348999999999888766554442223334455678899999864

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

>PF14369 zf-RING_3: zinc-finger

Probab=87.18  E-value=0.52  Score=25.45  Aligned_cols=27  Identities=22%  Similarity=0.423  Sum_probs=15.7

Q ss_pred             EEEcCCceeeeeeecCCCCCCCCCcce
Q 038108            4 VYVCSEEERELGRQQAPGSCPYCGGKV   30 (67)
Q Consensus         4 ~~vcde~~kv~~~~~ApG~Cp~CGG~v   30 (67)
                      +.-|++.=.+.......-+||+|+|+-
T Consensus         5 Ch~C~~~V~~~~~~~~~~~CP~C~~gF   31 (35)
T PF14369_consen    5 CHQCNRFVRIAPSPDSDVACPRCHGGF   31 (35)
T ss_pred             CccCCCEeEeCcCCCCCcCCcCCCCcE
Confidence            344444434433444555799999975

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

Probab=87.08  E-value=0.87  Score=25.02  Aligned_cols=13  Identities=46%  Similarity=1.111  Sum_probs=8.0

Q ss_pred             CCCCCCCCcceEE
Q 038108           20 PGSCPYCGGKVLA   32 (67)
Q Consensus        20 pG~Cp~CGG~v~a   32 (67)
                      +..||+||+.+..
T Consensus        21 ~~~Cp~CG~~~~~   33 (46)
T PRK00398         21 GVRCPYCGYRILF   33 (46)
T ss_pred             ceECCCCCCeEEE
Confidence            4567777666553

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

Probab=86.95  E-value=0.85  Score=26.57  Aligned_cols=38  Identities=26%  Similarity=0.690  Sum_probs=25.5

Q ss_pred             EEcCCceeeeeeecCCCCCC--CCCcceEEEEeceeeeEEEeeeEeeecceEEecccc
Q 038108            5 YVCSEEERELGRQQAPGSCP--YCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS   60 (67)
Q Consensus         5 ~vcde~~kv~~~~~ApG~Cp--~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~   60 (67)
                      +=+|+++||.+.+   -.||  +||.+|-.++-               +.|++|-.||
T Consensus         6 Ykvd~~Gkv~r~r---k~CP~~~CG~GvFMA~H---------------~dR~~CGKCg   45 (47)
T PF01599_consen    6 YKVDENGKVKRLR---KECPSPRCGAGVFMAEH---------------KDRHYCGKCG   45 (47)
T ss_dssp             CEEETTTEEEESS---EE-TSTTTTSSSEEEE----------------SSEEEETTTS
T ss_pred             EEECCCCcEEEhh---hcCCCcccCCceEeeec---------------CCCccCCCcc
Confidence            3468888887644   4699  99999865543               4577777776

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

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=86.67  E-value=0.78  Score=26.45  Aligned_cols=37  Identities=19%  Similarity=0.504  Sum_probs=23.3

Q ss_pred             cCCceeeeeeecCCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccccee
Q 038108            7 CSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRL   63 (67)
Q Consensus         7 cde~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L   63 (67)
                      +|.+ +|....+   -||+||..+.+.                ++.++.|..||...
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 6654443   899999752222                23688899998653

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

Probab=85.96  E-value=0.47  Score=32.49  Aligned_cols=24  Identities=25%  Similarity=0.689  Sum_probs=19.2

Q ss_pred             CCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccce
Q 038108           19 APGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRR   62 (67)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~   62 (67)
                      ..-.||.||.                    .+.|.+.|+.||..
T Consensus       308 tS~~C~~cg~--------------------~~~r~~~C~~cg~~  331 (364)
T COG0675         308 TSKTCPCCGH--------------------LSGRLFKCPRCGFV  331 (364)
T ss_pred             CcccccccCC--------------------ccceeEECCCCCCe
Confidence            3357999999                    45788999999964

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

Probab=85.75  E-value=0.98  Score=24.05  Aligned_cols=20  Identities=30%  Similarity=0.640  Sum_probs=14.1

Q ss_pred             eeeeeeecCCCCCCCCCcce
Q 038108           11 ERELGRQQAPGSCPYCGGKV   30 (67)
Q Consensus        11 ~kv~~~~~ApG~Cp~CGG~v   30 (67)
                      +-+.....+|..||-||.+-
T Consensus         9 G~i~~g~~~p~~CP~Cg~~~   28 (34)
T cd00729           9 GYIHEGEEAPEKCPICGAPK   28 (34)
T ss_pred             CCEeECCcCCCcCcCCCCch
Confidence            33434456899999999864

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.

>PRK10445 endonuclease VIII; Provisional

Probab=85.74  E-value=0.95  Score=32.92  Aligned_cols=29  Identities=28%  Similarity=0.728  Sum_probs=21.4

Q ss_pred             CCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccc
Q 038108           19 APGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS   60 (67)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~   60 (67)
                      +...||+||+.+.-+.+-.             ...|+|+.|-
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            4456999999999887753             5567777663

>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional

Probab=85.35  E-value=0.8  Score=33.45  Aligned_cols=26  Identities=15%  Similarity=0.583  Sum_probs=20.1

Q ss_pred             CCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccc
Q 038108           22 SCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS   60 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~   60 (67)
                      .||+||+.+.-..+..             ...|+|+.|-
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

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=84.91  E-value=0.38  Score=36.58  Aligned_cols=45  Identities=24%  Similarity=0.499  Sum_probs=34.2

Q ss_pred             cCCCCCCCCCcceEEEEe-----ceeeeEEEeeeEeeecc--eEEeccccce
Q 038108           18 QAPGSCPYCGGKVLAIDF-----ESQCRFCFLPICYNIKK--KYFCSLCSRR   62 (67)
Q Consensus        18 ~ApG~Cp~CGG~v~a~Dv-----es~~rfCflP~~~k~kr--~~~Ct~C~r~   62 (67)
                      ...|.||-||+.-++.-+     +...|+..=++|.--|+  |..|+.||..
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     34568888888876664  7899999864

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).

>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional

Probab=84.49  E-value=0.9  Score=33.27  Aligned_cols=27  Identities=22%  Similarity=0.688  Sum_probs=20.5

Q ss_pred             CCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccc
Q 038108           21 GSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS   60 (67)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~   60 (67)
                      ..||+||+.+.-.-+..             ...|+|+.|-
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

>PRK00420 hypothetical protein; Validated

Probab=84.26  E-value=0.87  Score=30.42  Aligned_cols=30  Identities=20%  Similarity=0.465  Sum_probs=22.1

Q ss_pred             CCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccceee
Q 038108           19 APGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      ....||.||.                |++.-...+.+|..||..+.
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

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=82.40  E-value=0.8  Score=35.00  Aligned_cols=43  Identities=21%  Similarity=0.496  Sum_probs=32.2

Q ss_pred             CCCCCCCCCcceEEE--Ee--ceeeeEEEeeeEeeecc--eEEeccccc
Q 038108           19 APGSCPYCGGKVLAI--DF--ESQCRFCFLPICYNIKK--KYFCSLCSR   61 (67)
Q Consensus        19 ApG~Cp~CGG~v~a~--Dv--es~~rfCflP~~~k~kr--~~~Ct~C~r   61 (67)
                      ..|.||-||+.-++.  +.  +...|++.=++|.--|+  |..|+.||.
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  34578888888876664  789999985

>PF12773 DZR: Double zinc ribbon

Probab=82.22  E-value=0.36  Score=26.45  Aligned_cols=14  Identities=21%  Similarity=0.418  Sum_probs=7.9

Q ss_pred             ecceEEecccccee
Q 038108           50 IKKKYFCSLCSRRL   63 (67)
Q Consensus        50 ~kr~~~Ct~C~r~L   63 (67)
                      .....+|+.||+.+
T Consensus        26 ~~~~~~C~~Cg~~~   39 (50)
T PF12773_consen   26 DQSKKICPNCGAEN   39 (50)
T ss_pred             cCCCCCCcCCcCCC
Confidence            34455666666654

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=82.05  E-value=1.6  Score=27.08  Aligned_cols=38  Identities=21%  Similarity=0.357  Sum_probs=26.4

Q ss_pred             CCCCCCcceEEEEeceeeeEEEeeeEeeecceEEec--cccceeeee
Q 038108           22 SCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCS--LCSRRLELY   66 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct--~C~r~L~~~   66 (67)
                      -||.||..+.+.|=+-..     +.  -..+.+.|+  .||.+.+++
T Consensus         3 ~CP~Cg~~a~irtSr~~s-----~~--~~~~Y~qC~N~eCg~tF~t~   42 (72)
T PRK09678          3 HCPLCQHAAHARTSRYIT-----DT--TKERYHQCQNVNCSATFITY   42 (72)
T ss_pred             cCCCCCCccEEEEChhcC-----hh--hheeeeecCCCCCCCEEEEE
Confidence            499999999665543222     22  245677899  999988775

>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg)

Probab=82.00  E-value=1.3  Score=32.25  Aligned_cols=26  Identities=27%  Similarity=0.733  Sum_probs=19.8

Q ss_pred             CCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccc
Q 038108           21 GSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLC   59 (67)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C   59 (67)
                      -.||+||+.+.-.-+..             ...|+|+.|
T Consensus       246 ~pC~~Cg~~I~~~~~~g-------------R~t~~CP~C  271 (272)
T TIGR00577       246 EPCRRCGTPIEKIKVGG-------------RGTHFCPQC  271 (272)
T ss_pred             CCCCCCCCeeEEEEECC-------------CCCEECCCC
Confidence            36999999998877763             566777766

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

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=81.85  E-value=1.6  Score=25.74  Aligned_cols=32  Identities=28%  Similarity=0.581  Sum_probs=21.9

Q ss_pred             CCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccceeee
Q 038108           21 GSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLEL   65 (67)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L~~   65 (67)
                      ..||.||..+..-|....             --+.|..||+.|..
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            479999998766543211             13588999988875

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.

>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=81.67  E-value=1.5  Score=23.83  Aligned_cols=29  Identities=38%  Similarity=0.840  Sum_probs=20.3

Q ss_pred             CCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccceee
Q 038108           22 SCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      .||+||..-...|-+              .-.++|+.||..|.
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              34568899998775

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.

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

Probab=81.56  E-value=1.1  Score=24.26  Aligned_cols=29  Identities=28%  Similarity=0.639  Sum_probs=13.9

Q ss_pred             CCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccc
Q 038108           22 SCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSR   61 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r   61 (67)
                      -||.||++++-.=.+-           -...|+.|+.||.
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           1344567888875

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

Probab=81.00  E-value=1.7  Score=31.63  Aligned_cols=28  Identities=25%  Similarity=0.777  Sum_probs=20.7

Q ss_pred             CCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccc
Q 038108           21 GSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSR   61 (67)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r   61 (67)
                      -.||+||+.+.-..+..             ...|+|+.|-+
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

>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=80.59  E-value=1.1  Score=23.16  Aligned_cols=17  Identities=18%  Similarity=0.192  Sum_probs=9.5

Q ss_pred             CCCCCCCcceEEEEece
Q 038108           21 GSCPYCGGKVLAIDFES   37 (67)
Q Consensus        21 G~Cp~CGG~v~a~Dves   37 (67)
                      .-||+||++...++=+.
T Consensus         4 rfC~~CG~~t~~~~~g~   20 (32)
T PF09297_consen    4 RFCGRCGAPTKPAPGGW   20 (32)
T ss_dssp             SB-TTT--BEEE-SSSS
T ss_pred             cccCcCCccccCCCCcC
Confidence            56999999988766543

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

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=80.52  E-value=1.8  Score=24.44  Aligned_cols=33  Identities=21%  Similarity=0.587  Sum_probs=19.4

Q ss_pred             CCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccc
Q 038108           22 SCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSR   61 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r   61 (67)
                      -||-||.+....+-+..+.---.       -.+.|+.||.
T Consensus         5 PCPFCG~~~~~~~~~~~~~~~~~-------~~V~C~~Cga   37 (61)
T PF14354_consen    5 PCPFCGSADVLIRQDEGFDYGMY-------YYVECTDCGA   37 (61)
T ss_pred             CCCCCCCcceEeecccCCCCCCE-------EEEEcCCCCC
Confidence            39999777766665433210000       3467888987

---

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	67
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	93.5
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	92.05
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	91.3
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	89.18
3ga8_A	78	HTH-type transcriptional regulator MQSA (YGIT/B30;	87.73
3u5c_f	152	40S ribosomal protein S31; translation, ribosome,	85.89
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	82.94
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	82.69
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	81.86
1k3x_A	262	Endonuclease VIII; hydrolase/DNA, hydrolase-DNA co	80.79
2xzf_A	271	Formamidopyrimidine-DNA glycosylase; hydrolase-DNA	80.24

>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=93.50  E-value=0.038  Score=31.66  Aligned_cols=38  Identities=21%  Similarity=0.535  Sum_probs=25.9

Q ss_pred             cCCceeeeeeecCCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccccee
Q 038108            7 CSEEERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRL   63 (67)
Q Consensus         7 cde~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L   63 (67)
                      +|+ +++.+.   --.||.||.++..            .   ++..++.|..|+-..
T Consensus         9 v~~-gki~~~---~~fCPkCG~~~~m------------a---~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A            9 IAD-GKLVRK---HRFCPRCGPGVFL------------A---EHADRYSCGRCGYTE   46 (55)
T ss_dssp             CCC-CCCCCS---SCCCTTTTTTCCC------------E---ECSSEEECTTTCCCE
T ss_pred             EcC-CEEEEc---cccCcCCCCceeE------------e---ccCCEEECCCCCCEE
Confidence            455 666542   4679999987722            1   445699999998653

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

Probab=92.05  E-value=0.12  Score=29.05  Aligned_cols=35  Identities=23%  Similarity=0.620  Sum_probs=23.9

Q ss_pred             ceeeeeeecCCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccce
Q 038108           10 EERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRR   62 (67)
Q Consensus        10 ~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~   62 (67)
                      ++||.+.   .--||.||.++..++               +..++.|..||-.
T Consensus        12 ~~kv~~~---~k~CP~CG~~~fm~~---------------~~~R~~C~kCG~t   46 (50)
T 3j20_Y           12 DGKVIRK---NKFCPRCGPGVFMAD---------------HGDRWACGKCGYT   46 (50)
T ss_dssp             SSCEECS---SEECSSSCSSCEEEE---------------CSSEEECSSSCCE
T ss_pred             CCEEEEe---cccCCCCCCceEEec---------------CCCeEECCCCCCE
Confidence            4566554   345999998875443               2467899999854

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

Probab=91.30  E-value=0.083  Score=38.70  Aligned_cols=45  Identities=22%  Similarity=0.455  Sum_probs=33.9

Q ss_pred             cCCCCCCCCCcceEEEEec-----eeeeEEEeeeEeeecc--eEEeccccce
Q 038108           18 QAPGSCPYCGGKVLAIDFE-----SQCRFCFLPICYNIKK--KYFCSLCSRR   62 (67)
Q Consensus        18 ~ApG~Cp~CGG~v~a~Dve-----s~~rfCflP~~~k~kr--~~~Ct~C~r~   62 (67)
                      ...|.||-||+.-++.-+.     ...|++.=.+|--.|+  +..|+.||..
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     5667877777755553  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=89.18  E-value=0.86  Score=27.61  Aligned_cols=43  Identities=14%  Similarity=0.339  Sum_probs=26.7

Q ss_pred             CCCCCCcceEEEEece-eeeEEEeeeEeeecceEEeccccceee
Q 038108           22 SCPYCGGKVLAIDFES-QCRFCFLPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves-~~rfCflP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      .||.||+.....+.++ ...+--.-+-.+.=..++|..||..+-
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 223333344444446789999998654

>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=87.73  E-value=1.2  Score=25.88  Aligned_cols=41  Identities=17%  Similarity=0.292  Sum_probs=24.4

Q ss_pred             CCCCCCcc-e--EEEEeceeeeEEEeeeEeeecceEEeccccceee
Q 038108           22 SCPYCGGK-V--LAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus        22 ~Cp~CGG~-v--~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      .||-||++ +  ...|+.-.+.=.-+  -.+.=...+|+.||..+-
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            59999986 3  22333333332322  224556889999998764

>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=85.89  E-value=0.62  Score=30.63  Aligned_cols=41  Identities=20%  Similarity=0.518  Sum_probs=29.3

Q ss_pred             EcCCceeeeeeecCCCCCCC--CCcceEEEEeceeeeEEEeeeEeeecceEEeccccceee
Q 038108            6 VCSEEERELGRQQAPGSCPY--CGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus         6 vcde~~kv~~~~~ApG~Cp~--CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      =+|+++||.+.+   -.||+  ||.+|-.++-               +.|++|-.|+-.+.
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            367888887654   35999  9988766544               35788888886653

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

Probab=82.94  E-value=0.82  Score=27.00  Aligned_cols=29  Identities=14%  Similarity=0.190  Sum_probs=21.0

Q ss_pred             CCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccceee
Q 038108           21 GSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      -+||.|+|++...+.               +....|+.|++.+-
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               35667888887654

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

Probab=82.69  E-value=0.98  Score=26.79  Aligned_cols=29  Identities=17%  Similarity=0.385  Sum_probs=20.8

Q ss_pred             CCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccceee
Q 038108           21 GSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      -+||.|+|++...+.               .....|+.|++.+-
T Consensus         9 L~CP~ck~~L~~~~~---------------~~~LiC~~cg~~YP   37 (70)
T 2js4_A            9 LVCPVCKGRLEFQRA---------------QAELVCNADRLAFP   37 (70)
T ss_dssp             CBCTTTCCBEEEETT---------------TTEEEETTTTEEEE
T ss_pred             eECCCCCCcCEEeCC---------------CCEEEcCCCCceec
Confidence            379999998875432               35667888887654

>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=81.86  E-value=0.99  Score=26.63  Aligned_cols=28  Identities=21%  Similarity=0.454  Sum_probs=20.6

Q ss_pred             CCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccceee
Q 038108           22 SCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRLE   64 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L~   64 (67)
                      +||.|+|++...+.               +....|+.|++.+-
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               45667888887654

>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=80.79  E-value=1  Score=31.59  Aligned_cols=26  Identities=23%  Similarity=0.706  Sum_probs=19.4

Q ss_pred             CCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccc
Q 038108           22 SCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS   60 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~   60 (67)
                      .||+||+++.-..+-             ....|+|+.|-
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             34556777763

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

Probab=80.24  E-value=1.2  Score=31.41  Aligned_cols=27  Identities=26%  Similarity=0.797  Sum_probs=20.8

Q ss_pred             CCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccc
Q 038108           22 SCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSR   61 (67)
Q Consensus        22 ~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r   61 (67)
                      .||+||+.+.-..+-             ....|+|+.|-+
T Consensus       244 pC~~CG~~I~~~~~~-------------gR~t~~CP~CQ~  270 (271)
T 2xzf_A          244 KCSRCGAEIQKIKVA-------------GRGTHFCPVCQQ  270 (271)
T ss_dssp             BCTTTCCBCEEEEET-------------TEEEEECTTTSC
T ss_pred             CCCCCCCEeeEEEEC-------------CCceEECCCCCC
Confidence            499999999887775             355677887754

---

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	67
d1k3xa3	40	Endonuclease VIII {Escherichia coli [TaxId: 562]}	91.06
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	91.01
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	89.65
d1k82a3	44	DNA repair protein MutM (Fpg) {Escherichia coli [T	87.68
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	85.84
d1tdza3	47	DNA repair protein MutM (Fpg) {Lactococcus lactis	85.24
d1r2za3	46	DNA repair protein MutM (Fpg) {Bacillus stearother	83.48
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	80.23

>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=91.06  E-value=0.09  Score=27.19  Aligned_cols=27  Identities=26%  Similarity=0.698  Sum_probs=20.4

Q ss_pred             CCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccc
Q 038108           20 PGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLC   59 (67)
Q Consensus        20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C   59 (67)
                      .-.|++||+.|.-+.+..             .+.|+|+.|
T Consensus        12 g~pC~~C~~~I~~~~~~g-------------R~t~~Cp~C   38 (40)
T d1k3xa3          12 GEPCERCGSIIEKTTLSS-------------RPFYWCPGC   38 (40)
T ss_dssp             TSBCTTTCCBCEEEEETT-------------EEEEECTTT
T ss_pred             CCccCcCCCEEEEEEECC-------------CCCEEChhh
Confidence            345999999999998864             355667666

>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=91.01  E-value=0.046  Score=38.08  Aligned_cols=45  Identities=22%  Similarity=0.438  Sum_probs=34.2

Q ss_pred             cCCCCCCCCCcceEEEEec-----eeeeEEEeeeEeeec--ceEEeccccce
Q 038108           18 QAPGSCPYCGGKVLAIDFE-----SQCRFCFLPICYNIK--KKYFCSLCSRR   62 (67)
Q Consensus        18 ~ApG~Cp~CGG~v~a~Dve-----s~~rfCflP~~~k~k--r~~~Ct~C~r~   62 (67)
                      ...|.||-||+.-++.-++     ...|++.=.+|.--|  .|..|+.||..
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     345888778876666  36688888754

>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=89.65  E-value=0.021  Score=28.57  Aligned_cols=13  Identities=38%  Similarity=0.928  Sum_probs=11.1

Q ss_pred             CCCCCCcceEEEE
Q 038108           22 SCPYCGGKVLAID   34 (67)
Q Consensus        22 ~Cp~CGG~v~a~D   34 (67)
                      .|||||+.|-|++
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=87.68  E-value=0.24  Score=25.73  Aligned_cols=27  Identities=22%  Similarity=0.824  Sum_probs=20.1

Q ss_pred             CCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccc
Q 038108           21 GSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS   60 (67)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~   60 (67)
                      -.||+||+.|..+.+..             .+.|+|+.|-
T Consensus        17 ~~C~~C~~~I~~~~~~~-------------R~t~~Cp~CQ   43 (44)
T d1k82a3          17 EPCRVCGTPIVATKHAQ-------------RATFYCRQCQ   43 (44)
T ss_dssp             SBCTTTCCBCEEEEETT-------------EEEEECTTTC
T ss_pred             CCcCCCCCEEEEEEECC-------------cccEEChhhc
Confidence            36999999999887764             3456777664

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

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

Probab=85.84  E-value=0.17  Score=28.35  Aligned_cols=34  Identities=24%  Similarity=0.656  Sum_probs=23.9

Q ss_pred             ceeeeeeecCCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccc
Q 038108           10 EERELGRQQAPGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSR   61 (67)
Q Consensus        10 ~~kv~~~~~ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r   61 (67)
                      ++|+.+.+   -.||+||-+|-.++               ++.|++|-.||-
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               567788888874

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

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

Probab=85.24  E-value=0.38  Score=25.22  Aligned_cols=29  Identities=24%  Similarity=0.771  Sum_probs=21.2

Q ss_pred             CCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEeccccc
Q 038108           20 PGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSR   61 (67)
Q Consensus        20 pG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r   61 (67)
                      .-.||+||..|.-+.+..             ...|+|+.|-+
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             34567777754

>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=83.48  E-value=0.65  Score=24.08  Aligned_cols=29  Identities=17%  Similarity=0.545  Sum_probs=20.9

Q ss_pred             CCCCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccc
Q 038108           19 APGSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCS   60 (67)
Q Consensus        19 ApG~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~   60 (67)
                      +.-.||+||..|.-+.+..             .+.|+|+.|-
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             4566777764

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

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

Probab=80.23  E-value=0.52  Score=24.99  Aligned_cols=29  Identities=28%  Similarity=0.543  Sum_probs=21.4

Q ss_pred             CCCCCCCcceEEEEeceeeeEEEeeeEeeecceEEecccccee
Q 038108           21 GSCPYCGGKVLAIDFESQCRFCFLPICYNIKKKYFCSLCSRRL   63 (67)
Q Consensus        21 G~Cp~CGG~v~a~Dves~~rfCflP~~~k~kr~~~Ct~C~r~L   63 (67)
                      ..||+||+.--..|.++--              ++|+.||..+
T Consensus         6 ~~Cp~Cgs~~iv~D~~~Ge--------------~vC~~CG~Vi   34 (50)
T d1pfta_           6 KVCPACESAELIYDPERGE--------------IVCAKCGYVI   34 (50)
T ss_dssp             CSCTTTSCCCEEEETTTTE--------------EEESSSCCBC
T ss_pred             ccCcCCCCCcEEEECCCCe--------------EecccCCcEe
Confidence            3699999987778866544              5667888665