Query 033169
Match_columns 125
No_of_seqs 105 out of 217
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 10:40:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033169.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033169hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00198 60S ribosomal protein 100.0 1.4E-66 3E-71 386.4 12.5 116 4-121 6-121 (122)
2 PF01776 Ribosomal_L22e: Ribos 100.0 1E-66 2.2E-71 382.6 8.3 112 12-125 1-112 (112)
3 KOG3434 60S ribosomal protein 100.0 1.7E-61 3.8E-66 360.0 6.8 123 1-125 2-124 (125)
4 PF02747 PCNA_C: Proliferating 62.2 56 0.0012 23.5 8.1 62 32-104 13-106 (128)
5 PF02576 DUF150: Uncharacteris 51.7 34 0.00073 25.1 4.5 32 17-48 61-93 (141)
6 PF12970 DUF3858: Domain of Un 46.0 20 0.00044 27.0 2.5 54 15-79 37-90 (116)
7 PF13202 EF-hand_5: EF hand; P 39.9 19 0.00042 19.3 1.2 14 28-41 12-25 (25)
8 PHA03383 PCNA-like protein; Pr 38.6 46 0.001 27.3 3.8 26 75-104 213-238 (262)
9 PF14728 PHTB1_C: PTHB1 C-term 35.6 69 0.0015 27.9 4.6 26 13-42 98-124 (377)
10 PF01485 IBR: IBR domain; Int 35.0 11 0.00023 23.1 -0.3 17 77-93 1-17 (64)
11 PF13543 KSR1-SAM: SAM like do 34.8 6.8 0.00015 29.7 -1.5 14 91-104 67-80 (129)
12 PRK14638 hypothetical protein; 31.6 1.4E+02 0.003 22.7 5.1 31 17-47 74-105 (150)
13 smart00647 IBR In Between Ring 29.1 42 0.0009 20.4 1.6 16 77-92 1-16 (64)
14 COG1018 Hmp Flavodoxin reducta 26.1 65 0.0014 26.4 2.7 33 14-47 51-90 (266)
15 TIGR00590 pcna proliferating c 25.2 36 0.00077 27.6 1.0 26 75-104 207-232 (259)
16 PF03192 DUF257: Pyrococcus pr 25.0 46 0.001 26.6 1.6 35 44-85 73-108 (210)
17 smart00054 EFh EF-hand, calciu 23.9 67 0.0015 14.9 1.6 18 26-43 11-28 (29)
18 PRK14646 hypothetical protein; 23.5 2E+02 0.0043 21.9 4.8 31 18-48 75-106 (155)
19 PF15547 DUF4654: Domain of un 23.0 51 0.0011 25.5 1.4 12 15-26 10-21 (138)
20 PRK15084 formate hydrogenlyase 22.8 56 0.0012 25.2 1.6 21 20-42 41-61 (133)
21 KOG1770 Translation initiation 22.6 86 0.0019 23.5 2.5 23 66-88 42-67 (112)
22 PF07450 HycH: Formate hydroge 22.3 60 0.0013 24.9 1.7 22 20-43 39-60 (131)
23 PRK14630 hypothetical protein; 22.1 2.3E+02 0.005 21.3 4.8 30 18-47 72-102 (143)
24 PF08980 DUF1883: Domain of un 21.6 52 0.0011 23.8 1.2 24 18-41 16-39 (94)
25 PF13833 EF-hand_8: EF-hand do 21.4 61 0.0013 19.1 1.3 20 25-44 35-54 (54)
26 cd02414 jag_KH jag_K homology 20.6 2.6E+02 0.0057 18.3 5.3 47 56-103 15-71 (77)
27 PRK07459 single-stranded DNA-b 20.4 1.4E+02 0.003 21.6 3.3 44 51-104 9-53 (121)
28 PRK10397 lipoprotein; Provisio 20.2 54 0.0012 25.4 1.1 27 92-118 66-92 (137)
29 PRK14640 hypothetical protein; 20.2 1.3E+02 0.0029 22.7 3.2 31 18-48 72-103 (152)
No 1
>PTZ00198 60S ribosomal protein L22; Provisional
Probab=100.00 E-value=1.4e-66 Score=386.42 Aligned_cols=116 Identities=57% Similarity=0.903 Sum_probs=109.0
Q ss_pred ccccccccCccceeEEEEeecCccCCCccchhhHHHhhhcceeeccccCCCCCceEEEEeCCEEEEEecccccchhhhhH
Q 033169 4 GAAAAGVKGKKKGATFVIDCGKPVEDKIMDIASLEKFLQERIKVGGKAGALGDSVTVTREKTKITVTSDSNFSKRYLKYL 83 (125)
Q Consensus 4 ~~~~~~~~~kk~~~kF~iDCt~PveD~I~d~a~fekfL~erIKV~gk~gnLg~~V~i~r~~~ki~V~s~~~fsKRYLKYL 83 (125)
++....+.++|..++|+||||+||||+|||+++||+|||||||||||+||||+.|+|++++++|+|+|++||||||||||
T Consensus 6 ~~~~~~~~~kk~~~kF~IDCt~PveD~I~d~a~fekfL~erIKV~GK~gnLg~~V~v~~~k~ki~V~s~~~FSKRYLKYL 85 (122)
T PTZ00198 6 RGRKRQKQVKKKKKKFKIDCTIPAEDGIIDLSGFEQFLQDRIKVDGKTGNLGNKVRVSREKNKITVTTTIPFSKRYLKYL 85 (122)
T ss_pred ccccccchhcccceEEEEEcCCcccCCcccHHHHHHHHHHhEEECCCcCccCCcEEEEEECCEEEEEecccccHHHHHHH
Confidence 44445566678889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhhccCCCceEEEEeccCCCCeEEEEeeeecCCCC
Q 033169 84 TKKYLKKHNVRDWLRVIASNKDRSVYELRYFNIAENEG 121 (125)
Q Consensus 84 tKKyLKk~~LRdwlrVvA~~K~~~~YeLrYfni~~d~~ 121 (125)
||||||||+|||||||||++| ++||||||||++|||
T Consensus 86 TKKyLKK~~LRDwlRVVA~~K--~~YELRYfnI~~d~~ 121 (122)
T PTZ00198 86 TKKYLKKKQLRDFLRVVATGK--GTYELKYFNIQDEEE 121 (122)
T ss_pred HHHHHhhhhhhheEEEEecCC--CeEEEEEEEecCcCC
Confidence 999999999999999999999 999999999976654
No 2
>PF01776 Ribosomal_L22e: Ribosomal L22e protein family; InterPro: IPR002671 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. 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 [, ]. Ribosomal protein L22e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. Rattus norvegicus (Rat) L22 is related to ribosomal proteins from other eukaryotes and is identical in amino acid sequence to human EAP, the EBER 1 (Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) encoded RNA) associated protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1D_M 4A1B_M 4A19_M 4A18_M 3IZR_W 3IZS_W.
Probab=100.00 E-value=1e-66 Score=382.62 Aligned_cols=112 Identities=69% Similarity=1.079 Sum_probs=91.3
Q ss_pred CccceeEEEEeecCccCCCccchhhHHHhhhcceeeccccCCCCCceEEEEeCCEEEEEecccccchhhhhHHHhhhhcc
Q 033169 12 GKKKGATFVIDCGKPVEDKIMDIASLEKFLQERIKVGGKAGALGDSVTVTREKTKITVTSDSNFSKRYLKYLTKKYLKKH 91 (125)
Q Consensus 12 ~kk~~~kF~iDCt~PveD~I~d~a~fekfL~erIKV~gk~gnLg~~V~i~r~~~ki~V~s~~~fsKRYLKYLtKKyLKk~ 91 (125)
+||+.++|+||||+||+|||||+|+||+|||+||||||++||||+.|+|++++++|+|+|++|||||||||||||||||+
T Consensus 1 kkk~~~kF~IDCt~pveD~I~d~~~fe~fL~erIKV~gk~gnlg~~V~i~~~~~ki~V~s~v~fsKrYLKYLTKKyLKK~ 80 (112)
T PF01776_consen 1 KKKQTLKFTIDCTHPVEDGIMDPADFEKFLQERIKVNGKTGNLGNKVTISRDKNKITVTSEVPFSKRYLKYLTKKYLKKN 80 (112)
T ss_dssp --EEEEEEEEE-HHSSSTS---SHHHHHHHHHHHHHHSCSSSSTTTEEEEE-SSEEEEEESSS-SHHHHHHHHHHHHTTS
T ss_pred CCcccEEEEEEeCCcccCceecHHHHHHHHHHheEeCCcccccCCeEEEEecCCEEEEEecccccHHHHHHHHHHHHhhc
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCceEEEEeccCCCCeEEEEeeeecCCCCCCCC
Q 033169 92 NVRDWLRVIASNKDRSVYELRYFNIAENEGEEED 125 (125)
Q Consensus 92 ~LRdwlrVvA~~K~~~~YeLrYfni~~d~~e~ee 125 (125)
+|||||||||++| ++||||||||++|||||||
T Consensus 81 ~LRdwlrVva~~K--~~YeLrYfni~~d~ee~e~ 112 (112)
T PF01776_consen 81 NLRDWLRVVASSK--DTYELRYFNINQDEEEEEE 112 (112)
T ss_dssp SSTTTEEECCSCS--TCEEEEE------------
T ss_pred chhheEEEEEcCC--CeEEEEEEecCCCcccccC
Confidence 9999999999999 9999999999999888886
No 3
>KOG3434 consensus 60S ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-61 Score=360.00 Aligned_cols=123 Identities=63% Similarity=0.979 Sum_probs=115.8
Q ss_pred CCcccccccccCccceeEEEEeecCccCCCccchhhHHHhhhcceeeccccCCCCCceEEEEeCCEEEEEecccccchhh
Q 033169 1 MSRGAAAAGVKGKKKGATFVIDCGKPVEDKIMDIASLEKFLQERIKVGGKAGALGDSVTVTREKTKITVTSDSNFSKRYL 80 (125)
Q Consensus 1 m~r~~~~~~~~~kk~~~kF~iDCt~PveD~I~d~a~fekfL~erIKV~gk~gnLg~~V~i~r~~~ki~V~s~~~fsKRYL 80 (125)
|||.+++...+++|..++|+||||+||||||||+|+||+|||||||||||+||||+.|+|++.+++|+|+|+++||+|||
T Consensus 2 ~~k~~~~~~~~~kKv~~~f~iDct~p~eDgI~d~A~fe~fLqerIKv~GK~gnLg~vv~ie~~kskitV~s~~~Fs~ryl 81 (125)
T KOG3434|consen 2 SAKKALRKTAKKKKVHLRFTIDCTNPVEDGILDIADLEKFLQERIKVNGKVGNLGNVVTIERSKSKITVVSTVHFSKRYL 81 (125)
T ss_pred chhhhhhhccccceeEEEEEEEecCccccccccHHHHHHHHHHHhhhcccccccCCeEEEecCCcEEEEEecCCccHHHH
Confidence 67777775567788899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHhhhhccCCCceEEEEeccCCCCeEEEEeeeecCCCCCCCC
Q 033169 81 KYLTKKYLKKHNVRDWLRVIASNKDRSVYELRYFNIAENEGEEED 125 (125)
Q Consensus 81 KYLtKKyLKk~~LRdwlrVvA~~K~~~~YeLrYfni~~d~~e~ee 125 (125)
||||||||||++|||||||||+++ ++||||||||+++++|+||
T Consensus 82 KyltkkYLkk~~LRdwlrvva~~k--~~yelryf~i~~~~~~~e~ 124 (125)
T KOG3434|consen 82 KYLTKKYLKKNNLRDWLRVVATDK--NTYELRYFQISDGEDEEEE 124 (125)
T ss_pred HHHHHHHHhhhhHHHHHHHhhccC--ceEEEEecccCCCcccccc
Confidence 999999999999999999999999 9999999999988766554
No 4
>PF02747 PCNA_C: Proliferating cell nuclear antigen, C-terminal domain; InterPro: IPR022649 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []. It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA replication []. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta. Homologues of PCNA have also been identified in the archaea (Euryarchaeota and Crenarchaeota) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. ; GO: 0003677 DNA binding, 0030337 DNA polymerase processivity factor activity, 0006275 regulation of DNA replication, 0043626 PCNA complex; PDB: 1IZ5_A 1IZ4_A 1GE8_A 1ISQ_A 3A2F_B 1RWZ_A 3P83_A 1RXM_A 1RXZ_A 1SXJ_F ....
Probab=62.16 E-value=56 Score=23.48 Aligned_cols=62 Identities=21% Similarity=0.416 Sum_probs=37.7
Q ss_pred cchhhHHHhhhcceeeccccCCCCCceEEEEeCCEEEEEecc--------------------------------cccchh
Q 033169 32 MDIASLEKFLQERIKVGGKAGALGDSVTVTREKTKITVTSDS--------------------------------NFSKRY 79 (125)
Q Consensus 32 ~d~a~fekfL~erIKV~gk~gnLg~~V~i~r~~~ki~V~s~~--------------------------------~fsKRY 79 (125)
|+.+.|.+.+++ ...+|+.|.|+.+++.|.+.++. .||=+|
T Consensus 13 m~S~~f~~~~kd-------l~~v~d~v~i~~~~~~~~f~~~Gd~~~~~v~~~~~~~~~~~~~~~~i~~~~~~~~~fsl~Y 85 (128)
T PF02747_consen 13 MPSSEFKKICKD-------LSSVGDTVTISADKDSVIFSAEGDIGSAEVEFKETESSEDDEELIEIEVKEPVSSSFSLDY 85 (128)
T ss_dssp EEHHHHHHHHHH-------HHTTCSEEEEEEETTEEEEEEEESSEEEEEEEEEEEEETTCTCESEEEESSEEEEEEEHHH
T ss_pred EEHHHHHHHHHH-------HHhcCCEEEEEEeCCEEEEEEEeccCcEEEEEeeccccccccccceeeeccceeeEEeHHH
Confidence 667778777754 33456677777666666553331 255555
Q ss_pred hhhHHHhhhhccCCCceEEEEeccC
Q 033169 80 LKYLTKKYLKKHNVRDWLRVIASNK 104 (125)
Q Consensus 80 LKYLtKKyLKk~~LRdwlrVvA~~K 104 (125)
|+. |.|-.+|-|-+.+--.+.
T Consensus 86 L~~----~~Ka~~ls~~V~l~l~~~ 106 (128)
T PF02747_consen 86 LND----FSKAAPLSDEVTLELGED 106 (128)
T ss_dssp HHH----HGGGGGTTSEEEEEEETT
T ss_pred HHh----hhccccCCceEEEEEcCC
Confidence 544 556677888777655544
No 5
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=51.66 E-value=34 Score=25.12 Aligned_cols=32 Identities=16% Similarity=0.472 Sum_probs=21.9
Q ss_pred eEEEEeecCcc-CCCccchhhHHHhhhcceeec
Q 033169 17 ATFVIDCGKPV-EDKIMDIASLEKFLQERIKVG 48 (125)
Q Consensus 17 ~kF~iDCt~Pv-eD~I~d~a~fekfL~erIKV~ 48 (125)
-.|++..|.|- +.-+....+|+.|+-+.|+|.
T Consensus 61 ~~y~LEVSSPG~~r~L~~~~~~~~~iG~~v~v~ 93 (141)
T PF02576_consen 61 EDYTLEVSSPGIDRPLKSPRDFERFIGRKVKVK 93 (141)
T ss_dssp S-EEEEEE--SSSS--SSHHHHHHH-SEEEEEE
T ss_pred cceEEEEeCCCCCCcCCCHHHHHHhcCCeEEEE
Confidence 47899999996 556666899999999999994
No 6
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=46.04 E-value=20 Score=26.97 Aligned_cols=54 Identities=24% Similarity=0.356 Sum_probs=32.9
Q ss_pred ceeEEEEeecCccCCCccchhhHHHhhhcceeeccccCCCCCceEEEEeCCEEEEEecccccchh
Q 033169 15 KGATFVIDCGKPVEDKIMDIASLEKFLQERIKVGGKAGALGDSVTVTREKTKITVTSDSNFSKRY 79 (125)
Q Consensus 15 ~~~kF~iDCt~PveD~I~d~a~fekfL~erIKV~gk~gnLg~~V~i~r~~~ki~V~s~~~fsKRY 79 (125)
....++|.|..- |++.. -.-..++++..|.+ .|+|..+++++.|+.++.++|+-
T Consensus 37 E~ytyti~~peg-----m~l~t----~~~~K~I~N~~Gk~--~isv~~~~~~~~V~rsL~L~Kql 90 (116)
T PF12970_consen 37 ETYTYTIELPEG-----MKLVT----PPMEKKIDNPVGKV--SISVKPEGNKIKVTRSLELKKQL 90 (116)
T ss_dssp EEEEEEEEE-TT------EE-S------S-EEEEETTEEE--EEEEEEETTEEEEEEEEEE--SE
T ss_pred cceEEEEEcCCC-----Ceeec----CccceeccCCcceE--EEEEEecCCeEEEEEEEEEeeee
Confidence 345677776433 33211 02234667777766 68899999999999999999863
No 7
>PF13202 EF-hand_5: EF hand; PDB: 3DD4_A 2Q4U_A 2BE4_A 1UHJ_B 1UHI_A 1UHH_B 1EJ3_B 1UHK_A 2ZFD_A 1UHN_A ....
Probab=39.85 E-value=19 Score=19.32 Aligned_cols=14 Identities=7% Similarity=0.361 Sum_probs=12.1
Q ss_pred CCCccchhhHHHhh
Q 033169 28 EDKIMDIASLEKFL 41 (125)
Q Consensus 28 eD~I~d~a~fekfL 41 (125)
.||.++.++|.+++
T Consensus 12 ~DG~is~~E~~~~~ 25 (25)
T PF13202_consen 12 GDGKISFEEFQRLV 25 (25)
T ss_dssp SSSEEEHHHHHHHH
T ss_pred CCCcCCHHHHHHHC
Confidence 68999999999874
No 8
>PHA03383 PCNA-like protein; Provisional
Probab=38.58 E-value=46 Score=27.32 Aligned_cols=26 Identities=23% Similarity=0.391 Sum_probs=16.1
Q ss_pred ccchhhhhHHHhhhhccCCCceEEEEeccC
Q 033169 75 FSKRYLKYLTKKYLKKHNVRDWLRVIASNK 104 (125)
Q Consensus 75 fsKRYLKYLtKKyLKk~~LRdwlrVvA~~K 104 (125)
||-|||+..+ |-..|-|-+.+--++.
T Consensus 213 ysl~YL~~~~----Ka~~ls~~V~i~l~~d 238 (262)
T PHA03383 213 FSLKYLTSFT----KASGMSSSVEIYLKES 238 (262)
T ss_pred EeHHHHHHhh----ccccCCCeEEEEEcCC
Confidence 6667776554 4667777766554443
No 9
>PF14728 PHTB1_C: PTHB1 C-terminus
Probab=35.60 E-value=69 Score=27.93 Aligned_cols=26 Identities=27% Similarity=0.502 Sum_probs=19.0
Q ss_pred ccceeEEEEeecCccCCCccchhh-HHHhhh
Q 033169 13 KKKGATFVIDCGKPVEDKIMDIAS-LEKFLQ 42 (125)
Q Consensus 13 kk~~~kF~iDCt~PveD~I~d~a~-fekfL~ 42 (125)
|....|.|||+++|.-+ .++ |..|+.
T Consensus 98 k~a~~KlTi~tn~~~v~----L~~lFpdf~~ 124 (377)
T PF14728_consen 98 KNAKHKLTIDTNKPPVS----LSDLFPDFLE 124 (377)
T ss_pred cccceEEEEeCCCCCcC----HHHHhhHhhc
Confidence 44578999999998643 444 777876
No 10
>PF01485 IBR: IBR domain; InterPro: IPR002867 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. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=35.05 E-value=11 Score=23.07 Aligned_cols=17 Identities=35% Similarity=0.733 Sum_probs=9.4
Q ss_pred chhhhhHHHhhhhccCC
Q 033169 77 KRYLKYLTKKYLKKHNV 93 (125)
Q Consensus 77 KRYLKYLtKKyLKk~~L 93 (125)
+||++++.++||..+..
T Consensus 1 eky~~~~~~~~~~~~~~ 17 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPN 17 (64)
T ss_dssp HCHHHCCCHS---S---
T ss_pred ChHHHHHHHHHHHCCCC
Confidence 48999999999965443
No 11
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=34.80 E-value=6.8 Score=29.73 Aligned_cols=14 Identities=36% Similarity=0.826 Sum_probs=11.7
Q ss_pred cCCCceEEEEeccC
Q 033169 91 HNVRDWLRVIASNK 104 (125)
Q Consensus 91 ~~LRdwlrVvA~~K 104 (125)
.+|++|||||.-+.
T Consensus 67 P~l~~WL~vVgl~~ 80 (129)
T PF13543_consen 67 PSLRQWLRVVGLRP 80 (129)
T ss_pred CcHHHHhhhcCCCH
Confidence 78999999997654
No 12
>PRK14638 hypothetical protein; Provisional
Probab=31.55 E-value=1.4e+02 Score=22.67 Aligned_cols=31 Identities=10% Similarity=0.288 Sum_probs=25.5
Q ss_pred eEEEEeecCcc-CCCccchhhHHHhhhcceee
Q 033169 17 ATFVIDCGKPV-EDKIMDIASLEKFLQERIKV 47 (125)
Q Consensus 17 ~kF~iDCt~Pv-eD~I~d~a~fekfL~erIKV 47 (125)
..|++.-|.|- +--+..+.+|..|.-..++|
T Consensus 74 ~~Y~LEVSSPGldRpL~~~~~f~r~~G~~v~V 105 (150)
T PRK14638 74 HSYTLEVSSPGLDRPLRGPKDYVRFTGKLAKI 105 (150)
T ss_pred CceEEEEeCCCCCCCCCCHHHHHHhCCCEEEE
Confidence 36888888884 66677799999999998888
No 13
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=29.07 E-value=42 Score=20.43 Aligned_cols=16 Identities=19% Similarity=0.559 Sum_probs=13.6
Q ss_pred chhhhhHHHhhhhccC
Q 033169 77 KRYLKYLTKKYLKKHN 92 (125)
Q Consensus 77 KRYLKYLtKKyLKk~~ 92 (125)
.||.+||++.||..+.
T Consensus 1 ~~y~~~~~~~~i~~~~ 16 (64)
T smart00647 1 EKYERLLLESYVESNP 16 (64)
T ss_pred ChHHHHHHHHHHhcCC
Confidence 4899999999998753
No 14
>COG1018 Hmp Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion]
Probab=26.06 E-value=65 Score=26.41 Aligned_cols=33 Identities=21% Similarity=0.353 Sum_probs=23.3
Q ss_pred cceeEEEEeecCccCCCcc-------chhhHHHhhhcceee
Q 033169 14 KKGATFVIDCGKPVEDKIM-------DIASLEKFLQERIKV 47 (125)
Q Consensus 14 k~~~kF~iDCt~PveD~I~-------d~a~fekfL~erIKV 47 (125)
...+-|+| |+.|.++... +...+-.|||+++|+
T Consensus 51 ~~~R~YSl-~s~p~~~~~~~isVk~~~~G~~S~~Lh~~lk~ 90 (266)
T COG1018 51 PLLRAYSL-SSAPDEDSLYRISVKREDGGGGSNWLHDHLKV 90 (266)
T ss_pred eeeEEEEe-ccCCCCCceEEEEEEEeCCCcccHHHHhcCCC
Confidence 55677888 8888776222 224567899999988
No 15
>TIGR00590 pcna proliferating cell nuclear antigen (pcna). All proteins in this family for which functions are known form sliding DNA clamps that are used in DNA replication processes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.16 E-value=36 Score=27.56 Aligned_cols=26 Identities=27% Similarity=0.471 Sum_probs=15.9
Q ss_pred ccchhhhhHHHhhhhccCCCceEEEEeccC
Q 033169 75 FSKRYLKYLTKKYLKKHNVRDWLRVIASNK 104 (125)
Q Consensus 75 fsKRYLKYLtKKyLKk~~LRdwlrVvA~~K 104 (125)
|+=+||+ .++|-.+|-|-+-+--++.
T Consensus 207 y~l~YL~----~~~Ka~~ls~~V~l~~~~~ 232 (259)
T TIGR00590 207 FAIKYLN----LFTKATPLSDRVTLSMSND 232 (259)
T ss_pred eeHHHHH----HhhhhccCCCeEEEEEcCC
Confidence 5545554 4666778888776554443
No 16
>PF03192 DUF257: Pyrococcus protein of unknown function, DUF257; InterPro: IPR005489 This family of proteins is of unknown function.; PDB: 2EKD_C.
Probab=25.03 E-value=46 Score=26.63 Aligned_cols=35 Identities=40% Similarity=0.715 Sum_probs=17.3
Q ss_pred ceeeccccCCCCCceEEEEeCCEEEEEeccc-ccchhhhhHHH
Q 033169 44 RIKVGGKAGALGDSVTVTREKTKITVTSDSN-FSKRYLKYLTK 85 (125)
Q Consensus 44 rIKV~gk~gnLg~~V~i~r~~~ki~V~s~~~-fsKRYLKYLtK 85 (125)
=||++|+. +.|+.| .+|.++++.+ |.|.|-.-+.+
T Consensus 73 VIKiGG~~-~~GnVv------~ri~~~~d~~~~~k~Y~~~~~~ 108 (210)
T PF03192_consen 73 VIKIGGRI-EVGNVV------GRIPITSDPSVYLKEYEEILEK 108 (210)
T ss_dssp EEEES-S----SEEE------EEE-----BBTTBHHHHHHHTT
T ss_pred EEEecCee-eeeeEE------EEEecccChHHHHHHHHHHHHH
Confidence 35667766 457666 4677788776 77777766654
No 17
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=23.93 E-value=67 Score=14.93 Aligned_cols=18 Identities=17% Similarity=0.313 Sum_probs=13.9
Q ss_pred ccCCCccchhhHHHhhhc
Q 033169 26 PVEDKIMDIASLEKFLQE 43 (125)
Q Consensus 26 PveD~I~d~a~fekfL~e 43 (125)
+-.+|.++..+|..++++
T Consensus 11 ~~~~g~i~~~e~~~~~~~ 28 (29)
T smart00054 11 KDGDGKIDFEEFKDLLKA 28 (29)
T ss_pred CCCCCcEeHHHHHHHHHh
Confidence 335789999999988764
No 18
>PRK14646 hypothetical protein; Provisional
Probab=23.52 E-value=2e+02 Score=21.92 Aligned_cols=31 Identities=16% Similarity=0.356 Sum_probs=26.1
Q ss_pred EEEEeecCc-cCCCccchhhHHHhhhcceeec
Q 033169 18 TFVIDCGKP-VEDKIMDIASLEKFLQERIKVG 48 (125)
Q Consensus 18 kF~iDCt~P-veD~I~d~a~fekfL~erIKV~ 48 (125)
.|++.-|.| ++--+..+.+|+.|+-..++|.
T Consensus 75 ~Y~LEVSSPGldRpL~~~~df~r~~G~~v~V~ 106 (155)
T PRK14646 75 SYVLEISSQGVSDELTSERDFKTFKGFPVNVE 106 (155)
T ss_pred CeEEEEcCCCCCCcCCCHHHHHHhCCCEEEEE
Confidence 588888888 4677788999999999999983
No 19
>PF15547 DUF4654: Domain of unknown function (DUF4654)
Probab=23.01 E-value=51 Score=25.50 Aligned_cols=12 Identities=50% Similarity=0.880 Sum_probs=9.5
Q ss_pred ceeEEEEeecCc
Q 033169 15 KGATFVIDCGKP 26 (125)
Q Consensus 15 ~~~kF~iDCt~P 26 (125)
-.+.|+|||+.-
T Consensus 10 AHlTFvIDCa~G 21 (138)
T PF15547_consen 10 AHLTFVIDCARG 21 (138)
T ss_pred cceEEEEEcCCC
Confidence 357999999864
No 20
>PRK15084 formate hydrogenlyase maturation protein HycH; Provisional
Probab=22.82 E-value=56 Score=25.16 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=17.9
Q ss_pred EEeecCccCCCccchhhHHHhhh
Q 033169 20 VIDCGKPVEDKIMDIASLEKFLQ 42 (125)
Q Consensus 20 ~iDCt~PveD~I~d~a~fekfL~ 42 (125)
+|||..|+ --++.++|++++.
T Consensus 41 vIDcle~~--L~~~~e~y~~wi~ 61 (133)
T PRK15084 41 VIDCLEAA--LTCPLDEYLAWIA 61 (133)
T ss_pred eEecchhh--hcCCHHHHHHHHH
Confidence 69999998 5688999999973
No 21
>KOG1770 consensus Translation initiation factor 1 (eIF-1/SUI1) [Translation, ribosomal structure and biogenesis]
Probab=22.63 E-value=86 Score=23.52 Aligned_cols=23 Identities=26% Similarity=0.457 Sum_probs=16.9
Q ss_pred EEEEEeccc--cc-chhhhhHHHhhh
Q 033169 66 KITVTSDSN--FS-KRYLKYLTKKYL 88 (125)
Q Consensus 66 ki~V~s~~~--fs-KRYLKYLtKKyL 88 (125)
+||..-.+| ++ ||-|++|-|+|-
T Consensus 42 tlTtVQgi~~Eyd~kril~~lKKef~ 67 (112)
T KOG1770|consen 42 TLTTVQGIPMEYDLKKILKSLKKEFA 67 (112)
T ss_pred EEEEecCChhhhhHHHHHHHHHHhcc
Confidence 355555676 77 889999988874
No 22
>PF07450 HycH: Formate hydrogenlyase maturation protein HycH; InterPro: IPR010005 This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form [].
Probab=22.26 E-value=60 Score=24.89 Aligned_cols=22 Identities=27% Similarity=0.516 Sum_probs=18.6
Q ss_pred EEeecCccCCCccchhhHHHhhhc
Q 033169 20 VIDCGKPVEDKIMDIASLEKFLQE 43 (125)
Q Consensus 20 ~iDCt~PveD~I~d~a~fekfL~e 43 (125)
+|||..|+ -.++.++|++++..
T Consensus 39 vIDcle~~--l~cp~~~y~~wi~~ 60 (131)
T PF07450_consen 39 VIDCLEKV--LECPLEEYERWIAQ 60 (131)
T ss_pred eEeechhh--ccCCHHHHHHHHHh
Confidence 69999998 66889999999843
No 23
>PRK14630 hypothetical protein; Provisional
Probab=22.11 E-value=2.3e+02 Score=21.31 Aligned_cols=30 Identities=23% Similarity=0.397 Sum_probs=25.2
Q ss_pred EEEEeecCcc-CCCccchhhHHHhhhcceee
Q 033169 18 TFVIDCGKPV-EDKIMDIASLEKFLQERIKV 47 (125)
Q Consensus 18 kF~iDCt~Pv-eD~I~d~a~fekfL~erIKV 47 (125)
.|++.-|.|- +--+..+.+|+.|+-+.++|
T Consensus 72 ~Y~LEVSSPGldRpL~~~~df~r~~G~~v~V 102 (143)
T PRK14630 72 NFSLEISTPGINRKIKSDREFKIFEGKKIKL 102 (143)
T ss_pred CeEEEEeCCCCCCcCCCHHHHHHhCCCEEEE
Confidence 5788888884 66677899999999999999
No 24
>PF08980 DUF1883: Domain of unknown function (DUF1883); InterPro: IPR015073 This family consist of hypothetical bacterial proteins. ; PDB: 2B1Y_A.
Probab=21.62 E-value=52 Score=23.78 Aligned_cols=24 Identities=17% Similarity=0.394 Sum_probs=10.1
Q ss_pred EEEEeecCccCCCccchhhHHHhh
Q 033169 18 TFVIDCGKPVEDKIMDIASLEKFL 41 (125)
Q Consensus 18 kF~iDCt~PveD~I~d~a~fekfL 41 (125)
.-.|.|+++..=-+||.++|+.|=
T Consensus 16 ~V~V~ls~~~nV~LMd~~Nf~~y~ 39 (94)
T PF08980_consen 16 TVVVRLSHQANVRLMDDSNFQRYK 39 (94)
T ss_dssp ------SSS-------HHHHHHHH
T ss_pred EEEEEeCCcccEEEcChhHhhhhc
Confidence 456899999988999999999984
No 25
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=21.37 E-value=61 Score=19.15 Aligned_cols=20 Identities=15% Similarity=0.257 Sum_probs=14.7
Q ss_pred CccCCCccchhhHHHhhhcc
Q 033169 25 KPVEDKIMDIASLEKFLQER 44 (125)
Q Consensus 25 ~PveD~I~d~a~fekfL~er 44 (125)
-+-.||.++..+|-.+++.|
T Consensus 35 D~~~~G~I~~~EF~~~~~~~ 54 (54)
T PF13833_consen 35 DTDGDGYISFDEFISMMQRR 54 (54)
T ss_dssp TTSSSSSEEHHHHHHHHHHH
T ss_pred ccCCCCCCCHHHHHHHHHhC
Confidence 34578888888888887654
No 26
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.57 E-value=2.6e+02 Score=18.30 Aligned_cols=47 Identities=23% Similarity=0.439 Sum_probs=30.7
Q ss_pred CceEEEEeCCEEEEEeccc-----ccch-----hhhhHHHhhhhccCCCceEEEEecc
Q 033169 56 DSVTVTREKTKITVTSDSN-----FSKR-----YLKYLTKKYLKKHNVRDWLRVIASN 103 (125)
Q Consensus 56 ~~V~i~r~~~ki~V~s~~~-----fsKR-----YLKYLtKKyLKk~~LRdwlrVvA~~ 103 (125)
..|.+..+.+.+.++-+.+ +-|+ =|.||+..++.++. ..+.||+-.-
T Consensus 15 ~~v~~~~~~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~~~-~~~~~v~lDv 71 (77)
T cd02414 15 ADVDVEEEGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNRNT-GEYVRITLDV 71 (77)
T ss_pred cEEEEEecCCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhhcc-CCceEEEEEC
Confidence 3455555555555443333 3333 47999999999875 8899988654
No 27
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=20.43 E-value=1.4e+02 Score=21.64 Aligned_cols=44 Identities=16% Similarity=0.225 Sum_probs=26.4
Q ss_pred cCCCCCceEEEEe-CCEEEEEecccccchhhhhHHHhhhhccCCCceEEEEeccC
Q 033169 51 AGALGDSVTVTRE-KTKITVTSDSNFSKRYLKYLTKKYLKKHNVRDWLRVIASNK 104 (125)
Q Consensus 51 ~gnLg~~V~i~r~-~~ki~V~s~~~fsKRYLKYLtKKyLKk~~LRdwlrVvA~~K 104 (125)
.|+||....+... +++-.++-.+..+++|-. .=-||++|+|-++
T Consensus 9 iGrL~~DPelr~t~~G~~v~~fslAv~~~~~~----------~~t~w~~v~~wg~ 53 (121)
T PRK07459 9 VGRAGRDPEVRYFESGSVVCNLTLAVNRRSRD----------DEPDWFNLEIWGK 53 (121)
T ss_pred EEEccCCCEEEEcCCCCEEEEEEEEecccccC----------CCceEEEEEEehH
Confidence 4566666555432 333444556666766633 2358999998765
No 28
>PRK10397 lipoprotein; Provisional
Probab=20.22 E-value=54 Score=25.35 Aligned_cols=27 Identities=26% Similarity=0.384 Sum_probs=16.2
Q ss_pred CCCceEEEEeccCCCCeEEEEeeeecC
Q 033169 92 NVRDWLRVIASNKDRSVYELRYFNIAE 118 (125)
Q Consensus 92 ~LRdwlrVvA~~K~~~~YeLrYfni~~ 118 (125)
.-|+|-||||..-.-....=+|+||+.
T Consensus 66 dCrqWqrvia~PGKlt~~~~~~~NVt~ 92 (137)
T PRK10397 66 DCRQWQRVIAVPGKLTLRSDDLTNVTV 92 (137)
T ss_pred eehhcceeeeccceeeeecCceEEeee
Confidence 358999999965321222335667663
No 29
>PRK14640 hypothetical protein; Provisional
Probab=20.17 E-value=1.3e+02 Score=22.67 Aligned_cols=31 Identities=16% Similarity=0.534 Sum_probs=26.4
Q ss_pred EEEEeecCc-cCCCccchhhHHHhhhcceeec
Q 033169 18 TFVIDCGKP-VEDKIMDIASLEKFLQERIKVG 48 (125)
Q Consensus 18 kF~iDCt~P-veD~I~d~a~fekfL~erIKV~ 48 (125)
.|++.-|.| ++--+..+.+|.+|+-..++|.
T Consensus 72 ~Y~LEVSSPGl~RpL~~~~~f~r~~G~~v~V~ 103 (152)
T PRK14640 72 EYYLEVSSPGLDRPLFKVAQFEKYVGQEAAVT 103 (152)
T ss_pred CeEEEEeCCCCCCcCCCHHHHHHhCCCeEEEE
Confidence 688888888 4777888999999999999883
Done!