Query psy15439
Match_columns 124
No_of_seqs 164 out of 1299
Neff 8.0
Searched_HMMs 46136
Date Fri Aug 16 21:05:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15439.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15439hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1701|consensus 99.9 6.1E-29 1.3E-33 192.1 0.4 118 5-122 275-404 (468)
2 KOG4577|consensus 99.7 1E-18 2.2E-23 130.3 -3.7 113 3-115 32-158 (383)
3 KOG2272|consensus 99.6 1.8E-16 3.9E-21 116.5 -1.6 119 4-123 73-206 (332)
4 PF00412 LIM: LIM domain; Int 99.6 5.7E-15 1.2E-19 86.4 4.7 56 7-62 1-58 (58)
5 KOG2272|consensus 99.4 9.5E-15 2.1E-19 107.5 -1.7 108 2-110 193-312 (332)
6 KOG1701|consensus 99.4 6.1E-14 1.3E-18 109.3 1.1 111 4-115 334-467 (468)
7 KOG1703|consensus 99.4 2.2E-13 4.7E-18 109.7 3.7 119 4-122 303-432 (479)
8 KOG1703|consensus 99.3 3.2E-13 6.9E-18 108.7 2.1 104 3-107 362-478 (479)
9 KOG1044|consensus 99.3 9.1E-13 2E-17 106.0 1.1 87 3-89 132-225 (670)
10 KOG1044|consensus 98.9 3.3E-10 7.2E-15 91.5 1.9 113 9-122 70-202 (670)
11 smart00132 LIM Zinc-binding do 98.7 1.1E-08 2.4E-13 54.5 2.6 37 6-42 1-38 (39)
12 KOG4577|consensus 98.2 4.7E-07 1E-11 68.3 0.4 58 4-61 92-153 (383)
13 KOG1700|consensus 97.9 3.2E-06 7E-11 61.2 0.6 59 5-63 8-67 (200)
14 KOG1700|consensus 97.8 3.8E-06 8.2E-11 60.9 0.2 62 3-64 107-169 (200)
15 KOG1702|consensus 97.5 1E-05 2.2E-10 58.6 -1.8 63 1-63 1-64 (264)
16 PF00412 LIM: LIM domain; Int 96.8 0.00037 8.1E-09 40.0 0.3 41 71-111 15-58 (58)
17 KOG0490|consensus 94.7 0.0033 7.1E-08 45.6 -2.3 97 9-106 1-115 (235)
18 PF08394 Arc_trans_TRASH: Arch 88.9 0.19 4.2E-06 26.7 0.7 32 7-41 1-33 (37)
19 PF14149 YhfH: YhfH-like prote 71.6 0.6 1.3E-05 24.8 -1.3 16 107-122 8-23 (37)
20 PF13240 zinc_ribbon_2: zinc-r 68.0 3.8 8.2E-05 19.2 1.2 11 7-17 2-12 (23)
21 COG1645 Uncharacterized Zn-fin 66.3 3.9 8.5E-05 27.8 1.5 23 33-59 30-52 (131)
22 PF11781 RRN7: RNA polymerase 61.8 4.5 9.7E-05 21.1 0.9 24 33-59 10-33 (36)
23 COG2191 Formylmethanofuran deh 60.3 4.1 8.9E-05 29.7 0.8 30 32-61 173-203 (206)
24 COG4357 Zinc finger domain con 56.6 1.5 3.2E-05 28.3 -1.8 49 7-55 38-87 (105)
25 PF09943 DUF2175: Uncharacteri 56.2 2.7 5.9E-05 27.3 -0.6 29 6-34 4-33 (101)
26 PF01258 zf-dskA_traR: Prokary 54.8 3 6.6E-05 21.5 -0.5 27 34-60 6-33 (36)
27 PF13248 zf-ribbon_3: zinc-rib 53.7 11 0.00023 18.0 1.4 12 6-17 4-15 (26)
28 PF06677 Auto_anti-p27: Sjogre 53.5 6.6 0.00014 21.2 0.7 22 33-57 19-40 (41)
29 PF14446 Prok-RING_1: Prokaryo 53.1 6.3 0.00014 22.7 0.6 29 4-32 5-36 (54)
30 PF04810 zf-Sec23_Sec24: Sec23 49.1 14 0.00031 19.5 1.6 31 4-39 2-32 (40)
31 PF02069 Metallothio_Pro: Prok 46.9 12 0.00027 21.3 1.2 27 33-59 9-37 (52)
32 PF12674 Zn_ribbon_2: Putative 44.6 8.8 0.00019 23.8 0.4 28 33-60 2-35 (81)
33 cd07451 CRD_SMO Cysteine-rich 42.6 13 0.00027 25.3 0.9 16 107-123 61-76 (132)
34 PRK14890 putative Zn-ribbon RN 42.0 21 0.00046 20.9 1.7 30 2-40 5-34 (59)
35 PF14471 DUF4428: Domain of un 41.6 16 0.00034 20.6 1.0 28 33-61 1-30 (51)
36 COG2888 Predicted Zn-ribbon RN 41.0 15 0.00032 21.6 0.9 16 108-123 5-20 (61)
37 PF04570 DUF581: Protein of un 40.8 16 0.00035 21.2 1.1 24 33-56 18-44 (58)
38 cd07447 CRD_Carboxypeptidase_Z 38.7 17 0.00036 24.6 1.0 16 107-123 62-77 (128)
39 KOG4739|consensus 36.7 18 0.0004 26.9 1.1 44 80-123 4-48 (233)
40 PF07754 DUF1610: Domain of un 35.2 38 0.00081 16.1 1.7 12 7-18 1-12 (24)
41 COG2174 RPL34A Ribosomal prote 34.7 20 0.00044 22.8 0.9 11 113-123 35-45 (93)
42 PF14255 Cys_rich_CPXG: Cystei 33.7 17 0.00036 20.7 0.3 30 6-35 2-31 (52)
43 TIGR02420 dksA RNA polymerase- 33.0 18 0.0004 23.4 0.5 10 114-123 82-91 (110)
44 PF10367 Vps39_2: Vacuolar sor 32.9 35 0.00076 21.2 1.8 12 32-43 79-90 (109)
45 PF01286 XPA_N: XPA protein N- 32.6 20 0.00044 18.5 0.5 14 5-18 4-17 (34)
46 cd07453 CRD_crescent Cysteine- 31.1 25 0.00054 24.0 0.9 15 107-123 58-72 (135)
47 PHA00080 DksA-like zinc finger 30.7 24 0.00053 21.3 0.7 11 114-124 33-43 (72)
48 PRK00420 hypothetical protein; 30.6 31 0.00068 22.8 1.3 25 32-59 24-48 (112)
49 PF12172 DUF35_N: Rubredoxin-l 30.4 13 0.00027 19.1 -0.5 13 108-120 7-19 (37)
50 smart00504 Ubox Modified RING 29.6 39 0.00085 18.8 1.5 31 32-62 2-32 (63)
51 PRK13715 conjugal transfer pro 29.6 18 0.0004 21.9 0.1 10 114-123 36-45 (73)
52 PRK14891 50S ribosomal protein 29.1 30 0.00064 23.5 1.0 28 1-28 1-31 (131)
53 TIGR02419 C4_traR_proteo phage 29.0 27 0.00058 20.5 0.7 12 112-123 31-42 (63)
54 PF06221 zf-C2HC5: Putative zi 28.5 31 0.00068 19.9 0.9 18 103-120 7-26 (57)
55 PF10013 DUF2256: Uncharacteri 28.5 41 0.00089 18.3 1.3 16 108-123 4-19 (42)
56 COG1734 DksA DnaK suppressor p 28.0 26 0.00056 23.4 0.6 10 114-123 82-91 (120)
57 cd07444 CRD_SFRP5 Cysteine-ric 27.4 32 0.0007 23.1 1.0 15 107-123 62-76 (127)
58 PRK11019 hypothetical protein; 26.5 31 0.00068 21.8 0.7 11 113-123 37-47 (88)
59 PF03854 zf-P11: P-11 zinc fin 26.4 13 0.00029 20.8 -0.8 26 98-123 19-46 (50)
60 PF11571 Med27: Mediator compl 25.6 12 0.00026 23.5 -1.3 24 98-121 40-63 (90)
61 PF12760 Zn_Tnp_IS1595: Transp 25.4 69 0.0015 17.2 1.9 8 32-39 19-26 (46)
62 PF01199 Ribosomal_L34e: Ribos 25.3 33 0.00071 22.0 0.7 12 112-123 41-52 (94)
63 PF00645 zf-PARP: Poly(ADP-rib 24.7 27 0.00059 21.0 0.2 15 3-17 6-20 (82)
64 KOG0978|consensus 23.8 18 0.0004 31.2 -0.9 45 32-76 644-693 (698)
65 cd07443 CRD_SFRP1 Cysteine-ric 23.5 41 0.0009 22.5 0.9 15 107-123 62-76 (124)
66 PF10886 DUF2685: Protein of u 22.7 55 0.0012 18.8 1.2 24 6-29 3-26 (54)
67 PF02591 DUF164: Putative zinc 22.6 22 0.00048 20.0 -0.5 25 33-57 24-52 (56)
68 PRK10778 dksA RNA polymerase-b 22.5 30 0.00066 23.9 0.1 12 113-124 112-123 (151)
69 PF06750 DiS_P_DiS: Bacterial 22.4 48 0.001 20.9 1.0 11 113-123 59-69 (92)
70 PF14569 zf-UDP: Zinc-binding 22.0 48 0.001 20.5 0.9 9 51-59 36-44 (80)
71 PLN03166 60S ribosomal protein 21.6 57 0.0012 20.9 1.2 12 112-123 41-52 (96)
72 COG4847 Uncharacterized protei 21.6 24 0.00052 22.7 -0.5 34 6-39 8-42 (103)
73 PF05502 Dynactin_p62: Dynacti 21.1 70 0.0015 26.4 2.0 35 7-42 29-63 (483)
74 PF07649 C1_3: C1-like domain; 21.0 43 0.00092 16.2 0.5 10 114-123 2-11 (30)
75 cd00162 RING RING-finger (Real 20.1 41 0.00089 16.7 0.3 8 7-14 2-9 (45)
No 1
>KOG1701|consensus
Probab=99.94 E-value=6.1e-29 Score=192.15 Aligned_cols=118 Identities=19% Similarity=0.372 Sum_probs=103.9
Q ss_pred CCCCCCCccccCCc-cEEEcCceecCCCeecCccCCCCC-CceeeeCCeecccchhhhhcC-CCCcee-----eecccCe
Q psy15439 5 KECGSCGRPITDRY-LLRVADISYHENCVACVECGHSLA-HSCFTRENKLYCRSDYDSRKK-GSQLVT-----VLFYSMY 76 (124)
Q Consensus 5 ~~C~~C~~~I~~~~-~i~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~g~~yC~~~y~~~f~-~~~c~~-----~i~~~~~ 76 (124)
..|.+|+|.|.++. .++||++.||..||+|..|++.|. ..||..|+++||+.||...+. |..|.+ .|.+.+.
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d~iLrA~Gk 354 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMDRILRALGK 354 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHHHHHHHHhccc
Confidence 47999999998754 479999999999999999999999 789999999999999987765 677765 4567788
Q ss_pred eeccCcEEeeeeC--CCCeeEe--EeCcEEEcccCccccCCCCCCCCCCc
Q psy15439 77 VHSVMKFHTITLP--LHTITIR--IQVTIIIIRNLSSLLAQPCTDSSRPI 122 (124)
Q Consensus 77 ~~h~~cf~c~~~~--~~~~~~~--~~~~~~~~~~~~~~~a~~c~~c~~~i 122 (124)
.||++||+|+++- |+++.|+ .+++|||++|||++|||+|+.|++||
T Consensus 355 ayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI 404 (468)
T KOG1701|consen 355 AYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPI 404 (468)
T ss_pred ccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCc
Confidence 9999999999964 7777655 56999999999999999999999999
No 2
>KOG4577|consensus
Probab=99.67 E-value=1e-18 Score=130.28 Aligned_cols=113 Identities=24% Similarity=0.535 Sum_probs=97.7
Q ss_pred CCCCCCCCCccccCCccEEEcCceecCCCeecCccCCCCCCceeeeCCeecccchhhhhcC--CCCceeeec-------c
Q psy15439 3 NMKECGSCGRPITDRYLLRVADISYHENCVACVECGHSLAHSCFTRENKLYCRSDYDSRKK--GSQLVTVLF-------Y 73 (124)
Q Consensus 3 ~~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~g~~yC~~~y~~~f~--~~~c~~~i~-------~ 73 (124)
..++|++|.+.|.+++++.+++++||..|++|+.|..+|.+++|.++|.+||+++|.++|+ |..|.+.|. +
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkA 111 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKA 111 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHh
Confidence 4689999999999999999999999999999999999999999999999999999999999 567766553 5
Q ss_pred cCeeeccCcEEeeeeC--C---CCeeEeEeCcEEEcccCccccCCCC
Q psy15439 74 SMYVHSVMKFHTITLP--L---HTITIRIQVTIIIIRNLSSLLAQPC 115 (124)
Q Consensus 74 ~~~~~h~~cf~c~~~~--~---~~~~~~~~~~~~~~~~~~~~~a~~c 115 (124)
.+.+||.+||.|.-+. | +.++++-+.+++|.+|+..-=+.-|
T Consensus 112 qd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 112 QDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred hcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 7889999999998754 4 3567777799999999976555544
No 3
>KOG2272|consensus
Probab=99.56 E-value=1.8e-16 Score=116.51 Aligned_cols=119 Identities=21% Similarity=0.382 Sum_probs=98.5
Q ss_pred CCCCCCCCccccCCccEEEcCceecCCCeecCccCCCCC-CceeeeCCeecccchhhh-------hcCCCCcee-----e
Q psy15439 4 MKECGSCGRPITDRYLLRVADISYHENCVACVECGHSLA-HSCFTRENKLYCRSDYDS-------RKKGSQLVT-----V 70 (124)
Q Consensus 4 ~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~g~~yC~~~y~~-------~f~~~~c~~-----~ 70 (124)
.|.|++|++.|.++ ++.+++.+||+.||+|..|++.|. ..++.-.|+.+|.+|..+ ++.|.+|.. .
T Consensus 73 aPcC~kC~EFiiGr-VikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~ 151 (332)
T KOG2272|consen 73 APCCGKCGEFIIGR-VIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQP 151 (332)
T ss_pred chhhcccccchhhH-HHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccccc
Confidence 57899999999999 789999999999999999999999 566667799999999877 445666654 4
Q ss_pred ecccCeeeccCcEEeeeeC--CCCeeEeEeCcEEEcccCccccCCCCCCCCCCcc
Q psy15439 71 LFYSMYVHSVMKFHTITLP--LHTITIRIQVTIIIIRNLSSLLAQPCTDSSRPIP 123 (124)
Q Consensus 71 i~~~~~~~h~~cf~c~~~~--~~~~~~~~~~~~~~~~~~~~~~a~~c~~c~~~i~ 123 (124)
|...+-.+|+--|.|.++. |....=.+.+++||++++-++=-|.|.+|.+||.
T Consensus 152 l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 152 LTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE 206 (332)
T ss_pred ccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchH
Confidence 4555667788888888865 4344444678899999999999999999999994
No 4
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.56 E-value=5.7e-15 Score=86.44 Aligned_cols=56 Identities=29% Similarity=0.816 Sum_probs=50.8
Q ss_pred CCCCCccccCCccE-EEcCceecCCCeecCccCCCCC-CceeeeCCeecccchhhhhc
Q psy15439 7 CGSCGRPITDRYLL-RVADISYHENCVACVECGHSLA-HSCFTRENKLYCRSDYDSRK 62 (124)
Q Consensus 7 C~~C~~~I~~~~~i-~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~g~~yC~~~y~~~f 62 (124)
|.+|+++|.+.+.+ .+.++.||++||+|..|+++|. ..++..+|++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 78999999987654 6999999999999999999999 55889999999999999876
No 5
>KOG2272|consensus
Probab=99.42 E-value=9.5e-15 Score=107.49 Aligned_cols=108 Identities=18% Similarity=0.331 Sum_probs=88.0
Q ss_pred CCCCCCCCCCccccCCccEEEcCceecCCCeecCccCCCCC-CceeeeCCeecccchhhhhcC--CCCcee-----eecc
Q psy15439 2 PNMKECGSCGRPITDRYLLRVADISYHENCVACVECGHSLA-HSCFTRENKLYCRSDYDSRKK--GSQLVT-----VLFY 73 (124)
Q Consensus 2 ~~~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~g~~yC~~~y~~~f~--~~~c~~-----~i~~ 73 (124)
.|.++|+.|.++|.++ ++.++|+.||.+.|+|..|.+|+- .+.|++.|..||+.+|.++|+ |..|.. .+++
T Consensus 193 mgipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~a 271 (332)
T KOG2272|consen 193 MGIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVSA 271 (332)
T ss_pred cCCcccccccCchHHH-HHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHHH
Confidence 5789999999999977 679999999999999999999976 899999999999999999998 444544 4455
Q ss_pred cCeeeccCcEEeeeeC--C--CCeeEeEeCcEEEcccCccc
Q psy15439 74 SMYVHSVMKFHTITLP--L--HTITIRIQVTIIIIRNLSSL 110 (124)
Q Consensus 74 ~~~~~h~~cf~c~~~~--~--~~~~~~~~~~~~~~~~~~~~ 110 (124)
..+.|-+.||.|+++. | -+-...++.-+.|.+++.++
T Consensus 272 l~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~rf 312 (332)
T KOG2272|consen 272 LNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDRF 312 (332)
T ss_pred hhhhhccccccccccccccccccceeeeccchHHHHHHhhc
Confidence 6778999999999864 2 23334456778888887654
No 6
>KOG1701|consensus
Probab=99.40 E-value=6.1e-14 Score=109.32 Aligned_cols=111 Identities=23% Similarity=0.407 Sum_probs=86.6
Q ss_pred CCCCCCCCccccCCccEEEcCceecCCCeecCccCCCCCCceee--eCCeecccchhhhhcCC--CCcee----------
Q psy15439 4 MKECGSCGRPITDRYLLRVADISYHENCVACVECGHSLAHSCFT--RENKLYCRSDYDSRKKG--SQLVT---------- 69 (124)
Q Consensus 4 ~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~~~~~~--~~g~~yC~~~y~~~f~~--~~c~~---------- 69 (124)
..+|..|++.|.+. ++.|+|+.||+.||+|..|++.|.+.-|. .++++||.+||+++|++ ..|.+
T Consensus 334 lekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~e 412 (468)
T KOG1701|consen 334 LEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDE 412 (468)
T ss_pred HHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcc
Confidence 35799999999999 78999999999999999999999955543 46899999999999994 34543
Q ss_pred --eecccCeeeccCcEEeeeeC--CC----Ce-eEeEeCcEEEcccCccccCCCC
Q psy15439 70 --VLFYSMYVHSVMKFHTITLP--LH----TI-TIRIQVTIIIIRNLSSLLAQPC 115 (124)
Q Consensus 70 --~i~~~~~~~h~~cf~c~~~~--~~----~~-~~~~~~~~~~~~~~~~~~a~~c 115 (124)
.|...+..+|+.|++|-.+. |+ +. =.-+++-++|-+|=.++.+..+
T Consensus 413 tvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl~~~~ 467 (468)
T KOG1701|consen 413 TVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRLQAGS 467 (468)
T ss_pred eEEEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhhhhhcccC
Confidence 33456678999999997754 32 22 2556778999888777766554
No 7
>KOG1703|consensus
Probab=99.39 E-value=2.2e-13 Score=109.65 Aligned_cols=119 Identities=13% Similarity=0.199 Sum_probs=100.7
Q ss_pred CCCCCCCCccccCCccEEEcCceecCCCeecCccCCCCC-CceeeeCCeecccchhhhhcC--CCCcee-----eecccC
Q psy15439 4 MKECGSCGRPITDRYLLRVADISYHENCVACVECGHSLA-HSCFTRENKLYCRSDYDSRKK--GSQLVT-----VLFYSM 75 (124)
Q Consensus 4 ~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~g~~yC~~~y~~~f~--~~~c~~-----~i~~~~ 75 (124)
.+.|..|+..|.+...+.++++.||+.+|.|..|+..+. ..+...+|++||.+||.+.+. |.+|.+ .|.+.+
T Consensus 303 ~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~ 382 (479)
T KOG1703|consen 303 RPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALG 382 (479)
T ss_pred cccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhcc
Confidence 378999999999944789999999999999999999998 667788999999999999887 567754 445668
Q ss_pred eeeccCcEEeeee--CCCCeeEe-EeCcEEEcccCccccCCCCCCCCCCc
Q psy15439 76 YVHSVMKFHTITL--PLHTITIR-IQVTIIIIRNLSSLLAQPCTDSSRPI 122 (124)
Q Consensus 76 ~~~h~~cf~c~~~--~~~~~~~~-~~~~~~~~~~~~~~~a~~c~~c~~~i 122 (124)
..||+.||.|..+ ++.+..+. .++.+||-+++..+|..+|..|.+||
T Consensus 383 ~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~ 432 (479)
T KOG1703|consen 383 RLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPV 432 (479)
T ss_pred CeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchh
Confidence 8999999999854 35555544 56899999999999999999999986
No 8
>KOG1703|consensus
Probab=99.34 E-value=3.2e-13 Score=108.73 Aligned_cols=104 Identities=17% Similarity=0.265 Sum_probs=85.5
Q ss_pred CCCCCCCCCccccCCccEEEcCceecCCCeecCccCCCCC-CceeeeCCeecccchhhhhcC--CCCc-------eeeec
Q psy15439 3 NMKECGSCGRPITDRYLLRVADISYHENCVACVECGHSLA-HSCFTRENKLYCRSDYDSRKK--GSQL-------VTVLF 72 (124)
Q Consensus 3 ~~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~g~~yC~~~y~~~f~--~~~c-------~~~i~ 72 (124)
..+.|.+|+++|.++ .|.++++.||++||.|..|+++|. ..++.+++.+||+.||++++. +..| ...+.
T Consensus 362 ~~p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie 440 (479)
T KOG1703|consen 362 FRPNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIE 440 (479)
T ss_pred hCccccccCCchHHh-HhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhhhHhh
Confidence 458899999999998 567889999999999999999999 788999999999999999996 3333 33556
Q ss_pred ccCeeeccCcEEeeeeC--CCCeeEeEe-CcEEEcccC
Q psy15439 73 YSMYVHSVMKFHTITLP--LHTITIRIQ-VTIIIIRNL 107 (124)
Q Consensus 73 ~~~~~~h~~cf~c~~~~--~~~~~~~~~-~~~~~~~~~ 107 (124)
+.+..||..||+|+-+. +.+.++... ..++|-..+
T Consensus 441 ~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 441 ADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred ccCccccccceehhhhhccccCCceeecCCccccccCC
Confidence 77889999999998865 565565543 678887654
No 9
>KOG1044|consensus
Probab=99.27 E-value=9.1e-13 Score=106.01 Aligned_cols=87 Identities=18% Similarity=0.351 Sum_probs=76.1
Q ss_pred CCCCCCCCCccccCCccEEEcCceecCCCeecCccCCCCCCceeeeCCeecccchhhhhcC--CCCc-----eeeecccC
Q psy15439 3 NMKECGSCGRPITDRYLLRVADISYHENCVACVECGHSLAHSCFTRENKLYCRSDYDSRKK--GSQL-----VTVLFYSM 75 (124)
Q Consensus 3 ~~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~~~~~~~~g~~yC~~~y~~~f~--~~~c-----~~~i~~~~ 75 (124)
+...|++|++.|.....+.|+++.||..||+|..|+..|..+|+.++|.+||+.||++.|+ |..| .+++.+++
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag~ 211 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAGD 211 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhccC
Confidence 4567999999998877789999999999999999999999999999999999999999998 3334 35677888
Q ss_pred eeeccCcEEeeeeC
Q psy15439 76 YVHSVMKFHTITLP 89 (124)
Q Consensus 76 ~~~h~~cf~c~~~~ 89 (124)
+.+|+.|-.|+-+.
T Consensus 212 kh~HPtCARCsRCg 225 (670)
T KOG1044|consen 212 KHFHPTCARCSRCG 225 (670)
T ss_pred cccCcchhhhhhhc
Confidence 89999999998764
No 10
>KOG1044|consensus
Probab=98.93 E-value=3.3e-10 Score=91.46 Aligned_cols=113 Identities=12% Similarity=0.203 Sum_probs=86.3
Q ss_pred CCCccccCCccEEEcCceecCCCeecCccCCCCC--CceeeeCCeecccchhhh-------hcC---CCCce------ee
Q psy15439 9 SCGRPITDRYLLRVADISYHENCVACVECGHSLA--HSCFTRENKLYCRSDYDS-------RKK---GSQLV------TV 70 (124)
Q Consensus 9 ~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~--~~~~~~~g~~yC~~~y~~-------~f~---~~~c~------~~ 70 (124)
.|...|.+. ++.++|+.||++||.|+.|+.+.. ++.-.-.....|..|-.. ..+ |.+|. ++
T Consensus 70 ~c~~~~~ge-vvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~ 148 (670)
T KOG1044|consen 70 DCRAFVEGE-VVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQA 148 (670)
T ss_pred chhhhccce-eEecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccce
Confidence 455455555 789999999999999999999987 344344445667666431 112 33443 46
Q ss_pred ecccCeeeccCcEEeeeeC--CCCeeEeEeCcEEEcccCccccCCCCCCCCCCc
Q psy15439 71 LFYSMYVHSVMKFHTITLP--LHTITIRIQVTIIIIRNLSSLLAQPCTDSSRPI 122 (124)
Q Consensus 71 i~~~~~~~h~~cf~c~~~~--~~~~~~~~~~~~~~~~~~~~~~a~~c~~c~~~i 122 (124)
+-+.+..||+.||.|.++. |.|-++..++-+||.+|+...|--||..|.+=|
T Consensus 149 llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fi 202 (670)
T KOG1044|consen 149 LLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFI 202 (670)
T ss_pred eeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhh
Confidence 6677889999999998876 677788888999999999999999999998866
No 11
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.70 E-value=1.1e-08 Score=54.46 Aligned_cols=37 Identities=35% Similarity=0.975 Sum_probs=32.9
Q ss_pred CCCCCCccccCC-ccEEEcCceecCCCeecCccCCCCC
Q psy15439 6 ECGSCGRPITDR-YLLRVADISYHENCVACVECGHSLA 42 (124)
Q Consensus 6 ~C~~C~~~I~~~-~~i~~~~~~~H~~Cf~C~~C~~~L~ 42 (124)
+|.+|+++|.+. ..+.+.++.||++||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 589999999885 5678899999999999999999884
No 12
>KOG4577|consensus
Probab=98.16 E-value=4.7e-07 Score=68.32 Aligned_cols=58 Identities=28% Similarity=0.740 Sum_probs=49.3
Q ss_pred CCCCCCCCccccCCccE-EEcCceecCCCeecCccCCCCC--Ccee-eeCCeecccchhhhh
Q psy15439 4 MKECGSCGRPITDRYLL-RVADISYHENCVACVECGHSLA--HSCF-TRENKLYCRSDYDSR 61 (124)
Q Consensus 4 ~~~C~~C~~~I~~~~~i-~~~~~~~H~~Cf~C~~C~~~L~--~~~~-~~~g~~yC~~~y~~~ 61 (124)
+.+|..|.+.|.+..++ .|.+..||.+||.|..|+.+|. ++|| +.|+++.|+.+|+.-
T Consensus 92 GTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~A 153 (383)
T KOG4577|consen 92 GTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETA 153 (383)
T ss_pred CCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHH
Confidence 35799999999886554 6788999999999999999998 6776 557999999999753
No 13
>KOG1700|consensus
Probab=97.90 E-value=3.2e-06 Score=61.24 Aligned_cols=59 Identities=19% Similarity=0.526 Sum_probs=52.2
Q ss_pred CCCCCCCccccCCccEEEcCceecCCCeecCccCCCCC-CceeeeCCeecccchhhhhcC
Q psy15439 5 KECGSCGRPITDRYLLRVADISYHENCVACVECGHSLA-HSCFTRENKLYCRSDYDSRKK 63 (124)
Q Consensus 5 ~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~g~~yC~~~y~~~f~ 63 (124)
..|..|++.++..+.+...+..||..||.|..|.+.|. ..+..+++.+||+.+|.+.++
T Consensus 8 ~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~ 67 (200)
T KOG1700|consen 8 DKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFG 67 (200)
T ss_pred chhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhC
Confidence 48999999999877777889999999999999999998 777889999999997776665
No 14
>KOG1700|consensus
Probab=97.84 E-value=3.8e-06 Score=60.87 Aligned_cols=62 Identities=23% Similarity=0.627 Sum_probs=54.0
Q ss_pred CCCCCCCCCccccCCccEEEcCceecCCCeecCccCCCCC-CceeeeCCeecccchhhhhcCC
Q psy15439 3 NMKECGSCGRPITDRYLLRVADISYHENCVACVECGHSLA-HSCFTRENKLYCRSDYDSRKKG 64 (124)
Q Consensus 3 ~~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~g~~yC~~~y~~~f~~ 64 (124)
....|..|.+.+++.+.+...+..||..||+|+.|+..|+ ..+...++.+||+..+.+++-.
T Consensus 107 ~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~ 169 (200)
T KOG1700|consen 107 EKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKG 169 (200)
T ss_pred cccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecC
Confidence 4567999999999988888999999999999999999999 6777889999998887776543
No 15
>KOG1702|consensus
Probab=97.50 E-value=1e-05 Score=58.63 Aligned_cols=63 Identities=22% Similarity=0.517 Sum_probs=52.1
Q ss_pred CCCCCCCCCCCccccCCccEEEcCceecCCCeecCccCCCCC-CceeeeCCeecccchhhhhcC
Q psy15439 1 MPNMKECGSCGRPITDRYLLRVADISYHENCVACVECGHSLA-HSCFTRENKLYCRSDYDSRKK 63 (124)
Q Consensus 1 ~~~~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~g~~yC~~~y~~~f~ 63 (124)
|.....|..|++.+++.+.+.-+++.||..||+|..|+..|. ..+--.+.++||..+|.+..+
T Consensus 1 ~~~k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 1 MSKKCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred CCccchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 344567889999999887788999999999999999999998 444446889999999976543
No 16
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=96.79 E-value=0.00037 Score=40.03 Aligned_cols=41 Identities=5% Similarity=-0.237 Sum_probs=31.8
Q ss_pred ecccCeeeccCcEEeeeeC--CCCe-eEeEeCcEEEcccCcccc
Q psy15439 71 LFYSMYVHSVMKFHTITLP--LHTI-TIRIQVTIIIIRNLSSLL 111 (124)
Q Consensus 71 i~~~~~~~h~~cf~c~~~~--~~~~-~~~~~~~~~~~~~~~~~~ 111 (124)
+.+.+..||..||+|..+. |.+. .+..++.+||-++|.++|
T Consensus 15 ~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 15 IKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp EEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred EEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 3567789999999998854 4433 455678999999998876
No 17
>KOG0490|consensus
Probab=94.69 E-value=0.0033 Score=45.61 Aligned_cols=97 Identities=30% Similarity=0.592 Sum_probs=64.5
Q ss_pred CCCccccCCccEEEcCceecCCCeecCccCCCCC--CceeeeCCeecccchhhh--hcC--CCCceeeec-------ccC
Q psy15439 9 SCGRPITDRYLLRVADISYHENCVACVECGHSLA--HSCFTRENKLYCRSDYDS--RKK--GSQLVTVLF-------YSM 75 (124)
Q Consensus 9 ~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~--~~~~~~~g~~yC~~~y~~--~f~--~~~c~~~i~-------~~~ 75 (124)
+|+..|.+.....+.+..||..|..|..|...|. ...+..+|..||..+|.+ .+. +.++...+. .-+
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~ 80 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFE 80 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHhhc
Confidence 4677888877777789999999999999999998 667766999999999998 443 333332221 122
Q ss_pred eeeccCcEEeeee---CCCCeeEeEe--CcEEEccc
Q psy15439 76 YVHSVMKFHTITL---PLHTITIRIQ--VTIIIIRN 106 (124)
Q Consensus 76 ~~~h~~cf~c~~~---~~~~~~~~~~--~~~~~~~~ 106 (124)
.+ |.-+|.|... .+.+-..+|+ ++..+...
T Consensus 81 ~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~ 115 (235)
T KOG0490|consen 81 KV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKD 115 (235)
T ss_pred CC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhh
Confidence 23 7778777652 2233344444 34544443
No 18
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=88.87 E-value=0.19 Score=26.68 Aligned_cols=32 Identities=25% Similarity=0.678 Sum_probs=22.6
Q ss_pred CCCCCccccCCcc-EEEcCceecCCCeecCccCCCC
Q psy15439 7 CGSCGRPITDRYL-LRVADISYHENCVACVECGHSL 41 (124)
Q Consensus 7 C~~C~~~I~~~~~-i~~~~~~~H~~Cf~C~~C~~~L 41 (124)
|..||.+|.+... +...++.|+ |-|..|...+
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f 33 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF 33 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence 6789999987654 577888887 5555565443
No 19
>PF14149 YhfH: YhfH-like protein
Probab=71.63 E-value=0.6 Score=24.76 Aligned_cols=16 Identities=25% Similarity=0.605 Sum_probs=13.7
Q ss_pred CccccCCCCCCCCCCc
Q psy15439 107 LSSLLAQPCTDSSRPI 122 (124)
Q Consensus 107 ~~~~~a~~c~~c~~~i 122 (124)
|-+|.+++|+.|++.|
T Consensus 8 frnLp~K~C~~CG~~i 23 (37)
T PF14149_consen 8 FRNLPPKKCTECGKEI 23 (37)
T ss_pred HHhCCCcccHHHHHHH
Confidence 5578899999999887
No 20
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=67.99 E-value=3.8 Score=19.20 Aligned_cols=11 Identities=45% Similarity=1.093 Sum_probs=7.2
Q ss_pred CCCCCccccCC
Q psy15439 7 CGSCGRPITDR 17 (124)
Q Consensus 7 C~~C~~~I~~~ 17 (124)
|..|+..|.+.
T Consensus 2 Cp~CG~~~~~~ 12 (23)
T PF13240_consen 2 CPNCGAEIEDD 12 (23)
T ss_pred CcccCCCCCCc
Confidence 66777777554
No 21
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=66.29 E-value=3.9 Score=27.78 Aligned_cols=23 Identities=26% Similarity=0.762 Sum_probs=18.8
Q ss_pred ecCccCCCCCCceeeeCCeecccchhh
Q psy15439 33 ACVECGHSLAHSCFTRENKLYCRSDYD 59 (124)
Q Consensus 33 ~C~~C~~~L~~~~~~~~g~~yC~~~y~ 59 (124)
.|..|+.+| |.++|.+||..|-.
T Consensus 30 hCp~Cg~PL----F~KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL----FRKDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc----eeeCCeEECCCCCc
Confidence 477889888 55999999999864
No 22
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=61.81 E-value=4.5 Score=21.14 Aligned_cols=24 Identities=21% Similarity=0.553 Sum_probs=16.2
Q ss_pred ecCccCCCCCCceeeeCCeecccchhh
Q psy15439 33 ACVECGHSLAHSCFTRENKLYCRSDYD 59 (124)
Q Consensus 33 ~C~~C~~~L~~~~~~~~g~~yC~~~y~ 59 (124)
.|..|+.. .+...+|..||..|.+
T Consensus 10 ~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe---EeEccCCEEEhhhCce
Confidence 46667653 5567789999977643
No 23
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=60.32 E-value=4.1 Score=29.70 Aligned_cols=30 Identities=20% Similarity=0.502 Sum_probs=24.1
Q ss_pred eecCccCCCCC-CceeeeCCeecccchhhhh
Q psy15439 32 VACVECGHSLA-HSCFTRENKLYCRSDYDSR 61 (124)
Q Consensus 32 f~C~~C~~~L~-~~~~~~~g~~yC~~~y~~~ 61 (124)
-+|+.|+.... ..-...+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 58999998877 4445778999999998754
No 24
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=56.58 E-value=1.5 Score=28.28 Aligned_cols=49 Identities=16% Similarity=0.328 Sum_probs=31.6
Q ss_pred CCCCCccccCCccEEEcCceecCCCeecCccCCCCC-CceeeeCCeeccc
Q psy15439 7 CGSCGRPITDRYLLRVADISYHENCVACVECGHSLA-HSCFTRENKLYCR 55 (124)
Q Consensus 7 C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~-~~~~~~~g~~yC~ 55 (124)
|..|...+.........-..+++.+..|..|.+.|. ..|...+.=+||.
T Consensus 38 Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C~ 87 (105)
T COG4357 38 CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYCQ 87 (105)
T ss_pred HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCcC
Confidence 445555665544445555677888888888888887 6666555555553
No 25
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=56.18 E-value=2.7 Score=27.26 Aligned_cols=29 Identities=28% Similarity=0.591 Sum_probs=21.0
Q ss_pred CCCCCCccccCCccEEEc-CceecCCCeec
Q psy15439 6 ECGSCGRPITDRYLLRVA-DISYHENCVAC 34 (124)
Q Consensus 6 ~C~~C~~~I~~~~~i~~~-~~~~H~~Cf~C 34 (124)
.|.-|+++|+.++..++. +..-|..||.=
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~ 33 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE 33 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence 588899999877666653 45678888764
No 26
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=54.80 E-value=3 Score=21.50 Aligned_cols=27 Identities=15% Similarity=0.460 Sum_probs=14.5
Q ss_pred cCccCCCCC-CceeeeCCeecccchhhh
Q psy15439 34 CVECGHSLA-HSCFTRENKLYCRSDYDS 60 (124)
Q Consensus 34 C~~C~~~L~-~~~~~~~g~~yC~~~y~~ 60 (124)
|..|+.++. .+.....+..+|.+|..+
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence 566666665 344455666677666543
No 27
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=53.70 E-value=11 Score=18.00 Aligned_cols=12 Identities=33% Similarity=0.747 Sum_probs=7.2
Q ss_pred CCCCCCccccCC
Q psy15439 6 ECGSCGRPITDR 17 (124)
Q Consensus 6 ~C~~C~~~I~~~ 17 (124)
.|..|+..|...
T Consensus 4 ~Cp~Cg~~~~~~ 15 (26)
T PF13248_consen 4 FCPNCGAEIDPD 15 (26)
T ss_pred CCcccCCcCCcc
Confidence 577777755433
No 28
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=53.46 E-value=6.6 Score=21.19 Aligned_cols=22 Identities=36% Similarity=0.936 Sum_probs=14.1
Q ss_pred ecCccCCCCCCceeeeCCeecccch
Q psy15439 33 ACVECGHSLAHSCFTRENKLYCRSD 57 (124)
Q Consensus 33 ~C~~C~~~L~~~~~~~~g~~yC~~~ 57 (124)
.|..|+.+|-. .++|+.||..|
T Consensus 19 ~Cp~C~~PL~~---~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMR---DKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEE---ecCCCEECCCC
Confidence 45567777632 46777888655
No 29
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=53.11 E-value=6.3 Score=22.66 Aligned_cols=29 Identities=24% Similarity=0.613 Sum_probs=17.2
Q ss_pred CCCCCCCCccccCCc-cE--EEcCceecCCCe
Q psy15439 4 MKECGSCGRPITDRY-LL--RVADISYHENCV 32 (124)
Q Consensus 4 ~~~C~~C~~~I~~~~-~i--~~~~~~~H~~Cf 32 (124)
..+|..|++.+.+.. ++ ..-+..+|.+|.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 467899999996432 22 223555666554
No 30
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=49.13 E-value=14 Score=19.45 Aligned_cols=31 Identities=16% Similarity=0.388 Sum_probs=14.4
Q ss_pred CCCCCCCCccccCCccEEEcCceecCCCeecCccCC
Q psy15439 4 MKECGSCGRPITDRYLLRVADISYHENCVACVECGH 39 (124)
Q Consensus 4 ~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~ 39 (124)
..+|..|+-.|.+-..+...++.| +|..|+.
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEE-----EETTT--
T ss_pred ccccCCCCCEECCcceEcCCCCEE-----ECcCCCC
Confidence 467888887776653344455555 5666654
No 31
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=46.91 E-value=12 Score=21.27 Aligned_cols=27 Identities=22% Similarity=0.653 Sum_probs=14.7
Q ss_pred ecCccCCCCC-CceeeeCCeeccc-chhh
Q psy15439 33 ACVECGHSLA-HSCFTRENKLYCR-SDYD 59 (124)
Q Consensus 33 ~C~~C~~~L~-~~~~~~~g~~yC~-~~y~ 59 (124)
.|..|...++ +.-+.+||+.||- .|..
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSHHHHH
T ss_pred cCCCCEeEECchHhHHhCCEeeecHHHhc
Confidence 4567777777 6778899999984 4443
No 32
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=44.64 E-value=8.8 Score=23.78 Aligned_cols=28 Identities=29% Similarity=0.694 Sum_probs=18.4
Q ss_pred ecCccCCCCC-Ccee--eeC---Ceecccchhhh
Q psy15439 33 ACVECGHSLA-HSCF--TRE---NKLYCRSDYDS 60 (124)
Q Consensus 33 ~C~~C~~~L~-~~~~--~~~---g~~yC~~~y~~ 60 (124)
.|..|+.||. +..+ ..| +.-||..||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 4788999998 3323 223 46789888854
No 33
>cd07451 CRD_SMO Cysteine-rich domain of the smoothened receptor (Smo) integral membrane protein. The cysteine-rich domain (CRD) is part of the smoothened receptor (Smo), an integral membrane protein and one of the key players in the Hedgehog (Hh) signaling pathway, critical for development, cell growth and migration, as well as stem cell maintenance. The CRD of Smo is conserved in vertebrates and can also be identified in invertebrates. The precise function of the CRD in Smo is unknown. Mutations in the Drosophila CRD disrupt Smo activity in vivo, while deletion of the CRD in mammalian cells does not seem to affect the activity of overexpressed Smo.
Probab=42.60 E-value=13 Score=25.33 Aligned_cols=16 Identities=19% Similarity=0.368 Sum_probs=12.2
Q ss_pred CccccCCCCCCCCCCcc
Q psy15439 107 LSSLLAQPCTDSSRPIP 123 (124)
Q Consensus 107 ~~~~~a~~c~~c~~~i~ 123 (124)
+-++|||+|.. .++|.
T Consensus 61 LCSly~P~C~~-~~~~~ 76 (132)
T cd07451 61 LCALYMPKCEN-GKVEL 76 (132)
T ss_pred eEeeECCcCCC-CCccC
Confidence 45899999987 66664
No 34
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=42.04 E-value=21 Score=20.86 Aligned_cols=30 Identities=30% Similarity=0.559 Sum_probs=19.8
Q ss_pred CCCCCCCCCCccccCCccEEEcCceecCCCeecCccCCC
Q psy15439 2 PNMKECGSCGRPITDRYLLRVADISYHENCVACVECGHS 40 (124)
Q Consensus 2 ~~~~~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~ 40 (124)
...++|..|+..|.+.+. .--|.|-.|+..
T Consensus 5 ~~~~~CtSCg~~i~~~~~---------~~~F~CPnCG~~ 34 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREK---------AVKFLCPNCGEV 34 (59)
T ss_pred ccCccccCCCCcccCCCc---------cCEeeCCCCCCe
Confidence 456789999988876541 112677777765
No 35
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=41.59 E-value=16 Score=20.58 Aligned_cols=28 Identities=14% Similarity=0.492 Sum_probs=18.9
Q ss_pred ecCccCCCCC--CceeeeCCeecccchhhhh
Q psy15439 33 ACVECGHSLA--HSCFTRENKLYCRSDYDSR 61 (124)
Q Consensus 33 ~C~~C~~~L~--~~~~~~~g~~yC~~~y~~~ 61 (124)
.|..|+..++ ..+-..|| ..|..|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 3677888877 33445666 5788888665
No 36
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=40.96 E-value=15 Score=21.57 Aligned_cols=16 Identities=25% Similarity=0.304 Sum_probs=12.5
Q ss_pred ccccCCCCCCCCCCcc
Q psy15439 108 SSLLAQPCTDSSRPIP 123 (124)
Q Consensus 108 ~~~~a~~c~~c~~~i~ 123 (124)
...+.+.|++|+..|.
T Consensus 5 ~~~~~~~CtSCg~~i~ 20 (61)
T COG2888 5 EMKDPPVCTSCGREIA 20 (61)
T ss_pred cccCCceeccCCCEec
Confidence 3455789999999883
No 37
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=40.78 E-value=16 Score=21.23 Aligned_cols=24 Identities=25% Similarity=0.592 Sum_probs=18.3
Q ss_pred ecCccCCCCC---CceeeeCCeecccc
Q psy15439 33 ACVECGHSLA---HSCFTRENKLYCRS 56 (124)
Q Consensus 33 ~C~~C~~~L~---~~~~~~~g~~yC~~ 56 (124)
.|..|++.|. +.|..++.+.+|..
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ 44 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSE 44 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccH
Confidence 5677888998 46667888999853
No 38
>cd07447 CRD_Carboxypeptidase_Z Cysteine-rich domain of carboxypeptidase Z, a member of the carboxypeptidase E family. The cysteine-rich-domain (CRD) is an essential part of carboxypeptidase Z, a member of the carboxypeptidase E family of metallocarboxypeptidases. This is a group of Zn-dependent enzymes implicated in the intra- and extracellular processing of proteins. Carboxypeptidase Z removes C-terminal basic amino acid residues from its substrates, particularly arginine. The CRD acts as a ligand-binding domain for Wnts involved in developmental processes. CPZ binds and may process Wnt-4, CPZ has also been found to enhance the induction of the homeobox gene Cdx1. During vertebrate embryogenesis, the CRD of CPZ upregulates Pax3, a Wnt reporter gene essential for patterning of somites and limb development.
Probab=38.70 E-value=17 Score=24.55 Aligned_cols=16 Identities=31% Similarity=0.488 Sum_probs=12.5
Q ss_pred CccccCCCCCCCCCCcc
Q psy15439 107 LSSLLAQPCTDSSRPIP 123 (124)
Q Consensus 107 ~~~~~a~~c~~c~~~i~ 123 (124)
+.++|||+|+. ++||+
T Consensus 62 LCSl~~P~C~~-~~~i~ 77 (128)
T cd07447 62 GCSVLAPRCEN-DKVIK 77 (128)
T ss_pred hhcccccccCC-CCccC
Confidence 56899999987 66664
No 39
>KOG4739|consensus
Probab=36.72 E-value=18 Score=26.92 Aligned_cols=44 Identities=11% Similarity=0.101 Sum_probs=32.1
Q ss_pred cCcEEeeeeCC-CCeeEeEeCcEEEcccCccccCCCCCCCCCCcc
Q psy15439 80 VMKFHTITLPL-HTITIRIQVTIIIIRNLSSLLAQPCTDSSRPIP 123 (124)
Q Consensus 80 ~~cf~c~~~~~-~~~~~~~~~~~~~~~~~~~~~a~~c~~c~~~i~ 123 (124)
++|.+|.-.|- .++.++-=.-+.|-.|+.--.++.|-.|.++|-
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIR 48 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccCCccccccccceee
Confidence 56667766554 455666556788888888888888998888863
No 40
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=35.17 E-value=38 Score=16.10 Aligned_cols=12 Identities=67% Similarity=1.356 Sum_probs=7.4
Q ss_pred CCCCCccccCCc
Q psy15439 7 CGSCGRPITDRY 18 (124)
Q Consensus 7 C~~C~~~I~~~~ 18 (124)
|..|+..|.+.+
T Consensus 1 C~sC~~~i~~r~ 12 (24)
T PF07754_consen 1 CTSCGRPIAPRE 12 (24)
T ss_pred CccCCCcccCcc
Confidence 556777776553
No 41
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=34.66 E-value=20 Score=22.79 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=9.4
Q ss_pred CCCCCCCCCcc
Q psy15439 113 QPCTDSSRPIP 123 (124)
Q Consensus 113 ~~c~~c~~~i~ 123 (124)
|+|++|+.|++
T Consensus 35 p~C~~cg~pL~ 45 (93)
T COG2174 35 PKCAICGRPLG 45 (93)
T ss_pred CcccccCCccC
Confidence 78999999875
No 42
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=33.74 E-value=17 Score=20.66 Aligned_cols=30 Identities=33% Similarity=0.701 Sum_probs=20.0
Q ss_pred CCCCCCccccCCccEEEcCceecCCCeecC
Q psy15439 6 ECGSCGRPITDRYLLRVADISYHENCVACV 35 (124)
Q Consensus 6 ~C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~ 35 (124)
.|..||+.+.-.--.+..++.|-.+|-.|.
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC 31 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCC 31 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcC
Confidence 588999988543123455788888886653
No 43
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=32.99 E-value=18 Score=23.39 Aligned_cols=10 Identities=20% Similarity=0.461 Sum_probs=8.9
Q ss_pred CCCCCCCCcc
Q psy15439 114 PCTDSSRPIP 123 (124)
Q Consensus 114 ~c~~c~~~i~ 123 (124)
.|-.|+.|||
T Consensus 82 ~C~~Cge~I~ 91 (110)
T TIGR02420 82 YCEECGEEIG 91 (110)
T ss_pred chhccCCccc
Confidence 7899999997
No 44
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=32.89 E-value=35 Score=21.19 Aligned_cols=12 Identities=33% Similarity=0.916 Sum_probs=8.3
Q ss_pred eecCccCCCCCC
Q psy15439 32 VACVECGHSLAH 43 (124)
Q Consensus 32 f~C~~C~~~L~~ 43 (124)
-.|..|+++|+.
T Consensus 79 ~~C~vC~k~l~~ 90 (109)
T PF10367_consen 79 TKCSVCGKPLGN 90 (109)
T ss_pred CCccCcCCcCCC
Confidence 457777777773
No 45
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=32.61 E-value=20 Score=18.50 Aligned_cols=14 Identities=43% Similarity=1.272 Sum_probs=5.1
Q ss_pred CCCCCCCccccCCc
Q psy15439 5 KECGSCGRPITDRY 18 (124)
Q Consensus 5 ~~C~~C~~~I~~~~ 18 (124)
+.|..|+++..+.+
T Consensus 4 ~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 4 PKCDECGKPFMDSY 17 (34)
T ss_dssp EE-TTT--EES-SS
T ss_pred chHhHhCCHHHHHH
Confidence 44555555554443
No 46
>cd07453 CRD_crescent Cysteine-rich domain of the crescent protein. The cysteine-rich domain (CRD) is an essential part of the crescent protein, a member of the secreted frizzled-related protein (SFRP) family, which regulates convergent extension movements (CEMs) during gastrulation and neurulation. Xenopus laevis crescent efficiently forms inhibitory complexes with Wnt5a and Wnt11, but this effect is cancelled in the presence of another member of the SFRP family, Frzb1. A potential role for Crescent in head formation is to regulate a non-canonical Wnt pathway positively in the adjacent posterior mesoderm, and negatively in the overlying anterior neuroectoderm.
Probab=31.09 E-value=25 Score=23.99 Aligned_cols=15 Identities=53% Similarity=0.747 Sum_probs=11.8
Q ss_pred CccccCCCCCCCCCCcc
Q psy15439 107 LSSLLAQPCTDSSRPIP 123 (124)
Q Consensus 107 ~~~~~a~~c~~c~~~i~ 123 (124)
+-++|||+|+ .+||+
T Consensus 58 LCSl~~P~C~--~~~i~ 72 (135)
T cd07453 58 LCSLFAPICW--DRPIY 72 (135)
T ss_pred hhhhcCccCC--CCCCC
Confidence 4578999998 67775
No 47
>PHA00080 DksA-like zinc finger domain containing protein
Probab=30.75 E-value=24 Score=21.26 Aligned_cols=11 Identities=36% Similarity=0.924 Sum_probs=9.4
Q ss_pred CCCCCCCCccC
Q psy15439 114 PCTDSSRPIPV 124 (124)
Q Consensus 114 ~c~~c~~~i~~ 124 (124)
.|.+|+.|||.
T Consensus 33 ~C~~Cg~~Ip~ 43 (72)
T PHA00080 33 HCEECGDPIPE 43 (72)
T ss_pred EecCCCCcCcH
Confidence 69999999983
No 48
>PRK00420 hypothetical protein; Validated
Probab=30.62 E-value=31 Score=22.76 Aligned_cols=25 Identities=20% Similarity=0.456 Sum_probs=15.9
Q ss_pred eecCccCCCCCCceeeeCCeecccchhh
Q psy15439 32 VACVECGHSLAHSCFTRENKLYCRSDYD 59 (124)
Q Consensus 32 f~C~~C~~~L~~~~~~~~g~~yC~~~y~ 59 (124)
-.|..|+.+| +-.++|+.||..|-.
T Consensus 24 ~~CP~Cg~pL---f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPL---FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcc---eecCCCceECCCCCC
Confidence 3566677666 223678888877744
No 49
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=30.38 E-value=13 Score=19.12 Aligned_cols=13 Identities=46% Similarity=0.813 Sum_probs=7.2
Q ss_pred ccccCCCCCCCCC
Q psy15439 108 SSLLAQPCTDSSR 120 (124)
Q Consensus 108 ~~~~a~~c~~c~~ 120 (124)
++|.+++|++|+.
T Consensus 7 ~~l~~~rC~~Cg~ 19 (37)
T PF12172_consen 7 GRLLGQRCRDCGR 19 (37)
T ss_dssp T-EEEEE-TTT--
T ss_pred CEEEEEEcCCCCC
Confidence 4677888988876
No 50
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=29.63 E-value=39 Score=18.84 Aligned_cols=31 Identities=10% Similarity=0.123 Sum_probs=20.2
Q ss_pred eecCccCCCCCCceeeeCCeecccchhhhhc
Q psy15439 32 VACVECGHSLAHSCFTRENKLYCRSDYDSRK 62 (124)
Q Consensus 32 f~C~~C~~~L~~~~~~~~g~~yC~~~y~~~f 62 (124)
|.|..|+..+.+-.....|..||+.+..+.+
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~ 32 (63)
T smart00504 2 FLCPISLEVMKDPVILPSGQTYERRAIEKWL 32 (63)
T ss_pred cCCcCCCCcCCCCEECCCCCEEeHHHHHHHH
Confidence 4566777766655555567888877766544
No 51
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=29.61 E-value=18 Score=21.89 Aligned_cols=10 Identities=40% Similarity=0.959 Sum_probs=9.2
Q ss_pred CCCCCCCCcc
Q psy15439 114 PCTDSSRPIP 123 (124)
Q Consensus 114 ~c~~c~~~i~ 123 (124)
.|.+|+.|||
T Consensus 36 ~C~~Cg~~Ip 45 (73)
T PRK13715 36 LCEACGNPIP 45 (73)
T ss_pred cHhhcCCcCC
Confidence 7999999998
No 52
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=29.06 E-value=30 Score=23.48 Aligned_cols=28 Identities=21% Similarity=0.311 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCccccCCcc---EEEcCceec
Q psy15439 1 MPNMKECGSCGRPITDRYL---LRVADISYH 28 (124)
Q Consensus 1 ~~~~~~C~~C~~~I~~~~~---i~~~~~~~H 28 (124)
|+....|..|+..|++... +...|+.|+
T Consensus 1 Mm~~e~CsFcG~kIyPG~G~~fVR~DGkvf~ 31 (131)
T PRK14891 1 MVETRTCDYTGEEIEPGTGTMFVRKDGTVLH 31 (131)
T ss_pred CCceeeecCcCCcccCCCCcEEEecCCCEEE
Confidence 7888899999999986432 455677776
No 53
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=28.98 E-value=27 Score=20.45 Aligned_cols=12 Identities=42% Similarity=0.999 Sum_probs=10.1
Q ss_pred CCCCCCCCCCcc
Q psy15439 112 AQPCTDSSRPIP 123 (124)
Q Consensus 112 a~~c~~c~~~i~ 123 (124)
...|..|+.|||
T Consensus 31 ~g~C~~Cg~~Ip 42 (63)
T TIGR02419 31 LRECEDCGEPIP 42 (63)
T ss_pred CCeeccCCCcCh
Confidence 457999999997
No 54
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=28.52 E-value=31 Score=19.94 Aligned_cols=18 Identities=17% Similarity=0.327 Sum_probs=12.5
Q ss_pred EcccCcccc--CCCCCCCCC
Q psy15439 103 IIRNLSSLL--AQPCTDSSR 120 (124)
Q Consensus 103 ~~~~~~~~~--a~~c~~c~~ 120 (124)
|...-|.|| |+.|..|++
T Consensus 7 C~a~~H~L~~~~~NCl~CGk 26 (57)
T PF06221_consen 7 CQARRHPLFPYAPNCLNCGK 26 (57)
T ss_pred cccccCCCccccccccccCh
Confidence 444556665 888888887
No 55
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.45 E-value=41 Score=18.25 Aligned_cols=16 Identities=31% Similarity=0.571 Sum_probs=12.7
Q ss_pred ccccCCCCCCCCCCcc
Q psy15439 108 SSLLAQPCTDSSRPIP 123 (124)
Q Consensus 108 ~~~~a~~c~~c~~~i~ 123 (124)
..|....|..|++|..
T Consensus 4 ~~lp~K~C~~C~rpf~ 19 (42)
T PF10013_consen 4 SNLPSKICPVCGRPFT 19 (42)
T ss_pred ccCCCCcCcccCCcch
Confidence 3577889999999863
No 56
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=27.96 E-value=26 Score=23.39 Aligned_cols=10 Identities=40% Similarity=1.052 Sum_probs=8.7
Q ss_pred CCCCCCCCcc
Q psy15439 114 PCTDSSRPIP 123 (124)
Q Consensus 114 ~c~~c~~~i~ 123 (124)
.|..|+.|||
T Consensus 82 ~Ce~cG~~Ip 91 (120)
T COG1734 82 ICEECGEPIP 91 (120)
T ss_pred chhccCCcCC
Confidence 6889999997
No 57
>cd07444 CRD_SFRP5 Cysteine-rich domain of the secreted frizzled-related protein 5 (SFRP5), a regulator of Wnt activity. The cysteine-rich domain (CRD) is an essential part of the secreted frizzled-related Protein 5 (SFRP5), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to the CRD domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs are also known to have functions unrelated to Wnt, as enhancers of procollagen cleavage by the TLD proteinases. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs.
Probab=27.37 E-value=32 Score=23.15 Aligned_cols=15 Identities=60% Similarity=0.906 Sum_probs=11.4
Q ss_pred CccccCCCCCCCCCCcc
Q psy15439 107 LSSLLAQPCTDSSRPIP 123 (124)
Q Consensus 107 ~~~~~a~~c~~c~~~i~ 123 (124)
+-++|||+|++ +||+
T Consensus 62 lCSl~~P~C~~--~~i~ 76 (127)
T cd07444 62 LCSLFAPVCLD--RPIY 76 (127)
T ss_pred hhhhcCCCCCC--CCCC
Confidence 46889999984 6664
No 58
>PRK11019 hypothetical protein; Provisional
Probab=26.52 E-value=31 Score=21.76 Aligned_cols=11 Identities=36% Similarity=1.020 Sum_probs=9.7
Q ss_pred CCCCCCCCCcc
Q psy15439 113 QPCTDSSRPIP 123 (124)
Q Consensus 113 ~~c~~c~~~i~ 123 (124)
..|..|+.|||
T Consensus 37 g~C~~CG~~Ip 47 (88)
T PRK11019 37 TECEECGEPIP 47 (88)
T ss_pred CeeCcCCCcCc
Confidence 47999999998
No 59
>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=26.41 E-value=13 Score=20.79 Aligned_cols=26 Identities=19% Similarity=0.508 Sum_probs=17.3
Q ss_pred eCcEEEcccCccccC--CCCCCCCCCcc
Q psy15439 98 QVTIIIIRNLSSLLA--QPCTDSSRPIP 123 (124)
Q Consensus 98 ~~~~~~~~~~~~~~a--~~c~~c~~~i~ 123 (124)
..-++|++++..++- ..|..|.+|+|
T Consensus 19 ~dHYLCl~CLt~ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 19 SDHYLCLNCLTLMLSRSDRCPICGKPLP 46 (50)
T ss_dssp SS-EEEHHHHHHT-SSSSEETTTTEE--
T ss_pred cchhHHHHHHHHHhccccCCCcccCcCc
Confidence 346788888888774 67888888876
No 60
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=25.59 E-value=12 Score=23.48 Aligned_cols=24 Identities=13% Similarity=0.394 Sum_probs=18.2
Q ss_pred eCcEEEcccCccccCCCCCCCCCC
Q psy15439 98 QVTIIIIRNLSSLLAQPCTDSSRP 121 (124)
Q Consensus 98 ~~~~~~~~~~~~~~a~~c~~c~~~ 121 (124)
..-+--+.-|..+|..+|+.|++=
T Consensus 40 ~~ll~~l~sY~~lfs~pC~~C~kl 63 (90)
T PF11571_consen 40 RSLLDWLSSYRNLFSTPCKKCGKL 63 (90)
T ss_pred HHHHHHHHHHhhhccchhhHHHhH
Confidence 333455677899999999999873
No 61
>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. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.37 E-value=69 Score=17.18 Aligned_cols=8 Identities=38% Similarity=1.173 Sum_probs=3.5
Q ss_pred eecCccCC
Q psy15439 32 VACVECGH 39 (124)
Q Consensus 32 f~C~~C~~ 39 (124)
|.|..|+.
T Consensus 19 ~~CP~Cg~ 26 (46)
T PF12760_consen 19 FVCPHCGS 26 (46)
T ss_pred CCCCCCCC
Confidence 44444443
No 62
>PF01199 Ribosomal_L34e: Ribosomal protein L34e; InterPro: IPR008195 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 [, ]. A number of eukaryotic and archaebacterial ribosomal proteins belong to the L34e family. These include, vertebrate L34, mosquito L31 [], plant L34 [], yeast putative ribosomal protein YIL052c and archaebacterial L34e.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_i 3IZS_i 4A19_L 4A1D_L 4A18_L 4A1B_L.
Probab=25.28 E-value=33 Score=21.95 Aligned_cols=12 Identities=25% Similarity=0.739 Sum_probs=7.3
Q ss_pred CCCCCCCCCCcc
Q psy15439 112 AQPCTDSSRPIP 123 (124)
Q Consensus 112 a~~c~~c~~~i~ 123 (124)
+|+|++|..||.
T Consensus 41 ~pkC~~cg~~L~ 52 (94)
T PF01199_consen 41 KPKCGDCGKPLN 52 (94)
T ss_dssp --BSTSSS-BSS
T ss_pred CCCcCccCCccc
Confidence 578999988764
No 63
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=24.69 E-value=27 Score=21.05 Aligned_cols=15 Identities=20% Similarity=0.598 Sum_probs=10.7
Q ss_pred CCCCCCCCCccccCC
Q psy15439 3 NMKECGSCGRPITDR 17 (124)
Q Consensus 3 ~~~~C~~C~~~I~~~ 17 (124)
+-..|.+|++.|...
T Consensus 6 ~Ra~Ck~C~~~I~kg 20 (82)
T PF00645_consen 6 GRAKCKGCKKKIAKG 20 (82)
T ss_dssp STEBETTTSCBE-TT
T ss_pred CCccCcccCCcCCCC
Confidence 446799999999643
No 64
>KOG0978|consensus
Probab=23.78 E-value=18 Score=31.15 Aligned_cols=45 Identities=11% Similarity=0.262 Sum_probs=30.0
Q ss_pred eecCccCCCCCCceeeeCCeecccchhhhhcC-----CCCceeeecccCe
Q psy15439 32 VACVECGHSLAHSCFTRENKLYCRSDYDSRKK-----GSQLVTVLFYSMY 76 (124)
Q Consensus 32 f~C~~C~~~L~~~~~~~~g~~yC~~~y~~~f~-----~~~c~~~i~~~~~ 76 (124)
.+|+.|+....+.....=+.+||..|-..++. |+.|..+.++.++
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence 57777775544444444467788888777665 7788877776653
No 65
>cd07443 CRD_SFRP1 Cysteine-rich domain of the secreted frizzled-related protein 1 (SFRP1), a regulator of Wnt activity. The cysteine-rich domain (CRD) is an essential part of the secreted frizzled-related protein 1 (SFRP1), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to the CRDs domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs are also known to have functions unrelated to Wnt, as enhancers of procollagen cleavage by the TLD proteinases. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs. SFRP1 is expressed in many tissues and is involved in the regulation of Wnt signaling in osteoblasts, leading to enhanced trabecular bone formation in adults; it has also been shown to control the gro
Probab=23.54 E-value=41 Score=22.53 Aligned_cols=15 Identities=53% Similarity=0.886 Sum_probs=11.1
Q ss_pred CccccCCCCCCCCCCcc
Q psy15439 107 LSSLLAQPCTDSSRPIP 123 (124)
Q Consensus 107 ~~~~~a~~c~~c~~~i~ 123 (124)
+-++|||+|.+ +||+
T Consensus 62 lCsl~~P~C~~--~~i~ 76 (124)
T cd07443 62 LCSLFAPVCLD--RPVY 76 (124)
T ss_pred hhheeccCCCC--CCCC
Confidence 46789999984 6664
No 66
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=22.70 E-value=55 Score=18.75 Aligned_cols=24 Identities=25% Similarity=0.513 Sum_probs=12.3
Q ss_pred CCCCCCccccCCccEEEcCceecC
Q psy15439 6 ECGSCGRPITDRYLLRVADISYHE 29 (124)
Q Consensus 6 ~C~~C~~~I~~~~~i~~~~~~~H~ 29 (124)
+|..|..+|.+...+...+..-|+
T Consensus 3 ~CvVCKqpi~~a~~v~T~~G~VH~ 26 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVETESGPVHP 26 (54)
T ss_pred eeeeeCCccCcceEEEcCCCccCc
Confidence 466666666554334444444443
No 67
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=22.62 E-value=22 Score=19.99 Aligned_cols=25 Identities=16% Similarity=0.483 Sum_probs=13.8
Q ss_pred ecCccCCCCC-Ccee---eeCCeecccch
Q psy15439 33 ACVECGHSLA-HSCF---TRENKLYCRSD 57 (124)
Q Consensus 33 ~C~~C~~~L~-~~~~---~~~g~~yC~~~ 57 (124)
+|+.|+..|. +.+. ..++..+|+.|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~C 52 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNC 52 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCC
Confidence 6677777776 2221 12355666665
No 68
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=22.55 E-value=30 Score=23.94 Aligned_cols=12 Identities=17% Similarity=0.315 Sum_probs=9.2
Q ss_pred CCCCCCCCCccC
Q psy15439 113 QPCTDSSRPIPV 124 (124)
Q Consensus 113 ~~c~~c~~~i~~ 124 (124)
-.|-.|+.|||+
T Consensus 112 G~Ce~CGe~I~~ 123 (151)
T PRK10778 112 GYCESCGVEIGI 123 (151)
T ss_pred ceeccCCCcccH
Confidence 468888888873
No 69
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=22.43 E-value=48 Score=20.87 Aligned_cols=11 Identities=36% Similarity=0.779 Sum_probs=6.0
Q ss_pred CCCCCCCCCcc
Q psy15439 113 QPCTDSSRPIP 123 (124)
Q Consensus 113 ~~c~~c~~~i~ 123 (124)
-||.-|.+||+
T Consensus 59 GrCr~C~~~I~ 69 (92)
T PF06750_consen 59 GRCRYCGAPIP 69 (92)
T ss_pred CCCcccCCCCC
Confidence 35555555554
No 70
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=22.03 E-value=48 Score=20.55 Aligned_cols=9 Identities=33% Similarity=0.637 Sum_probs=3.0
Q ss_pred eecccchhh
Q psy15439 51 KLYCRSDYD 59 (124)
Q Consensus 51 ~~yC~~~y~ 59 (124)
-+.|+.||.
T Consensus 36 fPvCr~CyE 44 (80)
T PF14569_consen 36 FPVCRPCYE 44 (80)
T ss_dssp ----HHHHH
T ss_pred CccchhHHH
Confidence 345666654
No 71
>PLN03166 60S ribosomal protein L34; Provisional
Probab=21.64 E-value=57 Score=20.95 Aligned_cols=12 Identities=17% Similarity=0.443 Sum_probs=9.3
Q ss_pred CCCCCCCCCCcc
Q psy15439 112 AQPCTDSSRPIP 123 (124)
Q Consensus 112 a~~c~~c~~~i~ 123 (124)
+|+|.+|..++.
T Consensus 41 ~pkC~~cg~~L~ 52 (96)
T PLN03166 41 GPKCPVTGKRIQ 52 (96)
T ss_pred CCcCCCCCCccC
Confidence 678888888763
No 72
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.60 E-value=24 Score=22.70 Aligned_cols=34 Identities=24% Similarity=0.386 Sum_probs=19.6
Q ss_pred CCCCCCccccCCccEEE-cCceecCCCeecCccCC
Q psy15439 6 ECGSCGRPITDRYLLRV-ADISYHENCVACVECGH 39 (124)
Q Consensus 6 ~C~~C~~~I~~~~~i~~-~~~~~H~~Cf~C~~C~~ 39 (124)
.|..|+++|...+..+. ...+.|-+|+.=+.-++
T Consensus 8 kC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k 42 (103)
T COG4847 8 KCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKK 42 (103)
T ss_pred eEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcC
Confidence 57777777765544443 23456767765444433
No 73
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=21.10 E-value=70 Score=26.36 Aligned_cols=35 Identities=23% Similarity=0.462 Sum_probs=24.2
Q ss_pred CCCCCccccCCccEEEcCceecCCCeecCccCCCCC
Q psy15439 7 CGSCGRPITDRYLLRVADISYHENCVACVECGHSLA 42 (124)
Q Consensus 7 C~~C~~~I~~~~~i~~~~~~~H~~Cf~C~~C~~~L~ 42 (124)
|..|...+...+ +...+..-..+||.|-.|...|.
T Consensus 29 Cp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~ 63 (483)
T PF05502_consen 29 CPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLS 63 (483)
T ss_pred CccccccCChhh-heeccceeccccccCCCCCCcce
Confidence 566665554443 24455556669999999999997
No 74
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=21.05 E-value=43 Score=16.23 Aligned_cols=10 Identities=30% Similarity=0.813 Sum_probs=3.5
Q ss_pred CCCCCCCCcc
Q psy15439 114 PCTDSSRPIP 123 (124)
Q Consensus 114 ~c~~c~~~i~ 123 (124)
+|..|++||.
T Consensus 2 ~C~~C~~~~~ 11 (30)
T PF07649_consen 2 RCDACGKPID 11 (30)
T ss_dssp --TTTS----
T ss_pred cCCcCCCcCC
Confidence 6888988874
No 75
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=20.08 E-value=41 Score=16.72 Aligned_cols=8 Identities=25% Similarity=0.671 Sum_probs=4.0
Q ss_pred CCCCCccc
Q psy15439 7 CGSCGRPI 14 (124)
Q Consensus 7 C~~C~~~I 14 (124)
|..|.+.+
T Consensus 2 C~iC~~~~ 9 (45)
T cd00162 2 CPICLEEF 9 (45)
T ss_pred CCcCchhh
Confidence 44555544
Done!