Query psy15597
Match_columns 204
No_of_seqs 98 out of 119
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 16:39:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15597.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15597hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4385|consensus 100.0 5.5E-52 1.2E-56 389.5 12.4 189 2-204 63-271 (581)
2 KOG4385|consensus 95.6 0.00097 2.1E-08 64.9 -3.4 67 133-203 132-198 (581)
3 PF00096 zf-C2H2: Zinc finger, 85.7 0.58 1.3E-05 26.1 1.6 20 148-168 4-23 (23)
4 PF13894 zf-C2H2_4: C2H2-type 81.3 1.5 3.2E-05 23.7 2.1 21 148-168 4-24 (24)
5 PF12756 zf-C2H2_2: C2H2 type 79.8 0.57 1.2E-05 33.2 0.0 41 148-188 3-43 (100)
6 PF13912 zf-C2H2_6: C2H2-type 78.9 1.6 3.4E-05 25.3 1.7 21 149-169 6-26 (27)
7 PF05605 zf-Di19: Drought indu 77.8 2.5 5.4E-05 28.7 2.7 27 147-174 5-31 (54)
8 PF12013 DUF3505: Protein of u 73.5 3.1 6.8E-05 31.6 2.5 33 137-169 75-109 (109)
9 COG4049 Uncharacterized protei 73.1 1.7 3.8E-05 32.0 1.0 27 144-170 17-43 (65)
10 PHA00616 hypothetical protein 70.2 2.9 6.4E-05 28.7 1.5 26 147-172 4-29 (44)
11 smart00355 ZnF_C2H2 zinc finge 68.2 6.3 0.00014 21.1 2.4 22 147-169 3-24 (26)
12 PF12874 zf-met: Zinc-finger o 63.5 5.3 0.00012 22.5 1.5 18 149-166 5-22 (25)
13 PF12756 zf-C2H2_2: C2H2 type 55.4 12 0.00025 26.4 2.5 28 142-171 50-77 (100)
14 KOG4377|consensus 54.5 5.8 0.00013 38.8 1.0 29 136-164 395-423 (480)
15 PF12171 zf-C2H2_jaz: Zinc-fin 50.8 6.8 0.00015 23.0 0.5 19 148-166 5-23 (27)
16 PF04696 Pinin_SDK_memA: pinin 49.1 36 0.00078 27.4 4.6 44 157-200 13-56 (131)
17 PF04968 CHORD: CHORD ; Inter 39.4 12 0.00026 27.4 0.4 30 133-162 25-54 (64)
18 KOG3915|consensus 38.5 43 0.00094 33.7 4.2 19 147-165 192-212 (641)
19 TIGR00741 yfiA ribosomal subun 36.6 35 0.00076 24.7 2.5 19 183-201 76-94 (95)
20 PF13611 Peptidase_S76: Serine 35.5 19 0.00042 29.5 1.1 20 147-166 78-97 (121)
21 smart00037 CNX Connexin homolo 34.2 8.2 0.00018 25.5 -1.0 17 147-163 16-32 (34)
22 KOG3608|consensus 32.8 23 0.00049 34.5 1.3 23 144-166 179-201 (467)
23 smart00307 ILWEQ I/LWEQ domain 30.8 77 0.0017 27.8 4.1 26 177-203 168-193 (200)
24 smart00451 ZnF_U1 U1-like zinc 30.2 43 0.00093 20.0 1.8 19 149-167 8-26 (35)
25 PF03262 Corona_6B_7B: Coronav 27.9 17 0.00036 32.3 -0.5 21 140-160 66-86 (209)
26 PF06348 DUF1059: Protein of u 27.5 58 0.0013 22.8 2.3 27 148-174 11-43 (57)
27 PF04780 DUF629: Protein of un 27.3 44 0.00096 32.8 2.2 33 140-174 55-87 (466)
28 TIGR02218 phg_TIGR02218 phage 26.3 28 0.0006 30.7 0.6 19 138-156 171-191 (229)
29 COG1544 Ribosome-associated pr 25.8 67 0.0015 25.5 2.6 18 184-201 79-96 (110)
30 PF02482 Ribosomal_S30AE: Sigm 24.2 57 0.0012 23.4 1.9 18 183-200 78-95 (97)
No 1
>KOG4385|consensus
Probab=100.00 E-value=5.5e-52 Score=389.51 Aligned_cols=189 Identities=39% Similarity=0.605 Sum_probs=149.2
Q ss_pred cccchhhhcccccccccCcchhHHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCC-CCCCC-CCC----CCCC
Q psy15597 2 HQMQEKLFIQHTSSQHIDGDKSAEAMHDMAFQQNQLIHQLEMTQRKYVLQHAIGLQSQASTS-RPGQP-MMM----PSGV 75 (204)
Q Consensus 2 EQLhLQLLqQqh~~qq~~k~~~~~a~qQLafQQQlL~QqlQ~qq~q~~~QhlL~LqRqgllS-~P~q~-~~~----~~~~ 75 (204)
|||++++++++ +++++... ...++++|+||++++ ||++.++ .|+|+|+++ +||+. +|+ ++||
T Consensus 63 ~qls~q~~~~~-agk~a~s~-~~~~n~~l~fQ~qL~-qm~~~q~---------~l~~~~~~tiqp~e~slplq~t~q~~m 130 (581)
T KOG4385|consen 63 PQLSLQLLQQQ-AGKNAKSQ-QSLLNQQLAFQQQLL-QMQQPQQ---------QLQRQGLLTIQPGESSLPLQTTPQAGM 130 (581)
T ss_pred cccchhhhhhc-cCcCCccc-cccccccchHHHHHH-HHhhhhh---------hhhhccccccCCCCCCCcccccCcccC
Confidence 78999999887 66664443 357889999999976 6555432 288999999 78877 433 4699
Q ss_pred CchhHhhhhhhcccC--CCCccCCCCCCCccc-----cccccccccccCcccCCCC----ccccccccccc---cccccc
Q psy15597 76 NQSDINSLWNNFSME--NQDVSIPAGDKSMFG-----INGLLVSMGISRREWMNGD----DQKANESYAEK---VHFLFG 141 (204)
Q Consensus 76 ~paelqqlWke~~~~--~~~~~~~~~~~~~~~-----~~~~~~s~~~~~~~~~nGq----~~~r~ss~~~~---~h~L~~ 141 (204)
+|+++++||||+..+ .++. .+++.+.++ ....+.+...+.|.++||+ ++|||+++++. +||||+
T Consensus 131 ~pt~~~~lw~e~~~a~psed~--~~~~l~ltt~~~~s~~ps~~s~~~nph~~~n~q~~~~~~r~ds~~~~~~~~shPl~~ 208 (581)
T KOG4385|consen 131 SPTPLQGLWKEGTPAHPSEDP--KHSGLDLTTTEASSTEPSKTSKVSNPHKVENGQHSVSSPRRDSSSMEEHPSSHPLYA 208 (581)
T ss_pred CCccHHHHhhccccCCcCCCc--cccceeeeecchhccCccccccCCCcccccccccccccccchhhhhhcccccCCccc
Confidence 999999999988432 2221 222222211 1112223333459999999 48999998874 999999
Q ss_pred CccccCCCCCcccccHHHHHHHhhhhcCCCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhhhC
Q psy15597 142 HGVCKWPGCEAVCEDVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLELQLQKERDRLQALKI 204 (204)
Q Consensus 142 ~g~CkWPgCe~~~ed~~~flkHL~~eH~lddrstaQcrvQ~qvVqqLE~qL~~EkerL~AM~~ 204 (204)
||+|||||||++||||+.||||||+||+||||||||||||||||++||.+|.||||||+|||+
T Consensus 209 hgvckwpgcE~~~ed~~~flKhln~eh~lddrstaQcrvQmQVvqqlE~ql~ke~erlqamm~ 271 (581)
T KOG4385|consen 209 HGVCKWPGCEAVCEDFGSFLKHLNTEHALDDRSTAQCRVQMQVVQQLEIQLSKESERLQAMMA 271 (581)
T ss_pred CCccCCCchhhhccchHHHHHhhccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999995
No 2
>KOG4385|consensus
Probab=95.61 E-value=0.00097 Score=64.90 Aligned_cols=67 Identities=9% Similarity=0.069 Sum_probs=61.8
Q ss_pred cccccccccCccccCCCCCcccccHHHHHHHhhhhcCCCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy15597 133 AEKVHFLFGHGVCKWPGCEAVCEDVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLELQLQKERDRLQALK 203 (204)
Q Consensus 133 ~~~~h~L~~~g~CkWPgCe~~~ed~~~flkHL~~eH~lddrstaQcrvQ~qvVqqLE~qL~~EkerL~AM~ 203 (204)
+-+.+-||.+|+|.||+|+. |.+...|..|+.++|...+++++=-+ +.|...|..+..+|.+..+|+
T Consensus 132 pt~~~~lw~e~~~a~psed~-~~~~l~ltt~~~~s~~ps~~s~~~np---h~~~n~q~~~~~~r~ds~~~~ 198 (581)
T KOG4385|consen 132 PTPLQGLWKEGTPAHPSEDP-KHSGLDLTTTEASSTEPSKTSKVSNP---HKVENGQHSVSSPRRDSSSME 198 (581)
T ss_pred CccHHHHhhccccCCcCCCc-cccceeeeecchhccCccccccCCCc---ccccccccccccccchhhhhh
Confidence 34678899999999999999 99999999999999999999999888 788899999999999999987
No 3
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=85.66 E-value=0.58 Score=26.13 Aligned_cols=20 Identities=20% Similarity=0.516 Sum_probs=18.3
Q ss_pred CCCCcccccHHHHHHHhhhhc
Q psy15597 148 PGCEAVCEDVQAFYKHLNKEH 168 (204)
Q Consensus 148 PgCe~~~ed~~~flkHL~~eH 168 (204)
|.|++.|.+...|.+|+.. |
T Consensus 4 ~~C~~~f~~~~~l~~H~~~-H 23 (23)
T PF00096_consen 4 PICGKSFSSKSNLKRHMRR-H 23 (23)
T ss_dssp TTTTEEESSHHHHHHHHHH-H
T ss_pred CCCCCccCCHHHHHHHHhH-C
Confidence 5899999999999999987 5
No 4
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=81.32 E-value=1.5 Score=23.68 Aligned_cols=21 Identities=19% Similarity=0.450 Sum_probs=18.0
Q ss_pred CCCCcccccHHHHHHHhhhhc
Q psy15597 148 PGCEAVCEDVQAFYKHLNKEH 168 (204)
Q Consensus 148 PgCe~~~ed~~~flkHL~~eH 168 (204)
|-|+..|.+..++.+|+.+.|
T Consensus 4 ~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 4 PICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp SSTS-EESSHHHHHHHHHHHS
T ss_pred cCCCCcCCcHHHHHHHHHhhC
Confidence 459999999999999999877
No 5
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=79.79 E-value=0.57 Score=33.16 Aligned_cols=41 Identities=17% Similarity=0.276 Sum_probs=0.0
Q ss_pred CCCCcccccHHHHHHHhhhhcCCCCchhHHHHHHHHHHHHH
Q psy15597 148 PGCEAVCEDVQAFYKHLNKEHNLDDRSTAQARVQMQVVSQL 188 (204)
Q Consensus 148 PgCe~~~ed~~~flkHL~~eH~lddrstaQcrvQ~qvVqqL 188 (204)
+-|+..|.+...+++|+...|..+-....-+.....++..+
T Consensus 3 ~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~ 43 (100)
T PF12756_consen 3 LFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYL 43 (100)
T ss_dssp -----------------------------------------
T ss_pred ccccccccccccccccccccccccccccccccccccccccc
Confidence 35999999999999999999999865433333344444444
No 6
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=78.87 E-value=1.6 Score=25.27 Aligned_cols=21 Identities=14% Similarity=0.311 Sum_probs=18.2
Q ss_pred CCCcccccHHHHHHHhhhhcC
Q psy15597 149 GCEAVCEDVQAFYKHLNKEHN 169 (204)
Q Consensus 149 gCe~~~ed~~~flkHL~~eH~ 169 (204)
-|++.|.+...|++|..+-|.
T Consensus 6 ~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 6 ECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp TTTEEESSHHHHHHHHCTTTT
T ss_pred ccCCccCChhHHHHHhHHhcC
Confidence 599999999999999976554
No 7
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=77.84 E-value=2.5 Score=28.72 Aligned_cols=27 Identities=19% Similarity=0.365 Sum_probs=23.2
Q ss_pred CCCCCcccccHHHHHHHhhhhcCCCCch
Q psy15597 147 WPGCEAVCEDVQAFYKHLNKEHNLDDRS 174 (204)
Q Consensus 147 WPgCe~~~ed~~~flkHL~~eH~lddrs 174 (204)
=|-|++ --|...|++|...+|..|.+.
T Consensus 5 CP~C~~-~~~~~~L~~H~~~~H~~~~~~ 31 (54)
T PF05605_consen 5 CPYCGK-GFSESSLVEHCEDEHRSESKN 31 (54)
T ss_pred CCCCCC-ccCHHHHHHHHHhHCcCCCCC
Confidence 378999 567899999999999998773
No 8
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=73.54 E-value=3.1 Score=31.64 Aligned_cols=33 Identities=24% Similarity=0.418 Sum_probs=30.2
Q ss_pred cccccCccc--cCCCCCcccccHHHHHHHhhhhcC
Q psy15597 137 HFLFGHGVC--KWPGCEAVCEDVQAFYKHLNKEHN 169 (204)
Q Consensus 137 h~L~~~g~C--kWPgCe~~~ed~~~flkHL~~eH~ 169 (204)
=|.|.+-.| .+++|.-++-+....-+|+..+|.
T Consensus 75 Lp~~~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 75 LPVYDGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCCCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 377888889 999999999999999999999994
No 9
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=73.05 E-value=1.7 Score=32.01 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=23.9
Q ss_pred cccCCCCCcccccHHHHHHHhhhhcCC
Q psy15597 144 VCKWPGCEAVCEDVQAFYKHLNKEHNL 170 (204)
Q Consensus 144 ~CkWPgCe~~~ed~~~flkHL~~eH~l 170 (204)
.-+-|-|+++|.+-.++++|.|..|..
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 346799999999999999999999964
No 10
>PHA00616 hypothetical protein
Probab=70.20 E-value=2.9 Score=28.70 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=23.4
Q ss_pred CCCCCcccccHHHHHHHhhhhcCCCC
Q psy15597 147 WPGCEAVCEDVQAFYKHLNKEHNLDD 172 (204)
Q Consensus 147 WPgCe~~~ed~~~flkHL~~eH~ldd 172 (204)
=|=|+..|-...++.+|+++.|.-|+
T Consensus 4 C~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 4 CLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred cchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 37799999999999999999998865
No 11
>smart00355 ZnF_C2H2 zinc finger.
Probab=68.20 E-value=6.3 Score=21.11 Aligned_cols=22 Identities=27% Similarity=0.563 Sum_probs=18.5
Q ss_pred CCCCCcccccHHHHHHHhhhhcC
Q psy15597 147 WPGCEAVCEDVQAFYKHLNKEHN 169 (204)
Q Consensus 147 WPgCe~~~ed~~~flkHL~~eH~ 169 (204)
.+-|+..|.+...|..|+. .|.
T Consensus 3 C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 3 CPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCcchhCCHHHHHHHHH-Hhc
Confidence 4559999999999999997 554
No 12
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=63.47 E-value=5.3 Score=22.55 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=16.4
Q ss_pred CCCcccccHHHHHHHhhh
Q psy15597 149 GCEAVCEDVQAFYKHLNK 166 (204)
Q Consensus 149 gCe~~~ed~~~flkHL~~ 166 (204)
=|++.|.+...|..|+++
T Consensus 5 ~C~~~f~s~~~~~~H~~s 22 (25)
T PF12874_consen 5 ICNKSFSSENSLRQHLRS 22 (25)
T ss_dssp TTTEEESSHHHHHHHHTT
T ss_pred CCCCCcCCHHHHHHHHCc
Confidence 389999999999999986
No 13
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=55.43 E-value=12 Score=26.37 Aligned_cols=28 Identities=21% Similarity=0.470 Sum_probs=22.0
Q ss_pred CccccCCCCCcccccHHHHHHHhhhhcCCC
Q psy15597 142 HGVCKWPGCEAVCEDVQAFYKHLNKEHNLD 171 (204)
Q Consensus 142 ~g~CkWPgCe~~~ed~~~flkHL~~eH~ld 171 (204)
.-.| +-|.+.|.+...+.+|+++.+..+
T Consensus 50 ~~~C--~~C~~~f~s~~~l~~Hm~~~~H~~ 77 (100)
T PF12756_consen 50 SFRC--PYCNKTFRSREALQEHMRSKHHKK 77 (100)
T ss_dssp SEEB--SSSS-EESSHHHHHHHHHHTTTTC
T ss_pred CCCC--CccCCCCcCHHHHHHHHcCccCCC
Confidence 4556 469999999999999999876554
No 14
>KOG4377|consensus
Probab=54.47 E-value=5.8 Score=38.75 Aligned_cols=29 Identities=28% Similarity=0.346 Sum_probs=24.0
Q ss_pred ccccccCccccCCCCCcccccHHHHHHHh
Q psy15597 136 VHFLFGHGVCKWPGCEAVCEDVQAFYKHL 164 (204)
Q Consensus 136 ~h~L~~~g~CkWPgCe~~~ed~~~flkHL 164 (204)
..-.+.|+.|.|+|||..+-+..+-..|-
T Consensus 395 ys~~cnhfhc~r~Gc~~tl~s~sqm~shk 423 (480)
T KOG4377|consen 395 YSGICNHFHCDRLGCEATLYSVSQMASHK 423 (480)
T ss_pred cccceeeeeecccCCceEEEehhhhhhhh
Confidence 34567899999999999999988887774
No 15
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=50.80 E-value=6.8 Score=22.97 Aligned_cols=19 Identities=11% Similarity=0.389 Sum_probs=17.2
Q ss_pred CCCCcccccHHHHHHHhhh
Q psy15597 148 PGCEAVCEDVQAFYKHLNK 166 (204)
Q Consensus 148 PgCe~~~ed~~~flkHL~~ 166 (204)
+-|++.|.|-..|-.|+++
T Consensus 5 ~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 5 DACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp TTTTBBBSSHHHHHCCTTS
T ss_pred ccCCCCcCCHHHHHHHHcc
Confidence 4699999999999999986
No 16
>PF04696 Pinin_SDK_memA: pinin/SDK/memA/ protein conserved region; InterPro: IPR006786 This conserved region is located adjacent and C-terminal to a N-terminal pinin/SKD domain IPR006787 from INTERPRO. Members of this family have very varied localisations within the eukaryotic cell. Pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque []. SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing []. MemA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions [].
Probab=49.10 E-value=36 Score=27.42 Aligned_cols=44 Identities=20% Similarity=0.379 Sum_probs=36.4
Q ss_pred HHHHHHHhhhhcCCCCchhHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy15597 157 VQAFYKHLNKEHNLDDRSTAQARVQMQVVSQLELQLQKERDRLQ 200 (204)
Q Consensus 157 ~~~flkHL~~eH~lddrstaQcrvQ~qvVqqLE~qL~~EkerL~ 200 (204)
||.++-||+.-=.-+++.+.+-.=+.+|-..||.++..|++.|.
T Consensus 13 FG~LlGTL~kf~~e~~k~~~~~~rR~eie~rleek~~~e~e~l~ 56 (131)
T PF04696_consen 13 FGGLLGTLQKFKKEEEKKTEQQKRRAEIEKRLEEKLKEEKEELR 56 (131)
T ss_pred HHHHHHHHHHHHHhHHhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67788888866665677788888889999999999999988775
No 17
>PF04968 CHORD: CHORD ; InterPro: IPR007051 Cysteine- and histidine-rich domains (CHORDs) are 60-amino acid modules that bind two zinc ions. They are usually arranged in tandem and are found in all tested eukaryotes, with the exception of yeast, where they are involved in processes ranging from pressure sensing in the heart to maintenance of diploidy in fungi, and exhibit distinct protein-protein interaction specificity. Six cysteine and two histidine residues are invariant within the CHORD domain. Three other residues are also invariant and some positions are confined to positive, negative, or aromatic amino acids [, ]. Silencing of the Caenorhabditis elegansCHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development. The CHORD domain is sometimes found N-terminal to the CS domain, IPR007052 from INTERPRO, in metazoan proteins, but occurs separately from the CS domain in plants. This association is thought to be indicative of an functional interaction between CS and CHORD domains []. ; PDB: 2XCM_E 2YRT_A.
Probab=39.39 E-value=12 Score=27.44 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=26.0
Q ss_pred cccccccccCccccCCCCCcccccHHHHHH
Q psy15597 133 AEKVHFLFGHGVCKWPGCEAVCEDVQAFYK 162 (204)
Q Consensus 133 ~~~~h~L~~~g~CkWPgCe~~~ed~~~flk 162 (204)
+-+..|.|..|+=.|-=|.+..-||.+|++
T Consensus 25 yHpG~PvFHeg~K~WsCC~~k~~dF~~Fl~ 54 (64)
T PF04968_consen 25 YHPGPPVFHEGMKGWSCCKKKVSDFDEFLK 54 (64)
T ss_dssp EBSS-EEEETTEEEETTTTEEESSHHHHTT
T ss_pred ecCCCceecCCceEEecCCCEeeCHHHHhc
Confidence 446788999999999999999999999985
No 18
>KOG3915|consensus
Probab=38.47 E-value=43 Score=33.67 Aligned_cols=19 Identities=42% Similarity=0.833 Sum_probs=16.4
Q ss_pred CCCCCcccc--cHHHHHHHhh
Q psy15597 147 WPGCEAVCE--DVQAFYKHLN 165 (204)
Q Consensus 147 WPgCe~~~e--d~~~flkHL~ 165 (204)
--|||.+|- -|.-|||||-
T Consensus 192 i~g~emiCLPQafdlFLKhlV 212 (641)
T KOG3915|consen 192 IEGCELICLPQAFDLFLKHLV 212 (641)
T ss_pred ecCceEEecHHHHHHHHHHHh
Confidence 469999997 6999999984
No 19
>TIGR00741 yfiA ribosomal subunit interface protein. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes.
Probab=36.56 E-value=35 Score=24.67 Aligned_cols=19 Identities=26% Similarity=0.440 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHhhh
Q psy15597 183 QVVSQLELQLQKERDRLQA 201 (204)
Q Consensus 183 qvVqqLE~qL~~EkerL~A 201 (204)
.++..||.||.++|+|+.+
T Consensus 76 ~a~~klerql~k~k~k~~~ 94 (95)
T TIGR00741 76 LAIDKLERQLRKLKEKRKE 94 (95)
T ss_pred HHHHHHHHHHHHHHhhhhc
Confidence 3789999999999999853
No 20
>PF13611 Peptidase_S76: Serine peptidase of plant viral polyprotein, P1
Probab=35.52 E-value=19 Score=29.49 Aligned_cols=20 Identities=20% Similarity=0.375 Sum_probs=18.5
Q ss_pred CCCCCcccccHHHHHHHhhh
Q psy15597 147 WPGCEAVCEDVQAFYKHLNK 166 (204)
Q Consensus 147 WPgCe~~~ed~~~flkHL~~ 166 (204)
|-||+-++++...||+|+|.
T Consensus 78 ~d~~~Dm~p~~r~fl~h~n~ 97 (121)
T PF13611_consen 78 KDGEDDMYPEDRSFLEHYNA 97 (121)
T ss_pred cCcccCCCHHHHHHHhcccc
Confidence 66999999999999999995
No 21
>smart00037 CNX Connexin homologues. Connexin channels participate in the regulation of signaling between developing and differentiated cell types.
Probab=34.20 E-value=8.2 Score=25.50 Aligned_cols=17 Identities=47% Similarity=0.800 Sum_probs=12.3
Q ss_pred CCCCCcccccHHHHHHH
Q psy15597 147 WPGCEAVCEDVQAFYKH 163 (204)
Q Consensus 147 WPgCe~~~ed~~~flkH 163 (204)
=|||+.+|-|.-.=|.|
T Consensus 16 QPGC~nvCyD~~fPiSh 32 (34)
T smart00037 16 QPGCENVCYDQAFPISH 32 (34)
T ss_pred CCCccceeccccccCcc
Confidence 59999999886544444
No 22
>KOG3608|consensus
Probab=32.84 E-value=23 Score=34.51 Aligned_cols=23 Identities=17% Similarity=0.595 Sum_probs=21.4
Q ss_pred cccCCCCCcccccHHHHHHHhhh
Q psy15597 144 VCKWPGCEAVCEDVQAFYKHLNK 166 (204)
Q Consensus 144 ~CkWPgCe~~~ed~~~flkHL~~ 166 (204)
+|+|-||-+.++|-..+.+|+.+
T Consensus 179 ~C~W~~Ct~~~~~k~~LreH~r~ 201 (467)
T KOG3608|consen 179 MCNWAMCTKHMGNKYRLREHIRT 201 (467)
T ss_pred eccchhhhhhhccHHHHHHHHHh
Confidence 79999999999999999999874
No 23
>smart00307 ILWEQ I/LWEQ domain. Thought to possess an F-actin binding function.
Probab=30.83 E-value=77 Score=27.83 Aligned_cols=26 Identities=23% Similarity=0.528 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy15597 177 QARVQMQVVSQLELQLQKERDRLQALK 203 (204)
Q Consensus 177 QcrvQ~qvVqqLE~qL~~EkerL~AM~ 203 (204)
...-|..|+ .||..|.++|.||-.|-
T Consensus 168 emE~Qv~IL-~lE~~L~~ar~~L~~lR 193 (200)
T smart00307 168 EMEQQVEIL-KLENELEAARKKLAEIR 193 (200)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 445566666 89999999999998873
No 24
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=30.18 E-value=43 Score=19.96 Aligned_cols=19 Identities=21% Similarity=0.302 Sum_probs=16.8
Q ss_pred CCCcccccHHHHHHHhhhh
Q psy15597 149 GCEAVCEDVQAFYKHLNKE 167 (204)
Q Consensus 149 gCe~~~ed~~~flkHL~~e 167 (204)
=|++.|.+-.++..|+++.
T Consensus 8 ~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 8 LCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred ccCCccCCHHHHHHHHChH
Confidence 4899999999999999865
No 25
>PF03262 Corona_6B_7B: Coronavirus 6B/7B protein; InterPro: IPR004945 The function of the Coronavirus 6B and 7B proteins is not known.
Probab=27.92 E-value=17 Score=32.26 Aligned_cols=21 Identities=29% Similarity=0.613 Sum_probs=16.5
Q ss_pred ccCccccCCCCCcccccHHHH
Q psy15597 140 FGHGVCKWPGCEAVCEDVQAF 160 (204)
Q Consensus 140 ~~~g~CkWPgCe~~~ed~~~f 160 (204)
..+-.|.|||-...-.|...|
T Consensus 66 ieGf~CtwPGf~~~a~DHiDf 86 (209)
T PF03262_consen 66 IEGFNCTWPGFQNPAHDHIDF 86 (209)
T ss_pred ccceeccCCCcccccccceeE
Confidence 456689999999988876655
No 26
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=27.49 E-value=58 Score=22.80 Aligned_cols=27 Identities=22% Similarity=0.481 Sum_probs=21.7
Q ss_pred CCCCccccc------HHHHHHHhhhhcCCCCch
Q psy15597 148 PGCEAVCED------VQAFYKHLNKEHNLDDRS 174 (204)
Q Consensus 148 PgCe~~~ed------~~~flkHL~~eH~lddrs 174 (204)
|||+..+.- +..+..|...+|..++-+
T Consensus 11 ~~C~~~~~a~tedEll~~~~~Ha~~~Hg~~~~~ 43 (57)
T PF06348_consen 11 PDCGFVIRAETEDELLEAVVEHAREVHGMTEIP 43 (57)
T ss_pred CCCCeEEeeCCHHHHHHHHHHHHHHhcCCccCC
Confidence 888887763 567889999999998743
No 27
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=27.26 E-value=44 Score=32.81 Aligned_cols=33 Identities=21% Similarity=0.541 Sum_probs=26.8
Q ss_pred ccCccccCCCCCcccccHHHHHHHhhhhcCCCCch
Q psy15597 140 FGHGVCKWPGCEAVCEDVQAFYKHLNKEHNLDDRS 174 (204)
Q Consensus 140 ~~~g~CkWPgCe~~~ed~~~flkHL~~eH~lddrs 174 (204)
|--=+| |-|++.|-|+.+|+.|+-.+|.-+-..
T Consensus 55 WrFWiC--p~CskkF~d~~~~~~H~~~eH~~~l~P 87 (466)
T PF04780_consen 55 WRFWIC--PRCSKKFSDAESCLSHMEQEHPAGLKP 87 (466)
T ss_pred eeEeeC--CcccceeCCHHHHHHHHHHhhhhhcCh
Confidence 444455 559999999999999999999987653
No 28
>TIGR02218 phg_TIGR02218 phage conserved hypothetical protein BR0599. This model describes a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.
Probab=26.28 E-value=28 Score=30.71 Aligned_cols=19 Identities=26% Similarity=0.676 Sum_probs=16.4
Q ss_pred ccccCccccC--CCCCccccc
Q psy15597 138 FLFGHGVCKW--PGCEAVCED 156 (204)
Q Consensus 138 ~L~~~g~CkW--PgCe~~~ed 156 (204)
.-|.+|+-+| |||++.|+.
T Consensus 171 g~f~~G~l~~~~~GCDk~~~T 191 (229)
T TIGR02218 171 GWFSRGRLEWTGAGCDKRFAT 191 (229)
T ss_pred ccccccEEEEeCCCCCCChhH
Confidence 4589999999 999998874
No 29
>COG1544 Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
Probab=25.82 E-value=67 Score=25.50 Aligned_cols=18 Identities=33% Similarity=0.661 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHhhh
Q psy15597 184 VVSQLELQLQKERDRLQA 201 (204)
Q Consensus 184 vVqqLE~qL~~EkerL~A 201 (204)
++..||.||.|-|+|+..
T Consensus 79 a~dKLerqlrK~K~K~~~ 96 (110)
T COG1544 79 AIDKLERQLRKHKEKLKD 96 (110)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 789999999999999864
No 30
>PF02482 Ribosomal_S30AE: Sigma 54 modulation protein / S30EA ribosomal protein; InterPro: IPR003489 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 [, ]. This family contains the sigma-54 modulation protein family and the S30Ae family of ribosomal proteins which includes the light-repressed protein (lrtA) [].; GO: 0005488 binding, 0044238 primary metabolic process; PDB: 1L4S_A 1VOX_a 1VOV_a 3V2E_Y 3V2C_Y 1N3G_A 1VOS_a 1VOZ_a 1VOQ_a 1IMU_A ....
Probab=24.24 E-value=57 Score=23.42 Aligned_cols=18 Identities=33% Similarity=0.586 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHhh
Q psy15597 183 QVVSQLELQLQKERDRLQ 200 (204)
Q Consensus 183 qvVqqLE~qL~~EkerL~ 200 (204)
.++..||.+|.+.|+|+.
T Consensus 78 ~a~dkl~rql~k~k~k~~ 95 (97)
T PF02482_consen 78 EAFDKLERQLRKYKEKLR 95 (97)
T ss_dssp HHHHHHHHHHHHHHHCCC
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 478999999999999875
Done!