Query 039685
Match_columns 111
No_of_seqs 18 out of 20
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 12:10:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039685.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039685hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10278 Med19: Mediator of RN 99.6 7.1E-17 1.5E-21 124.4 3.0 93 10-109 10-103 (178)
2 PF03854 zf-P11: P-11 zinc fin 40.8 8.7 0.00019 25.3 -0.1 11 33-43 39-49 (50)
3 PF05379 Peptidase_C23: Carlav 39.7 11 0.00024 26.0 0.3 14 56-69 35-48 (89)
4 TIGR02605 CxxC_CxxC_SSSS putat 38.0 13 0.00029 22.0 0.4 10 28-37 1-10 (52)
5 PRK03359 putative electron tra 36.5 28 0.0006 27.9 2.1 43 49-98 7-51 (256)
6 PRK12342 hypothetical protein; 33.5 37 0.00081 27.2 2.4 20 78-97 30-49 (254)
7 TIGR02542 B_forsyth_147 Bacter 32.2 32 0.0007 26.7 1.8 52 43-94 37-96 (145)
8 PF14799 FAM195: FAM195 family 26.5 47 0.001 23.5 1.7 16 74-89 73-88 (99)
9 PF03431 RNA_replicase_B: RNA 25.2 27 0.00058 32.0 0.3 32 4-39 359-391 (542)
10 PTZ00486 apyrase Superfamily; 24.1 34 0.00073 29.6 0.7 14 59-72 110-123 (352)
11 PF15137 DUF4571: Domain of un 23.1 52 0.0011 27.1 1.6 38 33-74 61-98 (219)
12 COG2086 FixA Electron transfer 22.9 49 0.0011 26.9 1.4 21 78-98 32-52 (260)
13 smart00834 CxxC_CXXC_SSSS Puta 20.6 43 0.00093 18.6 0.5 10 28-37 1-10 (41)
14 PHA00028 rep RNA replicase, be 20.4 62 0.0013 29.8 1.6 32 4-39 366-398 (561)
No 1
>PF10278 Med19: Mediator of RNA pol II transcription subunit 19 ; InterPro: IPR019403 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=99.64 E-value=7.1e-17 Score=124.43 Aligned_cols=93 Identities=30% Similarity=0.508 Sum_probs=82.7
Q ss_pred CCccccchhhhhhhhhcccccccccccccCccccccccccccCCCCeeeecC-CCcchhHHhhcCCCCCCCccccccHHH
Q 039685 10 RGPRELTGAVDLISHYKLLPHHDFFCKRSLPLSISDTHYLHNVVGDTEIRKG-EGMQLDQLIQNTSRDTSARIQPFDLDV 88 (111)
Q Consensus 10 ~gprEltgavDLis~ykL~~h~effCKr~lp~sisdthYL~nVvGDteirkg-eGmeLdQLiq~~~~~~~~~iqpFdl~v 88 (111)
.+.+|||||+|||+||.|-..|.-||+|.|..++| +||-||||++.++.+ |+..|-+||+..+- ..-.|+||+-..
T Consensus 10 p~~~eltG~~nL~~~y~L~~~y~kf~~kklke~lS--sFLp~lpG~~~~~~~~d~ssLrslIekPPi-~gkei~pL~~~~ 86 (178)
T PF10278_consen 10 PPDSELTGATNLITHYGLEHSYNKFCGKKLKESLS--SFLPHLPGNIDLPGSQDNSSLRSLIEKPPI-GGKEITPLSSSQ 86 (178)
T ss_pred CCccccccchhHHHHcCcHHHHHHHhCCcchhhHH--HHccCCCCcccCCCCcCcchHHHHhhCCCC-CCccCCcCCHHH
Confidence 46899999999999999999999999999999996 999999999999997 77779999999974 336799999999
Q ss_pred HHHhhccccCCCccCCCCCCC
Q 039685 89 LREAFQLRETSPVDLPPVRNP 109 (111)
Q Consensus 89 L~~aFqL~et~pi~Lp~aekG 109 (111)
| .+|.|.. || ||+..+.
T Consensus 87 L-~gFrL~p-Gp--lPE~yr~ 103 (178)
T PF10278_consen 87 L-AGFRLHP-GP--LPEQYRL 103 (178)
T ss_pred H-hhccCCC-CC--CchHHhh
Confidence 9 7999995 77 6766544
No 2
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=40.82 E-value=8.7 Score=25.28 Aligned_cols=11 Identities=36% Similarity=0.760 Sum_probs=5.7
Q ss_pred ccccccCcccc
Q 039685 33 FFCKRSLPLSI 43 (111)
Q Consensus 33 ffCKr~lp~si 43 (111)
=+|++|||+.|
T Consensus 39 ~iC~~~LPtki 49 (50)
T PF03854_consen 39 PICGKPLPTKI 49 (50)
T ss_dssp TTTTEE----S
T ss_pred CcccCcCcccc
Confidence 37999999986
No 3
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=39.67 E-value=11 Score=25.99 Aligned_cols=14 Identities=43% Similarity=0.878 Sum_probs=12.3
Q ss_pred eeeecCCCcchhHH
Q 039685 56 TEIRKGEGMQLDQL 69 (111)
Q Consensus 56 teirkgeGmeLdQL 69 (111)
.++|.|+|.++.+|
T Consensus 35 ~~l~~G~Gl~l~~l 48 (89)
T PF05379_consen 35 EELWSGEGLDLEDL 48 (89)
T ss_pred HHHHcCCCcCHHHH
Confidence 47899999999987
No 4
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. 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.
Probab=38.05 E-value=13 Score=22.00 Aligned_cols=10 Identities=20% Similarity=0.720 Sum_probs=8.3
Q ss_pred cccccccccc
Q 039685 28 LPHHDFFCKR 37 (111)
Q Consensus 28 ~~h~effCKr 37 (111)
||.|+|.|++
T Consensus 1 MP~Yey~C~~ 10 (52)
T TIGR02605 1 MPIYEYRCTA 10 (52)
T ss_pred CCCEEEEeCC
Confidence 6889999975
No 5
>PRK03359 putative electron transfer flavoprotein FixA; Reviewed
Probab=36.47 E-value=28 Score=27.89 Aligned_cols=43 Identities=26% Similarity=0.412 Sum_probs=28.5
Q ss_pred cccCCCCeeeecC-CCcchhHHhhcCCCC-CCCccccccHHHHHHhhccccC
Q 039685 49 LHNVVGDTEIRKG-EGMQLDQLIQNTSRD-TSARIQPFDLDVLREAFQLRET 98 (111)
Q Consensus 49 L~nVvGDteirkg-eGmeLdQLiq~~~~~-~~~~iqpFdl~vL~~aFqL~et 98 (111)
++.||-.++++-. ++..|+ |+ -..-|-|||..-|++|.+|||.
T Consensus 7 vKqVPD~~~~~~~~~~~~l~-------r~~~~~~iN~~D~~AlE~Alrlke~ 51 (256)
T PRK03359 7 YKCVPDEQDIAVNNADGSLD-------FSKADAKISQYDLNAIEAACQLKQQ 51 (256)
T ss_pred EEECcCCcceEEeCCCCeEE-------cCCCccccChhhHHHHHHHHHHhhh
Confidence 3456655565554 333333 22 2345999999999999999995
No 6
>PRK12342 hypothetical protein; Provisional
Probab=33.54 E-value=37 Score=27.21 Aligned_cols=20 Identities=40% Similarity=0.602 Sum_probs=17.8
Q ss_pred CCccccccHHHHHHhhcccc
Q 039685 78 SARIQPFDLDVLREAFQLRE 97 (111)
Q Consensus 78 ~~~iqpFdl~vL~~aFqL~e 97 (111)
..-|-|||..-|++|.+||+
T Consensus 30 ~~~iNp~D~~AlE~AlrLk~ 49 (254)
T PRK12342 30 EAKISQFDLNAIEAASQLAT 49 (254)
T ss_pred CccCChhhHHHHHHHHHHhh
Confidence 44599999999999999996
No 7
>TIGR02542 B_forsyth_147 Bacteroides forsythus 147-residue repeat. The longest predicted protein in Bacteroides forsythus ATCC 43037 is over 3000 residues long and lacks homology to other known proteins. Immediately after the signal sequence are four tandem repeats, approximately 147 residues long. This model describes that repeat. This model describes that repeat.
Probab=32.21 E-value=32 Score=26.66 Aligned_cols=52 Identities=33% Similarity=0.486 Sum_probs=35.6
Q ss_pred cccccccccCCC-----CeeeecCCCcchhH-HhhcCCCCCCCccccccH--HHHHHhhc
Q 039685 43 ISDTHYLHNVVG-----DTEIRKGEGMQLDQ-LIQNTSRDTSARIQPFDL--DVLREAFQ 94 (111)
Q Consensus 43 isdthYL~nVvG-----DteirkgeGmeLdQ-Liq~~~~~~~~~iqpFdl--~vL~~aFq 94 (111)
++|..||-+|-| |-.||-|.|-.-.- -||++++..++.+-|+++ ..||+.|.
T Consensus 37 ypdndal~~~~G~lE~vDg~i~IGs~q~~~sV~i~gTPsgnnv~F~PYTlT~~e~r~iF~ 96 (145)
T TIGR02542 37 YPDNDALLYVHGTLEQVDGNIRIGSGQTPASVRIQGTPSGNNVIFPPYTLTYNELRQIFR 96 (145)
T ss_pred cCCchhhheeeeehhhccCcEEEccCCCcccEEEecCCCCCceecCceeeeHHHHHHHHh
Confidence 455555555554 33488777754332 377888889999999976 67888884
No 8
>PF14799 FAM195: FAM195 family
Probab=26.48 E-value=47 Score=23.47 Aligned_cols=16 Identities=25% Similarity=0.526 Sum_probs=12.1
Q ss_pred CCCCCCccccccHHHH
Q 039685 74 SRDTSARIQPFDLDVL 89 (111)
Q Consensus 74 ~~~~~~~iqpFdl~vL 89 (111)
+...-..|.|||||.+
T Consensus 73 pnp~L~~FkPfDLE~w 88 (99)
T PF14799_consen 73 PNPSLKNFKPFDLEEW 88 (99)
T ss_pred CCCccCCCcccCHHHH
Confidence 3455567999999986
No 9
>PF03431 RNA_replicase_B: RNA replicase, beta-chain ; InterPro: IPR005093 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This is a family of Leviviridae RNA replicases.; GO: 0003968 RNA-directed RNA polymerase activity, 0019079 viral genome replication; PDB: 3MMP_G 3AVU_A 3AVW_A 3AGQ_A 3AGP_A 3AVT_A 3AVY_A 3AVX_A 3AVV_A.
Probab=25.23 E-value=27 Score=31.97 Aligned_cols=32 Identities=34% Similarity=0.527 Sum_probs=15.9
Q ss_pred cCCCCCCCc-cccchhhhhhhhhcccccccccccccC
Q 039685 4 EGKNFGRGP-RELTGAVDLISHYKLLPHHDFFCKRSL 39 (111)
Q Consensus 4 ~~~~fg~gp-rEltgavDLis~ykL~~h~effCKr~l 39 (111)
+.|.|..|| ||-||+ .+|.=..---|+||+|+
T Consensus 359 ~~KTF~~G~FRESCG~----h~f~g~DVtPfYik~pi 391 (542)
T PF03431_consen 359 LKKTFWTGPFRESCGA----HYFDGVDVTPFYIKRPI 391 (542)
T ss_dssp CCC-BSSSSEEEETTE----EEETTEE-------S--
T ss_pred cccccccccchhhhhh----hhcCCccccceEecccc
Confidence 568899898 999997 24444444568899976
No 10
>PTZ00486 apyrase Superfamily; Provisional
Probab=24.13 E-value=34 Score=29.59 Aligned_cols=14 Identities=36% Similarity=0.698 Sum_probs=12.0
Q ss_pred ecCCCcchhHHhhc
Q 039685 59 RKGEGMQLDQLIQN 72 (111)
Q Consensus 59 rkgeGmeLdQLiq~ 72 (111)
.+|+||||.+|+.=
T Consensus 110 ~~gRGmELSELv~F 123 (352)
T PTZ00486 110 EGGRGMELSELVSF 123 (352)
T ss_pred CCCCCcchhhhhee
Confidence 48999999999863
No 11
>PF15137 DUF4571: Domain of unknown function (DUF4571)
Probab=23.07 E-value=52 Score=27.10 Aligned_cols=38 Identities=29% Similarity=0.384 Sum_probs=32.6
Q ss_pred ccccccCccccccccccccCCCCeeeecCCCcchhHHhhcCC
Q 039685 33 FFCKRSLPLSISDTHYLHNVVGDTEIRKGEGMQLDQLIQNTS 74 (111)
Q Consensus 33 ffCKr~lp~sisdthYL~nVvGDteirkgeGmeLdQLiq~~~ 74 (111)
-.||--||.++..|.|= ||-+||=-|=--|.+|..=+.
T Consensus 61 CsCkTvLp~a~e~tsY~----g~LtIWFTd~s~Lg~LLNfTl 98 (219)
T PF15137_consen 61 CSCKTVLPSAVEQTSYS----GHLTIWFTDTSALGLLLNFTL 98 (219)
T ss_pred cccceeccccccccccc----CceEEEEecHHHHHHHHhhHh
Confidence 36999999999999996 999999999888888875543
No 12
>COG2086 FixA Electron transfer flavoprotein, beta subunit [Energy production and conversion]
Probab=22.86 E-value=49 Score=26.89 Aligned_cols=21 Identities=43% Similarity=0.816 Sum_probs=18.5
Q ss_pred CCccccccHHHHHHhhccccC
Q 039685 78 SARIQPFDLDVLREAFQLRET 98 (111)
Q Consensus 78 ~~~iqpFdl~vL~~aFqL~et 98 (111)
...|-|||..-+++|.||+|.
T Consensus 32 ~~~in~~D~~AvEeAlrLke~ 52 (260)
T COG2086 32 PLSINPFDLNAVEEALRLKEK 52 (260)
T ss_pred CcccChhhHHHHHHHHHhhcc
Confidence 345889999999999999994
No 13
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. 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.
Probab=20.60 E-value=43 Score=18.57 Aligned_cols=10 Identities=20% Similarity=0.766 Sum_probs=7.2
Q ss_pred cccccccccc
Q 039685 28 LPHHDFFCKR 37 (111)
Q Consensus 28 ~~h~effCKr 37 (111)
||.|+|.|..
T Consensus 1 Mp~Y~y~C~~ 10 (41)
T smart00834 1 MPIYEYRCED 10 (41)
T ss_pred CCCEEEEcCC
Confidence 5778888854
No 14
>PHA00028 rep RNA replicase, beta subunit
Probab=20.40 E-value=62 Score=29.79 Aligned_cols=32 Identities=38% Similarity=0.511 Sum_probs=23.3
Q ss_pred cCCCCCCCc-cccchhhhhhhhhcccccccccccccC
Q 039685 4 EGKNFGRGP-RELTGAVDLISHYKLLPHHDFFCKRSL 39 (111)
Q Consensus 4 ~~~~fg~gp-rEltgavDLis~ykL~~h~effCKr~l 39 (111)
..|.|=.|| ||-|||- +|+=..---|+||+|+
T Consensus 366 ~kKTF~~G~FRESCGaH----~f~GvDVtPFYik~pi 398 (561)
T PHA00028 366 LKKTFWTGPFRESCGAH----YFAGVDVTPFYIKRPL 398 (561)
T ss_pred CccccccCcchhhhhhh----hcCCCCccceEecccc
Confidence 347777787 9999982 4555555679999994
Done!