Citrus Sinensis ID: 039987

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-----
Protein Sequence
MSFSTSDNRTQLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDILLGEVCKLGHQMECYSLKFQLFEKELQQR
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHHHHcccccccccccccccccccEEEcccccccccccccccccccccccccccccccHHHHHHHHHHHcccccEEEHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHcccccEEEcccccccccccEEEEccccccEccccccccccccccccccccccHcHHHHHHHHHHHcccccEHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
msfstsdnrTQLKACEKcfnsskvlrtshtrenpnrkfwkckgcgafkwdddrkssecndfrgmvdrnmseNKIDILLGEVCKLGHQMECYSLKFQLFEKELQQR
Flexible Loop (DISEMBL)
msfstsdnrtqlkacekcfnsskvlrtshtrenpnrkfwkckgcgafkwdddrkssecndfrgmvdrnmSENKIDILLGEVCKLGHQMECYSLKFQLFEKELQQR
Low Complexity Region (SEG)
MSFSTSDNRTQLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDILLGEVCKLGHQMECYSLKFQLFEKELQQR
Disordered region (IsUnstruct)
***********************************RKFWKCKGCGAFKWDDD*****CNDFRGMVDRNMSENKIDILLGEVCKLGHQMECYSLKFQLF*******
Disordered Region (DISOPRED)
************KACEKCFNSSK*************KFWKCKGCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDILLGEVCKLGHQMECYSLKFQLFEKEL***
Disordered Region (DISEMBL)
**********QLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDILLGEVCKLGHQMECYSLKFQLFEKELQQR
Disordered Region (DISPRO)
*******NRTQLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDILLGEVCKLGHQMECYSLKFQLFEKELQ**
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSFSTSDNRTQLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDILLGEVCKLGHQMECYSLKFQLFEKELQQR
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

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

No hits with e-value below 0.001 by BLAST

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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	105
TAIR|locus:2010985	353	AT1G54930 [Arabidopsis thalian	0.333	0.099	0.472	9.8e-06

TAIR|locus:2010985 AT1G54930 [Arabidopsis thaliana (taxid:3702)]

 Score = 97 (39.2 bits), Expect = 9.8e-06, Sum P(2) = 9.8e-06
 Identities = 17/36 (47%), Positives = 23/36 (63%)

Query:    27 TSHTRENPNRKFWKCKGCGAFKWDDDRKSSECNDFR 62
             TS T +NPNR+F+ C  CG FKW D +   +C  F+
Sbjct:    51 TSKTEKNPNRRFYTCPSCGYFKWCD-QGLGDCGFFK 85

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	105
PF06839	45	zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc	99.65
KOG1956	758	consensus DNA topoisomerase III alpha [Replication	97.89
PF01396	39	zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc	97.09
PF05325	122	DUF730: Protein of unknown function (DUF730); Inte	96.93
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	96.38
PRK00464	154	nrdR transcriptional regulator NrdR; Validated	96.23
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	95.57
TIGR01384	104	TFS_arch transcription factor S, archaeal. There h	95.52
KOG4399	325	consensus C2HC-type Zn-finger protein [General fun	95.13
COG1594	113	RPB9 DNA-directed RNA polymerase, subunit M/Transc	93.98
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	93.7
PF12760	46	Zn_Tnp_IS1595: Transposase zinc-ribbon domain; Int	93.57
smart00661	52	RPOL9 RNA polymerase subunit 9.	92.73
PF01927	147	Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 T	92.59
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	92.21
PHA00626	59	hypothetical protein	91.94
KOG2907	116	consensus RNA polymerase I transcription factor TF	91.04
PF09855	64	DUF2082: Nucleic-acid-binding protein containing Z	90.47
PF04606	47	Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: I	90.21
PF14353	128	CpXC: CpXC protein	89.65
TIGR01385	299	TFSII transcription elongation factor S-II. This m	89.59
KOG2906	105	consensus RNA polymerase III subunit C11 [Transcri	89.43
PF04216	290	FdhE: Protein involved in formate dehydrogenase fo	89.14
KOG2691	113	consensus RNA polymerase II subunit 9 [Transcripti	89.06
PRK00432	50	30S ribosomal protein S27ae; Validated	88.35
PHA02998	195	RNA polymerase subunit; Provisional	88.22
PRK09678	72	DNA-binding transcriptional regulator; Provisional	87.74
KOG1294	335	consensus Apurinic/apyrimidinic endonuclease and r	84.6
PF07282	69	OrfB_Zn_ribbon: Putative transposase DNA-binding d	84.55
PRK07220	740	DNA topoisomerase I; Validated	84.25
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	84.02
PF03811	36	Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR0	83.61
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	83.12
PF11672	102	DUF3268: Protein of unknown function (DUF3268); In	82.79
PF14354	61	Lar_restr_allev: Restriction alleviation protein L	82.15
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	80.14

>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.65  E-value=1.5e-16  Score=96.08  Aligned_cols=38  Identities=47%  Similarity=1.070  Sum_probs=35.0

Q ss_pred             ccccccCCceeEEEeec-CCCCCCCceEeCC-----CCCeeEecCC
Q 039987           13 KACEKCFNSSKVLRTSH-TRENPNRKFWKCK-----GCGAFKWDDD   52 (105)
Q Consensus        13 ~~Cp~Cg~~~avlrTSk-T~~NPGRkFY~Cp-----sC~FFqW~De   52 (105)
                      +.|+ || .+++++||+ |++||||+||+||     +|+||+|.|+
T Consensus         1 p~C~-Cg-~~~~~~~s~k~~~N~GR~Fy~C~~~~~~~C~fF~W~De   44 (45)
T PF06839_consen    1 PKCP-CG-EPAVRRTSKKTGPNPGRRFYKCPNYKDKGCNFFQWEDE   44 (45)
T ss_pred             CCCC-CC-CEeEEEEEeCCCCCCCCcceECCCCCCCCcCCEEeccC
Confidence            4788 95 889999998 9999999999999     5999999997

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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding

>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]

Probab=97.89  E-value=4.6e-06  Score=75.29  Aligned_cols=38  Identities=32%  Similarity=0.719  Sum_probs=32.3

Q ss_pred             cccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEec
Q 039987           12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWD   50 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~   50 (105)
                      ...| .|+-..+.+++.+|++|.||+||+|+   +|+||+|+
T Consensus       718 ~~~c-~c~~ra~~l~v~k~~~nrGR~f~sc~~~k~c~ff~w~  758 (758)
T KOG1956|consen  718 EVTC-GCGTRAVKLLVAKTEPNRGRKFYSCLPEKSCNFFAWE  758 (758)
T ss_pred             cccc-CCcchhhhhhhhccCccCCCCCcccCCCCCcceEeeC
Confidence            4455 48655788888999999999999999   69999996

>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=97.09  E-value=0.001  Score=39.54  Aligned_cols=34  Identities=29%  Similarity=0.483  Sum_probs=29.0

Q ss_pred             ccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEecCC
Q 039987           13 KACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWDDD   52 (105)
Q Consensus        13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~De   52 (105)
                      ..||.|+ .+.++++++.+     .||.|.   .|.+..|..+
T Consensus         2 ~~CP~Cg-~~lv~r~~k~g-----~F~~Cs~yP~C~~~~~~~~   38 (39)
T PF01396_consen    2 EKCPKCG-GPLVLRRGKKG-----KFLGCSNYPECKYTEPLPK   38 (39)
T ss_pred             cCCCCCC-ceeEEEECCCC-----CEEECCCCCCcCCeEeCCC
Confidence            5799997 77888888766     999999   7999999764

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome

>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function

Probab=96.93  E-value=0.00098  Score=49.31  Aligned_cols=66  Identities=26%  Similarity=0.534  Sum_probs=50.2

Q ss_pred             ccCccccccccccCCceeEEEeecCCCCCCCceEeCC---------CCCeeEecCCCCCCccchhhhhhhhccccchhhh
Q 039987            6 SDNRTQLKACEKCFNSSKVLRTSHTRENPNRKFWKCK---------GCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDI   76 (105)
Q Consensus         6 ~~n~~~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---------sC~FFqW~De~~~~~~~~~~~~~~~n~~~~~~~~   76 (105)
                      +|++.+++-|- | +...++-||+.+-..|.-||.||         +|+|=.|+-..--++   | .|++.-+.|-|-|+
T Consensus        14 rrdkgv~ie~d-c-nakvvvats~dpvts~klyfscpyeisdg~g~~~gfkrwwtvalcde---f-dmikee~~emkkdl   87 (122)
T PF05325_consen   14 RRDKGVPIECD-C-NAKVVVATSRDPVTSGKLYFSCPYEISDGPGRGCGFKRWWTVALCDE---F-DMIKEETIEMKKDL   87 (122)
T ss_pred             ccCCCcceecc-C-CceEEEEeccCCcccceeeecCccccccCCCCCccceeEEeeeechh---h-hHHHHHHHHHHHHH
Confidence            56778899995 8 56689999999999999999999         799999996543332   2 35555566666665


Q ss_pred             H
Q 039987           77 L   77 (105)
Q Consensus        77 ~   77 (105)
                      -
T Consensus        88 e   88 (122)
T PF05325_consen   88 E   88 (122)
T ss_pred             H
Confidence            3

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=96.38  E-value=0.0068  Score=36.18  Aligned_cols=36  Identities=28%  Similarity=0.771  Sum_probs=29.7

Q ss_pred             cccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEec
Q 039987           14 ACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKWD   50 (105)
Q Consensus        14 ~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW~   50 (105)
                      .||.|++..++..++  +....|=-.||.|..|+. +|.
T Consensus         2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~-~w~   39 (40)
T smart00440        2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGH-RWR   39 (40)
T ss_pred             cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCC-EeC
Confidence            699999999998874  557778889999999984 564

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

>PRK00464 nrdR transcriptional regulator NrdR; Validated

Probab=96.23  E-value=0.0038  Score=46.73  Aligned_cols=33  Identities=24%  Similarity=0.481  Sum_probs=24.9

Q ss_pred             cccccCCceeEEEeecC--CCCCCCceEeCCCCCe
Q 039987           14 ACEKCFNSSKVLRTSHT--RENPNRKFWKCKGCGA   46 (105)
Q Consensus        14 ~Cp~Cg~~~avlrTSkT--~~NPGRkFY~CpsC~F   46 (105)
                      +||.||.....+++|+-  +-|--|+||.||.|++
T Consensus         2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~   36 (154)
T PRK00464          2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGK   36 (154)
T ss_pred             cCCCCCCCCCEeEeccccCCCCceeeeeeccccCC
Confidence            69999755547888874  4567788899996654

>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=95.57  E-value=0.017  Score=34.25  Aligned_cols=34  Identities=26%  Similarity=0.663  Sum_probs=26.0

Q ss_pred             ccccccCCceeEEEe--ecCCCCCCCceEeCCCCCe
Q 039987           13 KACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGA   46 (105)
Q Consensus        13 ~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~F   46 (105)
                      +.||.|+...++...  .+....|=-.||.|..|+.
T Consensus         1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~   36 (39)
T PF01096_consen    1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGH   36 (39)
T ss_dssp             S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTE
T ss_pred             CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCC
Confidence            479999999998887  4457788999999999984

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 ....

>TIGR01384 TFS_arch transcription factor S, archaeal

Probab=95.52  E-value=0.021  Score=38.38  Aligned_cols=40  Identities=25%  Similarity=0.657  Sum_probs=32.9

Q ss_pred             cccccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEecCC
Q 039987           12 LKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKWDDD   52 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW~De   52 (105)
                      ...||.||...|+..+.  +....|=-.||.|..|++ +|.+.
T Consensus        62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~-~w~~~  103 (104)
T TIGR01384        62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGY-VWREY  103 (104)
T ss_pred             cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCC-eeEeC
Confidence            57899999999988874  446778889999999995 78763

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.

>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]

Probab=95.13  E-value=0.016  Score=48.72  Aligned_cols=44  Identities=20%  Similarity=0.476  Sum_probs=37.7

Q ss_pred             cccccccccCCceeEEEeecCCCCCCCceEeCC-------CCCeeEecCCCCCC
Q 039987           10 TQLKACEKCFNSSKVLRTSHTRENPNRKFWKCK-------GCGAFKWDDDRKSS   56 (105)
Q Consensus        10 ~~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp-------sC~FFqW~De~~~~   56 (105)
                      +|-+.||   -+|+++..-+|.+---|+||+|.       -|+||+|.|+.-.|
T Consensus        11 ~~~P~C~---HGP~LLF~K~~~~E~~~~F~ACs~~R~d~kfC~F~~~~d~~~~g   61 (325)
T KOG4399|consen   11 VPAPLCP---HGPTLLFVKVTQKEETRRFYACSACRMDDKFCHFFMFEDEFFDG   61 (325)
T ss_pred             CCCCcCC---CCCeEEEEEccCcchheeeehhhhhhcchhccchhhhcccccCc
Confidence            4456666   48999999999999999999999       69999999997665

>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]

Probab=93.98  E-value=0.058  Score=38.32  Aligned_cols=38  Identities=29%  Similarity=0.803  Sum_probs=31.9

Q ss_pred             cccccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEec
Q 039987           12 LKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKWD   50 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW~   50 (105)
                      ...||.||+..+...+.  +....|==+||+|..|++ .|.
T Consensus        72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~-~wr  111 (113)
T COG1594          72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGY-RWR  111 (113)
T ss_pred             cccCCCCCCceeEEEeeehhccCCCceEEEEecccCC-Eee
Confidence            35699999999999884  448899999999999996 564

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=93.70  E-value=0.095  Score=32.26  Aligned_cols=35  Identities=26%  Similarity=0.493  Sum_probs=21.8

Q ss_pred             cccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987           12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF   47 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF   47 (105)
                      |+.||-||+. +....+..+..-++..|.|..|+.-
T Consensus         1 LkPCPfCGg~-~~~~~~~~~~~~~~~~~~C~~Cga~   35 (53)
T TIGR03655         1 LKPCPFCGGA-DVYLRRGFDPLDLSHYFECSTCGAS   35 (53)
T ss_pred             CCCCCCCCCc-ceeeEeccCCCCCEEEEECCCCCCC
Confidence            6789999765 4433333343344445579988763

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.

>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=93.57  E-value=0.086  Score=31.61  Aligned_cols=27  Identities=22%  Similarity=0.573  Sum_probs=19.2

Q ss_pred             ccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987           13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA   46 (105)
Q Consensus        13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F   46 (105)
                      ++||+||......+++       |.-|+|.+|+.
T Consensus        19 ~~CP~Cg~~~~~~~~~-------~~~~~C~~C~~   45 (46)
T PF12760_consen   19 FVCPHCGSTKHYRLKT-------RGRYRCKACRK   45 (46)
T ss_pred             CCCCCCCCeeeEEeCC-------CCeEECCCCCC
Confidence            6799998663333333       88999998873

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

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=92.73  E-value=0.17  Score=29.84  Aligned_cols=32  Identities=22%  Similarity=0.485  Sum_probs=20.4

Q ss_pred             cccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecC
Q 039987           14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDD   51 (105)
Q Consensus        14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~D   51 (105)
                      -||.||+    ++..+..  .++..|.||.|++-...+
T Consensus         2 FCp~Cg~----~l~~~~~--~~~~~~vC~~Cg~~~~~~   33 (52)
T smart00661        2 FCPKCGN----MLIPKEG--KEKRRFVCRKCGYEEPIE   33 (52)
T ss_pred             CCCCCCC----ccccccC--CCCCEEECCcCCCeEECC
Confidence            5999974    2222222  234589999999876554

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

Probab=92.59  E-value=0.14  Score=36.79  Aligned_cols=39  Identities=28%  Similarity=0.834  Sum_probs=27.8

Q ss_pred             cccccccCCceeEEEeecC---------CCCCCCceEeCCCCCeeEecCC
Q 039987           12 LKACEKCFNSSKVLRTSHT---------RENPNRKFWKCKGCGAFKWDDD   52 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT---------~~NPGRkFY~CpsC~FFqW~De   52 (105)
                      .-.|+.|+ .+ +..+++.         ..+....||.||+|+=..|...
T Consensus        91 ~sRC~~CN-~~-L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~Gs  138 (147)
T PF01927_consen   91 FSRCPKCN-GP-LRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGS  138 (147)
T ss_pred             CCccCCCC-cE-eeechhhccccccCccccccCCeEEECCCCCCEecccc
Confidence            57899995 43 3333444         2356778999999999999753

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

>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=92.21  E-value=0.098  Score=40.95  Aligned_cols=37  Identities=16%  Similarity=0.504  Sum_probs=20.3

Q ss_pred             cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEec
Q 039987           12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWD   50 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~   50 (105)
                      ...||-||..|..-.....+. .|+|+..|.-|++ +|.
T Consensus       172 ~g~CPvCGs~P~~s~l~~~~~-~G~R~L~Cs~C~t-~W~  208 (290)
T PF04216_consen  172 RGYCPVCGSPPVLSVLRGGER-EGKRYLHCSLCGT-EWR  208 (290)
T ss_dssp             -SS-TTT---EEEEEEE-------EEEEEETTT---EEE
T ss_pred             CCcCCCCCCcCceEEEecCCC-CccEEEEcCCCCC-eee
Confidence            579999998888888877766 8999999997763 554

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.

>PHA00626 hypothetical protein

Probab=91.94  E-value=0.14  Score=34.25  Aligned_cols=37  Identities=22%  Similarity=0.354  Sum_probs=23.7

Q ss_pred             cccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCC
Q 039987           14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDR   53 (105)
Q Consensus        14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~   53 (105)
                      .||.||....+ +-. +- +.-|.-|.|+.|+|+.=.|.-
T Consensus         2 ~CP~CGS~~Iv-rcg-~c-r~~snrYkCkdCGY~ft~~~~   38 (59)
T PHA00626          2 SCPKCGSGNIA-KEK-TM-RGWSDDYVCCDCGYNDSKDAF   38 (59)
T ss_pred             CCCCCCCceee-eec-ee-cccCcceEcCCCCCeechhhh
Confidence            69999743332 221 21 122677999999999877753

>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12

Probab=91.04  E-value=0.12  Score=38.23  Aligned_cols=38  Identities=18%  Similarity=0.391  Sum_probs=29.1

Q ss_pred             cccccccccCCceeEEEeecC-CCCCCC-ceEeCCCCCee
Q 039987           10 TQLKACEKCFNSSKVLRTSHT-RENPNR-KFWKCKGCGAF   47 (105)
Q Consensus        10 ~~l~~Cp~Cg~~~avlrTSkT-~~NPGR-kFY~CpsC~FF   47 (105)
                      +...+||+||.....--|--+ +++-|- .||+|+.|.|=
T Consensus        72 ~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k  111 (116)
T KOG2907|consen   72 VIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYK  111 (116)
T ss_pred             chhccCcccCCchhhhhhhhcccccCCceEEEEcCcccee
Confidence            336789999999888888333 566665 69999999874

2/RPA12 [Transcription]

>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=90.47  E-value=0.37  Score=31.85  Aligned_cols=43  Identities=26%  Similarity=0.466  Sum_probs=29.5

Q ss_pred             cccccCCceeEEEe-ecCCCCCC-------Cce--EeCCCCCeeEecCCCCCC
Q 039987           14 ACEKCFNSSKVLRT-SHTRENPN-------RKF--WKCKGCGAFKWDDDRKSS   56 (105)
Q Consensus        14 ~Cp~Cg~~~avlrT-SkT~~NPG-------RkF--Y~CpsC~FFqW~De~~~~   56 (105)
                      .||+|++....... +-|+.+-+       |+|  ..|+.|++=+|-....+.
T Consensus         2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y~~~~~~   54 (64)
T PF09855_consen    2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFYKAKTSN   54 (64)
T ss_pred             CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEEeecCcc
Confidence            69999987766555 33455443       334  579999999998765443

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

Probab=90.21  E-value=0.25  Score=29.94  Aligned_cols=32  Identities=28%  Similarity=0.612  Sum_probs=23.6

Q ss_pred             cccccCCceeEEEeecC-CCCCCCceEeCC--CCCe
Q 039987           14 ACEKCFNSSKVLRTSHT-RENPNRKFWKCK--GCGA   46 (105)
Q Consensus        14 ~Cp~Cg~~~avlrTSkT-~~NPGRkFY~Cp--sC~F   46 (105)
                      .||.|| .++.++||+. .+.-...+|.|.  .|+.
T Consensus         1 ~CP~Cg-~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~   35 (47)
T PF04606_consen    1 RCPHCG-SKARIRTSRQLSPLTRELYCQCTNPECGH   35 (47)
T ss_pred             CcCCCC-CeeEEEEchhhCcceEEEEEEECCCcCCC
Confidence            499996 6689999877 555666677888  4653

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

>PF14353 CpXC: CpXC protein

Probab=89.65  E-value=0.32  Score=33.61  Aligned_cols=32  Identities=22%  Similarity=0.494  Sum_probs=20.2

Q ss_pred             ccccccCCceeEEEeecCCCCCCCc-------------eEeCCCCCe
Q 039987           13 KACEKCFNSSKVLRTSHTRENPNRK-------------FWKCKGCGA   46 (105)
Q Consensus        13 ~~Cp~Cg~~~avlrTSkT~~NPGRk-------------FY~CpsC~F   46 (105)
                      +.||.|+.  ....+.+|.=|....             .|+||+||.
T Consensus         2 itCP~C~~--~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~   46 (128)
T PF14353_consen    2 ITCPHCGH--EFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGH   46 (128)
T ss_pred             cCCCCCCC--eeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCC
Confidence            68999963  233334454554444             599998874

>TIGR01385 TFSII transcription elongation factor S-II

Probab=89.59  E-value=0.47  Score=38.74  Aligned_cols=40  Identities=28%  Similarity=0.671  Sum_probs=31.7

Q ss_pred             ccccccccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEe
Q 039987            9 RTQLKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKW   49 (105)
Q Consensus         9 ~~~l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW   49 (105)
                      ...+..||.|+...++....  +....|=-.||.|..|+. +|
T Consensus       255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~-~w  296 (299)
T TIGR01385       255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGN-RW  296 (299)
T ss_pred             CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCC-ee
Confidence            44589999999888887664  456778899999999984 44

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.

>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]

Probab=89.43  E-value=0.24  Score=36.30  Aligned_cols=39  Identities=21%  Similarity=0.663  Sum_probs=32.3

Q ss_pred             cccccccCCceeEEEe--ecCCCCCCCceEeCCCCCeeEecC
Q 039987           12 LKACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGAFKWDD   51 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~FFqW~D   51 (105)
                      ...||.||...|....  .++..-|--.||+|-.|++ +|.|
T Consensus        65 ~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~-~Wre  105 (105)
T KOG2906|consen   65 EATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKH-RWRE  105 (105)
T ss_pred             cCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhcccc-cccC
Confidence            6789999998887655  6678889999999999984 6764

>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=89.14  E-value=0.22  Score=38.97  Aligned_cols=75  Identities=23%  Similarity=0.343  Sum_probs=35.4

Q ss_pred             ccccccCccccccccccCCceeEEEeec-CCCCCCCceEeCCCCC-eeEecCCCCCCccchhhhhhhhccccchhhhHhH
Q 039987            2 SFSTSDNRTQLKACEKCFNSSKVLRTSH-TRENPNRKFWKCKGCG-AFKWDDDRKSSECNDFRGMVDRNMSENKIDILLG   79 (105)
Q Consensus         2 ~~~~~~n~~~l~~Cp~Cg~~~avlrTSk-T~~NPGRkFY~CpsC~-FFqW~De~~~~~~~~~~~~~~~n~~~~~~~~~~~   79 (105)
                      |++.+.=+.+.+.||.||+.....+..- .+..++-+-+.|..|+ +++=-|........    .+--.+---.+||+..
T Consensus       201 s~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd~~~~~~~~----~~~dDl~tl~LD~~a~  276 (290)
T PF04216_consen  201 SLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVDREKDPELD----PVADDLATLHLDLLAQ  276 (290)
T ss_dssp             TTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEETTT-TT------HHHHHHTTHHHHHHHH
T ss_pred             CCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHhhhhCcccc----hhhHHhhhhhHHHHHH
Confidence            3455555666889999999988888877 5888899999999997 44444533222221    1222333345666665


Q ss_pred             h
Q 039987           80 E   80 (105)
Q Consensus        80 ~   80 (105)
                      |
T Consensus       277 e  277 (290)
T PF04216_consen  277 E  277 (290)
T ss_dssp             H
T ss_pred             h
Confidence            4

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.

>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]

Probab=89.06  E-value=0.41  Score=35.46  Aligned_cols=45  Identities=31%  Similarity=0.652  Sum_probs=35.8

Q ss_pred             cccCccc---cccccccCCceeEEEeecC--CCCCCCceEeCCCCCeeEec
Q 039987            5 TSDNRTQ---LKACEKCFNSSKVLRTSHT--RENPNRKFWKCKGCGAFKWD   50 (105)
Q Consensus         5 ~~~n~~~---l~~Cp~Cg~~~avlrTSkT--~~NPGRkFY~CpsC~FFqW~   50 (105)
                      ++|+.+|   ++.||+|+-..++...+.|  ..--=|-||.|-+|++ .|.
T Consensus        63 ~~DPTLPrts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h-~wt  112 (113)
T KOG2691|consen   63 ASDPTLPRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGH-RWT  112 (113)
T ss_pred             ccCCCcCccccccCCccCCcceEEEecccccccceEEEEEEeccccc-ccc
Confidence            4677776   7899999999999998655  5566789999999874 453

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=88.35  E-value=0.49  Score=29.60  Aligned_cols=30  Identities=23%  Similarity=0.664  Sum_probs=20.9

Q ss_pred             cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEec
Q 039987           12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWD   50 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~   50 (105)
                      ...||.||+.  .+.-..       ..|.|+.|+|-.|.
T Consensus        20 ~~fCP~Cg~~--~m~~~~-------~r~~C~~Cgyt~~~   49 (50)
T PRK00432         20 NKFCPRCGSG--FMAEHL-------DRWHCGKCGYTEFK   49 (50)
T ss_pred             cCcCcCCCcc--hheccC-------CcEECCCcCCEEec
Confidence            5689999754  332222       46899999998774

>PHA02998 RNA polymerase subunit; Provisional

Probab=88.22  E-value=0.6  Score=37.26  Aligned_cols=39  Identities=13%  Similarity=0.405  Sum_probs=31.5

Q ss_pred             cccccccCCceeEEEe--ecCCCCCCCceEeCCCCCeeEecC
Q 039987           12 LKACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGAFKWDD   51 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~FFqW~D   51 (105)
                      ...||.|++..+...+  .+...-|-=.||+|..|+. +|.-
T Consensus       143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~-~wkp  183 (195)
T PHA02998        143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKK-HFKP  183 (195)
T ss_pred             CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCC-ccCC
Confidence            5789999999888555  6667888899999999985 5543

>PRK09678 DNA-binding transcriptional regulator; Provisional

Probab=87.74  E-value=0.49  Score=31.92  Aligned_cols=33  Identities=24%  Similarity=0.603  Sum_probs=25.4

Q ss_pred             ccccccCCceeEEEeecC-CCCCCCceEeCC--CCCe
Q 039987           13 KACEKCFNSSKVLRTSHT-RENPNRKFWKCK--GCGA   46 (105)
Q Consensus        13 ~~Cp~Cg~~~avlrTSkT-~~NPGRkFY~Cp--sC~F   46 (105)
                      -.||.|| ..+.++||+. +..--|+.|.|.  .|+.
T Consensus         2 m~CP~Cg-~~a~irtSr~~s~~~~~~Y~qC~N~eCg~   37 (72)
T PRK09678          2 FHCPLCQ-HAAHARTSRYITDTTKERYHQCQNVNCSA   37 (72)
T ss_pred             ccCCCCC-CccEEEEChhcChhhheeeeecCCCCCCC
Confidence            3699996 5578888877 556778999999  6664

>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair]

Probab=84.60  E-value=0.54  Score=39.17  Aligned_cols=20  Identities=25%  Similarity=0.546  Sum_probs=17.6

Q ss_pred             eEEEeecCCCCCCCceEeCC
Q 039987           23 KVLRTSHTRENPNRKFWKCK   42 (105)
Q Consensus        23 avlrTSkT~~NPGRkFY~Cp   42 (105)
                      -.+++|++..|+||+||-|+
T Consensus       299 dy~~Vsk~~~n~~r~~~Ic~  318 (335)
T KOG1294|consen  299 DYILVSKPGPNNGRRFYICS  318 (335)
T ss_pred             eEEEecCcCCCCCceeeeec
Confidence            45566999999999999999

>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=84.55  E-value=0.78  Score=28.53  Aligned_cols=28  Identities=18%  Similarity=0.648  Sum_probs=20.8

Q ss_pred             cccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987           12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF   47 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF   47 (105)
                      -..||.||..        ...++..+-|.||.|++.
T Consensus        28 Sq~C~~CG~~--------~~~~~~~r~~~C~~Cg~~   55 (69)
T PF07282_consen   28 SQTCPRCGHR--------NKKRRSGRVFTCPNCGFE   55 (69)
T ss_pred             ccCccCcccc--------cccccccceEEcCCCCCE
Confidence            4579999733        112777889999999987

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

>PRK07220 DNA topoisomerase I; Validated

Probab=84.25  E-value=1.2  Score=39.97  Aligned_cols=36  Identities=19%  Similarity=0.417  Sum_probs=23.6

Q ss_pred             cccccccCCceeEEEeecCCCCCCCc--eEeCCCCCeeEecCCC
Q 039987           12 LKACEKCFNSSKVLRTSHTRENPNRK--FWKCKGCGAFKWDDDR   53 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT~~NPGRk--FY~CpsC~FFqW~De~   53 (105)
                      ...||.||.. .+...     +.|++  ||.||.|+|..|....
T Consensus       635 ~~~Cp~Cg~~-~~k~~-----~~g~~~~~~~Cp~C~~~~~~~~~  672 (740)
T PRK07220        635 DKVCEAHGLN-HIRII-----NGGKRPWDLGCPQCNFIEWQKKQ  672 (740)
T ss_pred             CCCCCCCCCc-eEEEE-----ecCCccceeeCCCCCCccccCCc
Confidence            3679999643 22222     22333  8999999999887644

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

Probab=84.02  E-value=0.7  Score=31.07  Aligned_cols=30  Identities=23%  Similarity=0.566  Sum_probs=18.2

Q ss_pred             cccccccCCceeEEEe--ecCCCCCCCceEeCCCCCe
Q 039987           12 LKACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGA   46 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~F   46 (105)
                      --.||.|| +..+.|-  .+.-.|    .|+||.|+|
T Consensus        27 ~F~CPnCG-e~~I~Rc~~CRk~g~----~Y~Cp~CGF   58 (61)
T COG2888          27 KFPCPNCG-EVEIYRCAKCRKLGN----PYRCPKCGF   58 (61)
T ss_pred             EeeCCCCC-ceeeehhhhHHHcCC----ceECCCcCc
Confidence            45688885 3333333  333444    499999998

>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=83.61  E-value=1.4  Score=26.16  Aligned_cols=33  Identities=18%  Similarity=0.529  Sum_probs=22.3

Q ss_pred             ccccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987           11 QLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG   45 (105)
Q Consensus        11 ~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~   45 (105)
                      ..+.||.|.....+.+--+  ...|.+=|.|.+|.
T Consensus         4 i~v~CP~C~s~~~v~k~G~--~~~G~qryrC~~C~   36 (36)
T PF03811_consen    4 IDVHCPRCQSTEGVKKNGK--SPSGHQRYRCKDCR   36 (36)
T ss_pred             EeeeCCCCCCCCcceeCCC--CCCCCEeEecCcCC
Confidence            3789999965443554322  23588999999884

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

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

Probab=83.12  E-value=1.1  Score=29.86  Aligned_cols=32  Identities=22%  Similarity=0.495  Sum_probs=19.6

Q ss_pred             cccccccccCCceeEEEee--cCCCCCCCceEeCCCCCe
Q 039987           10 TQLKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGA   46 (105)
Q Consensus        10 ~~l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~F   46 (105)
                      .+.-.||.|| +..+.|-+  +.-.|    -|+||.|||
T Consensus        23 ~~~F~CPnCG-~~~I~RC~~CRk~~~----~Y~CP~CGF   56 (59)
T PRK14890         23 AVKFLCPNCG-EVIIYRCEKCRKQSN----PYTCPKCGF   56 (59)
T ss_pred             cCEeeCCCCC-CeeEeechhHHhcCC----ceECCCCCC
Confidence            3456788885 43344442  23333    499999998

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

Probab=82.79  E-value=1.5  Score=31.26  Aligned_cols=40  Identities=15%  Similarity=0.262  Sum_probs=25.4

Q ss_pred             cccccccCCceeEEEeecC--CCC--CCCceEeCCCCCeeEecCC
Q 039987           12 LKACEKCFNSSKVLRTSHT--REN--PNRKFWKCKGCGAFKWDDD   52 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT--~~N--PGRkFY~CpsC~FFqW~De   52 (105)
                      .+.||.|| .++.+.++..  +..  .+.-+|.|..|+-..-.-+
T Consensus         2 p~~CpYCg-~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~H~   45 (102)
T PF11672_consen    2 PIICPYCG-GPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVGCHP   45 (102)
T ss_pred             CcccCCCC-CeeEEcccchhcCccCCCCceeEECCCCCceeeeeC
Confidence            47899996 5677766322  222  2444699998876665543

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

>PF14354 Lar_restr_allev: Restriction alleviation protein Lar

Probab=82.15  E-value=2  Score=26.18  Aligned_cols=35  Identities=31%  Similarity=0.562  Sum_probs=21.0

Q ss_pred             ccccccccCCceeEEEeecCCCCCCC-ceEeCCCCCe
Q 039987           11 QLKACEKCFNSSKVLRTSHTRENPNR-KFWKCKGCGA   46 (105)
Q Consensus        11 ~l~~Cp~Cg~~~avlrTSkT~~NPGR-kFY~CpsC~F   46 (105)
                      +|+.||-|| .+.+........+.|= -+-.|..|+.
T Consensus         2 ~LkPCPFCG-~~~~~~~~~~~~~~~~~~~V~C~~Cga   37 (61)
T PF14354_consen    2 ELKPCPFCG-SADVLIRQDEGFDYGMYYYVECTDCGA   37 (61)
T ss_pred             CCcCCCCCC-CcceEeecccCCCCCCEEEEEcCCCCC
Confidence            488999994 4444444433333332 4556998977

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

Probab=80.14  E-value=1.7  Score=25.53  Aligned_cols=31  Identities=26%  Similarity=0.527  Sum_probs=16.9

Q ss_pred             cccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987           14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK   48 (105)
Q Consensus        14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq   48 (105)
                      -||.|| .+...+   .++.-+|.=+.|++|++..
T Consensus         2 fC~~CG-~~l~~~---ip~gd~r~R~vC~~Cg~Ih   32 (34)
T PF14803_consen    2 FCPQCG-GPLERR---IPEGDDRERLVCPACGFIH   32 (34)
T ss_dssp             B-TTT---B-EEE-----TT-SS-EEEETTTTEEE
T ss_pred             cccccc-Chhhhh---cCCCCCccceECCCCCCEE
Confidence            599996 443333   3444577889999999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	105
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	97.11
3h0g_I	113	DNA-directed RNA polymerases I, II, and III subuni	96.3
1tfi_A	50	Transcriptional elongation factor SII; transcripti	96.05
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	95.8
3po3_S	178	Transcription elongation factor S-II; RNA polymera	93.84
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	93.69
1pqv_S	309	STP-alpha, transcription elongation factor S-II, D	92.73
2gai_A	633	DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A	89.68
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	86.25
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	86.24
1dl6_A	58	Transcription factor II B (TFIIB); zinc ribbon, ge	85.45
2fiy_A	309	Protein FDHE homolog; FDHE protein, structural gen	84.33

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

Probab=97.11  E-value=0.00069  Score=41.18  Aligned_cols=39  Identities=31%  Similarity=0.739  Sum_probs=32.3

Q ss_pred             cccccccCCceeEEEeecC--CCCCCCceEeCCCCCeeEecC
Q 039987           12 LKACEKCFNSSKVLRTSHT--RENPNRKFWKCKGCGAFKWDD   51 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT--~~NPGRkFY~CpsC~FFqW~D   51 (105)
                      .+.||.||...++-.+..+  ...|--.||.|..|+. .|.+
T Consensus        15 ~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~-~w~~   55 (57)
T 1qyp_A           15 KITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGH-TWRS   55 (57)
T ss_dssp             ECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCC-EEEC
T ss_pred             EeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCC-Eecc
Confidence            5789999998888888555  5578899999999986 6766

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

Probab=96.30  E-value=0.0049  Score=42.13  Aligned_cols=39  Identities=18%  Similarity=0.527  Sum_probs=32.5

Q ss_pred             cccccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEecC
Q 039987           12 LKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKWDD   51 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW~D   51 (105)
                      ...||+|+...|+..++  +....|--.||+|..|+. +|.+
T Consensus        72 ~~~Cp~C~~~~a~~~q~q~rsade~mt~fy~C~~C~~-~w~~  112 (113)
T 3h0g_I           72 DKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCGF-AFEE  112 (113)
T ss_dssp             CSCCSSSCCSCEEEECCCCSSCCCCCCCEEEESSSCC-CCCC
T ss_pred             ccCCCCCCCceEEEEEEecccCCCCCeeEEEcCCCCC-EEec
Confidence            37899999999999884  457889999999999984 5764

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

Probab=96.05  E-value=0.0079  Score=36.67  Aligned_cols=39  Identities=28%  Similarity=0.722  Sum_probs=31.9

Q ss_pred             cccccccccCCceeEEEeec--CCCCCCCceEeCCCCCeeEe
Q 039987           10 TQLKACEKCFNSSKVLRTSH--TRENPNRKFWKCKGCGAFKW   49 (105)
Q Consensus        10 ~~l~~Cp~Cg~~~avlrTSk--T~~NPGRkFY~CpsC~FFqW   49 (105)
                      ...+.||+|+...++..++-  ....|=-.||.|..|+. +|
T Consensus         7 t~~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~-~w   47 (50)
T 1tfi_A            7 TDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGN-RW   47 (50)
T ss_dssp             CCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCC-EE
T ss_pred             eCccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCC-eE
Confidence            44678999999999988854  46678899999999985 45

>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=95.80  E-value=0.014  Score=40.35  Aligned_cols=42  Identities=24%  Similarity=0.572  Sum_probs=35.2

Q ss_pred             cccccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEecCCCC
Q 039987           12 LKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKWDDDRK   54 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW~De~~   54 (105)
                      ...||.|+...|+..++  +....|--.||.|..|+. +|.+...
T Consensus        72 ~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~-~w~~nn~  115 (122)
T 1twf_I           72 DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSH-IFTSDQK  115 (122)
T ss_dssp             CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCC-EEECCTT
T ss_pred             CCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCC-EeccCCh
Confidence            57899999999999885  446778999999999996 7988653

>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=93.84  E-value=0.043  Score=40.31  Aligned_cols=38  Identities=26%  Similarity=0.649  Sum_probs=31.1

Q ss_pred             ccccccccCCceeEEEeecC--CCCCCCceEeCCCCCeeEe
Q 039987           11 QLKACEKCFNSSKVLRTSHT--RENPNRKFWKCKGCGAFKW   49 (105)
Q Consensus        11 ~l~~Cp~Cg~~~avlrTSkT--~~NPGRkFY~CpsC~FFqW   49 (105)
                      ....||.|+...|+..++.|  ...|-..||.|..|+. +|
T Consensus       136 ~~~~Cp~C~~~~a~~~q~Q~rsaDE~mt~f~~C~~C~~-~w  175 (178)
T 3po3_S          136 DRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGN-RW  175 (178)
T ss_dssp             SSSCCSSSCCSCEECCCCCCSCTTSCCCCCEEETTTCC-EE
T ss_pred             CCcCCCCCCCCceEEEEeecccCCCCCcEEEEcCCCCC-ee
Confidence            36789999999998888555  5678899999999985 45

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=93.69  E-value=0.012  Score=41.92  Aligned_cols=39  Identities=28%  Similarity=0.846  Sum_probs=0.0

Q ss_pred             cccccccCCceeEEEeec--CCCCCCCceEeCCCCCeeEecC
Q 039987           12 LKACEKCFNSSKVLRTSH--TRENPNRKFWKCKGCGAFKWDD   51 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSk--T~~NPGRkFY~CpsC~FFqW~D   51 (105)
                      ...||.|+...|+..++.  ....|--.||.|..|++ +|.+
T Consensus        92 ~~~CpkCg~~~a~f~q~Q~RsaDE~mT~fy~C~~C~~-~w~e  132 (133)
T 3qt1_I           92 DRECPKCHSRENVFFQLQIRSADEPMTTFYKCVNCGH-RWKE  132 (133)
T ss_dssp             ------------------------------------------
T ss_pred             cCCCCCCCCceEEEEEEeeecCCCCCcEEEEcCCCCC-EeCc
Confidence            578999999999888744  47788999999999984 5764

>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=92.73  E-value=0.1  Score=40.82  Aligned_cols=37  Identities=24%  Similarity=0.679  Sum_probs=31.0

Q ss_pred             cccccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEe
Q 039987           12 LKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKW   49 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW   49 (105)
                      ...||.|+...+...+.  +....|-..||.|-.|+. .|
T Consensus       268 ~~~C~~C~~~~~~~~q~Q~rsaDe~~t~f~~C~~Cg~-~w  306 (309)
T 1pqv_S          268 RFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGN-RW  306 (309)
T ss_pred             cccCCCCCCCeeEEEEeecccCCCCCcEEEEeCCCCC-ce
Confidence            67899999999988874  446779999999999986 45

>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga maritima} PDB: 2gaj_A*

Probab=89.68  E-value=0.079  Score=45.10  Aligned_cols=37  Identities=11%  Similarity=-0.104  Sum_probs=19.4

Q ss_pred             cccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEecCC
Q 039987           12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWDDD   52 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~De   52 (105)
                      .+.||.|+.++.+++.++    .|+.||.|.   .|.|-.|..+
T Consensus       572 ~G~CP~Cg~g~l~~r~~k----~G~~f~gCs~yp~C~f~~~~~p  611 (633)
T 2gai_A          572 YGFYLKCECGKTRSVKND----EIAVIDDGKIFLGRKDSESGSP  611 (633)
T ss_dssp             TEEEEECSSSCCEECCTT----SBCEEETTEEEC----------
T ss_pred             cccCcccCCCcceeeccc----CCCeEEeCCCCcCCCCeecCCc
Confidence            346999974566666553    477899996   7999999764

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

Probab=86.25  E-value=0.47  Score=37.49  Aligned_cols=53  Identities=17%  Similarity=0.147  Sum_probs=36.4

Q ss_pred             ccccccCccccccccccCCceeEEEeecCC-----CCCCCceEeCCCCC-eeEecCCCC
Q 039987            2 SFSTSDNRTQLKACEKCFNSSKVLRTSHTR-----ENPNRKFWKCKGCG-AFKWDDDRK   54 (105)
Q Consensus         2 ~~~~~~n~~~l~~Cp~Cg~~~avlrTSkT~-----~NPGRkFY~CpsC~-FFqW~De~~   54 (105)
                      |++.+.=+.+...||.||+..-+..-+-.+     ..++-+.+.|..|+ +++=-|...
T Consensus       212 s~C~t~W~~~R~~C~~Cg~~~~l~y~~~e~~~~~~~~~~~r~e~C~~C~~YlK~~~~~~  270 (309)
T 2fiy_A          212 SLCACEWHYVRIKCSHCEESKHLAYLSLEHDGQPAEKAVLRAETCPSCQGYLKQFYLEF  270 (309)
T ss_dssp             TTTCCEEECCTTSCSSSCCCSCCEEECCCC-CCCSTTCSEEEEEETTTTEEEEEEETTT
T ss_pred             CCCCCEEeecCcCCcCCCCCCCeeEEEecCccccCCCcceEEEEcccccchHhhhhhcc
Confidence            345555566789999998864433333344     45899999999998 666655543

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

Probab=86.24  E-value=0.75  Score=27.81  Aligned_cols=31  Identities=26%  Similarity=0.718  Sum_probs=21.6

Q ss_pred             cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEec
Q 039987           12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWD   50 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~   50 (105)
                      ..-||.||.. ......       ..-+.|+.|+|-.|.
T Consensus        19 ~k~CP~CG~~-~fm~~~-------~~R~~C~kCG~t~~~   49 (50)
T 3j20_Y           19 NKFCPRCGPG-VFMADH-------GDRWACGKCGYTEWK   49 (50)
T ss_dssp             SEECSSSCSS-CEEEEC-------SSEEECSSSCCEEEC
T ss_pred             cccCCCCCCc-eEEecC-------CCeEECCCCCCEEEC
Confidence            6789999743 333221       245899999999985

>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=85.45  E-value=1.9  Score=26.37  Aligned_cols=46  Identities=17%  Similarity=0.159  Sum_probs=29.0

Q ss_pred             ccccCccc-cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCCCCC
Q 039987            4 STSDNRTQ-LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKSS   56 (105)
Q Consensus         4 ~~~~n~~~-l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~~~~   56 (105)
                      |+|+-+.- ..+||.|++.+ ++.      +..+--+.|..||+-.=+.....+
T Consensus         2 ~~~~~~ll~~~~Cp~C~~~~-lv~------D~~~ge~vC~~CGlVl~e~~iD~g   48 (58)
T 1dl6_A            2 STSRLDALPRVTCPNHPDAI-LVE------DYRAGDMICPECGLVVGDRVIDVG   48 (58)
T ss_dssp             TTCSCCCCSCCSBTTBSSSC-CEE------CSSSCCEECTTTCCEECCSCCCCC
T ss_pred             ccchhhccccccCcCCCCCc-eeE------eCCCCeEEeCCCCCEEeccccccC
Confidence            45555554 44899998755 332      234455999999987755554444

>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=84.33  E-value=0.7  Score=36.52  Aligned_cols=36  Identities=11%  Similarity=0.308  Sum_probs=24.8

Q ss_pred             cccccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987           10 TQLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG   45 (105)
Q Consensus        10 ~~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~   45 (105)
                      -+...||-||+.+..-....++.--|.|+..|.-|+
T Consensus       180 ~~~~~CPvCGs~P~~s~l~~~g~~~G~R~l~Cs~C~  215 (309)
T 2fiy_A          180 ESRTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCA  215 (309)
T ss_dssp             TTCSSCTTTCCCEEEEEEEC----CCEEEEEETTTC
T ss_pred             ccCCCCCCCCCcCceeEEeecCCCCCcEEEEeCCCC
Confidence            347899999988876655555666798999998554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	105
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	95.32
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	95.23
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	93.39
d2fiya1	290	FdhE homolog PA4809 {Pseudomonas aeruginosa [TaxId	80.77

>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=95.32  E-value=0.0071  Score=36.67  Aligned_cols=39  Identities=28%  Similarity=0.743  Sum_probs=33.2

Q ss_pred             cccccccCCceeEEEe--ecCCCCCCCceEeCCCCCeeEecC
Q 039987           12 LKACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGAFKWDD   51 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~FFqW~D   51 (105)
                      .+.||+|+...++...  .+....|=-.||.|..|+. +|.|
T Consensus        15 ~~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~Cg~-~wre   55 (57)
T d1qypa_          15 KITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGH-TWRS   55 (57)
T ss_dssp             ECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCC-EEEC
T ss_pred             cCCCCCCCCCceEEEEeecccccCCCeEEEEeCCCCC-ccee
Confidence            5789999999998877  5558899999999999985 6765

>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=95.23  E-value=0.012  Score=37.15  Aligned_cols=42  Identities=21%  Similarity=0.556  Sum_probs=34.6

Q ss_pred             cccccccCCceeEEEe--ecCCCCCCCceEeCCCCCeeEecCCCC
Q 039987           12 LKACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGAFKWDDDRK   54 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~FFqW~De~~   54 (105)
                      ...||+|+...++...  .+....|=-.||.|..|++ .|..+..
T Consensus        23 ~~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h-~Wr~~~~   66 (72)
T d1twfi2          23 DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSH-IFTSDQK   66 (72)
T ss_dssp             CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCC-EEECCTT
T ss_pred             CCCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCC-Ccccccc
Confidence            5789999999998888  4447789999999999985 6776543

>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=93.39  E-value=0.04  Score=32.63  Aligned_cols=39  Identities=26%  Similarity=0.612  Sum_probs=31.1

Q ss_pred             CccccccccccCCceeEEEe--ecCCCCCCCceEeCCCCCe
Q 039987            8 NRTQLKACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGA   46 (105)
Q Consensus         8 n~~~l~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~F   46 (105)
                      ....+..||+|+...+...+  .++..-|-=.||.|..|+.
T Consensus         5 ~~T~~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~   45 (50)
T d1tfia_           5 TQTDLFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGN   45 (50)
T ss_dssp             EECCCSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCC
T ss_pred             cccCCEECCCCCCCccEEEEEEccCCCCCceEEEEccccCC
Confidence            34568899999988886655  5567788889999999984

>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=80.77  E-value=0.55  Score=35.03  Aligned_cols=37  Identities=14%  Similarity=0.442  Sum_probs=24.9

Q ss_pred             cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEe
Q 039987           12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKW   49 (105)
Q Consensus        12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW   49 (105)
                      ...||-||..|..-..-..+.--|.|+..|.-|+. +|
T Consensus       164 ~~~CPvCGs~P~~s~l~~~~~~~G~R~l~C~~C~t-eW  200 (290)
T d2fiya1         164 RTLCPACGSPPMAGMIRQGGKETGLRYLSCSLCAC-EW  200 (290)
T ss_dssp             CSSCTTTCCCEEEEEEEC----CCEEEEEETTTCC-EE
T ss_pred             CCcCCCCCCcchhheeeccCCCCCceEEECCCCCC-cc
Confidence            57899998777666655556667999999995553 45