Citrus Sinensis ID: 034528

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90--
Protein Sequence
MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVNNLEDDGAYEKA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccEEEEEEccccEEEEEcccccccEEEcccccccHHHHHHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccEEcccccccccEEEEEEEccccEEEEEEEEcccEEEEcccccccccHHHHHHHHHHHHHHHHcHccccccc
Coil and Loop (DISEMBL)
mgkrksrakpppkkrvdkldtvfscpfcnhgtsveCRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERvnnleddgayeka
Flexible Loop (DISEMBL)
mgkrksrakpppkkrvdkldtvfscpfcnhgtsVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVnnleddgayeka
Low Complexity Region (SEG)
MGkrksrakpppkkrVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVNNLEDDGAYEKA
Disordered region (IsUnstruct)
*****************KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVN***********
Disordered Region (DISOPRED)
**********************FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDEC***************
Disordered Region (DISEMBL)
***************VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVNNLEDDGAYEKA
Disordered Region (DISPRO)
***************VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVNNLE********
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVNNLEDDGAYEKA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	92	2.2.26 [Sep-21-2011]
Q8LHP0	89	Transcription elongation	yes	no	0.934	0.966	0.895	5e-41
Q8LEF3	120	Transcription elongation	yes	no	0.891	0.683	0.841	5e-36
P36053	145	Transcription elongation	yes	no	0.891	0.565	0.524	1e-20
O13868	107	Transcription elongation	yes	no	0.967	0.831	0.479	3e-20
Q9XVZ8	84	Transcription elongation	yes	no	0.891	0.976	0.518	1e-18
Q8MQI6	82	Transcription elongation	yes	no	0.880	0.987	0.475	3e-18
Q9U501	82	Transcription elongation	N/A	no	0.880	0.987	0.475	3e-18
Q54KR5	80	Transcription elongation	yes	no	0.858	0.987	0.512	6e-16
P60003	83	Transcription elongation	no	no	0.695	0.771	0.484	1e-12
P60002	83	Transcription elongation	yes	no	0.695	0.771	0.484	1e-12

>sp|Q8LHP0|ELOF1_ORYSJ Transcription elongation factor 1 homolog OS=Oryza sativa subsp. japonica GN=Os07g0631100 PE=3 SV=1

 Score =  166 bits (419), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 77/86 (89%), Positives = 82/86 (95%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKS AKPPPKKR+DKLDTVFSCPFCNHG+SVECRIDMKNLIGEA C ICQE+FSTT+
Sbjct: 1  MGKRKSAAKPPPKKRMDKLDTVFSCPFCNHGSSVECRIDMKNLIGEASCRICQENFSTTV 60

Query: 61 TALTEPIDIYSEWIDECERVNNLEDD 86
           ALTEPIDIYSEWIDECERVNN+EDD
Sbjct: 61 NALTEPIDIYSEWIDECERVNNVEDD 86

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8LEF3|ELOF1_ARATH Transcription elongation factor 1 homolog OS=Arabidopsis thaliana GN=At5g46030 PE=2 SV=1

 Score =  149 bits (376), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 69/82 (84%), Positives = 75/82 (91%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKSRAKP P KR+DKLDT+FSCPFCNHG+SVEC IDMK+LIG+A C IC+ESFSTTI
Sbjct: 1  MGKRKSRAKPAPTKRMDKLDTIFSCPFCNHGSSVECIIDMKHLIGKAACRICEESFSTTI 60

Query: 61 TALTEPIDIYSEWIDECERVNN 82
          TALTE IDIYSEWIDECERVN 
Sbjct: 61 TALTEAIDIYSEWIDECERVNT 82

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Arabidopsis thaliana (taxid: 3702)

>sp|P36053|ELF1_YEAST Transcription elongation factor 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ELF1 PE=1 SV=1

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 43/82 (52%), Positives = 55/82 (67%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRK   + P K+ V KLDT F+C FCNH  SV C +D KN IG   C IC +SF T I
Sbjct: 1  MGKRKKSTRKPTKRLVQKLDTKFNCLFCNHEKSVSCTLDKKNSIGTLSCKICGQSFQTRI 60

Query: 61 TALTEPIDIYSEWIDECERVNN 82
           +L++P+D+YS+W D  E VN+
Sbjct: 61 NSLSQPVDVYSDWFDAVEEVNS 82

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|O13868|ELOF1_SCHPO Transcription elongation factor 1 homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC1B3.02c PE=1 SV=1

 Score = 97.1 bits (240), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 46/96 (47%), Positives = 61/96 (63%), Gaps = 7/96 (7%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRK++AK  PK+R   LDT F+C FCNH  SV C +D ++ +G   C IC +S    I
Sbjct: 1  MGKRKAKAKVKPKRRAPPLDTTFTCLFCNHEKSVSCSLDKQSGVGNLHCKICGQSHQCLI 60

Query: 61 TALTEPIDIYSEWIDECE-------RVNNLEDDGAY 89
          TAL+ PID+YS+WID C+        V+N+ D  AY
Sbjct: 61 TALSAPIDVYSDWIDACDAVANQAKEVDNINDQEAY 96

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q9XVZ8|ELOF1_CAEEL Transcription elongation factor 1 homolog OS=Caenorhabditis elegans GN=Y54G11A.11 PE=3 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 43/83 (51%), Positives = 55/83 (66%), Gaps = 1/83 (1%)

Query: 1  MGKRKSRAKPPPK-KRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59
          MGKRKS+ K P K K V  LDT F+CPFCNH    E ++D +  +G   C +C E F T 
Sbjct: 1  MGKRKSKRKAPTKAKAVMPLDTQFNCPFCNHERVCEVKMDREKNVGYISCRVCSEDFQTN 60

Query: 60 ITALTEPIDIYSEWIDECERVNN 82
          I  L+EPID+YS+W+D CE+ NN
Sbjct: 61 INYLSEPIDVYSDWVDACEQANN 83

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Caenorhabditis elegans (taxid: 6239)

>sp|Q8MQI6|ELOF1_DROME Transcription elongation factor 1 homolog OS=Drosophila melanogaster GN=CG40228 PE=1 SV=1

 Score = 90.5 bits (223), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 39/82 (47%), Positives = 55/82 (67%), Gaps = 1/82 (1%)

Query: 1  MGKRKSRAKPPPKKR-VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59
          MG+RKS+ KPPPK++ ++ LD  F+CPFCNH  S E ++D      +  C +C E F T 
Sbjct: 1  MGRRKSKRKPPPKRKNIEPLDQQFNCPFCNHEKSCEVKMDKSRNTAKITCRVCLEDFQTG 60

Query: 60 ITALTEPIDIYSEWIDECERVN 81
          I  L+EPID+Y++W+D CE  N
Sbjct: 61 INFLSEPIDVYNDWVDACETAN 82

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Drosophila melanogaster (taxid: 7227)

>sp|Q9U501|ELOF1_MANSE Transcription elongation factor 1 homolog OS=Manduca sexta PE=3 SV=1

 Score = 90.1 bits (222), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 39/82 (47%), Positives = 54/82 (65%), Gaps = 1/82 (1%)

Query: 1  MGKRKSRAKPPPKKR-VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59
          MG+RKS+ KPPPK++ ++ LD  F+CPFCNH  S E ++D         C +C E F TT
Sbjct: 1  MGRRKSKRKPPPKRKAIEPLDQQFNCPFCNHEKSCEVKMDRAKNTAMIQCTVCLEDFHTT 60

Query: 60 ITALTEPIDIYSEWIDECERVN 81
             L+EPID+Y++W+D CE  N
Sbjct: 61 TNVLSEPIDVYNDWVDACESAN 82

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Manduca sexta (taxid: 7130)

>sp|Q54KR5|ELOF1_DICDI Transcription elongation factor 1 homolog OS=Dictyostelium discoideum GN=elof1 PE=3 SV=1

 Score = 82.8 bits (203), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 41/80 (51%), Positives = 52/80 (65%), Gaps = 1/80 (1%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKS +KPPPKK V KL   F C FC H  SV+C +D +   G A C +C  S+ T I
Sbjct: 1  MGKRKS-SKPPPKKVVQKLPKHFDCLFCAHSQSVDCILDRELGKGVAKCRVCNASYETPI 59

Query: 61 TALTEPIDIYSEWIDECERV 80
            L++ ID+YS+WID CE +
Sbjct: 60 HELSDAIDVYSDWIDACESI 79

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Dictyostelium discoideum (taxid: 44689)

>sp|P60003|ELOF1_MOUSE Transcription elongation factor 1 homolog OS=Mus musculus GN=Elof1 PE=1 SV=1

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/64 (48%), Positives = 41/64 (64%)

Query: 19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
          L+T F+CPFCNH  S + ++D     G   C +C E F T IT L+EP+D+YS+WID CE
Sbjct: 20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACE 79

Query: 79 RVNN 82
            N 
Sbjct: 80 AANQ 83

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Mus musculus (taxid: 10090)

>sp|P60002|ELOF1_HUMAN Transcription elongation factor 1 homolog OS=Homo sapiens GN=ELOF1 PE=2 SV=1

 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 31/64 (48%), Positives = 41/64 (64%)

Query: 19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
          L+T F+CPFCNH  S + ++D     G   C +C E F T IT L+EP+D+YS+WID CE
Sbjct: 20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACE 79

Query: 79 RVNN 82
            N 
Sbjct: 80 AANQ 83

Transcription elongation factor implicated in the maintenance of proper chromatin structure in actively transcribed regions.

Homo sapiens (taxid: 9606)

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	92
255563004	88	Transcription elongation factor, putativ	0.956	1.0	0.931	7e-43
297740448	128	unnamed protein product [Vitis vinifera]	0.978	0.703	0.922	7e-43
225443562	95	PREDICTED: transcription elongation fact	0.978	0.947	0.922	1e-42
224114575	157	predicted protein [Populus trichocarpa]	0.956	0.560	0.931	2e-42
224061282	88	predicted protein [Populus trichocarpa]	0.956	1.0	0.931	3e-42
118481651	88	unknown [Populus trichocarpa] gi|1184897	0.956	1.0	0.931	5e-42
449457009	88	PREDICTED: transcription elongation fact	0.956	1.0	0.931	1e-41
386278576	88	transcription elongation factor 1 [Verni	0.956	1.0	0.897	8e-41
225461576	92	PREDICTED: transcription elongation fact	0.956	0.956	0.863	5e-40
115473523	89	Os07g0631100 [Oryza sativa Japonica Grou	0.934	0.966	0.895	2e-39

>gi|255563004|ref|XP_002522506.1| Transcription elongation factor, putative [Ricinus communis] gi|223538197|gb|EEF39806.1| Transcription elongation factor, putative [Ricinus communis]

 Score =  177 bits (449), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 82/88 (93%), Positives = 87/88 (98%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKSRAKPPPKKR+DKLDTVFSCPFCNHGTSVECRIDMKNLIGEA+C ICQESFSTTI
Sbjct: 1  MGKRKSRAKPPPKKRMDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAVCAICQESFSTTI 60

Query: 61 TALTEPIDIYSEWIDECERVNNLEDDGA 88
          TALTEPID+YSEWIDECERVNN++DDGA
Sbjct: 61 TALTEPIDVYSEWIDECERVNNVDDDGA 88

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297740448|emb|CBI30630.3| unnamed protein product [Vitis vinifera]

 Score =  177 bits (449), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 83/90 (92%), Positives = 85/90 (94%)

Query: 1   MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
           MGKRKSRAKPPPKKR+DKLDTVFSCPFCNHGT VECRIDMKNLIGEA C ICQESFSTT+
Sbjct: 34  MGKRKSRAKPPPKKRMDKLDTVFSCPFCNHGTGVECRIDMKNLIGEASCRICQESFSTTV 93

Query: 61  TALTEPIDIYSEWIDECERVNNLEDDGAYE 90
           TALTEPIDIYSEWIDECERVNNLEDDG  E
Sbjct: 94  TALTEPIDIYSEWIDECERVNNLEDDGHLE 123

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443562|ref|XP_002277951.1| PREDICTED: transcription elongation factor 1 homolog isoform 1 [Vitis vinifera]

 Score =  176 bits (447), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 83/90 (92%), Positives = 85/90 (94%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKSRAKPPPKKR+DKLDTVFSCPFCNHGT VECRIDMKNLIGEA C ICQESFSTT+
Sbjct: 1  MGKRKSRAKPPPKKRMDKLDTVFSCPFCNHGTGVECRIDMKNLIGEASCRICQESFSTTV 60

Query: 61 TALTEPIDIYSEWIDECERVNNLEDDGAYE 90
          TALTEPIDIYSEWIDECERVNNLEDDG  E
Sbjct: 61 TALTEPIDIYSEWIDECERVNNLEDDGHLE 90

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114575|ref|XP_002316799.1| predicted protein [Populus trichocarpa] gi|222859864|gb|EEE97411.1| predicted protein [Populus trichocarpa]

 Score =  176 bits (446), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 82/88 (93%), Positives = 85/88 (96%)

Query: 1   MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
           MGKRKS AKPPPKKR+DKLDTVFSCPFCNHGTSVECRIDMKNLIGEA+C ICQESFS TI
Sbjct: 70  MGKRKSTAKPPPKKRMDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAVCGICQESFSMTI 129

Query: 61  TALTEPIDIYSEWIDECERVNNLEDDGA 88
           TALTEPIDIYSEWIDECERVN+LEDDGA
Sbjct: 130 TALTEPIDIYSEWIDECERVNSLEDDGA 157

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224061282|ref|XP_002300406.1| predicted protein [Populus trichocarpa] gi|222847664|gb|EEE85211.1| predicted protein [Populus trichocarpa]

 Score =  175 bits (444), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 82/88 (93%), Positives = 86/88 (97%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKSRAKPPPKKR+DKLDTVFSCPFCNHGTSVECRIDMKNLIGEA+C ICQE+FS TI
Sbjct: 1  MGKRKSRAKPPPKKRMDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAVCGICQENFSMTI 60

Query: 61 TALTEPIDIYSEWIDECERVNNLEDDGA 88
          TALTEPIDIYSEWIDECERVN+LEDDGA
Sbjct: 61 TALTEPIDIYSEWIDECERVNSLEDDGA 88

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118481651|gb|ABK92767.1| unknown [Populus trichocarpa] gi|118489754|gb|ABK96677.1| unknown [Populus trichocarpa x Populus deltoides]

 Score =  174 bits (442), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 82/88 (93%), Positives = 85/88 (96%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKS AKPPPKKR+DKLDTVFSCPFCNHGTSVECRIDMKNLIGEA+C ICQESFS TI
Sbjct: 1  MGKRKSTAKPPPKKRMDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAVCGICQESFSMTI 60

Query: 61 TALTEPIDIYSEWIDECERVNNLEDDGA 88
          TALTEPIDIYSEWIDECERVN+LEDDGA
Sbjct: 61 TALTEPIDIYSEWIDECERVNSLEDDGA 88

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449457009|ref|XP_004146241.1| PREDICTED: transcription elongation factor 1 homolog [Cucumis sativus]

 Score =  173 bits (439), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 82/88 (93%), Positives = 84/88 (95%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKSRAKPPPKKR+DKLDTVFSCPFCNHGTSVECRIDMKNLIGEA C ICQESFSTTI
Sbjct: 1  MGKRKSRAKPPPKKRMDKLDTVFSCPFCNHGTSVECRIDMKNLIGEASCRICQESFSTTI 60

Query: 61 TALTEPIDIYSEWIDECERVNNLEDDGA 88
          TAL+E IDIYSEWIDECERVNNLEDD A
Sbjct: 61 TALSEAIDIYSEWIDECERVNNLEDDAA 88

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|386278576|gb|AFJ04520.1| transcription elongation factor 1 [Vernicia fordii]

 Score =  170 bits (431), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 79/88 (89%), Positives = 84/88 (95%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKSRAKPPPKKR D+LDTVFSCPFCNHGTSVECRIDMKNLIGEA C ICQESFSTTI
Sbjct: 1  MGKRKSRAKPPPKKRTDRLDTVFSCPFCNHGTSVECRIDMKNLIGEAECAICQESFSTTI 60

Query: 61 TALTEPIDIYSEWIDECERVNNLEDDGA 88
          TAL+EPID+YSEWIDECERVNN++DDG 
Sbjct: 61 TALSEPIDVYSEWIDECERVNNVDDDGV 88

Source: Vernicia fordii

Species: Vernicia fordii

Genus: Vernicia

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461576|ref|XP_002285261.1| PREDICTED: transcription elongation factor 1 homolog isoform 1 [Vitis vinifera] gi|225461578|ref|XP_002285263.1| PREDICTED: transcription elongation factor 1 homolog isoform 2 [Vitis vinifera] gi|302142940|emb|CBI20235.3| unnamed protein product [Vitis vinifera]

 Score =  168 bits (425), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 76/88 (86%), Positives = 83/88 (94%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKSRAKPPPKKR+DKLDTVFSCPFCNHGTSVECRIDMKNLIGEA+C ICQESFS T+
Sbjct: 1  MGKRKSRAKPPPKKRMDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAVCRICQESFSMTV 60

Query: 61 TALTEPIDIYSEWIDECERVNNLEDDGA 88
           AL+EPID+YSEWIDECERVN L++D A
Sbjct: 61 NALSEPIDVYSEWIDECERVNTLDEDAA 88

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115473523|ref|NP_001060360.1| Os07g0631100 [Oryza sativa Japonica Group] gi|25453308|sp|Q8LHP0.1|ELOF1_ORYSJ RecName: Full=Transcription elongation factor 1 homolog gi|22296365|dbj|BAC10134.1| unknown protein [Oryza sativa Japonica Group] gi|113611896|dbj|BAF22274.1| Os07g0631100 [Oryza sativa Japonica Group] gi|125538787|gb|EAY85182.1| hypothetical protein OsI_06540 [Oryza sativa Indica Group] gi|125601184|gb|EAZ40760.1| hypothetical protein OsJ_25233 [Oryza sativa Japonica Group]

 Score =  166 bits (419), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 77/86 (89%), Positives = 82/86 (95%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MGKRKS AKPPPKKR+DKLDTVFSCPFCNHG+SVECRIDMKNLIGEA C ICQE+FSTT+
Sbjct: 1  MGKRKSAAKPPPKKRMDKLDTVFSCPFCNHGSSVECRIDMKNLIGEASCRICQENFSTTV 60

Query: 61 TALTEPIDIYSEWIDECERVNNLEDD 86
           ALTEPIDIYSEWIDECERVNN+EDD
Sbjct: 61 NALTEPIDIYSEWIDECERVNNVEDD 86

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	92
TAIR|locus:2161418	120	AT5G46030 "AT5G46030" [Arabido	0.826	0.633	0.789	4.9e-30
CGD|CAL0003980	128	orf19.6623 [Candida albicans (	0.652	0.468	0.616	1.6e-17
SGD|S000001643	145	ELF1 "Transcription elongation	0.728	0.462	0.537	4.1e-17
WB|WBGene00013219	84	Y54G11A.11.2 [Caenorhabditis e	0.695	0.761	0.5	3.7e-16
UNIPROTKB|Q9XVZ8	84	Y54G11A.11 "Transcription elon	0.695	0.761	0.5	3.7e-16
POMBASE|SPAC1B3.02c	107	SPAC1B3.02c "transcription elo	0.695	0.598	0.515	4.2e-15
UNIPROTKB|A4IFR3	83	ELOF1 "Transcription elongatio	0.684	0.759	0.492	8.8e-15
UNIPROTKB|P60002	83	ELOF1 "Transcription elongatio	0.684	0.759	0.492	8.8e-15
MGI|MGI:1913376	83	Elof1 "elongation factor 1 hom	0.684	0.759	0.492	8.8e-15
ZFIN|ZDB-GENE-040426-1385	83	elof1 "elongation factor 1 hom	0.684	0.759	0.492	8.8e-15

TAIR|locus:2161418 AT5G46030 "AT5G46030" [Arabidopsis thaliana (taxid:3702)]

 Score = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 60/76 (78%), Positives = 67/76 (88%)

Query:    16 VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWID 75
             +DKLDT+FSCPFCNHG+SVEC IDMK+LIG+A C IC+ESFSTTITALTE IDIYSEWID
Sbjct:    16 MDKLDTIFSCPFCNHGSSVECIIDMKHLIGKAACRICEESFSTTITALTEAIDIYSEWID 75

Query:    76 ECERVNNLEDDGAYEK 91
             ECERVN  EDD   E+
Sbjct:    76 ECERVNTAEDDVVQEE 91

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

CGD|CAL0003980 orf19.6623 [Candida albicans (taxid:5476)]

 Score = 214 (80.4 bits), Expect = 1.6e-17, P = 1.6e-17
 Identities = 37/60 (61%), Positives = 45/60 (75%)

Query:    19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
             LDT F+C FCNH  SV C ID KNL+GE  C IC +SF T I +L++P+DIYS+WID CE
Sbjct:    19 LDTTFTCLFCNHEKSVICTIDKKNLLGELHCKICGQSFQTAIHSLSQPVDIYSDWIDACE 78

GO:0008023 "transcription elongation factor complex" evidence=IEA

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0034401 "regulation of transcription by chromatin organization" evidence=IEA

GO:0000993 "RNA polymerase II core binding" evidence=IEA

SGD|S000001643 ELF1 "Transcription elongation factor with a conserved zinc finger domain" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 210 (79.0 bits), Expect = 4.1e-17, P = 4.1e-17
 Identities = 36/67 (53%), Positives = 46/67 (68%)

Query:    16 VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWID 75
             V KLDT F+C FCNH  SV C +D KN IG   C IC +SF T I +L++P+D+YS+W D
Sbjct:    16 VQKLDTKFNCLFCNHEKSVSCTLDKKNSIGTLSCKICGQSFQTRINSLSQPVDVYSDWFD 75

Query:    76 ECERVNN 82
               E VN+
Sbjct:    76 AVEEVNS 82

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0034401 "regulation of transcription by chromatin organization" evidence=IGI;IMP

GO:0008023 "transcription elongation factor complex" evidence=IDA

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=IGI;IMP

GO:0000993 "RNA polymerase II core binding" evidence=IDA

WB|WBGene00013219 Y54G11A.11.2 [Caenorhabditis elegans (taxid:6239)]

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 32/64 (50%), Positives = 43/64 (67%)

Query:    19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
             LDT F+CPFCNH    E ++D +  +G   C +C E F T I  L+EPID+YS+W+D CE
Sbjct:    20 LDTQFNCPFCNHERVCEVKMDREKNVGYISCRVCSEDFQTNINYLSEPIDVYSDWVDACE 79

Query:    79 RVNN 82
             + NN
Sbjct:    80 QANN 83

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q9XVZ8 Y54G11A.11 "Transcription elongation factor 1 homolog" [Caenorhabditis elegans (taxid:6239)]

 Score = 201 (75.8 bits), Expect = 3.7e-16, P = 3.7e-16
 Identities = 32/64 (50%), Positives = 43/64 (67%)

Query:    19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
             LDT F+CPFCNH    E ++D +  +G   C +C E F T I  L+EPID+YS+W+D CE
Sbjct:    20 LDTQFNCPFCNHERVCEVKMDREKNVGYISCRVCSEDFQTNINYLSEPIDVYSDWVDACE 79

Query:    79 RVNN 82
             + NN
Sbjct:    80 QANN 83

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

POMBASE|SPAC1B3.02c SPAC1B3.02c "transcription elongation factor, Elf1 family (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 191 (72.3 bits), Expect = 4.2e-15, P = 4.2e-15
 Identities = 33/64 (51%), Positives = 43/64 (67%)

Query:    19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
             LDT F+C FCNH  SV C +D ++ +G   C IC +S    ITAL+ PID+YS+WID C+
Sbjct:    19 LDTTFTCLFCNHEKSVSCSLDKQSGVGNLHCKICGQSHQCLITALSAPIDVYSDWIDACD 78

Query:    79 RVNN 82
              V N
Sbjct:    79 AVAN 82

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0006325 "chromatin organization" evidence=ISO

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=ISO

GO:0008270 "zinc ion binding" evidence=ISM

UNIPROTKB|A4IFR3 ELOF1 "Transcription elongation factor 1 homolog" [Bos taurus (taxid:9913)]

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 31/63 (49%), Positives = 41/63 (65%)

Query:    19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
             L+T F+CPFCNH  S + ++D     G   C +C E F T IT L+EP+D+YS+WID CE
Sbjct:    20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACE 79

Query:    79 RVN 81
               N
Sbjct:    80 AAN 82

GO:0005634 "nucleus" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|P60002 ELOF1 "Transcription elongation factor 1 homolog" [Homo sapiens (taxid:9606)]

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 31/63 (49%), Positives = 41/63 (65%)

Query:    19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
             L+T F+CPFCNH  S + ++D     G   C +C E F T IT L+EP+D+YS+WID CE
Sbjct:    20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACE 79

Query:    79 RVN 81
               N
Sbjct:    80 AAN 82

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:1913376 Elof1 "elongation factor 1 homolog (ELF1, S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 31/63 (49%), Positives = 41/63 (65%)

Query:    19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
             L+T F+CPFCNH  S + ++D     G   C +C E F T IT L+EP+D+YS+WID CE
Sbjct:    20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACE 79

Query:    79 RVN 81
               N
Sbjct:    80 AAN 82

GO:0003674 "molecular_function" evidence=ND

GO:0003746 "translation elongation factor activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006414 "translational elongation" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1385 elof1 "elongation factor 1 homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 188 (71.2 bits), Expect = 8.8e-15, P = 8.8e-15
 Identities = 31/63 (49%), Positives = 41/63 (65%)

Query:    19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
             LDT F+CPFCNH  S + +++     G   C +C E F T IT L+EP+D+YS+WID CE
Sbjct:    20 LDTQFTCPFCNHEKSCDVKMERSRNTGIISCTVCLEEFQTPITYLSEPVDVYSDWIDACE 79

Query:    79 RVN 81
               N
Sbjct:    80 AAN 82

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8LHP0	ELOF1_ORYSJ	No assigned EC number	0.8953	0.9347	0.9662	yes	no
O13868	ELOF1_SCHPO	No assigned EC number	0.4791	0.9673	0.8317	yes	no
Q8STS7	ELOF1_ENCCU	No assigned EC number	0.3896	0.8369	0.9625	yes	no
Q8MQI6	ELOF1_DROME	No assigned EC number	0.4756	0.8804	0.9878	yes	no
Q8LEF3	ELOF1_ARATH	No assigned EC number	0.8414	0.8913	0.6833	yes	no
Q54KR5	ELOF1_DICDI	No assigned EC number	0.5125	0.8586	0.9875	yes	no
Q9XVZ8	ELOF1_CAEEL	No assigned EC number	0.5180	0.8913	0.9761	yes	no

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

Your Input: eugene3.00110639 SubName- Full=Putative uncharacterized protein; (158 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	92
pfam05129	74	pfam05129, Elf1, Transcription elongation factor E	1e-33
COG4888	104	COG4888, COG4888, Uncharacterized Zn ribbon-contai	5e-26
PRK14892	99	PRK14892, PRK14892, putative transcription elongat	2e-04

>gnl|CDD|218451 pfam05129, Elf1, Transcription elongation factor Elf1 like

 Score =  110 bits (276), Expect = 1e-33
 Identities = 41/74 (55%), Positives = 49/74 (66%)

Query: 6  SRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTE 65
           + KPP KK+  KL TVF CPFCNH  SV  +ID K  I +  C +C  SF T I AL+E
Sbjct: 1  KKRKPPKKKKKYKLPTVFDCPFCNHKKSVSVKIDKKTGIAKLHCRVCGLSFQTEINALSE 60

Query: 66 PIDIYSEWIDECER 79
          PID+YS+WID CE 
Sbjct: 61 PIDVYSDWIDACEE 74

This family of short proteins contains a putative zinc binding domain with four conserved cysteines. ELF1 has been identified as a transcription elongation factor in Saccharomyces cerevisiae. Length = 74

>gnl|CDD|227225 COG4888, COG4888, Uncharacterized Zn ribbon-containing protein [General function prediction only]

 Score = 92.2 bits (229), Expect = 5e-26
 Identities = 27/82 (32%), Positives = 40/82 (48%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MG+R+ + +   K+R   L   F+CP C H     C +     IG A+C  C  SF   +
Sbjct: 1  MGRRRRKRRKIIKRRPQVLPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEV 60

Query: 61 TALTEPIDIYSEWIDECERVNN 82
            L+EP+D+YS W+D       
Sbjct: 61 PELSEPVDVYSAWVDAYLEGRG 82

Length = 104

>gnl|CDD|184886 PRK14892, PRK14892, putative transcription elongation factor Elf1; Provisional

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI 60
          MG+R+ + K   + +  KL  +F CP C     V   + +K  I    C  C       +
Sbjct: 1  MGRRRKKRKKIIRPKP-KLPKIFECPRCG---KVSISVKIKKNIAIITCGNCGLYTEFEV 56

Query: 61 TALTEPIDIYSEWID 75
           ++ + +D+Y+++ID
Sbjct: 57 PSVYDEVDVYNKFID 71

Length = 99

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	92
PF05129	81	Elf1: Transcription elongation factor Elf1 like; I	100.0
KOG3214	109	consensus Uncharacterized Zn ribbon-containing pro	100.0
COG4888	104	Uncharacterized Zn ribbon-containing protein [Gene	100.0
PRK14892	99	putative transcription elongation factor Elf1; Pro	100.0
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	97.23
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	97.01
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	96.72
PRK09710	64	lar restriction alleviation and modification prote	96.33
COG1327	156	Predicted transcriptional regulator, consists of a	96.25
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	96.23
TIGR00244	147	transcriptional regulator NrdR. Members of this al	96.22
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	96.21
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	96.1
TIGR00280	91	L37a ribosomal protein L37a. This model finds euka	95.5
PTZ00255	90	60S ribosomal protein L37a; Provisional	95.48
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	95.37
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	95.37
PF14255	52	Cys_rich_CPXG: Cysteine-rich CPXCG	95.2
PRK03976	90	rpl37ae 50S ribosomal protein L37Ae; Reviewed	95.1
PRK12286	57	rpmF 50S ribosomal protein L32; Reviewed	94.91
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	94.82
PF01780	90	Ribosomal_L37ae: Ribosomal L37ae protein family; I	94.79
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	94.74
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	94.52
PF14353	128	CpXC: CpXC protein	94.39
PRK09678	72	DNA-binding transcriptional regulator; Provisional	94.06
smart00778	37	Prim_Zn_Ribbon Zinc-binding domain of primase-heli	94.06
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	94.05
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	93.31
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	93.07
PF08792	33	A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: I	92.89
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	92.24
PHA00626	59	hypothetical protein	92.12
TIGR03829	89	YokU_near_AblA uncharacterized protein, YokU famil	91.77
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	91.71
PF04606	47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	91.11
PRK00432	50	30S ribosomal protein S27ae; Validated	90.83
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	90.8
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	90.64
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	90.58
PF09986	214	DUF2225: Uncharacterized protein conserved in bact	90.31
PRK13130	56	H/ACA RNA-protein complex component Nop10p; Review	90.25
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	89.96
PRK03988	138	translation initiation factor IF-2 subunit beta; V	89.81
TIGR00311	133	aIF-2beta translation initiation factor aIF-2, bet	89.79
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	89.36
smart00661	52	RPOL9 RNA polymerase subunit 9.	89.31
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	89.27
PF13453	41	zf-TFIIB: Transcription factor zinc-finger	89.13
COG3478	68	Predicted nucleic-acid-binding protein containing	88.8
PF06044	254	DRP: Dam-replacing family; InterPro: IPR010324 Dam	88.72
COG3677	129	Transposase and inactivated derivatives [DNA repli	88.53
PF14205	55	Cys_rich_KTR: Cysteine-rich KTR	87.7
PF08273	40	Prim_Zn_Ribbon: Zinc-binding domain of primase-hel	87.58
smart00653	110	eIF2B_5 domain present in translation initiation f	86.94
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	86.84
COG2051	67	RPS27A Ribosomal protein S27E [Translation, riboso	86.56
smart00531	147	TFIIE Transcription initiation factor IIE.	86.43
PF05605	54	zf-Di19: Drought induced 19 protein (Di19), zinc-b	86.26
PF01873	125	eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro:	86.24
TIGR02605	52	CxxC_CxxC_SSSS putative regulatory protein, FmdB f	86.14
PF09526	71	DUF2387: Probable metal-binding protein (DUF2387);	86.12
TIGR03831	46	YgiT_finger YgiT-type zinc finger domain. This dom	86.09
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	85.86
TIGR01385	299	TFSII transcription elongation factor S-II. This m	85.7
COG1405	285	SUA7 Transcription initiation factor TFIIIB, Brf1	85.45
TIGR02443	59	conserved hypothetical metal-binding protein. Memb	85.28
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	85.14
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	85.1
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	84.96
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	84.74
PF13248	26	zf-ribbon_3: zinc-ribbon domain	84.49
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	84.43
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	84.29
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	84.07
COG1779	201	C4-type Zn-finger protein [General function predic	83.82
PRK12336	201	translation initiation factor IF-2 subunit beta; P	83.82
PRK05978	148	hypothetical protein; Provisional	83.42
PF05180	66	zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc	83.42
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	83.39
PHA02540	337	61 DNA primase; Provisional	83.08
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	83.05
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	82.22
KOG0402	92	consensus 60S ribosomal protein L37 [Translation,	82.05
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	82.01
COG1326	201	Uncharacterized archaeal Zn-finger protein [Genera	81.93
PF03367	161	zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004	81.72
PF03966	68	Trm112p: Trm112p-like protein; InterPro: IPR005651	81.58
PF13465	26	zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A	81.55
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	81.54
PF05502	483	Dynactin_p62: Dynactin p62 family; InterPro: IPR00	81.51
PF10083	158	DUF2321: Uncharacterized protein conserved in bact	80.98
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	80.59
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	80.21
TIGR01562	305	FdhE formate dehydrogenase accessory protein FdhE.	80.21

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

Probab=100.00  E-value=5.3e-44  Score=234.07  Aligned_cols=80  Identities=59%  Similarity=1.065  Sum_probs=45.9

Q ss_pred             CCCccCCC-CCCCCCCCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528            2 GKRKSRAK-PPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV   80 (92)
Q Consensus         2 GkRK~k~k-~~~kk~~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~   80 (92)
                      ||||++++ ++++|++++|||.|+||||||++||+|+||++.++|+|+|++||++|+++|++|++||||||+|||+|+++
T Consensus         1 GkRK~~~k~~~~kk~~~~l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L~epiDVY~~wiD~~~~~   80 (81)
T PF05129_consen    1 GKRKKKRKKPPKKKKKPKLPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPLSEPIDVYSEWIDACEEG   80 (81)
T ss_dssp             -------------------SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS--TTHHHHHHHHHHH--
T ss_pred             CCCcccCCCCCccCcCCCCCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCccCcccchhHHHHHHHHhc
Confidence            89998887 67788899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             c
Q 034528           81 N   81 (92)
Q Consensus        81 n   81 (92)
                      |
T Consensus        81 n   81 (81)
T PF05129_consen   81 N   81 (81)
T ss_dssp             -
T ss_pred             C
Confidence            7

; PDB: 1WII_A.

>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]

Probab=100.00  E-value=1.7e-43  Score=241.69  Aligned_cols=90  Identities=66%  Similarity=1.134  Sum_probs=84.4

Q ss_pred             CCCCccCCCCCCC-CCCCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHh
Q 034528            1 MGKRKSRAKPPPK-KRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECER   79 (92)
Q Consensus         1 MGkRK~k~k~~~k-k~~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~   79 (92)
                      |||||+|++++++ |...+|+|.|+||||||+++|+|+||++.++|.++|++|+++|++.|++|++||||||+|||+|++
T Consensus         1 MgkRk~K~k~~~k~r~~~~ldt~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it~LsepIDVYSdWiDaCe~   80 (109)
T KOG3214|consen    1 MGKRKSKRKEPPKERRVEPLDTQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTITALSEPIDVYSDWIDACEA   80 (109)
T ss_pred             CCcccccccCCchhhhccchheeeccCccccccceeeeehhhcCcceeeeeehhhhhccchHhhccchHHHHHHHHHHHH
Confidence            9999999887766 789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCccccchhh
Q 034528           80 VNNLEDDGAYE   90 (92)
Q Consensus        80 ~n~~~~~~~~~   90 (92)
                      +|.-+.+++++
T Consensus        81 vn~a~~~~vd~   91 (109)
T KOG3214|consen   81 VNNAEDDVVDE   91 (109)
T ss_pred             hhccccchhhh
Confidence            99866666553

>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]

Probab=100.00  E-value=1.8e-38  Score=216.39  Aligned_cols=82  Identities=33%  Similarity=0.725  Sum_probs=78.7

Q ss_pred             CCCCccCCCCCCCCCCCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528            1 MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV   80 (92)
Q Consensus         1 MGkRK~k~k~~~kk~~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~   80 (92)
                      |||||++++.+.+++.++|||.|+||||||+++++|.++++.++|.++|++||++|++.||.|++||||||+|||+|+|+
T Consensus         1 MG~rr~krr~~ik~~~~~L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wvDay~eg   80 (104)
T COG4888           1 MGRRRRKRRKIIKRRPQVLPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVYSAWVDAYLEG   80 (104)
T ss_pred             CCcccccccccCcccCccCCceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHHHHHHHHHHhc
Confidence            99999888777778888899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q 034528           81 NN   82 (92)
Q Consensus        81 n~   82 (92)
                      +.
T Consensus        81 ~~   82 (104)
T COG4888          81 RG   82 (104)
T ss_pred             cc
Confidence            96

>PRK14892 putative transcription elongation factor Elf1; Provisional

Probab=100.00  E-value=1.7e-34  Score=195.72  Aligned_cols=77  Identities=25%  Similarity=0.505  Sum_probs=71.9

Q ss_pred             CCCCccCCCCCCCCCCCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528            1 MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV   80 (92)
Q Consensus         1 MGkRK~k~k~~~kk~~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~   80 (92)
                      |||||++++ +++|++.++|+.|+|||||+ .+|.|+|++  +++++.|.+||.+|.+.|++|++||||||+|||+|+++
T Consensus         1 MGkRk~~~k-~~~k~k~klpt~f~CP~Cge-~~v~v~~~k--~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wiD~~~eg   76 (99)
T PRK14892          1 MGRRRKKRK-KIIRPKPKLPKIFECPRCGK-VSISVKIKK--NIAIITCGNCGLYTEFEVPSVYDEVDVYNKFIDLYLEG   76 (99)
T ss_pred             CCCccccCC-CCcccccCCCcEeECCCCCC-eEeeeecCC--CcceEECCCCCCccCEECCccccchhhHHHHHHHHHhc
Confidence            999999976 44677899999999999995 799999987  89999999999999999999999999999999999999


Q ss_pred             c
Q 034528           81 N   81 (92)
Q Consensus        81 n   81 (92)
                      .
T Consensus        77 ~   77 (99)
T PRK14892         77 K   77 (99)
T ss_pred             C
Confidence            8

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=97.23  E-value=0.00032  Score=42.04  Aligned_cols=34  Identities=32%  Similarity=0.570  Sum_probs=24.5

Q ss_pred             cCCCCCCCCeEEEE--eecCCceEEEEcCccCCeeEe
Q 034528           24 SCPFCNHGTSVECR--IDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        24 ~CPfC~~~~sV~vk--idk~~~~g~l~C~~Cg~~~~~   58 (92)
                      .|||||.. .+.+.  .+-....+...|..||.+...
T Consensus         3 PCPfCGg~-~~~~~~~~~~~~~~~~~~C~~Cga~~~~   38 (53)
T TIGR03655         3 PCPFCGGA-DVYLRRGFDPLDLSHYFECSTCGASGPV   38 (53)
T ss_pred             CCCCCCCc-ceeeEeccCCCCCEEEEECCCCCCCccc
Confidence            69999984 45454  444556677799999987654

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.

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=97.01  E-value=0.0011  Score=39.93  Aligned_cols=33  Identities=27%  Similarity=0.437  Sum_probs=23.2

Q ss_pred             ccccCCCCCCCCeEEEEeecCCce---EEEEcCccCC
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLI---GEAICNICQE   54 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~---g~l~C~~Cg~   54 (92)
                      ++-.|||||. ..+.+.-+.....   ..|.|..||.
T Consensus         2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence            3457999987 4566665443222   7899999998

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=96.72  E-value=0.0027  Score=38.97  Aligned_cols=37  Identities=24%  Similarity=0.596  Sum_probs=26.5

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe-ecCC
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST-TITA   62 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~-~i~~   62 (92)
                      .|.||.||.  ++++  .....-.++.|..||..|+- ..++
T Consensus         2 ~~~CP~CG~--~iev--~~~~~GeiV~Cp~CGaeleVv~~~p   39 (54)
T TIGR01206         2 QFECPDCGA--EIEL--ENPELGELVICDECGAELEVVSLDP   39 (54)
T ss_pred             ccCCCCCCC--EEec--CCCccCCEEeCCCCCCEEEEEeCCC
Confidence            589999997  3444  33333458899999999986 4444

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.

>PRK09710 lar restriction alleviation and modification protein; Reviewed

Probab=96.33  E-value=0.0055  Score=39.07  Aligned_cols=34  Identities=35%  Similarity=0.631  Sum_probs=27.3

Q ss_pred             CCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528           19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES   55 (92)
Q Consensus        19 l~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~   55 (92)
                      .+++=.|||||- ++|.++-  ..+...+.|..||..
T Consensus         3 ~d~lKPCPFCG~-~~~~v~~--~~g~~~v~C~~CgA~   36 (64)
T PRK09710          3 YDNVKPCPFCGC-PSVTVKA--ISGYYRAKCNGCESR   36 (64)
T ss_pred             cccccCCCCCCC-ceeEEEe--cCceEEEEcCCCCcC
Confidence            466778999997 5677765  577888999999986

>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]

Probab=96.25  E-value=0.0024  Score=46.81  Aligned_cols=35  Identities=29%  Similarity=0.543  Sum_probs=24.0

Q ss_pred             cCCCCCCCCeEEEEeecC-CceE---EEEcCccCCeeEe
Q 034528           24 SCPFCNHGTSVECRIDMK-NLIG---EAICNICQESFST   58 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~-~~~g---~l~C~~Cg~~~~~   58 (92)
                      .||||+|+.|=.+.=-.. .|-+   .=.|..||.+|+|
T Consensus         2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTT   40 (156)
T COG1327           2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTT   40 (156)
T ss_pred             CCCCCCCCCCeeeecccccccchhhhhhcccccccccch
Confidence            599999998755443222 2222   2579999999987

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=96.23  E-value=0.011  Score=33.59  Aligned_cols=35  Identities=23%  Similarity=0.556  Sum_probs=24.1

Q ss_pred             ccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeE
Q 034528           23 FSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFS   57 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~   57 (92)
                      |+||.|||.+.+-..+.-.    .+.-...|..||..|.
T Consensus         1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr   39 (39)
T PF01096_consen    1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR   39 (39)
T ss_dssp             S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred             CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence            6899999998888766332    3567789999998763

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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>TIGR00244 transcriptional regulator NrdR

Probab=96.22  E-value=0.0047  Score=44.85  Aligned_cols=36  Identities=28%  Similarity=0.574  Sum_probs=25.5

Q ss_pred             cCCCCCCCCeEEEEeec-CCceEE---EEcCccCCeeEee
Q 034528           24 SCPFCNHGTSVECRIDM-KNLIGE---AICNICQESFSTT   59 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk-~~~~g~---l~C~~Cg~~~~~~   59 (92)
                      .||||||+++=.+.=-. .+|.++   =.|..||.+|+|-
T Consensus         2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTy   41 (147)
T TIGR00244         2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTF   41 (147)
T ss_pred             CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcccee
Confidence            59999998876554322 344443   5799999999873

Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.

>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=96.21  E-value=0.0045  Score=35.44  Aligned_cols=32  Identities=25%  Similarity=0.562  Sum_probs=22.5

Q ss_pred             ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528           23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT   59 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~   59 (92)
                      |.||.|++..   +..|  ...|.+.|..||.--+..
T Consensus         1 m~Cp~Cg~~~---~~~D--~~~g~~vC~~CG~Vl~e~   32 (43)
T PF08271_consen    1 MKCPNCGSKE---IVFD--PERGELVCPNCGLVLEEN   32 (43)
T ss_dssp             ESBTTTSSSE---EEEE--TTTTEEEETTT-BBEE-T
T ss_pred             CCCcCCcCCc---eEEc--CCCCeEECCCCCCEeecc
Confidence            6899999843   4555  445888999999876653

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.

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=96.10  E-value=0.0025  Score=35.28  Aligned_cols=34  Identities=18%  Similarity=0.382  Sum_probs=22.7

Q ss_pred             cccCCCCCCCCeEEEEeecC-CceEEEEcCccCCeeE
Q 034528           22 VFSCPFCNHGTSVECRIDMK-NLIGEAICNICQESFS   57 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~-~~~g~l~C~~Cg~~~~   57 (92)
                      .+.||.|+..  ..|.-+.. ...+.+.|.+||..|.
T Consensus         2 ~~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~~   36 (38)
T TIGR02098         2 RIQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVWY   36 (38)
T ss_pred             EEECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEEE
Confidence            3789999974  33333222 2234899999998875

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>TIGR00280 L37a ribosomal protein L37a

Probab=95.50  E-value=0.038  Score=37.29  Aligned_cols=44  Identities=23%  Similarity=0.534  Sum_probs=31.6

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhh
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIY   70 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY   70 (92)
                      ..+.||||+...   |+   ...+|+-.|+.||..|.--.-.++.|.-+.
T Consensus        34 a~y~CpfCgk~~---vk---R~a~GIW~C~~C~~~~AGGAy~p~T~~~~t   77 (91)
T TIGR00280        34 AKYVCPFCGKKT---VK---RGSTGIWTCRKCGAKFAGGAYTPVTPAGKT   77 (91)
T ss_pred             cCccCCCCCCCc---eE---EEeeEEEEcCCCCCEEeCCccccccchhHH
Confidence            578999999732   22   367899999999999986544445554444

This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.

>PTZ00255 60S ribosomal protein L37a; Provisional

Probab=95.48  E-value=0.038  Score=37.25  Aligned_cols=45  Identities=20%  Similarity=0.536  Sum_probs=31.2

Q ss_pred             CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhh
Q 034528           20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIY   70 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY   70 (92)
                      -..+.||||+...   |+   ...+|+-.|+.|+..|.--.-.++.|.-+.
T Consensus        34 ~a~y~CpfCgk~~---vk---R~a~GIW~C~~C~~~~AGGAy~~~T~~~~t   78 (90)
T PTZ00255         34 HAKYFCPFCGKHA---VK---RQAVGIWRCKGCKKTVAGGAWTLSTPAAST   78 (90)
T ss_pred             hCCccCCCCCCCc---ee---eeeeEEEEcCCCCCEEeCCccccccchhHH
Confidence            3679999999642   22   356799999999999886444444444433

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

Probab=95.37  E-value=0.034  Score=32.09  Aligned_cols=34  Identities=15%  Similarity=0.352  Sum_probs=24.2

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeec
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI   60 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i   60 (92)
                      ..|.||.||..    +.++...  ..+.|..||..+.+..
T Consensus         2 ~~y~C~~CG~~----~~~~~~~--~~~~Cp~CG~~~~~~~   35 (46)
T PRK00398          2 AEYKCARCGRE----VELDEYG--TGVRCPYCGYRILFKE   35 (46)
T ss_pred             CEEECCCCCCE----EEECCCC--CceECCCCCCeEEEcc
Confidence            46899999973    3444333  3789999998877643

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=95.37  E-value=0.045  Score=31.27  Aligned_cols=34  Identities=15%  Similarity=0.479  Sum_probs=25.9

Q ss_pred             ccCCCCCCCCeEEEEeecC----CceEEEEcCccCCee
Q 034528           23 FSCPFCNHGTSVECRIDMK----NLIGEAICNICQESF   56 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~   56 (92)
                      |.||.|||..++-..+...    .+.-...|..||-.+
T Consensus         1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w   38 (40)
T smart00440        1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW   38 (40)
T ss_pred             CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence            6899999998887766321    346678999999765

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG

Probab=95.20  E-value=0.037  Score=33.70  Aligned_cols=48  Identities=13%  Similarity=0.346  Sum_probs=29.8

Q ss_pred             ccCCCCCCCCeEEEEeecCCceEEEEcCccCC--eeEeecCCCCcchhhh
Q 034528           23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQE--SFSTTITALTEPIDIY   70 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~--~~~~~i~~L~epVDVY   70 (92)
                      .+||+||+...+.+.......-..--|.+|-.  .+...+.....-|.|+
T Consensus         1 i~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d~~~~~v~v~   50 (52)
T PF14255_consen    1 IQCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVTVDEDEPSVSVR   50 (52)
T ss_pred             CCCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEEECCCCCEEEEE
Confidence            37999999655544444444456788999986  4455555554444443

>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed

Probab=95.10  E-value=0.058  Score=36.33  Aligned_cols=44  Identities=18%  Similarity=0.375  Sum_probs=31.2

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhh
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIY   70 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY   70 (92)
                      ..+.||||+..   .|+   ...+|+-.|+.|+..|.--.-.++.|.-+.
T Consensus        35 a~y~CpfCgk~---~vk---R~a~GIW~C~~C~~~~AGGAy~~~T~~~~t   78 (90)
T PRK03976         35 AKHVCPVCGRP---KVK---RVGTGIWECRKCGAKFAGGAYTPETPAGKT   78 (90)
T ss_pred             cCccCCCCCCC---ceE---EEEEEEEEcCCCCCEEeCCccccccchhhh
Confidence            57899999863   222   367899999999999876544444554443

>PRK12286 rpmF 50S ribosomal protein L32; Reviewed

Probab=94.91  E-value=0.031  Score=34.49  Aligned_cols=28  Identities=21%  Similarity=0.497  Sum_probs=22.4

Q ss_pred             CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528           17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES   55 (92)
Q Consensus        17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~   55 (92)
                      -.+|.+..||.||+.           ...+-.|..||..
T Consensus        22 l~~~~l~~C~~CG~~-----------~~~H~vC~~CG~Y   49 (57)
T PRK12286         22 LKAPGLVECPNCGEP-----------KLPHRVCPSCGYY   49 (57)
T ss_pred             ccCCcceECCCCCCc-----------cCCeEECCCCCcC
Confidence            467899999999973           3468899999954

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=94.82  E-value=0.042  Score=39.80  Aligned_cols=35  Identities=29%  Similarity=0.602  Sum_probs=22.7

Q ss_pred             cCCCCCCCCeEEEEeec-CCc--e-EEEEcCccCCeeEe
Q 034528           24 SCPFCNHGTSVECRIDM-KNL--I-GEAICNICQESFST   58 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk-~~~--~-g~l~C~~Cg~~~~~   58 (92)
                      .||+||++.+-.+.=.- ..|  + -.-.|..||-+|.+
T Consensus         2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~   40 (154)
T PRK00464          2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT   40 (154)
T ss_pred             cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence            69999997743333221 111  1 23789999999986

>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=94.79  E-value=0.018  Score=38.78  Aligned_cols=42  Identities=24%  Similarity=0.565  Sum_probs=28.3

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchh
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPID   68 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVD   68 (92)
                      ..+.||||+.. +  |+-   ..+|+-.|+.|+..|.--.-.++.|.-
T Consensus        34 ~ky~Cp~Cgk~-~--vkR---~a~GIW~C~~C~~~~AGGAy~~~T~~~   75 (90)
T PF01780_consen   34 AKYTCPFCGKT-S--VKR---VATGIWKCKKCGKKFAGGAYTPSTPAA   75 (90)
T ss_dssp             S-BEESSSSSS-E--EEE---EETTEEEETTTTEEEE-BSSSSS-HHH
T ss_pred             CCCcCCCCCCc-e--eEE---eeeEEeecCCCCCEEeCCCccccchHH
Confidence            56899999984 2  332   456889999999999875555555543

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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=94.74  E-value=0.024  Score=31.82  Aligned_cols=33  Identities=21%  Similarity=0.423  Sum_probs=23.8

Q ss_pred             ccCCCCCCCCeEEEEeec-CCceEEEEcCccCCeeE
Q 034528           23 FSCPFCNHGTSVECRIDM-KNLIGEAICNICQESFS   57 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk-~~~~g~l~C~~Cg~~~~   57 (92)
                      .+||.|+..  ..|.-++ ..+.+.+.|..|+..|.
T Consensus         3 i~CP~C~~~--f~v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    3 ITCPNCQTR--FRVPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             EECCCCCce--EEcCHHHcccCCcEEECCCCCcEee
Confidence            589999973  4444432 24567999999999874

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=94.52  E-value=0.016  Score=32.48  Aligned_cols=34  Identities=18%  Similarity=0.435  Sum_probs=22.5

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF   56 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~   56 (92)
                      .+.||.|+..-.|.=..- ......+.|..||..|
T Consensus         2 ~i~Cp~C~~~y~i~d~~i-p~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    2 IITCPNCQAKYEIDDEKI-PPKGRKVRCSKCGHVF   35 (36)
T ss_pred             EEECCCCCCEEeCCHHHC-CCCCcEEECCCCCCEe
Confidence            368999998533322221 2445689999999876

>PF14353 CpXC: CpXC protein

Probab=94.39  E-value=0.049  Score=37.03  Aligned_cols=39  Identities=21%  Similarity=0.496  Sum_probs=26.5

Q ss_pred             ccCCCCCCCCeEEEEe--ec-----------CCceEEEEcCccCCeeEeecC
Q 034528           23 FSCPFCNHGTSVECRI--DM-----------KNLIGEAICNICQESFSTTIT   61 (92)
Q Consensus        23 F~CPfC~~~~sV~vki--dk-----------~~~~g~l~C~~Cg~~~~~~i~   61 (92)
                      -+||.|+|+..+++--  +-           ...+....|..||..+....+
T Consensus         2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p   53 (128)
T PF14353_consen    2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYP   53 (128)
T ss_pred             cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCC
Confidence            4799999976555432  21           135568999999998765433

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=94.06  E-value=0.049  Score=35.18  Aligned_cols=44  Identities=23%  Similarity=0.458  Sum_probs=26.6

Q ss_pred             ccCCCCCCCCeEEEEeec-C--CceEEEEcC--ccCCeeEeec---CCCCcch
Q 034528           23 FSCPFCNHGTSVECRIDM-K--NLIGEAICN--ICQESFSTTI---TALTEPI   67 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk-~--~~~g~l~C~--~Cg~~~~~~i---~~L~epV   67 (92)
                      |.||+||+.. ...+=.. .  ...-.-.|.  .||.+|.+..   +.|+.|.
T Consensus         2 m~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~es~s~tis~p~   53 (72)
T PRK09678          2 FHCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATFITYESVQRYIVKPG   53 (72)
T ss_pred             ccCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEEEEEEEEEEEEcCCC
Confidence            7899999854 2222211 1  223456788  7999998742   3455553

>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase

Probab=94.06  E-value=0.038  Score=31.55  Aligned_cols=29  Identities=28%  Similarity=0.676  Sum_probs=25.2

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQE   54 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~   54 (92)
                      .||.|+-.....  ++.+.+.|...|+.|+.
T Consensus         5 pCP~CGG~DrFr--~~d~~g~G~~~C~~Cg~   33 (37)
T smart00778        5 PCPNCGGSDRFR--FDDKDGRGTWFCSVCGA   33 (37)
T ss_pred             CCCCCCCccccc--cccCCCCcCEEeCCCCC
Confidence            699999988777  77788899999999975

This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.

>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins

Probab=94.05  E-value=0.13  Score=32.48  Aligned_cols=48  Identities=15%  Similarity=0.470  Sum_probs=31.2

Q ss_pred             ccCCCCCCCCeEEEE-----------eecC-CceEEEEcCccCCe--eEeecCCCCcchhhh
Q 034528           23 FSCPFCNHGTSVECR-----------IDMK-NLIGEAICNICQES--FSTTITALTEPIDIY   70 (92)
Q Consensus        23 F~CPfC~~~~sV~vk-----------idk~-~~~g~l~C~~Cg~~--~~~~i~~L~epVDVY   70 (92)
                      +.||-||++.--.=.           +|-. +..-.++|..||-+  |....+.|++-+|.+
T Consensus         1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y~~~~~~~~~i~D~~   62 (64)
T PF09855_consen    1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFYKAKTSNGSNILDFF   62 (64)
T ss_pred             CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEEeecCcccchhhhhh
Confidence            579999996422111           1211 23346899999954  667888888887764

>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=93.31  E-value=0.076  Score=30.74  Aligned_cols=32  Identities=25%  Similarity=0.691  Sum_probs=21.9

Q ss_pred             CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528           18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE   54 (92)
Q Consensus        18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~   54 (92)
                      .-+.-|.||+||+.+  ...|   ...+.-.|..|+.
T Consensus        14 RW~~g~~CP~Cg~~~--~~~~---~~~~~~~C~~C~~   45 (46)
T PF12760_consen   14 RWPDGFVCPHCGSTK--HYRL---KTRGRYRCKACRK   45 (46)
T ss_pred             cCCCCCCCCCCCCee--eEEe---CCCCeEECCCCCC
Confidence            345669999999852  2222   2267889999974

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

>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]

Probab=93.07  E-value=0.088  Score=35.51  Aligned_cols=32  Identities=25%  Similarity=0.588  Sum_probs=25.0

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      ....||+|+..   .|+-   ...|+-.|+.||..|.-
T Consensus        34 ~~~~Cp~C~~~---~VkR---~a~GIW~C~kCg~~fAG   65 (89)
T COG1997          34 AKHVCPFCGRT---TVKR---IATGIWKCRKCGAKFAG   65 (89)
T ss_pred             cCCcCCCCCCc---ceee---eccCeEEcCCCCCeecc
Confidence            46899999984   3333   56799999999999864

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

Probab=92.89  E-value=0.12  Score=28.65  Aligned_cols=30  Identities=23%  Similarity=0.451  Sum_probs=22.4

Q ss_pred             ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      -.|+-|||+.-+.      ...+...|..||.+|++
T Consensus         4 ~~C~~C~~~~i~~------~~~~~~~C~~Cg~~~~~   33 (33)
T PF08792_consen    4 KKCSKCGGNGIVN------KEDDYEVCIFCGSSFPY   33 (33)
T ss_pred             eEcCCCCCCeEEE------ecCCeEEcccCCcEeeC
Confidence            4699999975221      33478999999999874

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

Probab=92.24  E-value=0.3  Score=27.18  Aligned_cols=28  Identities=21%  Similarity=0.516  Sum_probs=21.2

Q ss_pred             CCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528           25 CPFCNHGTSVECRIDMKNLIGEAICNICQESFS   57 (92)
Q Consensus        25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~   57 (92)
                      ||.||+  -+.++=++...+   .|+.|+-.++
T Consensus         4 Cp~C~n--lL~p~~~~~~~~---~C~~C~Y~~~   31 (35)
T PF02150_consen    4 CPECGN--LLYPKEDKEKRV---ACRTCGYEEP   31 (35)
T ss_dssp             ETTTTS--BEEEEEETTTTE---EESSSS-EEE
T ss_pred             CCCCCc--cceEcCCCccCc---CCCCCCCccC
Confidence            999996  577777776666   9999997654

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

>PHA00626 hypothetical protein

Probab=92.12  E-value=0.18  Score=31.69  Aligned_cols=34  Identities=24%  Similarity=0.425  Sum_probs=24.0

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      .||.||+.+-+-+.+-++ ....-.|..||-.|+-
T Consensus         2 ~CP~CGS~~Ivrcg~cr~-~snrYkCkdCGY~ft~   35 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRG-WSDDYVCCDCGYNDSK   35 (59)
T ss_pred             CCCCCCCceeeeeceecc-cCcceEcCCCCCeech
Confidence            599999976565555333 1356789999988864

>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family

Probab=91.77  E-value=0.29  Score=32.90  Aligned_cols=35  Identities=11%  Similarity=0.456  Sum_probs=23.8

Q ss_pred             cCCCCCCC----CeEEEEeecCC--------ceEEEEcCccCCeeEe
Q 034528           24 SCPFCNHG----TSVECRIDMKN--------LIGEAICNICQESFST   58 (92)
Q Consensus        24 ~CPfC~~~----~sV~vkidk~~--------~~g~l~C~~Cg~~~~~   58 (92)
                      .|+.|++.    ..+++..+..+        ++-.+.|..||+.|.+
T Consensus         1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~   47 (89)
T TIGR03829         1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQD   47 (89)
T ss_pred             CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeec
Confidence            49999663    34455555543        3345899999999875

Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.

>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=91.71  E-value=0.4  Score=36.88  Aligned_cols=49  Identities=14%  Similarity=0.300  Sum_probs=27.3

Q ss_pred             cccCCCCCCCCeEEEEee---cCCceEEEEcCccCCeeEeecCCCCcchhhh
Q 034528           22 VFSCPFCNHGTSVECRID---MKNLIGEAICNICQESFSTTITALTEPIDIY   70 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkid---k~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY   70 (92)
                      ...||+||+++......-   -..+.-.-.|..|+.+.-+--...+..+|.+
T Consensus       211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd~~~~~~~~~~  262 (290)
T PF04216_consen  211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVDREKDPELDPV  262 (290)
T ss_dssp             TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEETTT-TT--HH
T ss_pred             CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHhhhhCcccchh
Confidence            457999999988877764   3456778899999997766335666666655

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.

>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr

Probab=91.11  E-value=0.44  Score=27.73  Aligned_cols=36  Identities=17%  Similarity=0.462  Sum_probs=22.7

Q ss_pred             cCCCCCCCCeEEEEeecC--CceEEEEcCc--cCCeeEee
Q 034528           24 SCPFCNHGTSVECRIDMK--NLIGEAICNI--CQESFSTT   59 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~--~~~g~l~C~~--Cg~~~~~~   59 (92)
                      .||+||+.-.+.-.-...  .......|.+  ||.+|.+.
T Consensus         1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~   40 (47)
T PF04606_consen    1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVAN   40 (47)
T ss_pred             CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEE
Confidence            499999854332222222  2334678888  99999875

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=90.83  E-value=0.15  Score=30.53  Aligned_cols=26  Identities=23%  Similarity=0.487  Sum_probs=18.1

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESF   56 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~   56 (92)
                      -||.||++  +-  ....   +...|+.||.++
T Consensus        22 fCP~Cg~~--~m--~~~~---~r~~C~~Cgyt~   47 (50)
T PRK00432         22 FCPRCGSG--FM--AEHL---DRWHCGKCGYTE   47 (50)
T ss_pred             cCcCCCcc--hh--eccC---CcEECCCcCCEE
Confidence            79999973  21  1111   688999999865

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=90.80  E-value=0.13  Score=28.23  Aligned_cols=31  Identities=26%  Similarity=0.465  Sum_probs=21.4

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQES   55 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~   55 (92)
                      .|.|+.||+.-.+...+  .. -..+.|-.||..
T Consensus         5 ~y~C~~Cg~~fe~~~~~--~~-~~~~~CP~Cg~~   35 (41)
T smart00834        5 EYRCEDCGHTFEVLQKI--SD-DPLATCPECGGD   35 (41)
T ss_pred             EEEcCCCCCEEEEEEec--CC-CCCCCCCCCCCc
Confidence            58999999853333333  22 467889999983

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>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=90.64  E-value=0.31  Score=37.45  Aligned_cols=36  Identities=14%  Similarity=0.281  Sum_probs=18.6

Q ss_pred             ccCCCCCCCCeEEEEeecCC-ceEEEEcCccCCeeEe
Q 034528           23 FSCPFCNHGTSVECRIDMKN-LIGEAICNICQESFST   58 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk~~-~~g~l~C~~Cg~~~~~   58 (92)
                      =.||.||..-++++-..... |.=.+.|..||..+.+
T Consensus       173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~  209 (290)
T PF04216_consen  173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRF  209 (290)
T ss_dssp             SS-TTT---EEEEEEE------EEEEEETTT--EEE-
T ss_pred             CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeee
Confidence            48999999766665554432 6788999999987654

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.

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=90.58  E-value=0.093  Score=26.87  Aligned_cols=21  Identities=24%  Similarity=0.672  Sum_probs=13.4

Q ss_pred             CCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528           25 CPFCNHGTSVECRIDMKNLIGEAICNICQES   55 (92)
Q Consensus        25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~   55 (92)
                      ||.||++..-          +..-|..||..
T Consensus         2 Cp~CG~~~~~----------~~~fC~~CG~~   22 (23)
T PF13240_consen    2 CPNCGAEIED----------DAKFCPNCGTP   22 (23)
T ss_pred             CcccCCCCCC----------cCcchhhhCCc
Confidence            8999986422          22348888863

>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function

Probab=90.31  E-value=0.43  Score=35.64  Aligned_cols=44  Identities=16%  Similarity=0.345  Sum_probs=27.2

Q ss_pred             CccccCCCCCCCCeEEEEeecCCc---------------------eEEEEcCccCCeeEe-ecCCCCc
Q 034528           20 DTVFSCPFCNHGTSVECRIDMKNL---------------------IGEAICNICQESFST-TITALTE   65 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~~~---------------------~g~l~C~~Cg~~~~~-~i~~L~e   65 (92)
                      ++..+||+|+++  ...+.-+...                     --...|..||-.+.. ..+.|+.
T Consensus         3 ~k~~~CPvC~~~--F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l~~   68 (214)
T PF09986_consen    3 DKKITCPVCGKE--FKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEKLSP   68 (214)
T ss_pred             CCceECCCCCCe--eeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccccccCCH
Confidence            578899999985  3333222111                     135899999977654 3555553

>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed

Probab=90.25  E-value=0.25  Score=30.57  Aligned_cols=45  Identities=20%  Similarity=0.462  Sum_probs=35.5

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHH
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE   78 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~   78 (92)
                      .-.|+.||.   .+.         ...|.+||.......++-+.|.|-|++.-=++.
T Consensus         5 mr~C~~Cgv---YTL---------k~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~k   49 (56)
T PRK13130          5 IRKCPKCGV---YTL---------KEICPVCGGKTKNPHPPRFSPEDKYGKYRRALK   49 (56)
T ss_pred             ceECCCCCC---EEc---------cccCcCCCCCCCCCCCCCCCCCCccHHHHHHHH
Confidence            346888885   222         348999999999999999999999998765543

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=89.96  E-value=0.16  Score=29.08  Aligned_cols=30  Identities=23%  Similarity=0.447  Sum_probs=23.3

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQE   54 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~   54 (92)
                      .|.|+-|||.-.+...|  .+ ...+.|-.||.
T Consensus         5 ey~C~~Cg~~fe~~~~~--~~-~~~~~CP~Cg~   34 (42)
T PF09723_consen    5 EYRCEECGHEFEVLQSI--SE-DDPVPCPECGS   34 (42)
T ss_pred             EEEeCCCCCEEEEEEEc--CC-CCCCcCCCCCC
Confidence            58999999965555555  33 67889999998

The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PRK03988 translation initiation factor IF-2 subunit beta; Validated

Probab=89.81  E-value=0.5  Score=33.66  Aligned_cols=33  Identities=18%  Similarity=0.358  Sum_probs=26.1

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF   56 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~   56 (92)
                      ..=.||.|+.+++.-++   +..+-.+.|..||...
T Consensus       101 ~yVlC~~C~spdT~l~k---~~r~~~l~C~ACGa~~  133 (138)
T PRK03988        101 EYVICPECGSPDTKLIK---EGRIWVLKCEACGAET  133 (138)
T ss_pred             hcEECCCCCCCCcEEEE---cCCeEEEEcccCCCCC
Confidence            34579999998876554   5678899999999864

>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative

Probab=89.79  E-value=0.49  Score=33.52  Aligned_cols=34  Identities=15%  Similarity=0.333  Sum_probs=26.2

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS   57 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~   57 (92)
                      ..=.||.|+.+.+.-++   +..+-.+.|..||....
T Consensus        96 ~yVlC~~C~sPdT~l~k---~~r~~~l~C~ACGa~~~  129 (133)
T TIGR00311        96 KYVICRECNRPDTRIIK---EGRVSLLKCEACGAKAP  129 (133)
T ss_pred             heEECCCCCCCCcEEEE---eCCeEEEecccCCCCCc
Confidence            44579999998876554   46677899999998643

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

Probab=89.36  E-value=0.41  Score=26.73  Aligned_cols=29  Identities=28%  Similarity=0.523  Sum_probs=17.4

Q ss_pred             CCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528           25 CPFCNHGTSVECRIDMKNLIGEAICNICQES   55 (92)
Q Consensus        25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~   55 (92)
                      ||.||+.  ++..|-..+..-...|..||.-
T Consensus         3 C~~CG~~--l~~~ip~gd~r~R~vC~~Cg~I   31 (34)
T PF14803_consen    3 CPQCGGP--LERRIPEGDDRERLVCPACGFI   31 (34)
T ss_dssp             -TTT--B---EEE--TT-SS-EEEETTTTEE
T ss_pred             cccccCh--hhhhcCCCCCccceECCCCCCE
Confidence            9999984  7888876677889999999963

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=89.31  E-value=0.4  Score=27.53  Aligned_cols=28  Identities=18%  Similarity=0.400  Sum_probs=16.6

Q ss_pred             CCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528           25 CPFCNHGTSVECRIDMKNLIGEAICNICQESF   56 (92)
Q Consensus        25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~   56 (92)
                      ||.||+  -+..+-+  .......|..||..+
T Consensus         3 Cp~Cg~--~l~~~~~--~~~~~~vC~~Cg~~~   30 (52)
T smart00661        3 CPKCGN--MLIPKEG--KEKRRFVCRKCGYEE   30 (52)
T ss_pred             CCCCCC--ccccccC--CCCCEEECCcCCCeE
Confidence            899987  2333221  111378899999544

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=89.27  E-value=1.2  Score=29.21  Aligned_cols=40  Identities=20%  Similarity=0.361  Sum_probs=28.8

Q ss_pred             CCCc-cccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeE
Q 034528           18 KLDT-VFSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFS   57 (92)
Q Consensus        18 kl~~-~F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~   57 (92)
                      .+|+ ...||.|||...+-..+...    .+.-.-.|-.||..+.
T Consensus        57 ~~~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~  101 (104)
T TIGR01384        57 TLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWR  101 (104)
T ss_pred             CCCcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeE
Confidence            4444 79999999998877766332    2445678999997653

There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.

>PF13453 zf-TFIIB: Transcription factor zinc-finger

Probab=89.13  E-value=0.7  Score=25.98  Aligned_cols=27  Identities=22%  Similarity=0.591  Sum_probs=20.1

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQE   54 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~   54 (92)
                      +||.|++ .-....+   .++..-.|..||=
T Consensus         1 ~CP~C~~-~l~~~~~---~~~~id~C~~C~G   27 (41)
T PF13453_consen    1 KCPRCGT-ELEPVRL---GDVEIDVCPSCGG   27 (41)
T ss_pred             CcCCCCc-ccceEEE---CCEEEEECCCCCe
Confidence            5999998 3445555   5678888999984

>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=88.80  E-value=0.62  Score=30.00  Aligned_cols=45  Identities=24%  Similarity=0.473  Sum_probs=27.7

Q ss_pred             CccccCCCCCCCCeEEEEeec-----------C-CceEEEEcCccCCe--eEeecCCCC
Q 034528           20 DTVFSCPFCNHGTSVECRIDM-----------K-NLIGEAICNICQES--FSTTITALT   64 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk-----------~-~~~g~l~C~~Cg~~--~~~~i~~L~   64 (92)
                      ...|.||-||..+-.+=.|.-           . +..-.++|.+||-+  |+-.+..+.
T Consensus         2 ~~~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY~a~~st~~   60 (68)
T COG3478           2 KNAFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFYSAKISTTG   60 (68)
T ss_pred             CccccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhheeccccccc
Confidence            346889999986544433322           1 23456999999954  454554433

>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements

Probab=88.72  E-value=0.37  Score=37.86  Aligned_cols=60  Identities=20%  Similarity=0.431  Sum_probs=25.5

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeec--CCCCcch--hhhhhHHHHHHhhcCc
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI--TALTEPI--DIYSEWIDECERVNNL   83 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i--~~L~epV--DVYs~WiD~~~~~n~~   83 (92)
                      .+-||.||+..  --.+.-..-++-..|..|++.||.+-  ..|+.-|  -.|+--|+.+...+.+
T Consensus        31 n~yCP~Cg~~~--L~~f~NN~PVaDF~C~~C~eeyELKSk~~~l~~~I~dGAY~Tmi~Ri~s~~NP   94 (254)
T PF06044_consen   31 NMYCPNCGSKP--LSKFENNRPVADFYCPNCNEEYELKSKKKKLSNKINDGAYHTMIERITSDNNP   94 (254)
T ss_dssp             H---TTT--SS---EE--------EEE-TTT--EEEEEEEESS--SEEEEEEHHHHHHHHHTT---
T ss_pred             CCcCCCCCChh--HhhccCCCccceeECCCCchHHhhhhhccccCCcccCccHHHHHHHhhccCCC
Confidence            46799999853  23445567789999999999999743  3333332  2577777766655443

The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.

>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=88.53  E-value=0.44  Score=33.38  Aligned_cols=41  Identities=20%  Similarity=0.503  Sum_probs=28.8

Q ss_pred             ccCCCCCCCCeEEEEeec-CCceEEEEcCccCCeeEeec-CCCCc
Q 034528           23 FSCPFCNHGTSVECRIDM-KNLIGEAICNICQESFSTTI-TALTE   65 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk-~~~~g~l~C~~Cg~~~~~~i-~~L~e   65 (92)
                      =.||+|++..  .+++.. ..+...-.|..|+-+|+-.. .+|..
T Consensus        31 ~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~~~~~~~~~   73 (129)
T COG3677          31 VNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTVETGSPLSK   73 (129)
T ss_pred             CcCCCCCccc--eeeECCccccccccccCCcCcceeeeccCcccc
Confidence            4799999987  334433 34578899999999998743 33443

>PF14205 Cys_rich_KTR: Cysteine-rich KTR

Probab=87.70  E-value=0.65  Score=28.83  Aligned_cols=38  Identities=21%  Similarity=0.402  Sum_probs=27.1

Q ss_pred             ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeec
Q 034528           23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI   60 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i   60 (92)
                      --||.||+..-+.+.-|-...-.-+.|..|.+..-..|
T Consensus         5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v   42 (55)
T PF14205_consen    5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDV   42 (55)
T ss_pred             EECCCCCCccceeeecCceeccccccCCCCCceEEEEe
Confidence            35999998765666665555667799999998654433

>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4

Probab=87.58  E-value=0.37  Score=27.87  Aligned_cols=29  Identities=28%  Similarity=0.553  Sum_probs=17.7

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccC
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQ   53 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg   53 (92)
                      .||.|+-..-..|--|+ .+.|.-.|+.|+
T Consensus         5 pCP~CGG~DrFri~~d~-~~~G~~~C~~C~   33 (40)
T PF08273_consen    5 PCPICGGKDRFRIFDDK-DGRGTWICRQCG   33 (40)
T ss_dssp             --TTTT-TTTEEEETT-----S-EEETTTT
T ss_pred             CCCCCcCccccccCcCc-ccCCCEECCCCC
Confidence            69999998877766655 556999999994

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.

>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5

Probab=86.94  E-value=1  Score=30.85  Aligned_cols=32  Identities=19%  Similarity=0.329  Sum_probs=24.2

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES   55 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~   55 (92)
                      ..=-||.|+.+.+.-+   +++++-.+.|..||..
T Consensus        79 ~yVlC~~C~spdT~l~---k~~r~~~l~C~aCGa~  110 (110)
T smart00653       79 EYVLCPECGSPDTELI---KENRLFFLKCEACGAR  110 (110)
T ss_pred             hcEECCCCCCCCcEEE---EeCCeEEEEccccCCC
Confidence            3457999999875443   3477889999999973

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=86.84  E-value=0.34  Score=28.30  Aligned_cols=31  Identities=19%  Similarity=0.383  Sum_probs=21.8

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT   59 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~   59 (92)
                      .|.|..||++  ++  ++   ..+.+.|..||-+--++
T Consensus         2 ~Y~C~~Cg~~--~~--~~---~~~~irC~~CG~rIlyK   32 (44)
T smart00659        2 IYICGECGRE--NE--IK---SKDVVRCRECGYRILYK   32 (44)
T ss_pred             EEECCCCCCE--ee--cC---CCCceECCCCCceEEEE
Confidence            4789999985  33  33   34779999999765443

present in RNA polymerase I, II and III

>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]

Probab=86.56  E-value=1.1  Score=28.89  Aligned_cols=30  Identities=20%  Similarity=0.541  Sum_probs=22.6

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      .||-|+|+   .+.+.+.  .-.+.|.+||..--.
T Consensus        21 kCpdC~N~---q~vFsha--st~V~C~~CG~~l~~   50 (67)
T COG2051          21 KCPDCGNE---QVVFSHA--STVVTCLICGTTLAE   50 (67)
T ss_pred             ECCCCCCE---EEEeccC--ceEEEecccccEEEe
Confidence            79999995   5666554  367899999986544

>smart00531 TFIIE Transcription initiation factor IIE

Probab=86.43  E-value=0.2  Score=35.19  Aligned_cols=40  Identities=18%  Similarity=0.462  Sum_probs=24.9

Q ss_pred             CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528           20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT   59 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~   59 (92)
                      ...|.||+|+..=+..=-+......|...|..||..-...
T Consensus        97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~  136 (147)
T smart00531       97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED  136 (147)
T ss_pred             CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence            4689999999643221111111235779999999876543

>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins

Probab=86.26  E-value=0.31  Score=28.81  Aligned_cols=32  Identities=25%  Similarity=0.837  Sum_probs=19.4

Q ss_pred             cccCCCCCCCCeEEEE-e------ecCCceEEEEcCccCCe
Q 034528           22 VFSCPFCNHGTSVECR-I------DMKNLIGEAICNICQES   55 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vk-i------dk~~~~g~l~C~~Cg~~   55 (92)
                      .|.||||+..  ++.. +      .-......+.|.+|...
T Consensus         2 ~f~CP~C~~~--~~~~~L~~H~~~~H~~~~~~v~CPiC~~~   40 (54)
T PF05605_consen    2 SFTCPYCGKG--FSESSLVEHCEDEHRSESKNVVCPICSSR   40 (54)
T ss_pred             CcCCCCCCCc--cCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence            5999999973  3221 1      00122336899999864

Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.

>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []

Probab=86.24  E-value=0.73  Score=32.23  Aligned_cols=32  Identities=19%  Similarity=0.327  Sum_probs=25.0

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES   55 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~   55 (92)
                      +.--||.|+.+.+.-++-   .++-.+.|..||.+
T Consensus        92 ~yVlC~~C~spdT~l~k~---~r~~~l~C~aCGa~  123 (125)
T PF01873_consen   92 EYVLCPECGSPDTELIKE---GRLIFLKCKACGAS  123 (125)
T ss_dssp             HHSSCTSTSSSSEEEEEE---TTCCEEEETTTSCE
T ss_pred             HEEEcCCCCCCccEEEEc---CCEEEEEecccCCc
Confidence            445799999988654443   77789999999985

Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....

>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family

Probab=86.14  E-value=0.38  Score=27.92  Aligned_cols=30  Identities=23%  Similarity=0.438  Sum_probs=21.5

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQE   54 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~   54 (92)
                      .|.|+.||+.-.+...++.   ...+.|-.||.
T Consensus         5 ey~C~~Cg~~fe~~~~~~~---~~~~~CP~Cg~   34 (52)
T TIGR02605         5 EYRCTACGHRFEVLQKMSD---DPLATCPECGG   34 (52)
T ss_pred             EEEeCCCCCEeEEEEecCC---CCCCCCCCCCC
Confidence            5899999986545444432   35678999997

This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.

>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC

Probab=86.12  E-value=1.8  Score=27.75  Aligned_cols=36  Identities=17%  Similarity=0.217  Sum_probs=27.8

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecC
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTIT   61 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~   61 (92)
                      .||-|+.-+++..  -+.+++-.+.|-.||-+.+.+..
T Consensus        10 ~CP~C~~~D~i~~--~~e~~ve~vECV~CGy~e~~~~~   45 (71)
T PF09526_consen   10 VCPKCQAMDTIMM--WRENGVEYVECVECGYTERQPDQ   45 (71)
T ss_pred             cCCCCcCccEEEE--EEeCCceEEEecCCCCeeccCCc
Confidence            6999999875554  44667999999999987665444

Members are found in various proteobacteria.

>TIGR03831 YgiT_finger YgiT-type zinc finger domain

Probab=86.09  E-value=1.7  Score=23.91  Aligned_cols=12  Identities=25%  Similarity=0.775  Sum_probs=9.2

Q ss_pred             EEcCccCCeeEe
Q 034528           47 AICNICQESFST   58 (92)
Q Consensus        47 l~C~~Cg~~~~~   58 (92)
                      ..|..||+.|-+
T Consensus        33 ~~C~~CGE~~~~   44 (46)
T TIGR03831        33 LVCPQCGEEYLD   44 (46)
T ss_pred             cccccCCCEeeC
Confidence            469999997743

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.

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=85.86  E-value=0.35  Score=25.50  Aligned_cols=24  Identities=25%  Similarity=0.652  Sum_probs=15.1

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFS   57 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~   57 (92)
                      +||.|+++-          ..+...|..||-.|+
T Consensus         2 ~CP~C~~~V----------~~~~~~Cp~CG~~F~   25 (26)
T PF10571_consen    2 TCPECGAEV----------PESAKFCPHCGYDFE   25 (26)
T ss_pred             cCCCCcCCc----------hhhcCcCCCCCCCCc
Confidence            588888742          234456778877664

Several members are annotated as putative helicases.

>TIGR01385 TFSII transcription elongation factor S-II

Probab=85.70  E-value=1.4  Score=34.86  Aligned_cols=40  Identities=13%  Similarity=0.463  Sum_probs=29.2

Q ss_pred             CCCccccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeE
Q 034528           18 KLDTVFSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFS   57 (92)
Q Consensus        18 kl~~~F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~   57 (92)
                      .....|.||.|+|.+++-..+.-.    -+.-...|..||.++.
T Consensus       254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~  297 (299)
T TIGR01385       254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK  297 (299)
T ss_pred             CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence            344579999999988776655221    3456789999998765

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.

>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]

Probab=85.45  E-value=0.45  Score=37.44  Aligned_cols=41  Identities=32%  Similarity=0.538  Sum_probs=29.7

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHH
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWID   75 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD   75 (92)
                      .||.||..     .+..+..-|.+.|..||+--+      +..||-..+|--
T Consensus         3 ~CpeCg~~-----~~~~d~~~ge~VC~~CG~Vi~------~~~id~gpewr~   43 (285)
T COG1405           3 SCPECGST-----NIITDYERGEIVCADCGLVLE------DSLIDPGPEWRA   43 (285)
T ss_pred             CCCCCCCc-----cceeeccCCeEEeccCCEEec------cccccCCCCccc
Confidence            69999974     333344479999999998543      357788888873

>TIGR02443 conserved hypothetical metal-binding protein

Probab=85.28  E-value=1.6  Score=27.40  Aligned_cols=33  Identities=21%  Similarity=0.368  Sum_probs=26.6

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      .||-|+.-+++.  +-+.+++-.+.|-.||-+-+-
T Consensus        11 ~CP~C~~~Dtl~--~~~e~~~e~vECv~Cg~~~~~   43 (59)
T TIGR02443        11 VCPACSAQDTLA--MWKENNIELVECVECGYQEQQ   43 (59)
T ss_pred             cCCCCcCccEEE--EEEeCCceEEEeccCCCcccc
Confidence            699999988774  446788899999999976543

Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=85.14  E-value=0.41  Score=42.57  Aligned_cols=37  Identities=22%  Similarity=0.569  Sum_probs=28.6

Q ss_pred             CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      ...|.|..|||+  +.+.+++..----..|..|+.++++
T Consensus       262 ~afFrC~vC~~~--~~ve~drg~i~eP~~C~~C~~~~~~  298 (804)
T KOG0478|consen  262 EAFFRCSVCGHE--IAVESDRGRIKEPMLCKECGTTNSF  298 (804)
T ss_pred             hHhhhhhhcCce--EEEEeecCccCCCcccccccCcccc
Confidence            368999999995  7777776554455789999988665

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

Probab=85.10  E-value=0.74  Score=32.91  Aligned_cols=27  Identities=26%  Similarity=0.517  Sum_probs=20.0

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF   56 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~   56 (92)
                      --+||-||.+      +.+  ..|.+.|-+||.++
T Consensus        28 ~~hCp~Cg~P------LF~--KdG~v~CPvC~~~~   54 (131)
T COG1645          28 AKHCPKCGTP------LFR--KDGEVFCPVCGYRE   54 (131)
T ss_pred             HhhCcccCCc------cee--eCCeEECCCCCceE
Confidence            3579999975      222  55999999999543

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=84.96  E-value=1.1  Score=31.23  Aligned_cols=44  Identities=18%  Similarity=0.403  Sum_probs=27.6

Q ss_pred             CCCCCCCCeEEEEeecCCceEEEEcCccCCeeE----e-ecCCCCcchhhhhhHHHHHHhhc
Q 034528           25 CPFCNHGTSVECRIDMKNLIGEAICNICQESFS----T-TITALTEPIDIYSEWIDECERVN   81 (92)
Q Consensus        25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~----~-~i~~L~epVDVYs~WiD~~~~~n   81 (92)
                      ||.||++          ..+-.+.|..|+...+    . ++..|+.. |  -+||-.+....
T Consensus         1 CPvCg~~----------l~vt~l~C~~C~t~i~G~F~l~~~~~L~~E-~--~~Fi~~Fi~~r   49 (113)
T PF09862_consen    1 CPVCGGE----------LVVTRLKCPSCGTEIEGEFELPWFARLSPE-Q--LEFIKLFIKNR   49 (113)
T ss_pred             CCCCCCc----------eEEEEEEcCCCCCEEEeeeccchhhcCCHH-H--HHHHHHHHHhc
Confidence            9999984          3456789999998643    3 34445433 2  34555555444

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=84.74  E-value=0.51  Score=29.64  Aligned_cols=34  Identities=24%  Similarity=0.429  Sum_probs=19.1

Q ss_pred             CccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528           20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE   54 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~   54 (92)
                      -+.|.||.||.+.-..+.-=++.+ ..-.|..||.
T Consensus        23 ~~~F~CPnCG~~~I~RC~~CRk~~-~~Y~CP~CGF   56 (59)
T PRK14890         23 AVKFLCPNCGEVIIYRCEKCRKQS-NPYTCPKCGF   56 (59)
T ss_pred             cCEeeCCCCCCeeEeechhHHhcC-CceECCCCCC
Confidence            378999999973222222222222 3456777775

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=84.49  E-value=0.45  Score=24.62  Aligned_cols=22  Identities=23%  Similarity=0.537  Sum_probs=15.3

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQES   55 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~   55 (92)
                      .||.||++.          ..+...|..||..
T Consensus         4 ~Cp~Cg~~~----------~~~~~fC~~CG~~   25 (26)
T PF13248_consen    4 FCPNCGAEI----------DPDAKFCPNCGAK   25 (26)
T ss_pred             CCcccCCcC----------CcccccChhhCCC
Confidence            599999842          2345678888864

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=84.43  E-value=0.79  Score=35.80  Aligned_cols=32  Identities=25%  Similarity=0.508  Sum_probs=22.7

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      .-.||.||..   .+..|  ..-|.+.|..||.-.+.
T Consensus        11 ~~~Cp~Cg~~---~iv~d--~~~Ge~vC~~CG~Vl~e   42 (310)
T PRK00423         11 KLVCPECGSD---KLIYD--YERGEIVCADCGLVIEE   42 (310)
T ss_pred             CCcCcCCCCC---CeeEE--CCCCeEeecccCCcccc
Confidence            3469999963   34344  35699999999986543

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

Probab=84.29  E-value=0.55  Score=24.57  Aligned_cols=12  Identities=33%  Similarity=0.911  Sum_probs=10.0

Q ss_pred             CCCccccCCCCC
Q 034528           18 KLDTVFSCPFCN   29 (92)
Q Consensus        18 kl~~~F~CPfC~   29 (92)
                      ..-..|.||.||
T Consensus        12 ~~~v~f~CPnCG   23 (24)
T PF07754_consen   12 EQAVPFPCPNCG   23 (24)
T ss_pred             ccCceEeCCCCC
Confidence            346799999998

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

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=84.07  E-value=0.9  Score=36.32  Aligned_cols=38  Identities=18%  Similarity=0.468  Sum_probs=25.9

Q ss_pred             CccccCCCCCCCCeEEE-EeecCCceEEEEcCccCCeeE
Q 034528           20 DTVFSCPFCNHGTSVEC-RIDMKNLIGEAICNICQESFS   57 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~v-kidk~~~~g~l~C~~Cg~~~~   57 (92)
                      +..=.||.||..-.+++ .+.-..|.-.+.|..|+....
T Consensus       185 ~~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~  223 (309)
T PRK03564        185 EQRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWH  223 (309)
T ss_pred             cCCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccc
Confidence            45678999998765553 343456777888888887543

>COG1779 C4-type Zn-finger protein [General function prediction only]

Probab=83.82  E-value=1.3  Score=33.77  Aligned_cols=38  Identities=21%  Similarity=0.640  Sum_probs=26.1

Q ss_pred             CCCccccCCCCCCCCeEEEEeec-------CCceEEEEcCccCCeeE
Q 034528           18 KLDTVFSCPFCNHGTSVECRIDM-------KNLIGEAICNICQESFS   57 (92)
Q Consensus        18 kl~~~F~CPfC~~~~sV~vkidk-------~~~~g~l~C~~Cg~~~~   57 (92)
                      -..+.-+||.||+  .+...+..       .-.+-+..|..||-++.
T Consensus        10 ~~~~~~~CPvCg~--~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~   54 (201)
T COG1779          10 EFETRIDCPVCGG--TLKAHMYLYDIPYFGEVLISTGVCERCGYRST   54 (201)
T ss_pred             eeeeeecCCcccc--eeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence            3456779999998  34433322       23567899999998764

>PRK12336 translation initiation factor IF-2 subunit beta; Provisional

Probab=83.82  E-value=1.5  Score=32.60  Aligned_cols=35  Identities=11%  Similarity=0.226  Sum_probs=26.6

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      ..=.||.|+++.+--+   ++..+-.+.|..||.....
T Consensus        97 ~yV~C~~C~~pdT~l~---k~~~~~~l~C~aCGa~~~v  131 (201)
T PRK12336         97 EYVICSECGLPDTRLV---KEDRVLMLRCDACGAHRPV  131 (201)
T ss_pred             heEECCCCCCCCcEEE---EcCCeEEEEcccCCCCccc
Confidence            3457999999876544   3467889999999987543

>PRK05978 hypothetical protein; Provisional

Probab=83.42  E-value=0.52  Score=34.11  Aligned_cols=31  Identities=29%  Similarity=0.566  Sum_probs=21.5

Q ss_pred             ccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           23 FSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      =.||.||..+     |-+.--.-.-+|.+||+.|+.
T Consensus        34 grCP~CG~G~-----LF~g~Lkv~~~C~~CG~~~~~   64 (148)
T PRK05978         34 GRCPACGEGK-----LFRAFLKPVDHCAACGEDFTH   64 (148)
T ss_pred             CcCCCCCCCc-----ccccccccCCCccccCCcccc
Confidence            3699999754     223333345689999998875

>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.42  E-value=1.4  Score=28.12  Aligned_cols=35  Identities=14%  Similarity=0.333  Sum_probs=23.1

Q ss_pred             cccCCCCCCCCeEEEEeecC---CceEEEEcCccCCeeEe
Q 034528           22 VFSCPFCNHGTSVECRIDMK---NLIGEAICNICQESFST   58 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~---~~~g~l~C~~Cg~~~~~   58 (92)
                      .|+|..|++..+  =.|.+.   .|+-.+.|..|+..+-.
T Consensus         4 ~FTC~~C~~Rs~--~~~sk~aY~~GvViv~C~gC~~~HlI   41 (66)
T PF05180_consen    4 TFTCNKCGTRSA--KMFSKQAYHKGVVIVQCPGCKNRHLI   41 (66)
T ss_dssp             EEEETTTTEEEE--EEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred             EEEcCCCCCccc--eeeCHHHHhCCeEEEECCCCcceeee
Confidence            699999997322  233333   79999999999987654

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. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=83.39  E-value=3.6  Score=32.93  Aligned_cols=60  Identities=15%  Similarity=0.293  Sum_probs=39.2

Q ss_pred             cccCCCCCCCCeEEEE-eecC-CceEEEEcCccCCeeEe---ecCCCCcch--hhhhhHHHHHHhhc
Q 034528           22 VFSCPFCNHGTSVECR-IDMK-NLIGEAICNICQESFST---TITALTEPI--DIYSEWIDECERVN   81 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vk-idk~-~~~g~l~C~~Cg~~~~~---~i~~L~epV--DVYs~WiD~~~~~n   81 (92)
                      .-.||+||+.+.+..- ++-. ..+-.-+|..|+.+.-+   ..++..+|+  |+-+--+|..-+..
T Consensus       226 R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~p~adDlatL~LDl~a~e~  292 (309)
T PRK03564        226 RVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQEKDPKVEAVADDLASLVLDARMEQE  292 (309)
T ss_pred             CccCCCCCCCCceeeeeecCCCcceEeeecccccccceecccccCCCCCcchhHHhhhHhHHHHHhc
Confidence            3479999987766643 4433 34556799999987554   233444455  77888888776543

>PHA02540 61 DNA primase; Provisional

Probab=83.08  E-value=1.4  Score=35.53  Aligned_cols=50  Identities=24%  Similarity=0.347  Sum_probs=34.5

Q ss_pred             ccccCCCCCCCC------eEEEEeecCCceEEEEcCccCCe-----eEeecCCCCcchhhhhhHHHHH
Q 034528           21 TVFSCPFCNHGT------SVECRIDMKNLIGEAICNICQES-----FSTTITALTEPIDIYSEWIDEC   77 (92)
Q Consensus        21 ~~F~CPfC~~~~------sV~vkidk~~~~g~l~C~~Cg~~-----~~~~i~~L~epVDVYs~WiD~~   77 (92)
                      =.|.|||||..+      |..|.-++.  ...-+|-.||.+     |-+.+..|+     |.+|+-..
T Consensus        26 ~~~~CPf~~ds~~~~~kpsF~V~p~k~--~~~yhCFgCGa~Gd~i~Flme~e~ls-----f~Eav~~l   86 (337)
T PHA02540         26 YNFRCPICGDSQKDKNKARGWIYEKKD--GGVFKCHNCGYHRPFGNFLKDYEPDL-----YREYIMER   86 (337)
T ss_pred             EEecCCCCCCccccCcCCcEEEeccCC--ceEEEecCCCCCCCHHHHHHHhcCCC-----hHHHHHHH
Confidence            478999999743      566655444  578899999986     556666664     55676633

>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=83.05  E-value=0.61  Score=28.34  Aligned_cols=36  Identities=19%  Similarity=0.356  Sum_probs=24.8

Q ss_pred             CCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeec
Q 034528           19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI   60 (92)
Q Consensus        19 l~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i   60 (92)
                      --|.=.||.||+...-      ........|..||..+.--+
T Consensus        25 ~~TSq~C~~CG~~~~~------~~~~r~~~C~~Cg~~~~rD~   60 (69)
T PF07282_consen   25 AYTSQTCPRCGHRNKK------RRSGRVFTCPNCGFEMDRDV   60 (69)
T ss_pred             CCCccCccCccccccc------ccccceEEcCCCCCEECcHH
Confidence            3366789999984311      34556899999998765433

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

>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases

Probab=82.22  E-value=1.8  Score=24.39  Aligned_cols=30  Identities=20%  Similarity=0.403  Sum_probs=17.9

Q ss_pred             ccCCCCCCCCeEEEEeec-CCceEEEEcCccC
Q 034528           23 FSCPFCNHGTSVECRIDM-KNLIGEAICNICQ   53 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk-~~~~g~l~C~~Cg   53 (92)
                      -.||+|+...+| ++--+ ..|.-.-.|..|.
T Consensus         6 v~CP~C~s~~~v-~k~G~~~~G~qryrC~~C~   36 (36)
T PF03811_consen    6 VHCPRCQSTEGV-KKNGKSPSGHQRYRCKDCR   36 (36)
T ss_pred             eeCCCCCCCCcc-eeCCCCCCCCEeEecCcCC
Confidence            479999986533 22222 2455567777773

Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated

>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]

Probab=82.05  E-value=0.6  Score=31.53  Aligned_cols=31  Identities=19%  Similarity=0.722  Sum_probs=23.5

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFS   57 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~   57 (92)
                      ..++|+|||.. +    | +..-+|+-.|+.|...+.
T Consensus        35 aky~CsfCGK~-~----v-KR~AvGiW~C~~C~kv~a   65 (92)
T KOG0402|consen   35 AKYTCSFCGKK-T----V-KRKAVGIWKCGSCKKVVA   65 (92)
T ss_pred             hhhhhhhcchh-h----h-hhhceeEEecCCccceec
Confidence            56899999973 2    2 235789999999997654

>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=82.01  E-value=0.94  Score=38.04  Aligned_cols=55  Identities=18%  Similarity=0.342  Sum_probs=45.5

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhhc
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVN   81 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~n   81 (92)
                      ..=+||-|.      |.|.+.+|--.-+|..||+.|-.--..+..|.|.|.-|-|...+-.
T Consensus       367 N~krCP~C~------v~IEr~eGCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~~s~c~  421 (445)
T KOG1814|consen  367 NSKRCPKCK------VVIERSEGCNKMHCTKCGTYFCWICAELLYPENPYKHFSEPGSECY  421 (445)
T ss_pred             cCCCCCccc------ceeecCCCccceeeccccccceeehhhhcCCCChhhhhcCCcCccc
Confidence            345799998      3567788889999999999999999999999999999887654443

>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]

Probab=81.93  E-value=0.59  Score=35.60  Aligned_cols=34  Identities=18%  Similarity=0.362  Sum_probs=23.1

Q ss_pred             cccCCCCCCCCeEEEEeecC-CceEEEEcCccCCee
Q 034528           22 VFSCPFCNHGTSVECRIDMK-NLIGEAICNICQESF   56 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~-~~~g~l~C~~Cg~~~   56 (92)
                      ...||.|+.+. +.=.+-+. ..-..+.|..||.-+
T Consensus         6 y~~Cp~Cg~ee-v~hEVik~~g~~~lvrC~eCG~V~   40 (201)
T COG1326           6 YIECPSCGSEE-VSHEVIKERGREPLVRCEECGTVH   40 (201)
T ss_pred             EEECCCCCcch-hhHHHHHhcCCceEEEccCCCcEe
Confidence            46899999543 42233333 344789999999988

>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=81.72  E-value=2.2  Score=30.78  Aligned_cols=34  Identities=18%  Similarity=0.383  Sum_probs=18.6

Q ss_pred             cCCCCCCCCeEEEEee-----cCCceEEEEcCccCCeeE
Q 034528           24 SCPFCNHGTSVECRID-----MKNLIGEAICNICQESFS   57 (92)
Q Consensus        24 ~CPfC~~~~sV~vkid-----k~~~~g~l~C~~Cg~~~~   57 (92)
                      .||.|++.....+.+.     +.--+-...|..||-++.
T Consensus         3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~   41 (161)
T PF03367_consen    3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNN   41 (161)
T ss_dssp             E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEE
T ss_pred             cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEee
Confidence            5999998654433332     234556789999997754

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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.

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

Probab=81.58  E-value=0.38  Score=29.77  Aligned_cols=24  Identities=21%  Similarity=0.552  Sum_probs=16.4

Q ss_pred             EEEeecCCceEEEEcCccCCeeEe
Q 034528           35 ECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        35 ~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      .+-++-.-.-|.+.|..||..|-.
T Consensus        42 ~~l~~~~i~eg~L~Cp~c~r~YPI   65 (68)
T PF03966_consen   42 HVLLEVEIVEGELICPECGREYPI   65 (68)
T ss_dssp             EHHCTEETTTTEEEETTTTEEEEE
T ss_pred             hhhhcccccCCEEEcCCCCCEEeC
Confidence            333333444589999999998854

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

>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A

Probab=81.55  E-value=0.58  Score=24.00  Aligned_cols=11  Identities=27%  Similarity=1.298  Sum_probs=8.8

Q ss_pred             CccccCCCCCC
Q 034528           20 DTVFSCPFCNH   30 (92)
Q Consensus        20 ~~~F~CPfC~~   30 (92)
                      ++.|.||.|+.
T Consensus        12 ~k~~~C~~C~k   22 (26)
T PF13465_consen   12 EKPYKCPYCGK   22 (26)
T ss_dssp             SSSEEESSSSE
T ss_pred             CCCCCCCCCcC
Confidence            46799999984

...

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=81.54  E-value=1.4  Score=37.26  Aligned_cols=33  Identities=21%  Similarity=0.519  Sum_probs=25.8

Q ss_pred             ccCCCCCCCCeEE---EEeec--CCceEEEEcCccCCe
Q 034528           23 FSCPFCNHGTSVE---CRIDM--KNLIGEAICNICQES   55 (92)
Q Consensus        23 F~CPfC~~~~sV~---vkidk--~~~~g~l~C~~Cg~~   55 (92)
                      ..||.|||.+.+.   ++.+.  ....+...|..||..
T Consensus       201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~  238 (557)
T PF05876_consen  201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCE  238 (557)
T ss_pred             ccCCCCCCCccccccceeecCCCCccceEEECCCCcCC
Confidence            4799999998876   55543  356789999999975

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein

Probab=81.51  E-value=1.5  Score=36.66  Aligned_cols=48  Identities=21%  Similarity=0.406  Sum_probs=32.0

Q ss_pred             ccccCCCCCCCCeEEEEeecC------------CceEEEEcCccCCeeEeecCC-CCcchhhhh
Q 034528           21 TVFSCPFCNHGTSVECRIDMK------------NLIGEAICNICQESFSTTITA-LTEPIDIYS   71 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~------------~~~g~l~C~~Cg~~~~~~i~~-L~epVDVYs   71 (92)
                      .-|+||.|.+.  +++.....            .+...+.|.-|.=+.. .|+- .+.|=+++.
T Consensus        51 ~Cf~CP~C~~~--L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~Wss~-~igi~Fdkpt~l~~  111 (483)
T PF05502_consen   51 NCFDCPICFSP--LSVRASDTPPSPPDPSSDSGGKPYYLSCSYCRWSSR-DIGIKFDKPTGLRA  111 (483)
T ss_pred             ccccCCCCCCc--ceeEecccccccccccccCCCCCEEEECCCceeecc-ccCccccCchhHHH
Confidence            57999999984  55554432            4677899999986532 3333 355656665

p62 binds directly to the Arp1 subunit of dynactin [, ].

>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454

Probab=80.98  E-value=0.27  Score=36.18  Aligned_cols=60  Identities=25%  Similarity=0.406  Sum_probs=39.7

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceE--------EEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhhcCccccc
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIG--------EAICNICQESFSTTITALTEPIDIYSEWIDECERVNNLEDDG   87 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g--------~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~n~~~~~~   87 (92)
                      +.-.||.|++.  +.=.- .-.++.        --.|.+||..|-...+.|    +.+.+-+++.++....+++.
T Consensus        38 tI~~Cp~C~~~--IrG~y-~v~gv~~~g~~~~~PsYC~~CGkpyPWt~~~L----~aa~el~ee~eeLs~deke~  105 (158)
T PF10083_consen   38 TITSCPNCSTP--IRGDY-HVEGVFGLGGHYEAPSYCHNCGKPYPWTENAL----EAANELIEEDEELSPDEKEQ  105 (158)
T ss_pred             HHHHCcCCCCC--CCCce-ecCCeeeeCCCCCCChhHHhCCCCCchHHHHH----HHHHHHHHHhhcCCHHHHHH
Confidence            45689999984  21110 012333        348999999997766555    77888899888887665554

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=80.59  E-value=2.5  Score=33.69  Aligned_cols=59  Identities=15%  Similarity=0.345  Sum_probs=34.8

Q ss_pred             cccCCCCCCCCeEE-EEeec---CCceEEEEcCccCCeeEe---ecCCCCcch--hhhhhHHHHHHhh
Q 034528           22 VFSCPFCNHGTSVE-CRIDM---KNLIGEAICNICQESFST---TITALTEPI--DIYSEWIDECERV   80 (92)
Q Consensus        22 ~F~CPfC~~~~sV~-vkidk---~~~~g~l~C~~Cg~~~~~---~i~~L~epV--DVYs~WiD~~~~~   80 (92)
                      .-.||+||+.+.+. ..++-   ..++-.-+|..|+.+.-+   ...+..+|+  |+=|--+|...+.
T Consensus       224 R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~~~~adDlaSL~LD~~a~e  291 (305)
T TIGR01562       224 RVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLKILYQEKDPHADAVADDLASLALDMRMAE  291 (305)
T ss_pred             CccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchhhhccccCCccCchHHHHhhhHhhHHHHh
Confidence            34699999877664 33433   123445589999976433   233444555  6666666665543

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).

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=80.21  E-value=0.72  Score=29.19  Aligned_cols=34  Identities=24%  Similarity=0.372  Sum_probs=19.5

Q ss_pred             CccccCCCCCCCCeEEEEeecCCceEEEEcCccCC
Q 034528           20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQE   54 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~   54 (92)
                      -..|.||.||.+.-..+..=++. -..-.|..||.
T Consensus        25 ~v~F~CPnCGe~~I~Rc~~CRk~-g~~Y~Cp~CGF   58 (61)
T COG2888          25 AVKFPCPNCGEVEIYRCAKCRKL-GNPYRCPKCGF   58 (61)
T ss_pred             eeEeeCCCCCceeeehhhhHHHc-CCceECCCcCc
Confidence            36899999996322222222222 23457888885

>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE

Probab=80.21  E-value=1  Score=35.91  Aligned_cols=36  Identities=14%  Similarity=0.349  Sum_probs=24.0

Q ss_pred             cccCCCCCCCCeEEEEee--cCCceEEEEcCccCCeeE
Q 034528           22 VFSCPFCNHGTSVECRID--MKNLIGEAICNICQESFS   57 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkid--k~~~~g~l~C~~Cg~~~~   57 (92)
                      .=.||.||..-.+++-..  .+.|.-.++|..|+..+.
T Consensus       184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~  221 (305)
T TIGR01562       184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWH  221 (305)
T ss_pred             CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccc
Confidence            448999998765554333  246677888888876543

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).

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	92
1wii_A	85	Solution Structure Of Rsgi Ruh-025, A Duf701 Domain		2e-13

>pdb|1WII|A Chain A, Solution Structure Of Rsgi Ruh-025, A Duf701 Domain From Mouse Cdna Length = 85

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 40/60 (66%)
Query: 19 LDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE 78
          L+T F+CPFCNH  S + ++D     G   C +C E F T IT L+EP+D+YS+WID CE
Sbjct: 20 LETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACE 79

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	92
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	8e-34
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	1e-06

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4 Length = 85

 Score =  110 bits (276), Expect = 8e-34
 Identities = 36/83 (43%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 2  GKRKSRAK--PPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59
          G   S  +  PP KK    L+T F+CPFCNH  S + ++D     G   C +C E F T 
Sbjct: 1  GSSGSSGRKPPPKKKMTGTLETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTP 60

Query: 60 ITALTEPIDIYSEWIDECERVNN 82
          IT L+EP+D+YS+WID CE   +
Sbjct: 61 ITYLSEPVDVYSDWIDACESGPS 83

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 20/78 (25%)

Query: 1  MGKRKSRAKPPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLI-----GEAICNICQES 55
          M  R+S  K   ++  + L+ V +CP        EC++    ++     G+ +C +C   
Sbjct: 1  MMTRESIDKRAGRRGPN-LNIVLTCP--------ECKVYPPKIVERFSEGDVVCALCGLV 51

Query: 56 FSTTITALTEPIDIYSEW 73
           S  +      +D  SEW
Sbjct: 52 LSDKL------VDTRSEW 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	92
1wii_A	85	Hypothetical UPF0222 protein MGC4549; domain of un	100.0
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	96.02
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	95.86
4a17_Y	103	RPL37A, 60S ribosomal protein L32; eukaryotic ribo	95.67
3iz5_m	92	60S ribosomal protein L43 (L37AE); eukaryotic ribo	95.27
3j21_i	83	50S ribosomal protein L37AE; archaea, archaeal, KI	95.19
3izc_m	92	60S ribosomal protein RPL43 (L37AE); eukaryotic ri	95.07
1ffk_W	73	Ribosomal protein L37AE; ribosome assembly, RNA-RN	95.06
3jyw_9	72	60S ribosomal protein L43; eukaryotic ribosome, RA	94.89
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	94.76
1k81_A	36	EIF-2-beta, probable translation initiation factor	94.43
3cc2_Z	116	50S ribosomal protein L37AE, 50S ribosomal protein	93.73
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	93.59
3ga8_A	78	HTH-type transcriptional regulator MQSA (YGIT/B30;	93.18
1tfi_A	50	Transcriptional elongation factor SII; transcripti	92.96
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	92.24
2js4_A	70	UPF0434 protein BB2007; NESG, northeast structural	90.53
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	90.32
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	89.71
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	89.2
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	88.98
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	88.92
2pk7_A	69	Uncharacterized protein; NESG, PLR1, putative tetr	88.61
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	88.4
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	87.91
2hf1_A	68	Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A	87.82
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	87.79
2apo_B	60	Ribosome biogenesis protein NOP10; protein-protein	87.7
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	87.2
1nui_A	255	DNA primase/helicase; zinc-biding domain, toprim f	87.17
2e9h_A	157	EIF-5, eukaryotic translation initiation factor 5;	86.91
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	86.84
2aus_D	60	NOP10, ribosome biogenesis protein NOP10; isomeras	86.34
4esj_A	257	Type-2 restriction enzyme DPNI; restriction endonu	85.76
2kpi_A	56	Uncharacterized protein SCO3027; zinc finger, PSI-	85.14
1gh9_A	71	8.3 kDa protein (gene MTH1184); beta+alpha complex	83.81
2jny_A	67	Uncharacterized BCR; structure, CGR1, NESG, struct	83.76
4bbr_M	345	Transcription initiation factor IIB; RNA polymeras	83.46
2g2k_A	170	EIF-5, eukaryotic translation initiation factor 5;	82.65
2xzm_6	81	RPS27E; ribosome, translation; 3.93A {Tetrahymena	82.47
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	82.47
3k7a_M	345	Transcription initiation factor IIB; RNA polymeras	81.9
3po3_S	178	Transcription elongation factor S-II; RNA polymera	81.59

>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function, zinc finger, metal-binding protein, structural genomics; NMR {Mus musculus} SCOP: g.41.3.4

Probab=100.00  E-value=2.6e-45  Score=242.00  Aligned_cols=82  Identities=45%  Similarity=0.916  Sum_probs=75.0

Q ss_pred             CCCccCCCCCCCCC-CCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhh
Q 034528            2 GKRKSRAKPPPKKR-VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERV   80 (92)
Q Consensus         2 GkRK~k~k~~~kk~-~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~   80 (92)
                      |||||++||++|++ .++|||+|+||||||++||+|+||++.++|+|+|++||++|+++||+|+|||||||+|||+|+++
T Consensus         2 ~rRKs~~k~~~k~k~~~~L~t~F~CPfCnh~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epiDVYs~WiDac~~~   81 (85)
T 1wii_A            2 SSGSSGRKPPPKKKMTGTLETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACESG   81 (85)
T ss_dssp             CCCCCCCCCCCCCCCCCCCSSCCCCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEEECCSSCCTTHHHHHHHHHHHHC
T ss_pred             CCccccCCCCCCcccCCCCCCeEcCCCCCCCCeEEEEEEccCCEEEEEcccCCCeEEeccCccCcchhhHHHHHHHHHHH
Confidence            45666667776665 48999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCc
Q 034528           81 NNL   83 (92)
Q Consensus        81 n~~   83 (92)
                      |++
T Consensus        82 ~~~   84 (85)
T 1wii_A           82 PSS   84 (85)
T ss_dssp             CCC
T ss_pred             hhc
Confidence            974

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=96.02  E-value=0.0028  Score=40.80  Aligned_cols=45  Identities=20%  Similarity=0.342  Sum_probs=31.8

Q ss_pred             CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhh
Q 034528           20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIY   70 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY   70 (92)
                      ...|.|||||.+. +     .....|+..|..||..|.--.-.++.|.-+.
T Consensus        25 ~~~y~Cp~CG~~~-v-----~r~atGiW~C~~Cg~~~aggay~~~t~~~~~   69 (83)
T 1vq8_Z           25 NEDHACPNCGEDR-V-----DRQGTGIWQCSYCDYKFTGGSYKPETPGGKT   69 (83)
T ss_dssp             HSCEECSSSCCEE-E-----EEEETTEEEETTTCCEEECCSSSSSCHHHHH
T ss_pred             cccCcCCCCCCcc-e-----eccCCCeEECCCCCCEecCCEecccchHHHH
Confidence            4689999999731 1     1234689999999999987655555665544

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

Probab=95.86  E-value=0.0045  Score=35.40  Aligned_cols=33  Identities=27%  Similarity=0.540  Sum_probs=24.4

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      ..+.||.|+..   .+..|..  .|.+.|..||+.|..
T Consensus         4 ~~~~CP~C~~~---~l~~d~~--~gelvC~~CG~v~~e   36 (50)
T 1pft_A            4 KQKVCPACESA---ELIYDPE--RGEIVCAKCGYVIEE   36 (50)
T ss_dssp             SCCSCTTTSCC---CEEEETT--TTEEEESSSCCBCCC
T ss_pred             ccEeCcCCCCc---ceEEcCC--CCeEECcccCCcccc
Confidence            45789999974   2445544  467999999998865

>4a17_Y RPL37A, 60S ribosomal protein L32; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_Y 4a1c_Y 4a1e_Y

Probab=95.67  E-value=0.0052  Score=41.39  Aligned_cols=58  Identities=17%  Similarity=0.438  Sum_probs=37.9

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhh-hhHHHHHHhhcCcc
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIY-SEWIDECERVNNLE   84 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY-s~WiD~~~~~n~~~   84 (92)
                      ..+.|||||..   .|+-   ..+|+-.|+.|+..|.--.-.++.|.-+. ..=|..+.|..+++
T Consensus        35 aky~CpfCgk~---~vKR---~a~GIW~C~kCg~~~AGGAy~~~T~~a~tv~~~irrl~e~~~~~   93 (103)
T 4a17_Y           35 AKYGCPFCGKV---AVKR---AAVGIWKCKPCKKIIAGGAWELTTPPAVTAKTTMNRLKKLQEEQ   93 (103)
T ss_dssp             SCEECTTTCCE---EEEE---EETTEEEETTTTEEEECCSSCSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCc---eeee---cCcceEEcCCCCCEEeCCcccCCCcHHHHHHHHHHHHHHHHHHH
Confidence            57899999973   3333   45789999999999987555555554433 22355555555443

>3j21_i 50S ribosomal protein L37AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=95.19  E-value=0.0081  Score=38.96  Aligned_cols=40  Identities=20%  Similarity=0.446  Sum_probs=28.7

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcc
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEP   66 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~ep   66 (92)
                      ..+.||||+...   |+-   ..+|+-.|+.|+..|.--.-.++.|
T Consensus        34 ~ky~CpfCGk~~---vkR---~a~GIW~C~kCg~~~AGGAy~~~T~   73 (83)
T 3j21_i           34 QKHTCPVCGRKA---VKR---ISTGIWQCQKCGATFAGGAYLPVTP   73 (83)
T ss_dssp             SCBCCSSSCSSC---EEE---EETTEEEETTTCCEEECCSSSSSCH
T ss_pred             cccCCCCCCCce---eEe---cCcCeEEcCCCCCEEeCCccccCcc
Confidence            478999999853   322   4578999999999987654444444

>1ffk_W Ribosomal protein L37AE; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1jj2_Y 1k73_1* 1k8a_1* 1k9m_1* 1kc8_1* 1kd1_1* 1kqs_Y* 1m1k_1* 1m90_1* 1n8r_1* 1nji_1* 1q7y_1* 1q81_1* 1q82_1* 1q86_1* 1qvf_Y 1qvg_Y 1w2b_Y 3cxc_Y*

Probab=95.06  E-value=0.024  Score=35.85  Aligned_cols=36  Identities=17%  Similarity=0.452  Sum_probs=26.7

Q ss_pred             CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee
Q 034528           18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT   59 (92)
Q Consensus        18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~   59 (92)
                      .....+.||||+.. +|  +-   ..+|+-.|+.|+..|.--
T Consensus        23 ~q~~ky~C~fCgk~-~v--kR---~a~GIW~C~~C~~~~AGG   58 (73)
T 1ffk_W           23 KHKKKYKCPVCGFP-KL--KR---ASTSIWVCGHCGYKIAGG   58 (73)
T ss_pred             hcccCccCCCCCCc-ee--EE---EEeEEEECCCCCcEEECC
Confidence            44678999999963 22  22   347999999999987654

>3jyw_9 60S ribosomal protein L43; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}

Probab=94.89  E-value=0.0067  Score=38.40  Aligned_cols=40  Identities=18%  Similarity=0.537  Sum_probs=28.6

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcc
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEP   66 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~ep   66 (92)
                      ..+.||||+...     |.+ ..+|+-.|+.|+..|.--.-.++.|
T Consensus        25 ~ky~C~fCgk~~-----vkR-~a~GIW~C~~C~~~~AGGAy~~~T~   64 (72)
T 3jyw_9           25 ARYDCSFCGKKT-----VKR-GAAGIWTCSCCKKTVAGGAYTVSTA   64 (72)
T ss_dssp             SCBCCSSCCSSC-----BSB-CSSSCBCCSSSCCCCCCSSSSSCCH
T ss_pred             cCccCCCCCCce-----eEe-cCCCeEECCCCCCEEeCCccccCCc
Confidence            578999999753     433 5689999999999886544333333

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

Probab=94.76  E-value=0.01  Score=35.52  Aligned_cols=36  Identities=19%  Similarity=0.288  Sum_probs=26.1

Q ss_pred             CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      +|...-.||.|+..+   +..|  ...|.+.|..||+.++.
T Consensus         7 ~ll~~~~Cp~C~~~~---lv~D--~~~ge~vC~~CGlVl~e   42 (58)
T 1dl6_A            7 DALPRVTCPNHPDAI---LVED--YRAGDMICPECGLVVGD   42 (58)
T ss_dssp             CCCSCCSBTTBSSSC---CEEC--SSSCCEECTTTCCEECC
T ss_pred             hccccccCcCCCCCc---eeEe--CCCCeEEeCCCCCEEec
Confidence            455566899999865   3334  34578999999998765

>1k81_A EIF-2-beta, probable translation initiation factor 2 beta subunit; zinc ribbon; NMR {Methanocaldococcus jannaschii} SCOP: g.59.1.1

Probab=94.43  E-value=0.047  Score=29.86  Aligned_cols=31  Identities=13%  Similarity=0.259  Sum_probs=24.3

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFS   57 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~   57 (92)
                      .||.|+.+.+.-++   +++.-.+.|..||....
T Consensus         2 lC~~C~~peT~l~~---~~~~~~l~C~aCG~~~~   32 (36)
T 1k81_A            2 ICRECGKPDTKIIK---EGRVHLLKCMACGAIRP   32 (36)
T ss_dssp             CCSSSCSCEEEEEE---ETTEEEEEEETTTEEEE
T ss_pred             CCcCCCCCCcEEEE---eCCcEEEEhhcCCCccc
Confidence            49999998765444   56889999999998654

>3cc2_Z 50S ribosomal protein L37AE, 50S ribosomal protein L32E; genomic sequnece for R-proteins, ribonucleoprotein, ribosoma protein, RNA-binding; HET: 1MA OMU OMG UR3 PSU; 2.40A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 3cc4_Z* 3cc7_Z* 3cce_Z* 3ccj_Z* 3ccl_Z* 3ccm_Z* 3ccq_Z* 3ccr_Z* 3ccs_Z* 3ccu_Z* 3ccv_Z* 3cd6_Z* 3cma_Z* 3cme_Z* 3i55_Z* 3i56_Z* 3cpw_Y* 4adx_Z

Probab=93.73  E-value=0.04  Score=37.68  Aligned_cols=45  Identities=18%  Similarity=0.304  Sum_probs=31.9

Q ss_pred             CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhh
Q 034528           20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIY   70 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVY   70 (92)
                      ...+.|||||..   .++-   ..+|+-.|+.|+..|.--.-.++.|.-+.
T Consensus        58 ~akytCPfCGk~---~vKR---~avGIW~C~~Cgk~fAGGAy~~~T~~~~t  102 (116)
T 3cc2_Z           58 NEDHACPNCGED---RVDR---QGTGIWQCSYCDYKFTGGSYKPETPGGKT  102 (116)
T ss_dssp             HSCEECSSSCCE---EEEE---EETTEEEETTTCCEEECCSSSSSCHHHHH
T ss_pred             ccCCcCCCCCCc---eeEe---cCceeEECCCCCCEEECCCcccccchhhh
Confidence            467899999962   3332   23589999999999987655555665544

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=93.59  E-value=0.15  Score=29.70  Aligned_cols=38  Identities=18%  Similarity=0.394  Sum_probs=27.5

Q ss_pred             ccccCCCCCCCCeEEEEeec----CCceEEEEcCccCCeeEe
Q 034528           21 TVFSCPFCNHGTSVECRIDM----KNLIGEAICNICQESFST   58 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk----~~~~g~l~C~~Cg~~~~~   58 (92)
                      +.+.||.|||...+--.+.-    ..+.....|..||-.+..
T Consensus        14 ~~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~w~~   55 (57)
T 1qyp_A           14 TKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWRS   55 (57)
T ss_dssp             EECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEEC
T ss_pred             eEeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCEecc
Confidence            36899999997766555532    235678899999987653

>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=93.18  E-value=0.1  Score=32.01  Aligned_cols=35  Identities=26%  Similarity=0.597  Sum_probs=23.0

Q ss_pred             cCCCCCCCC----eEEEEeecCC------ceEEEEcCccCCeeEe
Q 034528           24 SCPFCNHGT----SVECRIDMKN------LIGEAICNICQESFST   58 (92)
Q Consensus        24 ~CPfC~~~~----sV~vkidk~~------~~g~l~C~~Cg~~~~~   58 (92)
                      .||+|+...    ...+.++.+.      ++--..|..||+.|-+
T Consensus         4 ~Cp~Cg~~~l~~~~~~~~~~~~G~~~~I~~Vp~~~C~~CGE~~~~   48 (78)
T 3ga8_A            4 KCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMN   48 (78)
T ss_dssp             BCTTTSSSBEEEEEEEEEEEETTEEEEEEEEEEEEETTTCCEECC
T ss_pred             ECCCCCCCeeEeEEEEEEEEECCEEEEEcCceeEECCCCCCEEEC
Confidence            699999762    3334454443      3345689999997754

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=92.96  E-value=0.25  Score=28.61  Aligned_cols=37  Identities=16%  Similarity=0.547  Sum_probs=28.1

Q ss_pred             ccccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeE
Q 034528           21 TVFSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFS   57 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~   57 (92)
                      +.+.||.|||...+-..+...    .+.-...|..||-++.
T Consensus         8 ~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~w~   48 (50)
T 1tfi_A            8 DLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK   48 (50)
T ss_dssp             CCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred             CccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCeEE
Confidence            468999999999887766432    3556788999998764

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=92.24  E-value=0.21  Score=33.41  Aligned_cols=32  Identities=25%  Similarity=0.237  Sum_probs=26.2

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeE
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFS   57 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~   57 (92)
                      =||.||+  -+.++-++..+...+.|+.||-.+.
T Consensus         6 FCp~Cgn--lL~~~~~~~~~~~~~~C~~C~y~~~   37 (122)
T 1twf_I            6 FCRDCNN--MLYPREDKENNRLLFECRTCSYVEE   37 (122)
T ss_dssp             BCSSSCC--BCEEEEETTTTEEEEECSSSSCEEE
T ss_pred             cccccCc--cCcccccCcCCCCEEECCcCCCeee
Confidence            3999996  5777777777889999999997664

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

Probab=90.53  E-value=0.12  Score=32.10  Aligned_cols=41  Identities=22%  Similarity=0.553  Sum_probs=29.8

Q ss_pred             CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee--cCCC
Q 034528           17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT--ITAL   63 (92)
Q Consensus        17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~--i~~L   63 (92)
                      +.|-....||.|..+  +...  ..  -|.+.|..||..|-..  |+-|
T Consensus         3 ~~LL~iL~CP~ck~~--L~~~--~~--~~~LiC~~cg~~YPI~dGIPvm   45 (70)
T 2js4_A            3 SRLLDILVCPVCKGR--LEFQ--RA--QAELVCNADRLAFPVRDGVPIM   45 (70)
T ss_dssp             CCCCCCCBCTTTCCB--EEEE--TT--TTEEEETTTTEEEEEETTEECC
T ss_pred             hHHhhheECCCCCCc--CEEe--CC--CCEEEcCCCCceecCCCCeeee
Confidence            357778899999973  4433  22  3789999999999763  5554

>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=90.32  E-value=0.45  Score=36.58  Aligned_cols=58  Identities=16%  Similarity=0.305  Sum_probs=36.6

Q ss_pred             cccCCCCCCCCeEEEE-eec------CCceEEEEcCccCCeeEeecCCCCcch-----hhhhhHHHHHHh
Q 034528           22 VFSCPFCNHGTSVECR-IDM------KNLIGEAICNICQESFSTTITALTEPI-----DIYSEWIDECER   79 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vk-idk------~~~~g~l~C~~Cg~~~~~~i~~L~epV-----DVYs~WiD~~~~   79 (92)
                      ...||+||+.+.++.- ++.      ...+-.-.|..||.+.-+--...+..+     |+-+--+|..-+
T Consensus       222 R~~C~~Cg~~~~l~y~~~e~~~~~~~~~~~r~e~C~~C~~YlK~~~~~~d~~~dp~adDlatL~LDl~a~  291 (309)
T 2fiy_A          222 RIKCSHCEESKHLAYLSLEHDGQPAEKAVLRAETCPSCQGYLKQFYLEFDRHADALADDLASLALDMRLA  291 (309)
T ss_dssp             TTSCSSSCCCSCCEEECCCC-CCCSTTCSEEEEEETTTTEEEEEEETTTCTTCCHHHHHHTTHHHHHHHH
T ss_pred             CcCCcCCCCCCCeeEEEecCccccCCCcceEEEEcccccchHhhhhhccCCCCCcchhHHHHHHHHHHHH
Confidence            4689999998877665 443      266778899999987655322223333     344445555443

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

Probab=89.71  E-value=0.2  Score=30.85  Aligned_cols=41  Identities=15%  Similarity=0.277  Sum_probs=29.3

Q ss_pred             CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee--cCCC
Q 034528           17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT--ITAL   63 (92)
Q Consensus        17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~--i~~L   63 (92)
                      +.|-....||.|..+  +...  ..  -+.+.|..||..|-..  |+-|
T Consensus         3 ~~LL~iL~CP~ck~~--L~~~--~~--~~~LiC~~cg~~YPI~dGIPvm   45 (68)
T 2jr6_A            3 KKFLDILVCPVTKGR--LEYH--QD--KQELWSRQAKLAYPIKDGIPYM   45 (68)
T ss_dssp             CSSSCCCBCSSSCCB--CEEE--TT--TTEEEETTTTEEEEEETTEECC
T ss_pred             hHHhhheECCCCCCc--CeEe--CC--CCEEEcCCCCcEecCCCCeeee
Confidence            356678899999973  4443  22  3789999999999763  5544

>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=89.20  E-value=0.53  Score=30.32  Aligned_cols=35  Identities=29%  Similarity=0.649  Sum_probs=20.9

Q ss_pred             cCCCCCCCCeE----EEEeecCC------ceEEEEcCccCCeeEe
Q 034528           24 SCPFCNHGTSV----ECRIDMKN------LIGEAICNICQESFST   58 (92)
Q Consensus        24 ~CPfC~~~~sV----~vkidk~~------~~g~l~C~~Cg~~~~~   58 (92)
                      .||+|+.+..+    ...++-+.      ++-...|..||+.+-.
T Consensus         4 ~Cp~Cg~~~~~~~~~~~~~~~kg~~~~v~~v~~~~C~~CGE~~~d   48 (133)
T 3o9x_A            4 KCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMN   48 (133)
T ss_dssp             BCTTTSSSBEEEEEEEEEEEETTEEEEEEEEEEEEESSSSCEECC
T ss_pred             CCCcCCCCceeeceEEEEEEECCEEEEECCCceeECCCCCCEeec
Confidence            69999986432    22222232      2335679999987643

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

Probab=88.98  E-value=0.34  Score=28.09  Aligned_cols=27  Identities=22%  Similarity=0.412  Sum_probs=18.4

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESF   56 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~   56 (92)
                      -||.||+. .+...  .   .....|+.||.++
T Consensus        21 ~CP~CG~~-~fm~~--~---~~R~~C~kCG~t~   47 (50)
T 3j20_Y           21 FCPRCGPG-VFMAD--H---GDRWACGKCGYTE   47 (50)
T ss_dssp             ECSSSCSS-CEEEE--C---SSEEECSSSCCEE
T ss_pred             cCCCCCCc-eEEec--C---CCeEECCCCCCEE
Confidence            49999984 22221  1   2578999999865

>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=88.92  E-value=0.47  Score=36.47  Aligned_cols=39  Identities=13%  Similarity=0.302  Sum_probs=27.5

Q ss_pred             CccccCCCCCCCCeEEEEee--cCCceEEEEcCccCCeeEe
Q 034528           20 DTVFSCPFCNHGTSVECRID--MKNLIGEAICNICQESFST   58 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkid--k~~~~g~l~C~~Cg~~~~~   58 (92)
                      ...=.||.||..-++++-..  ...|.-.++|..||..+.+
T Consensus       180 ~~~~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~t~W~~  220 (309)
T 2fiy_A          180 ESRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHY  220 (309)
T ss_dssp             TTCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEEC
T ss_pred             ccCCCCCCCCCcCceeEEeecCCCCCcEEEEeCCCCCEEee
Confidence            55668999999876664332  2466678999999987654

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

Probab=88.61  E-value=0.17  Score=31.22  Aligned_cols=40  Identities=20%  Similarity=0.378  Sum_probs=29.0

Q ss_pred             CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee--cCCC
Q 034528           18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT--ITAL   63 (92)
Q Consensus        18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~--i~~L   63 (92)
                      .|-....||.|..+  +..  +.  .-+.+.|..||..|...  |+-|
T Consensus         4 ~LLeiL~CP~ck~~--L~~--~~--~~~~LiC~~cg~~YPI~dGIPvm   45 (69)
T 2pk7_A            4 KLLDILACPICKGP--LKL--SA--DKTELISKGAGLAYPIRDGIPVM   45 (69)
T ss_dssp             CGGGTCCCTTTCCC--CEE--CT--TSSEEEETTTTEEEEEETTEECC
T ss_pred             HHHhheeCCCCCCc--CeE--eC--CCCEEEcCCCCcEecCcCCeeee
Confidence            56678899999974  433  22  34789999999999863  5554

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=88.40  E-value=0.88  Score=30.29  Aligned_cols=42  Identities=19%  Similarity=0.433  Sum_probs=30.4

Q ss_pred             CCC-ccccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeEee
Q 034528           18 KLD-TVFSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFSTT   59 (92)
Q Consensus        18 kl~-~~F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~~~   59 (92)
                      .+| +.+.||.|||...+-..+...    .+.-...|..||-.+..+
T Consensus        67 t~p~t~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~w~~n  113 (122)
T 1twf_I           67 TLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSD  113 (122)
T ss_dssp             TSCCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEECC
T ss_pred             cccccCCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCEeccC
Confidence            444 358999999998877766321    355578899999887653

>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=87.91  E-value=0.34  Score=28.61  Aligned_cols=29  Identities=21%  Similarity=0.391  Sum_probs=20.6

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF   56 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~   56 (92)
                      ...||.||+.--++      .......|+.||.++
T Consensus        18 ~~fCPkCG~~~~ma------~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           18 HRFCPRCGPGVFLA------EHADRYSCGRCGYTE   46 (55)
T ss_dssp             SCCCTTTTTTCCCE------ECSSEEECTTTCCCE
T ss_pred             cccCcCCCCceeEe------ccCCEEECCCCCCEE
Confidence            67899999843222      112489999999875

>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=87.82  E-value=0.17  Score=31.21  Aligned_cols=41  Identities=22%  Similarity=0.440  Sum_probs=29.4

Q ss_pred             CCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee--cCCC
Q 034528           17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT--ITAL   63 (92)
Q Consensus        17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~--i~~L   63 (92)
                      +.|-....||.|..+  +....  .  -+.+.|..||..|-..  |+-|
T Consensus         3 ~~LL~iL~CP~ck~~--L~~~~--~--~~~LiC~~cg~~YPI~dGIPvm   45 (68)
T 2hf1_A            3 AKFLEILVCPLCKGP--LVFDK--S--KDELICKGDRLAFPIKDGIPMM   45 (68)
T ss_dssp             CCCEEECBCTTTCCB--CEEET--T--TTEEEETTTTEEEEEETTEECC
T ss_pred             hHHhhheECCCCCCc--CeEeC--C--CCEEEcCCCCcEecCCCCeeee
Confidence            356678899999973  44432  2  4789999999999763  5554

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=87.79  E-value=0.24  Score=32.69  Aligned_cols=30  Identities=27%  Similarity=0.377  Sum_probs=23.9

Q ss_pred             CCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528           25 CPFCNHGTSVECRIDMKNLIGEAICNICQESF   56 (92)
Q Consensus        25 CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~   56 (92)
                      ||.||+  -+.++.+...+.-.+.|+.||-.+
T Consensus         7 Cp~Cgn--~L~~~~~~~~~~~~~~C~~C~y~~   36 (113)
T 3h0g_I            7 CIECNN--MLYPREDKVDRVLRLACRNCDYSE   36 (113)
T ss_dssp             CSSSCC--CCEECCCTTTCCCCEECSSSCCEE
T ss_pred             CcCCCC--EeeEcccCCCCeeEEECCCCCCeE
Confidence            999997  477777665667789999999755

>2apo_B Ribosome biogenesis protein NOP10; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: g.41.16.1 PDB: 2aqc_A

Probab=87.70  E-value=0.21  Score=30.40  Aligned_cols=44  Identities=18%  Similarity=0.310  Sum_probs=34.2

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHH
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDEC   77 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~   77 (92)
                      .-.||.|+.   -+.         .-.|..||......-++-+.|-|-|++.-=++
T Consensus         6 mr~C~~Cgv---YTL---------k~~CP~CG~~T~~~hParfSp~Dky~~yR~~~   49 (60)
T 2apo_B            6 MKKCPKCGL---YTL---------KEICPKCGEKTVIPKPPKFSLEDRWGKYRRML   49 (60)
T ss_dssp             CEECTTTCC---EES---------SSBCSSSCSBCBCCCCCCCCTTCTTHHHHHHH
T ss_pred             ceeCCCCCC---Eec---------cccCcCCCCcCCCCCCCCCCCCcchHHHHHHH
Confidence            346999975   222         12599999999999999999999999876444

>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A

Probab=87.20  E-value=0.64  Score=35.40  Aligned_cols=38  Identities=16%  Similarity=0.427  Sum_probs=27.6

Q ss_pred             ccccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeEe
Q 034528           21 TVFSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFST   58 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~~   58 (92)
                      +.|.||.|||...+--.+...    .+.-...|..||-++.+
T Consensus       267 ~~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C~~Cg~~w~f  308 (309)
T 1pqv_S          267 DRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWKF  308 (309)
T ss_pred             ccccCCCCCCCeeEEEEeecccCCCCCcEEEEeCCCCCceec
Confidence            479999999988766555321    34557899999987653

>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA-direct polymerase, primosome, late protein, ATP-binding; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2

Probab=87.17  E-value=0.25  Score=35.61  Aligned_cols=31  Identities=13%  Similarity=0.321  Sum_probs=22.5

Q ss_pred             CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCe
Q 034528           20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQES   55 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~   55 (92)
                      ...+.||.||..+...+-  . .+  ...|..||..
T Consensus        12 ~~~~~CP~Cg~~d~~~~~--~-dg--~~~C~~Cg~~   42 (255)
T 1nui_A           12 LYHIPCDNCGSSDGNSLF--S-DG--HTFCYVCEKW   42 (255)
T ss_dssp             EEEECCSSSCCSSCEEEE--T-TS--CEEETTTCCE
T ss_pred             ecCCcCCCCCCCCCceEe--C-CC--CeecccCCCc
Confidence            346899999986665544  2 23  5899999975

>2e9h_A EIF-5, eukaryotic translation initiation factor 5; zinc binding, C4 type zinc finger, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=86.91  E-value=0.97  Score=31.98  Aligned_cols=36  Identities=17%  Similarity=0.263  Sum_probs=28.1

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      .=.||.|+.+.+.-+ ++++..+-.+.|..||....-
T Consensus       103 YVlC~~C~sPdT~L~-~~~~~r~~~l~C~ACGa~~~V  138 (157)
T 2e9h_A          103 FVLCPECENPETDLH-VNPKKQTIGNSCKACGYRGML  138 (157)
T ss_dssp             TTSCTTTCCSCCEEE-EETTTTEEEEECSSSCCEEEC
T ss_pred             eEECCCCCCCccEEE-EecCCCEEEEEccCCCCCCcc
Confidence            457999999886544 456788999999999987544

>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=86.84  E-value=0.59  Score=30.77  Aligned_cols=40  Identities=20%  Similarity=0.353  Sum_probs=27.1

Q ss_pred             CCCC-ccccCCCCCCCCeEEEEeec----CCceEEEEcCccCCee
Q 034528           17 DKLD-TVFSCPFCNHGTSVECRIDM----KNLIGEAICNICQESF   56 (92)
Q Consensus        17 ~kl~-~~F~CPfC~~~~sV~vkidk----~~~~g~l~C~~Cg~~~   56 (92)
                      +.|| +.+.||.|||..++--.+..    ..+.-...|..||-++
T Consensus        66 ~tlp~~~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~~w  110 (113)
T 3h0g_I           66 PTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGFAF  110 (113)
T ss_dssp             SSSCBCCSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCCCC
T ss_pred             ccCCCcccCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCCEE
Confidence            3455 45999999998876655432    1244567899999765

>2aus_D NOP10, ribosome biogenesis protein NOP10; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_B 3lwo_B* 3lwq_B* 3lwp_B 3lwv_B 3hax_C* 2hvy_C* 3hay_C* 2ey4_E 3hjw_B* 2rfk_B* 3hjy_B 3mqk_B

Probab=86.34  E-value=0.37  Score=29.36  Aligned_cols=45  Identities=22%  Similarity=0.515  Sum_probs=34.2

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHH
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE   78 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~   78 (92)
                      .-.||.||. -+    + +      -.|.+||......-++-+.|-|-|++.-=++.
T Consensus         5 mr~C~~Cg~-YT----L-k------~~CP~CG~~t~~ahParfSP~Dky~~yR~~lK   49 (60)
T 2aus_D            5 IRKCPKCGR-YT----L-K------ETCPVCGEKTKVAHPPRFSPEDPYGEYRRRLK   49 (60)
T ss_dssp             CEECTTTCC-EE----S-S------SBCTTTCSBCEESSCCCCCSCCTTHHHHHHHH
T ss_pred             ceECCCCCC-EE----c-c------ccCcCCCCccCCCCCCCCCCCCchHHHHHHHH
Confidence            346999975 11    1 1      15999999999999999999999998765443

>4esj_A Type-2 restriction enzyme DPNI; restriction endonuclease-DNA complex, type IIM, type IIE, RE enzyme, DPNI; HET: DNA 6MA; 2.05A {Streptococcus pneumoniae}

Probab=85.76  E-value=0.44  Score=36.39  Aligned_cols=60  Identities=20%  Similarity=0.448  Sum_probs=39.0

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee--cCCCCcch--hhhhhHHHHHHhhcCc
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT--ITALTEPI--DIYSEWIDECERVNNL   83 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~--i~~L~epV--DVYs~WiD~~~~~n~~   83 (92)
                      .+-||.||+.. + -.+.-..-+|--.|..|++.||-+  =..|+.-|  -.|+--|+.+...+.+
T Consensus        34 n~yCPnCG~~~-l-~~f~nN~PVaDF~C~~C~EeyELKSk~~~~~~~I~dGAY~Tmi~Ri~s~~NP   97 (257)
T 4esj_A           34 QSYCPNCGNNP-L-NHFENNRPVADFYCNHCSEEFELKSKKGNFSSTINDGAYATMMKRVQADNNP   97 (257)
T ss_dssp             HCCCTTTCCSS-C-EEC----CCCEEECTTTCCEEEEEEEESSCCSEEEEEEHHHHHHHHHTTCCC
T ss_pred             CCcCCCCCChh-h-hhccCCCcccccccCCcchhheeccccCccCccccCchHHHHHHHHhccCCC
Confidence            46799999843 2 245556788999999999999963  23344333  2688777777766644

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

Probab=85.14  E-value=0.82  Score=26.96  Aligned_cols=39  Identities=28%  Similarity=0.584  Sum_probs=28.3

Q ss_pred             CCCCccccCCCCCCCCeEEEEeecCCceEEEEcC--ccCCeeEee--cCCC
Q 034528           17 DKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICN--ICQESFSTT--ITAL   63 (92)
Q Consensus        17 ~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~--~Cg~~~~~~--i~~L   63 (92)
                      +.|-....||.|..+  ++.  +.    +.+.|.  .||..|-..  |+-|
T Consensus         5 ~~lL~iL~CP~c~~~--L~~--~~----~~L~C~~~~c~~~YPI~dGIPvl   47 (56)
T 2kpi_A            5 AGLLEILACPACHAP--LEE--RD----AELICTGQDCGLAYPVRDGIPVL   47 (56)
T ss_dssp             CSCTTSCCCSSSCSC--EEE--ET----TEEEECSSSCCCEEEEETTEECC
T ss_pred             HHHHhheeCCCCCCc--cee--cC----CEEEcCCcCCCcEEeeECCEeee
Confidence            356678899999974  333  22    889999  999999763  5443

>1gh9_A 8.3 kDa protein (gene MTH1184); beta+alpha complex structure, structural genomics, PSI, protein structure initiative; NMR {Methanothermobacterthermautotrophicus} SCOP: g.41.6.1

Probab=83.81  E-value=1.3  Score=27.53  Aligned_cols=53  Identities=13%  Similarity=0.327  Sum_probs=34.4

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHhhcC
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECERVNN   82 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~~n~   82 (92)
                      +|-|| |+.-   .+.   +.+.....|. ||..++..=-.+.-.+|=+.+=.++....+.
T Consensus         4 vv~C~-C~~~---~~~---~~~~kT~~C~-CG~~~~~~k~rif~~~~d~~eA~e~~~~lqa   56 (71)
T 1gh9_A            4 IFRCD-CGRA---LYS---REGAKTRKCV-CGRTVNVKDRRIFGRADDFEEASELVRKLQE   56 (71)
T ss_dssp             EEEET-TSCC---EEE---ETTCSEEEET-TTEEEECCSSSCBSCCSSHHHHHHHHHHHSS
T ss_pred             EEECC-CCCE---EEE---cCCCcEEECC-CCCeeeeceEEEEEecCCHHHHHHHHHHHHh
Confidence            68999 9973   222   2355688997 9999998533333337766666655555543

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

Probab=83.76  E-value=0.3  Score=30.04  Aligned_cols=40  Identities=15%  Similarity=0.119  Sum_probs=28.4

Q ss_pred             CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEee--cCCC
Q 034528           18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT--ITAL   63 (92)
Q Consensus        18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~--i~~L   63 (92)
                      .|-....||.|..+  +..  +.  .-|.+.|..||..|-..  |+-|
T Consensus         6 ~LLeiL~CP~ck~~--L~~--~~--~~g~LvC~~c~~~YPI~dGIPvm   47 (67)
T 2jny_A            6 QLLEVLACPKDKGP--LRY--LE--SEQLLVNERLNLAYRIDDGIPVL   47 (67)
T ss_dssp             GGTCCCBCTTTCCB--CEE--ET--TTTEEEETTTTEEEEEETTEECC
T ss_pred             HHHHHhCCCCCCCc--CeE--eC--CCCEEEcCCCCccccCCCCEeee
Confidence            46667899999973  333  22  24789999999999763  5544

>4bbr_M Transcription initiation factor IIB; RNA polymerase, TFIIB; 3.40A {Saccharomyces cerevisiae} PDB: 3k7a_M 4bbs_M

Probab=83.46  E-value=0.64  Score=35.73  Aligned_cols=50  Identities=26%  Similarity=0.536  Sum_probs=30.5

Q ss_pred             CCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHH
Q 034528           16 VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWI   74 (92)
Q Consensus        16 ~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~Wi   74 (92)
                      .+-|.-.-.||.|+... -.+..|.  .-|.+.|..||+-.+.      ..||.=++|-
T Consensus        15 ~~~l~~~~~Cp~C~~~~-~~lv~D~--~~G~~vC~~CGlVl~e------~~iD~g~EWR   64 (345)
T 4bbr_M           15 GPNLNIVLTCPECKVYP-PKIVERF--SEGDVVCALCGLVLSD------KLVDTRSEWR   64 (345)
T ss_dssp             -------CCCSSCCCSS-CCEEEEG--GGTEEEETTTCBEEES------CCBCHHHHHT
T ss_pred             CcccccCCcCCCCCCCC-CceeEEC--CCCcEEeCCCCCCccC------cccccCcccc
Confidence            45666666899999721 1233343  4589999999987654      4578888886

>2g2k_A EIF-5, eukaryotic translation initiation factor 5; EIF125 fold; NMR {Homo sapiens}

Probab=82.65  E-value=1.6  Score=31.30  Aligned_cols=34  Identities=18%  Similarity=0.255  Sum_probs=25.9

Q ss_pred             cccCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528           22 VFSCPFCNHGTSVECRIDMKNLIGEAICNICQESF   56 (92)
Q Consensus        22 ~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~   56 (92)
                      +=.||.|+.+.+.-++ +.+.++-.+.|..||...
T Consensus        96 YVlC~~C~sPdT~L~k-~~~~r~~~l~C~ACGa~~  129 (170)
T 2g2k_A           96 FVLCPECENPETDLHV-NPKKQTIGNSCKACGYRG  129 (170)
T ss_dssp             HHSCTTTSSSCEEEEE-ETTTTEEEEEETTTCCCC
T ss_pred             eEECCCCCCCccEEEE-ecCCCEEEEEccccCCcc
Confidence            3479999998765443 436778889999999853

>2xzm_6 RPS27E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_6

Probab=82.47  E-value=1.8  Score=27.83  Aligned_cols=38  Identities=16%  Similarity=0.532  Sum_probs=28.2

Q ss_pred             CCCCCccc---cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           16 VDKLDTVF---SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        16 ~~kl~~~F---~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      ++...+.|   .||-|++   +.+.++...  -.+.|.+||.....
T Consensus        23 v~~PnS~Fm~VkCp~C~n---~q~VFShA~--t~V~C~~Cg~~L~~   63 (81)
T 2xzm_6           23 IQAPNSYFMDVKCAQCQN---IQMIFSNAQ--STIICEKCSAILCK   63 (81)
T ss_dssp             SCCCSCCEEEEECSSSCC---EEEEETTCS--SCEECSSSCCEEEE
T ss_pred             eeCCCCcEEEeECCCCCC---eeEEEecCc--cEEEccCCCCEEee
Confidence            45556888   9999998   566676554  56899999986544

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae}

Probab=82.47  E-value=1.3  Score=32.67  Aligned_cols=54  Identities=24%  Similarity=0.450  Sum_probs=37.7

Q ss_pred             CCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHH
Q 034528           16 VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECE   78 (92)
Q Consensus        16 ~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~   78 (92)
                      .+-|...-.||.|+... ..+..|  ...|.+.|..||+-.+      +..||-=++|--.-.
T Consensus        15 ~~~ln~~~~CPECGs~~-t~IV~D--~erGE~VCsdCGLVLE------EriID~GPEWRAFsn   68 (197)
T 3k1f_M           15 GPNLNIVLTCPECKVYP-PKIVER--FSEGDVVCALCGLVLS------DKLVDTRSEWRTFSN   68 (197)
T ss_dssp             SSCCCCCCCCTTTCCSS-CCEEEE--GGGTEEEETTTCBBCC------CCCBCHHHHHHHHHC
T ss_pred             ccccccCeECcCCCCcC-CeEEEe--CCCCEEEEcCCCCCcC------CceeECCCCCcCcCC
Confidence            45666677899999732 223333  3348999999998643      356899999986553

>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, DNA-binding, DNA- directed RNA polymerase, isopeptide bond, magnesium; 3.80A {Saccharomyces cerevisiae}

Probab=81.90  E-value=0.25  Score=37.70  Aligned_cols=49  Identities=27%  Similarity=0.567  Sum_probs=31.4

Q ss_pred             CCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhH
Q 034528           16 VDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEW   73 (92)
Q Consensus        16 ~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~W   73 (92)
                      .+-|...-.||.|+...+ .+..  +...|.+.|..||.--+.      ..||-=++|
T Consensus        15 ~~~~~~~~~Cp~Cg~~~~-~iv~--D~~~G~~vC~~CG~Vl~e------~~id~~~Ew   63 (345)
T 3k7a_M           15 GPNLNIVLTCPECKVYPP-KIVE--RFSEGDVVCALCGLVLSD------KLVDTRSEW   63 (345)
T ss_dssp             --CCCCCCCCSTTCCSCC-CCCC--CSSSCSCCCSSSCCCCCC------CCCCTTCCC
T ss_pred             CccccCCCcCcCCCCCCC-ceEE--ECCCCCEecCCCCeEccc------ccccCCccc
Confidence            346666778999998521 1222  345689999999986543      345665666

>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A

Probab=81.59  E-value=0.45  Score=33.82  Aligned_cols=38  Identities=16%  Similarity=0.419  Sum_probs=26.0

Q ss_pred             CccccCCCCCCCCeEEEEeec----CCceEEEEcCccCCeeE
Q 034528           20 DTVFSCPFCNHGTSVECRIDM----KNLIGEAICNICQESFS   57 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk----~~~~g~l~C~~Cg~~~~   57 (92)
                      ...|.||.|||..++--.+..    ..+.-...|..||-.+.
T Consensus       135 t~~~~Cp~C~~~~a~~~q~Q~rsaDE~mt~f~~C~~C~~~w~  176 (178)
T 3po3_S          135 TDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRWK  176 (178)
T ss_dssp             BSSSCCSSSCCSCEECCCCCCSCTTSCCCCCEEETTTCCEEC
T ss_pred             cCCcCCCCCCCCceEEEEeecccCCCCCcEEEEcCCCCCeec
Confidence            347999999998765433321    12455788999998764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	92
d1wiia_	85	g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549	2e-38

>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Putative zinc binding domain
domain: Hypothetical UPF0222 protein MGC4549
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  121 bits (304), Expect = 2e-38
 Identities = 36/83 (43%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 2  GKRKSRAK--PPPKKRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTT 59
          G   S  +  PP KK    L+T F+CPFCNH  S + ++D     G   C +C E F T 
Sbjct: 1  GSSGSSGRKPPPKKKMTGTLETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTP 60

Query: 60 ITALTEPIDIYSEWIDECERVNN 82
          IT L+EP+D+YS+WID CE   +
Sbjct: 61 ITYLSEPVDVYSDWIDACESGPS 83

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	92
d1wiia_	85	Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m	100.0
d1vqoz1	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	95.46
d1jj2y_	73	Ribosomal protein L37ae {Archaeon Haloarcula maris	95.35
d1pfta_	50	Transcription initiation factor TFIIB, N-terminal	94.51
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	94.3
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	93.63
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	93.06
d1dl6a_	58	Transcription initiation factor TFIIB, N-terminal	92.79
d1k81a_	36	Zinc-binding domain of translation initiation fact	90.6
d1neea2	37	Zinc-binding domain of translation initiation fact	88.06
d2epqa1	32	PATZ1 {Human (Homo sapiens) [TaxId: 9606]}	88.0
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	86.43
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	86.15
d2ct1a2	36	Transcriptional repressor CTCF {Human (Homo sapien	82.96
d6rxna_	45	Rubredoxin {Desulfovibrio desulfuricans, strain 27	82.74
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	81.1

>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Putative zinc binding domain
domain: Hypothetical UPF0222 protein MGC4549
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=1.7e-44  Score=236.86  Aligned_cols=82  Identities=46%  Similarity=0.925  Sum_probs=74.2

Q ss_pred             CCCccC-CCCCCC-CCCCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCCCcchhhhhhHHHHHHh
Q 034528            2 GKRKSR-AKPPPK-KRVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITALTEPIDIYSEWIDECER   79 (92)
Q Consensus         2 GkRK~k-~k~~~k-k~~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L~epVDVYs~WiD~~~~   79 (92)
                      |+||++ |+++++ |.+++|||+|+||||||++||+|+||++.++|.|+|++||++|++.||+|+|||||||+|||+||+
T Consensus         1 g~~~~s~rk~~pkkk~~~kL~t~F~CPfCnh~~sV~vk~dkk~~~g~l~C~vCg~~~~~~i~~L~epiDVYs~WiDace~   80 (85)
T d1wiia_           1 GSSGSSGRKPPPKKKMTGTLETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACES   80 (85)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCSSCCCCTTTCCSSCEEEEEETTTTEEEEEESSSCCEEEEECCSSCCTTHHHHHHHHHHHH
T ss_pred             CCCcccCCCCCCCccccCCCCceEcCCCCCCCCeEEEEEEecCCEEEEEEecCCCeEEecccccCccHhHHHHHHHHHHH
Confidence            777754 455444 446899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCc
Q 034528           80 VNNL   83 (92)
Q Consensus        80 ~n~~   83 (92)
                      +|..
T Consensus        81 ~n~~   84 (85)
T d1wiia_          81 GPSS   84 (85)
T ss_dssp             CCCC
T ss_pred             hccC
Confidence            9973

>d1vqoz1 g.41.8.1 (Z:10-82) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=95.46  E-value=0.0031  Score=38.63  Aligned_cols=34  Identities=21%  Similarity=0.478  Sum_probs=26.0

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeec
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTI   60 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i   60 (92)
                      ..+.|||||...   |+   ...+|+-.|..|+..|.--.
T Consensus        26 ~ky~Cp~Cgk~~---vk---R~a~GIW~C~kC~~~~AGGA   59 (73)
T d1vqoz1          26 EDHACPNCGEDR---VD---RQGTGIWQCSYCDYKFTGGS   59 (73)
T ss_dssp             SCBCCSSSSCSC---EE---EEETTEEEETTTCCEEECCS
T ss_pred             CCccCCCCCCce---eE---EEEEEEEECCCCCCEEeCCe
Confidence            468999999742   22   25679999999999987643

>d1jj2y_ g.41.8.1 (Y:) Ribosomal protein L37ae {Archaeon Haloarcula marismortui [TaxId: 2238]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein L37ae
domain: Ribosomal protein L37ae
species: Archaeon Haloarcula marismortui [TaxId: 2238]

Probab=95.35  E-value=0.0033  Score=38.50  Aligned_cols=37  Identities=16%  Similarity=0.378  Sum_probs=26.9

Q ss_pred             ccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCC
Q 034528           21 TVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITAL   63 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L   63 (92)
                      ..+.|||||...   |+   ...+|+-.|+.|+..|.-..-.+
T Consensus        26 ~ky~Cp~Cgk~~---vk---R~a~GIW~C~kC~~~~AGgAy~p   62 (73)
T d1jj2y_          26 KKHKCPVCGFKK---LK---RAGTGIWMCGHCGYKIAGGCYQP   62 (73)
T ss_dssp             SCBCCSSSCCSC---EE---EEETTEEEETTTCCEEECCSSSS
T ss_pred             CCccCCCCCCCc---eE---EEEEEEEECCCCCCEEeCcccee
Confidence            468999999742   22   25678999999999987644333

>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=94.51  E-value=0.0071  Score=34.05  Aligned_cols=34  Identities=24%  Similarity=0.536  Sum_probs=23.9

Q ss_pred             CccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           20 DTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      ++.-.||.||..+   +..|...  |.+.|..||+--+.
T Consensus         3 ~~~~~Cp~Cgs~~---iv~D~~~--Ge~vC~~CG~Viee   36 (50)
T d1pfta_           3 NKQKVCPACESAE---LIYDPER--GEIVCAKCGYVIEE   36 (50)
T ss_dssp             SSCCSCTTTSCCC---EEEETTT--TEEEESSSCCBCCC
T ss_pred             cccccCcCCCCCc---EEEECCC--CeEecccCCcEecc
Confidence            4455799999743   4455444  79999999985543

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.30  E-value=0.043  Score=32.97  Aligned_cols=42  Identities=19%  Similarity=0.427  Sum_probs=31.6

Q ss_pred             CCCC-ccccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeEe
Q 034528           17 DKLD-TVFSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFST   58 (92)
Q Consensus        17 ~kl~-~~F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~~   58 (92)
                      +.|| +...||.|+|.+.+-..+.-.    .+.-...|-.||-.+..
T Consensus        17 Ptlp~t~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h~Wr~   63 (72)
T d1twfi2          17 PTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTS   63 (72)
T ss_dssp             TTSCCCCCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCEEEC
T ss_pred             CCCCccCCCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCCCccc
Confidence            3444 468999999988777766432    46668999999998876

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=93.63  E-value=0.067  Score=30.69  Aligned_cols=37  Identities=19%  Similarity=0.391  Sum_probs=29.1

Q ss_pred             ccccCCCCCCCCeEEEEeec----CCceEEEEcCccCCeeE
Q 034528           21 TVFSCPFCNHGTSVECRIDM----KNLIGEAICNICQESFS   57 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkidk----~~~~g~l~C~~Cg~~~~   57 (92)
                      +.+.||.|+|..++-..+.-    ..+.-...|..||-.|.
T Consensus        14 ~~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~Cg~~wr   54 (57)
T d1qypa_          14 TKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTWR   54 (57)
T ss_dssp             EECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCEEE
T ss_pred             ccCCCCCCCCCceEEEEeecccccCCCeEEEEeCCCCCcce
Confidence            46899999998888776643    23667899999998874

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=93.06  E-value=0.11  Score=29.15  Aligned_cols=38  Identities=16%  Similarity=0.533  Sum_probs=27.0

Q ss_pred             CccccCCCCCCCCeEEEEeecC----CceEEEEcCccCCeeE
Q 034528           20 DTVFSCPFCNHGTSVECRIDMK----NLIGEAICNICQESFS   57 (92)
Q Consensus        20 ~~~F~CPfC~~~~sV~vkidk~----~~~g~l~C~~Cg~~~~   57 (92)
                      -..|.||.|++.+.....+.-.    -..-.+.|..||.++-
T Consensus         7 T~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~~Wr   48 (50)
T d1tfia_           7 TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRWK   48 (50)
T ss_dssp             CCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEEE
T ss_pred             cCCEECCCCCCCccEEEEEEccCCCCCceEEEEccccCCeee
Confidence            3578999999988655554221    2455799999998763

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

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

Probab=92.79  E-value=0.028  Score=32.42  Aligned_cols=36  Identities=19%  Similarity=0.288  Sum_probs=25.5

Q ss_pred             CCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           18 KLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        18 kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      .+.....||.|+..+   +..|  ...|.+.|..||+--+.
T Consensus         7 ~~~~~~~Cp~Cgs~~---ii~D--~~~Ge~vC~~CG~Vlee   42 (58)
T d1dl6a_           7 DALPRVTCPNHPDAI---LVED--YRAGDMICPECGLVVGD   42 (58)
T ss_dssp             CCCSCCSBTTBSSSC---CEEC--SSSCCEECTTTCCEECC
T ss_pred             ccccccCCCCCCCCC---EEEE--CCCCcEecccCCCEecc
Confidence            445577899999743   3333  44588999999986544

>d1k81a_ g.59.1.1 (A:) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=90.60  E-value=0.13  Score=27.11  Aligned_cols=32  Identities=13%  Similarity=0.244  Sum_probs=25.1

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEe
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESFST   58 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~   58 (92)
                      .|+-|+.+++.-++   .+.+-.|.|..||.+..-
T Consensus         2 ~C~~C~spDT~l~k---e~R~~~l~C~aCGa~r~V   33 (36)
T d1k81a_           2 ICRECGKPDTKIIK---EGRVHLLKCMACGAIRPI   33 (36)
T ss_dssp             CCSSSCSCEEEEEE---ETTEEEEEEETTTEEEEE
T ss_pred             CCCCCCCCCCEEEE---cCCEEEEEeccCCCCCcc
Confidence            59999987765444   567899999999987643

>d1neea2 g.59.1.1 (A:99-135) Zinc-binding domain of translation initiation factor 2 beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Small proteins
fold: Zinc-binding domain of translation initiation factor 2 beta
superfamily: Zinc-binding domain of translation initiation factor 2 beta
family: Zinc-binding domain of translation initiation factor 2 beta
domain: Zinc-binding domain of translation initiation factor 2 beta
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=88.06  E-value=0.068  Score=28.49  Aligned_cols=30  Identities=23%  Similarity=0.412  Sum_probs=24.3

Q ss_pred             cCCCCCCCCeEEEEeecCCceEEEEcCccCCee
Q 034528           24 SCPFCNHGTSVECRIDMKNLIGEAICNICQESF   56 (92)
Q Consensus        24 ~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~   56 (92)
                      .|+-|+.+++.-++   ...+-.|.|..||.+.
T Consensus         3 ~C~~C~spDT~l~k---e~R~~~l~C~aCGa~r   32 (37)
T d1neea2           3 ICHECNRPDTRIIR---EGRISLLKCEACGAKA   32 (37)
T ss_dssp             HHTCCSSCSSCCEE---ETTTTEEECSTTSCCC
T ss_pred             ECCCCCCCCCEEEE---cCCEEEEEeccCCCCc
Confidence            59999999876665   4567899999999864

>d2epqa1 g.37.1.1 (A:380-411) PATZ1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: PATZ1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.00  E-value=0.058  Score=27.79  Aligned_cols=11  Identities=36%  Similarity=1.135  Sum_probs=8.6

Q ss_pred             CccccCCCCCC
Q 034528           20 DTVFSCPFCNH   30 (92)
Q Consensus        20 ~~~F~CPfC~~   30 (92)
                      ++.|+||.|+.
T Consensus         1 ekp~~cpic~q   11 (32)
T d2epqa1           1 EKPYSCPVCGL   11 (32)
T ss_dssp             CCSSEETTTTE
T ss_pred             CCCcccchHHH
Confidence            46789999984

>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=86.43  E-value=0.39  Score=34.84  Aligned_cols=38  Identities=13%  Similarity=0.287  Sum_probs=25.5

Q ss_pred             ccccCCCCCCCCeEEEEee--cCCceEEEEcCccCCeeEe
Q 034528           21 TVFSCPFCNHGTSVECRID--MKNLIGEAICNICQESFST   58 (92)
Q Consensus        21 ~~F~CPfC~~~~sV~vkid--k~~~~g~l~C~~Cg~~~~~   58 (92)
                      ..=.||.||..-.+++-..  ...|.=.++|+.|+....+
T Consensus       163 ~~~~CPvCGs~P~~s~l~~~~~~~G~R~l~C~~C~teW~~  202 (290)
T d2fiya1         163 SRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCACEWHY  202 (290)
T ss_dssp             TCSSCTTTCCCEEEEEEEC----CCEEEEEETTTCCEEEC
T ss_pred             cCCcCCCCCCcchhheeeccCCCCCceEEECCCCCCcccc
Confidence            3345999999765555443  3466778999999887543

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.15  E-value=0.69  Score=26.53  Aligned_cols=55  Identities=16%  Similarity=0.362  Sum_probs=36.4

Q ss_pred             CCCCCCccccCCCCCCCCeEEEEeecCCceEEEEcCccCCeeEeecCCC------CcchhhhhhHHH
Q 034528           15 RVDKLDTVFSCPFCNHGTSVECRIDMKNLIGEAICNICQESFSTTITAL------TEPIDIYSEWID   75 (92)
Q Consensus        15 ~~~kl~~~F~CPfC~~~~sV~vkidk~~~~g~l~C~~Cg~~~~~~i~~L------~epVDVYs~WiD   75 (92)
                      ....-|..--||.|+..  |    .+..+.-.+.|..||..|-+.-...      ...=+-|.+|-+
T Consensus        11 ~l~~~~~~k~CP~C~~~--~----~~~~~~~~~~C~~C~~~fC~~C~~~w~~~H~~~tC~~~~~wk~   71 (73)
T d2ct7a1          11 VLMRDPKFLWCAQCSFG--F----IYEREQLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKR   71 (73)
T ss_dssp             CCCSCCCEECCSSSCCC--E----ECCCSCSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHHHH
T ss_pred             HHHHCCCCCCCCCCCCE--e----EECCCCCEEEcCCCCCeECcccCcchhcCCCCCCHHHHHHHHH
Confidence            34556778899999973  2    2345566789999999987643322      234456777743

>d2ct1a2 g.37.1.1 (A:8-43) Transcriptional repressor CTCF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Transcriptional repressor CTCF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.96  E-value=0.18  Score=26.05  Aligned_cols=11  Identities=18%  Similarity=0.836  Sum_probs=9.5

Q ss_pred             CccccCCCCCC
Q 034528           20 DTVFSCPFCNH   30 (92)
Q Consensus        20 ~~~F~CPfC~~   30 (92)
                      +++|.|++||.
T Consensus         6 ekP~~C~~C~k   16 (36)
T d2ct1a2           6 EKPYECYICHA   16 (36)
T ss_dssp             CCSEECTTTCC
T ss_pred             CCCEeCCCCcc
Confidence            67899999995

>d6rxna_ g.41.5.1 (A:) Rubredoxin {Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio desulfuricans, strain 27774 [TaxId: 876]

Probab=82.74  E-value=0.2  Score=27.44  Aligned_cols=18  Identities=28%  Similarity=0.750  Sum_probs=14.9

Q ss_pred             CCCCCccccCCCCCCCCe
Q 034528           16 VDKLDTVFSCPFCNHGTS   33 (92)
Q Consensus        16 ~~kl~~~F~CPfC~~~~s   33 (92)
                      -..||..|.||.|+..++
T Consensus        23 Fe~LP~dw~CP~C~a~K~   40 (45)
T d6rxna_          23 FDQLPDDWCCPVCGVSKD   40 (45)
T ss_dssp             GGGSCTTCBCTTTCCBGG
T ss_pred             HHHCCCCCCCcCCCCcHH
Confidence            356899999999998764

>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=81.10  E-value=1.2  Score=32.17  Aligned_cols=36  Identities=14%  Similarity=0.422  Sum_probs=25.4

Q ss_pred             ccCCCCCCCCeEEEEeecCC-------ceEEEEcCccCCeeEe
Q 034528           23 FSCPFCNHGTSVECRIDMKN-------LIGEAICNICQESFST   58 (92)
Q Consensus        23 F~CPfC~~~~sV~vkidk~~-------~~g~l~C~~Cg~~~~~   58 (92)
                      ..||+||+.+......-...       .+=.-.|..|+.+.-+
T Consensus       205 ~~C~~Cg~~~~~~~~~~~~~~~~~~~~~~r~e~C~~C~~Y~K~  247 (290)
T d2fiya1         205 IKCSHCEESKHLAYLSLEHDGQPAEKAVLRAETCPSCQGYLKQ  247 (290)
T ss_dssp             TSCSSSCCCSCCEEECCCC-CCCSTTCSEEEEEETTTTEEEEE
T ss_pred             ccCCCCCCCCCcceEEEecCCCcccccceEEEEcCCcCCeEEE
Confidence            47999999887776653321       2445689999987655