Query 034188
Match_columns 102
No_of_seqs 111 out of 1030
Neff 9.3
Searched_HMMs 46136
Date Fri Mar 29 10:45:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034188.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034188hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00412 LIM: LIM domain; Int 99.6 6E-15 1.3E-19 78.1 5.8 57 10-66 1-58 (58)
2 KOG4577 Transcription factor L 99.5 1E-15 2.2E-20 102.4 -3.1 75 6-81 32-107 (383)
3 KOG1701 Focal adhesion adaptor 99.4 3.4E-14 7.4E-19 99.2 -1.4 76 4-80 331-408 (468)
4 KOG1044 Actin-binding LIM Zn-f 99.1 1.4E-11 3E-16 89.1 1.6 81 6-87 132-213 (670)
5 KOG2272 Focal adhesion protein 99.1 4E-12 8.7E-17 84.1 -1.5 81 8-88 13-97 (332)
6 KOG2272 Focal adhesion protein 99.1 1E-11 2.2E-16 82.2 -1.4 78 5-83 193-271 (332)
7 KOG1701 Focal adhesion adaptor 99.0 1.9E-11 4.1E-16 85.7 -2.1 69 8-77 275-345 (468)
8 KOG1703 Adaptor protein Enigma 98.9 3.9E-10 8.5E-15 81.6 1.3 68 5-73 361-428 (479)
9 KOG4577 Transcription factor L 98.8 2.1E-09 4.5E-14 72.5 0.8 63 8-70 93-158 (383)
10 smart00132 LIM Zinc-binding do 98.7 1.3E-08 2.8E-13 49.1 2.5 37 9-45 1-38 (39)
11 KOG1700 Regulatory protein MLP 98.6 3.1E-08 6.7E-13 64.5 2.3 77 1-77 1-78 (200)
12 KOG1700 Regulatory protein MLP 98.4 5.6E-08 1.2E-12 63.3 0.2 70 5-74 106-175 (200)
13 KOG1703 Adaptor protein Enigma 98.2 1.5E-06 3.3E-11 63.2 3.0 76 7-82 303-379 (479)
14 KOG1702 Nebulin repeat protein 98.1 1E-07 2.2E-12 61.7 -3.3 59 8-66 5-63 (264)
15 KOG1044 Actin-binding LIM Zn-f 97.2 0.0002 4.3E-09 52.9 1.7 52 9-61 18-70 (670)
16 KOG0490 Transcription factor, 93.9 0.011 2.4E-07 38.8 -0.8 58 13-71 2-63 (235)
17 PF09943 DUF2175: Uncharacteri 84.8 0.5 1.1E-05 27.6 1.0 32 9-40 4-36 (101)
18 PF14446 Prok-RING_1: Prokaryo 83.6 0.65 1.4E-05 24.0 1.0 28 8-35 6-36 (54)
19 PF10367 Vps39_2: Vacuolar sor 81.2 1.2 2.6E-05 25.6 1.7 11 9-19 80-90 (109)
20 PF08394 Arc_trans_TRASH: Arch 80.5 1.2 2.6E-05 21.2 1.2 23 10-32 1-24 (37)
21 PF00645 zf-PARP: Poly(ADP-rib 70.5 2.9 6.2E-05 23.1 1.3 16 6-21 6-21 (82)
22 KOG3579 Predicted E3 ubiquitin 67.4 1.9 4.1E-05 30.0 0.1 46 9-59 270-315 (352)
23 COG1645 Uncharacterized Zn-fin 67.3 3.2 7E-05 25.4 1.1 22 36-62 30-51 (131)
24 PF13240 zinc_ribbon_2: zinc-r 65.8 3.2 7E-05 17.4 0.7 9 10-18 2-10 (23)
25 COG4357 Zinc finger domain con 65.2 0.38 8.2E-06 27.8 -3.0 16 30-45 58-73 (105)
26 KOG0978 E3 ubiquitin ligase in 59.2 2.9 6.3E-05 32.5 -0.2 47 35-82 644-694 (698)
27 COG2191 Formylmethanofuran deh 57.7 3.1 6.7E-05 27.4 -0.2 31 35-65 173-203 (206)
28 COG4847 Uncharacterized protei 51.7 6.9 0.00015 22.7 0.6 36 8-43 7-43 (103)
29 PF04810 zf-Sec23_Sec24: Sec23 51.3 11 0.00023 18.0 1.2 24 7-30 2-25 (40)
30 PF02069 Metallothio_Pro: Prok 49.7 13 0.00028 19.1 1.4 25 36-60 9-33 (52)
31 PRK00807 50S ribosomal protein 48.5 17 0.00036 18.5 1.7 24 8-31 2-28 (52)
32 COG0266 Nei Formamidopyrimidin 47.2 13 0.00028 25.7 1.5 9 9-17 247-255 (273)
33 PF01258 zf-dskA_traR: Prokary 46.2 4.4 9.4E-05 18.8 -0.7 11 9-19 5-15 (36)
34 PF11781 RRN7: RNA polymerase 44.1 18 0.00039 16.9 1.3 22 36-61 10-31 (36)
35 PF06677 Auto_anti-p27: Sjogre 41.3 9.8 0.00021 18.4 0.2 8 52-59 31-38 (41)
36 PF14471 DUF4428: Domain of un 39.9 31 0.00067 17.4 1.9 28 37-65 2-30 (51)
37 cd02336 ZZ_RSC8 Zinc finger, Z 39.2 29 0.00063 17.1 1.7 29 36-64 2-32 (45)
38 PRK00420 hypothetical protein; 36.0 17 0.00036 21.7 0.6 10 52-61 37-46 (112)
39 PF14255 Cys_rich_CPXG: Cystei 35.8 16 0.00035 18.6 0.5 31 9-39 2-32 (52)
40 PF10886 DUF2685: Protein of u 33.9 31 0.00068 17.8 1.3 10 9-18 3-12 (54)
41 PF00569 ZZ: Zinc finger, ZZ t 33.6 61 0.0013 15.7 2.4 10 55-64 28-37 (46)
42 PF12674 Zn_ribbon_2: Putative 33.6 19 0.0004 20.1 0.5 27 37-63 3-34 (81)
43 KOG0320 Predicted E3 ubiquitin 32.8 29 0.00063 22.5 1.4 48 31-78 128-179 (187)
44 cd02249 ZZ Zinc finger, ZZ typ 32.1 39 0.00085 16.3 1.5 9 56-64 24-32 (46)
45 smart00504 Ubox Modified RING 32.1 74 0.0016 15.9 3.5 33 35-68 2-34 (63)
46 PRK14890 putative Zn-ribbon RN 32.0 41 0.0009 17.7 1.6 18 4-21 4-21 (59)
47 PF14835 zf-RING_6: zf-RING of 31.9 32 0.0007 18.5 1.2 37 35-71 8-44 (65)
48 PF06750 DiS_P_DiS: Bacterial 31.7 20 0.00043 20.5 0.4 37 7-45 33-69 (92)
49 PF04502 DUF572: Family of unk 31.6 31 0.00066 24.3 1.4 39 7-45 40-88 (324)
50 PF13923 zf-C3HC4_2: Zinc fing 31.5 61 0.0013 14.8 2.7 31 38-68 2-32 (39)
51 PRK14810 formamidopyrimidine-D 31.3 32 0.00069 23.6 1.4 15 30-44 240-254 (272)
52 PRK14811 formamidopyrimidine-D 30.6 32 0.0007 23.5 1.4 32 29-61 230-261 (269)
53 smart00291 ZnF_ZZ Zinc-binding 30.4 44 0.00096 16.0 1.5 10 55-64 27-36 (44)
54 PF04570 DUF581: Protein of un 29.7 33 0.00072 17.9 1.0 25 36-60 18-44 (58)
55 PRK01103 formamidopyrimidine/5 29.5 36 0.00077 23.3 1.5 12 34-45 245-256 (274)
56 PF10080 DUF2318: Predicted me 29.4 46 0.001 19.5 1.7 47 27-77 28-79 (102)
57 PF07754 DUF1610: Domain of un 29.3 36 0.00077 14.5 0.9 11 10-20 1-11 (24)
58 PRK13945 formamidopyrimidine-D 28.8 34 0.00074 23.5 1.3 17 29-45 249-265 (282)
59 PF13719 zinc_ribbon_5: zinc-r 28.6 38 0.00083 15.7 1.1 11 7-17 25-35 (37)
60 TIGR00577 fpg formamidopyrimid 27.8 39 0.00084 23.1 1.4 16 30-45 241-256 (272)
61 KOG2186 Cell growth-regulating 27.6 13 0.00028 25.5 -0.9 40 9-49 5-44 (276)
62 PF05502 Dynactin_p62: Dynacti 27.0 34 0.00074 25.6 1.1 39 8-47 27-65 (483)
63 TIGR02420 dksA RNA polymerase- 25.6 14 0.00031 21.6 -0.9 17 6-23 79-95 (110)
64 PRK10445 endonuclease VIII; Pr 25.4 46 0.00099 22.7 1.4 11 35-45 236-246 (263)
65 cd00162 RING RING-finger (Real 25.1 37 0.0008 15.3 0.7 8 55-62 20-27 (45)
66 PRK00398 rpoP DNA-directed RNA 24.8 47 0.001 16.0 1.0 27 9-44 5-31 (46)
67 PF11077 DUF2616: Protein of u 24.0 27 0.00057 22.5 0.1 31 36-66 138-171 (173)
68 COG1656 Uncharacterized conser 23.4 35 0.00075 21.8 0.5 36 7-42 97-138 (165)
69 cd02341 ZZ_ZZZ3 Zinc finger, Z 23.1 69 0.0015 15.9 1.5 10 55-64 26-35 (48)
70 COG1998 RPS31 Ribosomal protei 22.3 41 0.0009 17.1 0.5 6 10-15 22-27 (51)
71 PF06943 zf-LSD1: LSD1 zinc fi 22.3 46 0.00099 14.3 0.6 6 9-14 18-23 (25)
72 PF01927 Mut7-C: Mut7-C RNAse 21.6 59 0.0013 20.0 1.3 13 8-20 92-104 (147)
73 PF08746 zf-RING-like: RING-li 21.1 25 0.00054 17.0 -0.4 10 10-19 1-10 (43)
74 TIGR03831 YgiT_finger YgiT-typ 20.6 61 0.0013 15.1 1.0 11 9-19 34-44 (46)
75 PF13248 zf-ribbon_3: zinc-rib 20.4 50 0.0011 13.9 0.6 10 9-18 4-13 (26)
No 1
>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=99.58 E-value=6e-15 Score=78.09 Aligned_cols=57 Identities=35% Similarity=0.815 Sum_probs=52.2
Q ss_pred cccccceeecCceE-EecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHh
Q 034188 10 CKVCEKTVYPVEQL-SADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66 (102)
Q Consensus 10 C~~C~~~i~~~~~~-~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~ 66 (102)
|.+|++.|.+.+.+ .+.++.||.+||+|..|+.+|....++..++++||..||.++|
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 78999999877764 7999999999999999999999888889999999999999876
No 2
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.48 E-value=1e-15 Score=102.42 Aligned_cols=75 Identities=25% Similarity=0.460 Sum_probs=67.6
Q ss_pred CccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCCCC
Q 034188 6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSPAK 81 (102)
Q Consensus 6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~~~ 81 (102)
..++|++|+++|.+..++.+.++.||..|++|+.|..+|.. .++.+++.+||+.+|.++|+++|+ |+.+|.+.+|
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqV 107 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQV 107 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHH
Confidence 45789999999988777899999999999999999999974 578899999999999999999998 8888887765
No 3
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.37 E-value=3.4e-14 Score=99.20 Aligned_cols=76 Identities=25% Similarity=0.530 Sum_probs=65.1
Q ss_pred cCCccccccccceeecCceEEecCccccccCcccccccccCcCcceEe-eCCeeeeHHHHHHHhCCCCC-CCCCCCCCC
Q 034188 4 IGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSS-MEGVLYCKPHFEQLFKESGN-FNKNFQSPA 80 (102)
Q Consensus 4 ~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~-~~~~~~C~~~~~~~~~~~c~-~~~~~~~~~ 80 (102)
..+..+|..|++.|++. ++.+.++.||+.||+|.+|.+.|.+..|.. .++.+||..||+++|+++|+ |.+.|.+.+
T Consensus 331 q~tlekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~ 408 (468)
T KOG1701|consen 331 QDTLEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRD 408 (468)
T ss_pred HHHHHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCC
Confidence 34556899999999653 479999999999999999999999888776 59999999999999999999 666666655
No 4
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.14 E-value=1.4e-11 Score=89.06 Aligned_cols=81 Identities=26% Similarity=0.490 Sum_probs=69.0
Q ss_pred CccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCCCCCCC
Q 034188 6 TQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSPAKSAE 84 (102)
Q Consensus 6 ~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~~~~~~ 84 (102)
+...|++|++.|..+..+.+.++.||..||+|..|..-|. ++|...++.+||+.+|...|+-+|. |.+-|....+.+.
T Consensus 132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag 210 (670)
T KOG1044|consen 132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAG 210 (670)
T ss_pred CCccccchhhhhhccceeeeeccceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhcc
Confidence 5668999999998888889999999999999999999886 6789999999999999999999988 5555666666665
Q ss_pred CCC
Q 034188 85 KLT 87 (102)
Q Consensus 85 ~~~ 87 (102)
+.+
T Consensus 211 ~kh 213 (670)
T KOG1044|consen 211 DKH 213 (670)
T ss_pred Ccc
Confidence 543
No 5
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.13 E-value=4e-12 Score=84.06 Aligned_cols=81 Identities=23% Similarity=0.538 Sum_probs=70.0
Q ss_pred cccccccceeecCce-EEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCCCCCCCCCCCC---C
Q 034188 8 QKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNKNFQSPAKS---A 83 (102)
Q Consensus 8 ~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~~~~~~~~~~~---~ 83 (102)
..|.+|..++.+.+. +...+.+||..||.|..|-.++.++.|+..+|+.||+.+|..+|+|.|.-+..|..++|. +
T Consensus 13 ~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVikamn 92 (332)
T KOG2272|consen 13 MVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIKAMN 92 (332)
T ss_pred HHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHHhhc
Confidence 479999999988886 688899999999999999999999999999999999999999999999966677766665 4
Q ss_pred CCCCh
Q 034188 84 EKLTP 88 (102)
Q Consensus 84 ~~~~~ 88 (102)
..|+|
T Consensus 93 nSwHp 97 (332)
T KOG2272|consen 93 NSWHP 97 (332)
T ss_pred cccCc
Confidence 44443
No 6
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.07 E-value=1e-11 Score=82.20 Aligned_cols=78 Identities=23% Similarity=0.413 Sum_probs=67.3
Q ss_pred CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCCCCCC
Q 034188 5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSPAKSA 83 (102)
Q Consensus 5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~~~~~ 83 (102)
.+.+.|..|...|. ...+.++++.||.+.|+|.+|.+|+-+...+++.|..||+.+|.++|+.-|. |+..+.++++++
T Consensus 193 mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~a 271 (332)
T KOG2272|consen 193 MGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVSA 271 (332)
T ss_pred cCCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccHHHH
Confidence 46689999999994 3347899999999999999999998877889999999999999999999998 666777777663
No 7
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.01 E-value=1.9e-11 Score=85.69 Aligned_cols=69 Identities=23% Similarity=0.557 Sum_probs=58.6
Q ss_pred cccccccceeecCce-EEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCC
Q 034188 8 QKCKVCEKTVYPVEQ-LSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQ 77 (102)
Q Consensus 8 ~~C~~C~~~i~~~~~-~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~ 77 (102)
.+|.+|++.|..... .+++++.||..||.|..|.+.|....|+..++++||+.||+..+. +|. |.+.|+
T Consensus 275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tle-kC~~Cg~~I~ 345 (468)
T KOG1701|consen 275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLE-KCNKCGEPIM 345 (468)
T ss_pred hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHH-HHhhhhhHHH
Confidence 389999999977665 799999999999999999999998899999999999999987653 444 554443
No 8
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.90 E-value=3.9e-10 Score=81.63 Aligned_cols=68 Identities=29% Similarity=0.679 Sum_probs=59.6
Q ss_pred CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCCC
Q 034188 5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFN 73 (102)
Q Consensus 5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~~ 73 (102)
...+.|.+|++.|. .+.+.+.+..||++||.|..|.+++....|+..++.+||+.||..++.++|..+
T Consensus 361 ~~~p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~ 428 (479)
T KOG1703|consen 361 PFRPNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYC 428 (479)
T ss_pred hhCccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhc
Confidence 34678999999995 445677799999999999999999998899999999999999999998887644
No 9
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.76 E-value=2.1e-09 Score=72.50 Aligned_cols=63 Identities=29% Similarity=0.653 Sum_probs=52.6
Q ss_pred cccccccceeecCceE-EecCccccccCcccccccccCcCcc-eE-eeCCeeeeHHHHHHHhCCCC
Q 034188 8 QKCKVCEKTVYPVEQL-SADGIVYHKSCFKCSHCKGTLKLSN-YS-SMEGVLYCKPHFEQLFKESG 70 (102)
Q Consensus 8 ~~C~~C~~~i~~~~~~-~~~~~~~h~~Cf~C~~C~~~l~~~~-~~-~~~~~~~C~~~~~~~~~~~c 70 (102)
.+|..|.++|.+..++ .+.+.+||+.||.|..|.+.|..+. |+ ..++++.|+.+|+......|
T Consensus 93 TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 93 TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 3899999999776654 7889999999999999999999875 44 46999999999987644444
No 10
>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=1.3e-08 Score=49.11 Aligned_cols=37 Identities=43% Similarity=0.767 Sum_probs=32.2
Q ss_pred ccccccceeecC-ceEEecCccccccCcccccccccCc
Q 034188 9 KCKVCEKTVYPV-EQLSADGIVYHKSCFKCSHCKGTLK 45 (102)
Q Consensus 9 ~C~~C~~~i~~~-~~~~~~~~~~h~~Cf~C~~C~~~l~ 45 (102)
+|..|++.|.+. ..+...+..||..||.|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 588999999776 4578899999999999999998874
No 11
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.58 E-value=3.1e-08 Score=64.49 Aligned_cols=77 Identities=53% Similarity=0.966 Sum_probs=65.2
Q ss_pred CCccCCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCC
Q 034188 1 MSFIGTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQ 77 (102)
Q Consensus 1 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~ 77 (102)
|++.+....|..|++.++..+++...+..||..||.|..|...|....+...++.+||..+|...++++.. ...+++
T Consensus 1 ~~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~ 78 (200)
T KOG1700|consen 1 SSFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQ 78 (200)
T ss_pred CCcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccccc
Confidence 45556667999999999988888899999999999999999999988899999999999977788887654 555444
No 12
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.41 E-value=5.6e-08 Score=63.29 Aligned_cols=70 Identities=54% Similarity=1.205 Sum_probs=61.1
Q ss_pred CCccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCCCCC
Q 034188 5 GTQQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGNFNK 74 (102)
Q Consensus 5 ~~~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~~~~ 74 (102)
+....|.+|.+.+++.+.+...+..||..||+|..|...|....+....+.++|..++..+|-.+.....
T Consensus 106 g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~~~ 175 (200)
T KOG1700|consen 106 GEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNYNE 175 (200)
T ss_pred ccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCCcccc
Confidence 4567899999999999989999999999999999999999998899999999998888887666555543
No 13
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.16 E-value=1.5e-06 Score=63.20 Aligned_cols=76 Identities=17% Similarity=0.369 Sum_probs=65.4
Q ss_pred ccccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC-CCCCCCCCCCC
Q 034188 7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN-FNKNFQSPAKS 82 (102)
Q Consensus 7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~-~~~~~~~~~~~ 82 (102)
.+.|..|+..|.....+..+++.||..+|.|..|...+..+.+...+|.+||..+|...+++.|. |...+.+..+.
T Consensus 303 ~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~ 379 (479)
T KOG1703|consen 303 RPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVC 379 (479)
T ss_pred cccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhh
Confidence 47899999999654668999999999999999999999888888889999999999999999998 55566665555
No 14
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=98.12 E-value=1e-07 Score=61.74 Aligned_cols=59 Identities=41% Similarity=0.836 Sum_probs=52.6
Q ss_pred cccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeHHHHHHHh
Q 034188 8 QKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 66 (102)
Q Consensus 8 ~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~ 66 (102)
..|..|++.+++.+.+...++.||..||.|..|+..|....+-+.+.++||..+|....
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence 46888999999999999999999999999999999998888888899999999986543
No 15
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=97.17 E-value=0.0002 Score=52.87 Aligned_cols=52 Identities=29% Similarity=0.622 Sum_probs=44.9
Q ss_pred ccccccceeecCceEEecCccccccCcccccccccCcCcceEee-CCeeeeHHH
Q 034188 9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSM-EGVLYCKPH 61 (102)
Q Consensus 9 ~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~-~~~~~C~~~ 61 (102)
.|..|.+.- .++++.+.++.||..||.|..|+..|..+.|+.. +.++|+...
T Consensus 18 ~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~ 70 (670)
T KOG1044|consen 18 KCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDD 70 (670)
T ss_pred ehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccceeecccc
Confidence 799999998 5788999999999999999999999998888775 667777643
No 16
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=93.87 E-value=0.011 Score=38.77 Aligned_cols=58 Identities=26% Similarity=0.639 Sum_probs=44.0
Q ss_pred ccceeecCceEEecCccccccCcccccccccCc--CcceEeeCCeeeeHHHHHH--HhCCCCC
Q 034188 13 CEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLK--LSNYSSMEGVLYCKPHFEQ--LFKESGN 71 (102)
Q Consensus 13 C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~~~~~--~~~~~c~ 71 (102)
|+..|.+...+...+..||..|..|..|...+. ...+.. ++..||..+|.+ .+..+|.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~ 63 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCA 63 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcccccc
Confidence 566665555566678999999999999999987 334555 999999999987 5544444
No 17
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=84.84 E-value=0.5 Score=27.62 Aligned_cols=32 Identities=25% Similarity=0.540 Sum_probs=23.4
Q ss_pred ccccccceeecCceEEe-cCccccccCcccccc
Q 034188 9 KCKVCEKTVYPVEQLSA-DGIVYHKSCFKCSHC 40 (102)
Q Consensus 9 ~C~~C~~~i~~~~~~~~-~~~~~h~~Cf~C~~C 40 (102)
+|..|++.|..++++.+ ...+-|..||.-..-
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~ 36 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKAS 36 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHHh
Confidence 68999999988887654 335678888875443
No 18
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=83.61 E-value=0.65 Score=24.05 Aligned_cols=28 Identities=32% Similarity=0.702 Sum_probs=20.0
Q ss_pred cccccccceeecCc-eE--EecCccccccCc
Q 034188 8 QKCKVCEKTVYPVE-QL--SADGIVYHKSCF 35 (102)
Q Consensus 8 ~~C~~C~~~i~~~~-~~--~~~~~~~h~~Cf 35 (102)
.+|..|++.|.+.+ .+ ..=+.+||.+|+
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 48999999996444 33 334667888887
No 19
>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=81.15 E-value=1.2 Score=25.55 Aligned_cols=11 Identities=45% Similarity=0.881 Sum_probs=5.8
Q ss_pred ccccccceeec
Q 034188 9 KCKVCEKTVYP 19 (102)
Q Consensus 9 ~C~~C~~~i~~ 19 (102)
.|..|++.+..
T Consensus 80 ~C~vC~k~l~~ 90 (109)
T PF10367_consen 80 KCSVCGKPLGN 90 (109)
T ss_pred CccCcCCcCCC
Confidence 45555555543
No 20
>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=80.46 E-value=1.2 Score=21.22 Aligned_cols=23 Identities=17% Similarity=0.304 Sum_probs=14.5
Q ss_pred cccccceeecCce-EEecCccccc
Q 034188 10 CKVCEKTVYPVEQ-LSADGIVYHK 32 (102)
Q Consensus 10 C~~C~~~i~~~~~-~~~~~~~~h~ 32 (102)
|.-|+..|..... +...++.|+.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~f 24 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYF 24 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEE
Confidence 5667777753333 5677777763
No 21
>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=70.48 E-value=2.9 Score=23.06 Aligned_cols=16 Identities=38% Similarity=0.655 Sum_probs=12.0
Q ss_pred CccccccccceeecCc
Q 034188 6 TQQKCKVCEKTVYPVE 21 (102)
Q Consensus 6 ~~~~C~~C~~~i~~~~ 21 (102)
+...|..|++.|..++
T Consensus 6 ~Ra~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 6 GRAKCKGCKKKIAKGE 21 (82)
T ss_dssp STEBETTTSCBE-TTS
T ss_pred CCccCcccCCcCCCCC
Confidence 3458999999997666
No 22
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.43 E-value=1.9 Score=29.97 Aligned_cols=46 Identities=24% Similarity=0.577 Sum_probs=32.2
Q ss_pred ccccccceeecCceEEecCccccccCcccccccccCcCcceEeeCCeeeeH
Q 034188 9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCK 59 (102)
Q Consensus 9 ~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~ 59 (102)
.|.-|++.+.+..++..-...-|.-||-|+.=. +.-....+.+||.
T Consensus 270 cCTLC~ERLEDTHFVQCPSVp~HKFCFPCSRes-----IK~Qg~sgevYCP 315 (352)
T KOG3579|consen 270 CCTLCHERLEDTHFVQCPSVPSHKFCFPCSRES-----IKQQGASGEVYCP 315 (352)
T ss_pred eehhhhhhhccCceeecCCCcccceecccCHHH-----HHhhcCCCceeCC
Confidence 688899998777678888888898888886521 2223335577873
No 23
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=67.32 E-value=3.2 Score=25.43 Aligned_cols=22 Identities=23% Similarity=0.591 Sum_probs=14.9
Q ss_pred ccccccccCcCcceEeeCCeeeeHHHH
Q 034188 36 KCSHCKGTLKLSNYSSMEGVLYCKPHF 62 (102)
Q Consensus 36 ~C~~C~~~l~~~~~~~~~~~~~C~~~~ 62 (102)
.|..|+.+| |..+|.+||+.|-
T Consensus 30 hCp~Cg~PL-----F~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL-----FRKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc-----eeeCCeEECCCCC
Confidence 366776665 3378888887764
No 24
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=65.78 E-value=3.2 Score=17.41 Aligned_cols=9 Identities=22% Similarity=0.715 Sum_probs=5.4
Q ss_pred cccccceee
Q 034188 10 CKVCEKTVY 18 (102)
Q Consensus 10 C~~C~~~i~ 18 (102)
|..|+..|.
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 556666663
No 25
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=65.22 E-value=0.38 Score=27.85 Aligned_cols=16 Identities=19% Similarity=0.646 Sum_probs=7.5
Q ss_pred ccccCcccccccccCc
Q 034188 30 YHKSCFKCSHCKGTLK 45 (102)
Q Consensus 30 ~h~~Cf~C~~C~~~l~ 45 (102)
++..+..|.+|...|.
T Consensus 58 ~~~~~iiCGvC~~~LT 73 (105)
T COG4357 58 FNPKAIICGVCRKLLT 73 (105)
T ss_pred cCCccEEhhhhhhhhh
Confidence 3444444555544444
No 26
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=59.15 E-value=2.9 Score=32.46 Aligned_cols=47 Identities=19% Similarity=0.370 Sum_probs=31.1
Q ss_pred cccccccccCcCcceEeeCCeeeeHHHHHHHhCC---CCC-CCCCCCCCCCC
Q 034188 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE---SGN-FNKNFQSPAKS 82 (102)
Q Consensus 35 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~---~c~-~~~~~~~~~~~ 82 (102)
.+|..|+..+.. .....-+.+||..|-..++.+ +|. |+..|++..+.
T Consensus 644 LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~ 694 (698)
T KOG0978|consen 644 LKCSVCNTRWKD-AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVH 694 (698)
T ss_pred eeCCCccCchhh-HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccc
Confidence 467777755532 122346677898888877753 676 77788887764
No 27
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=57.75 E-value=3.1 Score=27.41 Aligned_cols=31 Identities=26% Similarity=0.502 Sum_probs=23.0
Q ss_pred cccccccccCcCcceEeeCCeeeeHHHHHHH
Q 034188 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 65 (102)
Q Consensus 35 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~ 65 (102)
-+|..|+.......-...+|++.|..|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 4788888777654455579999999998643
No 28
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=51.73 E-value=6.9 Score=22.67 Aligned_cols=36 Identities=25% Similarity=0.350 Sum_probs=24.2
Q ss_pred cccccccceeecCceEEec-CccccccCccccccccc
Q 034188 8 QKCKVCEKTVYPVEQLSAD-GIVYHKSCFKCSHCKGT 43 (102)
Q Consensus 8 ~~C~~C~~~i~~~~~~~~~-~~~~h~~Cf~C~~C~~~ 43 (102)
-+|..|+..|..++++.+- ..+-|-+|+.-+.-+++
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKP 43 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCc
Confidence 3799999998888865443 33568788775554443
No 29
>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=51.26 E-value=11 Score=17.99 Aligned_cols=24 Identities=21% Similarity=0.577 Sum_probs=11.9
Q ss_pred ccccccccceeecCceEEecCccc
Q 034188 7 QQKCKVCEKTVYPVEQLSADGIVY 30 (102)
Q Consensus 7 ~~~C~~C~~~i~~~~~~~~~~~~~ 30 (102)
+.+|..|+..|-+--.+...++.|
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w 25 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTW 25 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEE
T ss_pred ccccCCCCCEECCcceEcCCCCEE
Confidence 458899988885544455555555
No 30
>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=49.67 E-value=13 Score=19.07 Aligned_cols=25 Identities=20% Similarity=0.566 Sum_probs=13.2
Q ss_pred ccccccccCcCcceEeeCCeeeeHH
Q 034188 36 KCSHCKGTLKLSNYSSMEGVLYCKP 60 (102)
Q Consensus 36 ~C~~C~~~l~~~~~~~~~~~~~C~~ 60 (102)
.|..|...++...-..++|+.||..
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~ 33 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSE 33 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSH
T ss_pred cCCCCEeEECchHhHHhCCEeeecH
Confidence 3566776666556677899999843
No 31
>PRK00807 50S ribosomal protein L24e; Validated
Probab=48.55 E-value=17 Score=18.52 Aligned_cols=24 Identities=25% Similarity=0.609 Sum_probs=15.4
Q ss_pred cccccccceeecCce---EEecCcccc
Q 034188 8 QKCKVCEKTVYPVEQ---LSADGIVYH 31 (102)
Q Consensus 8 ~~C~~C~~~i~~~~~---~~~~~~~~h 31 (102)
..|..|+..|.++.. +...+++|.
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~ 28 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY 28 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE
Confidence 368888888875552 345566654
No 32
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=47.25 E-value=13 Score=25.74 Aligned_cols=9 Identities=22% Similarity=0.947 Sum_probs=4.8
Q ss_pred cccccccee
Q 034188 9 KCKVCEKTV 17 (102)
Q Consensus 9 ~C~~C~~~i 17 (102)
.|.+|+..|
T Consensus 247 pC~~CGt~I 255 (273)
T COG0266 247 PCRRCGTPI 255 (273)
T ss_pred CCCccCCEe
Confidence 455555555
No 33
>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=46.18 E-value=4.4 Score=18.78 Aligned_cols=11 Identities=18% Similarity=0.582 Sum_probs=6.6
Q ss_pred ccccccceeec
Q 034188 9 KCKVCEKTVYP 19 (102)
Q Consensus 9 ~C~~C~~~i~~ 19 (102)
.|..|++.|..
T Consensus 5 ~C~~CGe~I~~ 15 (36)
T PF01258_consen 5 ICEDCGEPIPE 15 (36)
T ss_dssp B-TTTSSBEEH
T ss_pred CccccCChHHH
Confidence 47777777743
No 34
>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=44.11 E-value=18 Score=16.89 Aligned_cols=22 Identities=27% Similarity=0.693 Sum_probs=12.8
Q ss_pred ccccccccCcCcceEeeCCeeeeHHH
Q 034188 36 KCSHCKGTLKLSNYSSMEGVLYCKPH 61 (102)
Q Consensus 36 ~C~~C~~~l~~~~~~~~~~~~~C~~~ 61 (102)
.|..|+. ..+...+|..||..+
T Consensus 10 ~C~~C~~----~~~~~~dG~~yC~~c 31 (36)
T PF11781_consen 10 PCPVCGS----RWFYSDDGFYYCDRC 31 (36)
T ss_pred cCCCCCC----eEeEccCCEEEhhhC
Confidence 3666643 234556888888544
No 35
>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=41.30 E-value=9.8 Score=18.44 Aligned_cols=8 Identities=38% Similarity=1.107 Sum_probs=4.0
Q ss_pred eCCeeeeH
Q 034188 52 MEGVLYCK 59 (102)
Q Consensus 52 ~~~~~~C~ 59 (102)
++++.||.
T Consensus 31 k~g~~~Cv 38 (41)
T PF06677_consen 31 KDGKIYCV 38 (41)
T ss_pred cCCCEECC
Confidence 45555553
No 36
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=39.94 E-value=31 Score=17.42 Aligned_cols=28 Identities=25% Similarity=0.661 Sum_probs=15.2
Q ss_pred cccccccCcCcc-eEeeCCeeeeHHHHHHH
Q 034188 37 CSHCKGTLKLSN-YSSMEGVLYCKPHFEQL 65 (102)
Q Consensus 37 C~~C~~~l~~~~-~~~~~~~~~C~~~~~~~ 65 (102)
|..|+..++.-. +-..|| ..|..|+.+.
T Consensus 2 C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 2 CAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCccccccccccceeccCc-cchHHHHHHh
Confidence 556666554322 223455 4677777654
No 37
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=39.19 E-value=29 Score=17.10 Aligned_cols=29 Identities=14% Similarity=0.424 Sum_probs=15.6
Q ss_pred ccccccccCcCcceEe--eCCeeeeHHHHHH
Q 034188 36 KCSHCKGTLKLSNYSS--MEGVLYCKPHFEQ 64 (102)
Q Consensus 36 ~C~~C~~~l~~~~~~~--~~~~~~C~~~~~~ 64 (102)
.|..|+..+....|.- .....+|..||.+
T Consensus 2 ~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 2 HCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred cccCCCCccCceEEEecCCCccccChHHHhC
Confidence 3556666554333322 1345678888853
No 38
>PRK00420 hypothetical protein; Validated
Probab=35.98 E-value=17 Score=21.73 Aligned_cols=10 Identities=30% Similarity=0.727 Sum_probs=4.6
Q ss_pred eCCeeeeHHH
Q 034188 52 MEGVLYCKPH 61 (102)
Q Consensus 52 ~~~~~~C~~~ 61 (102)
.+|..||..|
T Consensus 37 k~g~~~Cp~C 46 (112)
T PRK00420 37 KDGEVVCPVH 46 (112)
T ss_pred CCCceECCCC
Confidence 3445555433
No 39
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=35.83 E-value=16 Score=18.65 Aligned_cols=31 Identities=23% Similarity=0.501 Sum_probs=18.5
Q ss_pred ccccccceeecCceEEecCccccccCccccc
Q 034188 9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSH 39 (102)
Q Consensus 9 ~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~ 39 (102)
.|.-|++.+...--....++.|-..|..|..
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~ 32 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCR 32 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCC
Confidence 5888999884211133446677777765543
No 40
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=33.87 E-value=31 Score=17.80 Aligned_cols=10 Identities=30% Similarity=0.856 Sum_probs=4.9
Q ss_pred ccccccceee
Q 034188 9 KCKVCEKTVY 18 (102)
Q Consensus 9 ~C~~C~~~i~ 18 (102)
+|..|+.+|.
T Consensus 3 ~CvVCKqpi~ 12 (54)
T PF10886_consen 3 ICVVCKQPID 12 (54)
T ss_pred eeeeeCCccC
Confidence 3455555553
No 41
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=33.63 E-value=61 Score=15.73 Aligned_cols=10 Identities=20% Similarity=0.477 Sum_probs=6.7
Q ss_pred eeeeHHHHHH
Q 034188 55 VLYCKPHFEQ 64 (102)
Q Consensus 55 ~~~C~~~~~~ 64 (102)
.-+|..||..
T Consensus 28 ~dLC~~C~~~ 37 (46)
T PF00569_consen 28 YDLCEDCFSK 37 (46)
T ss_dssp -EEEHHHHHH
T ss_pred CchhhHHHhC
Confidence 4468888865
No 42
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=33.55 E-value=19 Score=20.13 Aligned_cols=27 Identities=19% Similarity=0.406 Sum_probs=13.5
Q ss_pred cccccccCcCcceEe-----eCCeeeeHHHHH
Q 034188 37 CSHCKGTLKLSNYSS-----MEGVLYCKPHFE 63 (102)
Q Consensus 37 C~~C~~~l~~~~~~~-----~~~~~~C~~~~~ 63 (102)
|..|+.||.....++ ..+.-||..||.
T Consensus 3 CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~ 34 (81)
T PF12674_consen 3 CQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQ 34 (81)
T ss_pred CCcCcCccCCccccccccCCCCchhHHHHHhc
Confidence 566666665443221 133346666663
No 43
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.81 E-value=29 Score=22.55 Aligned_cols=48 Identities=15% Similarity=0.376 Sum_probs=32.7
Q ss_pred cccCcccccccccCcCcc-eEeeCCeeeeHHHHHHHh--CCCCC-CCCCCCC
Q 034188 31 HKSCFKCSHCKGTLKLSN-YSSMEGVLYCKPHFEQLF--KESGN-FNKNFQS 78 (102)
Q Consensus 31 h~~Cf~C~~C~~~l~~~~-~~~~~~~~~C~~~~~~~~--~~~c~-~~~~~~~ 78 (102)
...+|.|-.|........ +...-|.+||..|-.... +.+|- |-+.+..
T Consensus 128 ~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred cccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 456788888887776554 446789999999987654 34666 4444443
No 44
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=32.13 E-value=39 Score=16.35 Aligned_cols=9 Identities=11% Similarity=0.493 Sum_probs=5.1
Q ss_pred eeeHHHHHH
Q 034188 56 LYCKPHFEQ 64 (102)
Q Consensus 56 ~~C~~~~~~ 64 (102)
-+|..||..
T Consensus 24 dLC~~Cf~~ 32 (46)
T cd02249 24 DLCSSCYAK 32 (46)
T ss_pred cCHHHHHCc
Confidence 356666653
No 45
>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=32.07 E-value=74 Score=15.93 Aligned_cols=33 Identities=18% Similarity=0.212 Sum_probs=21.2
Q ss_pred cccccccccCcCcceEeeCCeeeeHHHHHHHhCC
Q 034188 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE 68 (102)
Q Consensus 35 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~ 68 (102)
|.|..|...+.. ......|..||..+..+.+..
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~ 34 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLS 34 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHH
Confidence 356667666653 344457788998888766543
No 46
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=32.03 E-value=41 Score=17.70 Aligned_cols=18 Identities=28% Similarity=0.573 Sum_probs=13.2
Q ss_pred cCCccccccccceeecCc
Q 034188 4 IGTQQKCKVCEKTVYPVE 21 (102)
Q Consensus 4 ~~~~~~C~~C~~~i~~~~ 21 (102)
....+.|..|+..|.+.+
T Consensus 4 ~~~~~~CtSCg~~i~~~~ 21 (59)
T PRK14890 4 MMEPPKCTSCGIEIAPRE 21 (59)
T ss_pred cccCccccCCCCcccCCC
Confidence 344568999999987655
No 47
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=31.93 E-value=32 Score=18.47 Aligned_cols=37 Identities=16% Similarity=0.288 Sum_probs=14.0
Q ss_pred cccccccccCcCcceEeeCCeeeeHHHHHHHhCCCCC
Q 034188 35 FKCSHCKGTLKLSNYSSMEGVLYCKPHFEQLFKESGN 71 (102)
Q Consensus 35 f~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~c~ 71 (102)
.+|+.|..-|..-.....=...||..|-...++..|.
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CP 44 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECP 44 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-S
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCC
Confidence 4566665555432223445566676666666665554
No 48
>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=31.65 E-value=20 Score=20.47 Aligned_cols=37 Identities=14% Similarity=0.309 Sum_probs=18.2
Q ss_pred ccccccccceeecCceEEecCccccccCcccccccccCc
Q 034188 7 QQKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLK 45 (102)
Q Consensus 7 ~~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~ 45 (102)
...|..|++.+...+.+-..+ |-..--+|..|+.+++
T Consensus 33 rS~C~~C~~~L~~~~lIPi~S--~l~lrGrCr~C~~~I~ 69 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIPILS--YLLLRGRCRYCGAPIP 69 (92)
T ss_pred CCcCcCCCCcCcccccchHHH--HHHhCCCCcccCCCCC
Confidence 456777777765444322221 2222335566665554
No 49
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=31.60 E-value=31 Score=24.33 Aligned_cols=39 Identities=21% Similarity=0.527 Sum_probs=24.8
Q ss_pred ccccccccceeecCceEEecCc-----ccc-----ccCcccccccccCc
Q 034188 7 QQKCKVCEKTVYPVEQLSADGI-----VYH-----KSCFKCSHCKGTLK 45 (102)
Q Consensus 7 ~~~C~~C~~~i~~~~~~~~~~~-----~~h-----~~Cf~C~~C~~~l~ 45 (102)
...|..|+..|+-+.++.+.-+ .|+ .--++|..|...+.
T Consensus 40 ~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~ 88 (324)
T PF04502_consen 40 NIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIE 88 (324)
T ss_pred cCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEe
Confidence 5689999999987766544322 132 22446777876654
No 50
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=31.50 E-value=61 Score=14.81 Aligned_cols=31 Identities=19% Similarity=0.361 Sum_probs=16.8
Q ss_pred ccccccCcCcceEeeCCeeeeHHHHHHHhCC
Q 034188 38 SHCKGTLKLSNYSSMEGVLYCKPHFEQLFKE 68 (102)
Q Consensus 38 ~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~ 68 (102)
..|...+........=|..||..+..+.+..
T Consensus 2 ~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 2 PICLDELRDPVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp TTTTSB-SSEEEECTTSEEEEHHHHHHHHHC
T ss_pred CCCCCcccCcCEECCCCCchhHHHHHHHHHC
Confidence 3444444331133457788888887665443
No 51
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=31.27 E-value=32 Score=23.58 Aligned_cols=15 Identities=27% Similarity=0.751 Sum_probs=6.8
Q ss_pred ccccCcccccccccC
Q 034188 30 YHKSCFKCSHCKGTL 44 (102)
Q Consensus 30 ~h~~Cf~C~~C~~~l 44 (102)
|...--.|-.|+..+
T Consensus 240 y~R~g~pCprCG~~I 254 (272)
T PRK14810 240 YQRTGEPCLNCKTPI 254 (272)
T ss_pred cCCCCCcCCCCCCee
Confidence 333334455555554
No 52
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=30.58 E-value=32 Score=23.53 Aligned_cols=32 Identities=19% Similarity=0.446 Sum_probs=13.8
Q ss_pred cccccCcccccccccCcCcceEeeCCeeeeHHH
Q 034188 29 VYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPH 61 (102)
Q Consensus 29 ~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~ 61 (102)
+|...--.|..|+..+..... ..-+-.||+.|
T Consensus 230 Vy~R~g~pC~~Cg~~I~~~~~-~gR~ty~Cp~C 261 (269)
T PRK14811 230 VYGREGQPCPRCGTPIEKIVV-GGRGTHFCPQC 261 (269)
T ss_pred ecCCCcCCCCcCCCeeEEEEE-CCCCcEECCCC
Confidence 343333445556655543211 12333456544
No 53
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=30.36 E-value=44 Score=16.03 Aligned_cols=10 Identities=20% Similarity=0.517 Sum_probs=5.8
Q ss_pred eeeeHHHHHH
Q 034188 55 VLYCKPHFEQ 64 (102)
Q Consensus 55 ~~~C~~~~~~ 64 (102)
.-+|..||..
T Consensus 27 ~dlC~~Cf~~ 36 (44)
T smart00291 27 YDLCQSCFAK 36 (44)
T ss_pred ccchHHHHhC
Confidence 3357777653
No 54
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=29.75 E-value=33 Score=17.94 Aligned_cols=25 Identities=24% Similarity=0.511 Sum_probs=16.6
Q ss_pred ccccccccCcCc-c-eEeeCCeeeeHH
Q 034188 36 KCSHCKGTLKLS-N-YSSMEGVLYCKP 60 (102)
Q Consensus 36 ~C~~C~~~l~~~-~-~~~~~~~~~C~~ 60 (102)
.|..|++.|..+ . |--++...||..
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ 44 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSE 44 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccH
Confidence 467788888843 3 444677788844
No 55
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=29.52 E-value=36 Score=23.30 Aligned_cols=12 Identities=17% Similarity=0.523 Sum_probs=6.2
Q ss_pred CcccccccccCc
Q 034188 34 CFKCSHCKGTLK 45 (102)
Q Consensus 34 Cf~C~~C~~~l~ 45 (102)
--.|..|+..+.
T Consensus 245 g~pC~~Cg~~I~ 256 (274)
T PRK01103 245 GEPCRRCGTPIE 256 (274)
T ss_pred CCCCCCCCCeeE
Confidence 334555665554
No 56
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=29.38 E-value=46 Score=19.47 Aligned_cols=47 Identities=21% Similarity=0.212 Sum_probs=29.5
Q ss_pred CccccccCcccccccccCcCcceEeeCCeeeeHHHHHH----HhC-CCCCCCCCCC
Q 034188 27 GIVYHKSCFKCSHCKGTLKLSNYSSMEGVLYCKPHFEQ----LFK-ESGNFNKNFQ 77 (102)
Q Consensus 27 ~~~~h~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~----~~~-~~c~~~~~~~ 77 (102)
+..+...=-.|..| ....|+.+++.+.|..|-.+ ..+ .++.|+.-..
T Consensus 28 dg~~~va~daCeiC----~~~GY~q~g~~lvC~~C~~~~~~~~ig~~~GGCNP~P~ 79 (102)
T PF10080_consen 28 DGSYRVAFDACEIC----GPKGYYQEGDQLVCKNCGVRFNLPTIGGKSGGCNPIPL 79 (102)
T ss_pred CCCEEEEEEecccc----CCCceEEECCEEEEecCCCEEehhhcccccCCCCccCC
Confidence 33444444458888 34578899999999888633 234 5566765333
No 57
>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=29.31 E-value=36 Score=14.49 Aligned_cols=11 Identities=27% Similarity=0.927 Sum_probs=5.8
Q ss_pred cccccceeecC
Q 034188 10 CKVCEKTVYPV 20 (102)
Q Consensus 10 C~~C~~~i~~~ 20 (102)
|..|+..|.+.
T Consensus 1 C~sC~~~i~~r 11 (24)
T PF07754_consen 1 CTSCGRPIAPR 11 (24)
T ss_pred CccCCCcccCc
Confidence 44566665443
No 58
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.77 E-value=34 Score=23.52 Aligned_cols=17 Identities=24% Similarity=0.694 Sum_probs=8.3
Q ss_pred cccccCcccccccccCc
Q 034188 29 VYHKSCFKCSHCKGTLK 45 (102)
Q Consensus 29 ~~h~~Cf~C~~C~~~l~ 45 (102)
+|+..--.|..|+..+.
T Consensus 249 Vy~R~g~pC~~Cg~~I~ 265 (282)
T PRK13945 249 VYRRTGKPCRKCGTPIE 265 (282)
T ss_pred EeCCCcCCCCcCCCeeE
Confidence 34333344555665554
No 59
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=28.58 E-value=38 Score=15.69 Aligned_cols=11 Identities=18% Similarity=0.706 Sum_probs=5.7
Q ss_pred cccccccccee
Q 034188 7 QQKCKVCEKTV 17 (102)
Q Consensus 7 ~~~C~~C~~~i 17 (102)
..+|+.|+..+
T Consensus 25 ~vrC~~C~~~f 35 (37)
T PF13719_consen 25 KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCcEe
Confidence 34566565543
No 60
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.80 E-value=39 Score=23.14 Aligned_cols=16 Identities=19% Similarity=0.584 Sum_probs=7.5
Q ss_pred ccccCcccccccccCc
Q 034188 30 YHKSCFKCSHCKGTLK 45 (102)
Q Consensus 30 ~h~~Cf~C~~C~~~l~ 45 (102)
|...--.|..|+..+.
T Consensus 241 y~r~g~pC~~Cg~~I~ 256 (272)
T TIGR00577 241 YGRKGEPCRRCGTPIE 256 (272)
T ss_pred eCCCCCCCCCCCCeeE
Confidence 3333334555555554
No 61
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=27.59 E-value=13 Score=25.50 Aligned_cols=40 Identities=23% Similarity=0.496 Sum_probs=26.0
Q ss_pred ccccccceeecCceEEecCccccccCcccccccccCcCcce
Q 034188 9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLSNY 49 (102)
Q Consensus 9 ~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~~~ 49 (102)
.|..|++.|--..+-..+. .+|-.+|.|.+|++.+....|
T Consensus 5 tCnvCgEsvKKp~vekH~s-rCrn~~fSCIDC~k~F~~~sY 44 (276)
T KOG2186|consen 5 TCNVCGESVKKPQVEKHMS-RCRNAYFSCIDCGKTFERVSY 44 (276)
T ss_pred ehhhhhhhccccchHHHHH-hccCCeeEEeecccccccchh
Confidence 6889999884333212222 245588999999987765443
No 62
>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=26.96 E-value=34 Score=25.59 Aligned_cols=39 Identities=23% Similarity=0.479 Sum_probs=25.5
Q ss_pred cccccccceeecCceEEecCccccccCcccccccccCcCc
Q 034188 8 QKCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTLKLS 47 (102)
Q Consensus 8 ~~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l~~~ 47 (102)
..|..|-..+...+ +...+.....+||.|-.|...|...
T Consensus 27 ~yCp~CL~~~p~~e-~~~~~nrC~r~Cf~CP~C~~~L~~~ 65 (483)
T PF05502_consen 27 YYCPNCLFEVPSSE-ARSEKNRCSRNCFDCPICFSPLSVR 65 (483)
T ss_pred eECccccccCChhh-heeccceeccccccCCCCCCcceeE
Confidence 35777766663332 3344445556899999999988754
No 63
>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=25.56 E-value=14 Score=21.63 Aligned_cols=17 Identities=18% Similarity=0.481 Sum_probs=11.4
Q ss_pred CccccccccceeecCceE
Q 034188 6 TQQKCKVCEKTVYPVEQL 23 (102)
Q Consensus 6 ~~~~C~~C~~~i~~~~~~ 23 (102)
+...|..|++.|. .+++
T Consensus 79 ~yG~C~~Cge~I~-~~RL 95 (110)
T TIGR02420 79 EYGYCEECGEEIG-LRRL 95 (110)
T ss_pred CCCchhccCCccc-HHHH
Confidence 3458999999984 3443
No 64
>PRK10445 endonuclease VIII; Provisional
Probab=25.36 E-value=46 Score=22.69 Aligned_cols=11 Identities=27% Similarity=0.860 Sum_probs=5.5
Q ss_pred cccccccccCc
Q 034188 35 FKCSHCKGTLK 45 (102)
Q Consensus 35 f~C~~C~~~l~ 45 (102)
-.|-.|+..+.
T Consensus 236 ~~Cp~Cg~~I~ 246 (263)
T PRK10445 236 EACERCGGIIE 246 (263)
T ss_pred CCCCCCCCEeE
Confidence 34555555553
No 65
>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=25.11 E-value=37 Score=15.26 Aligned_cols=8 Identities=13% Similarity=0.800 Sum_probs=3.3
Q ss_pred eeeeHHHH
Q 034188 55 VLYCKPHF 62 (102)
Q Consensus 55 ~~~C~~~~ 62 (102)
..||..+.
T Consensus 20 H~~c~~C~ 27 (45)
T cd00162 20 HVFCRSCI 27 (45)
T ss_pred ChhcHHHH
Confidence 33444444
No 66
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=24.81 E-value=47 Score=16.04 Aligned_cols=27 Identities=26% Similarity=0.464 Sum_probs=15.7
Q ss_pred ccccccceeecCceEEecCccccccCcccccccccC
Q 034188 9 KCKVCEKTVYPVEQLSADGIVYHKSCFKCSHCKGTL 44 (102)
Q Consensus 9 ~C~~C~~~i~~~~~~~~~~~~~h~~Cf~C~~C~~~l 44 (102)
+|..|+..+...... . -+.|..|+.++
T Consensus 5 ~C~~CG~~~~~~~~~----~-----~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYG----T-----GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCC----C-----ceECCCCCCeE
Confidence 788888877433211 1 35667776544
No 67
>PF11077 DUF2616: Protein of unknown function (DUF2616); InterPro: IPR020201 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf52; it is a family of uncharacterised viral proteins.
Probab=24.00 E-value=27 Score=22.55 Aligned_cols=31 Identities=26% Similarity=0.564 Sum_probs=19.4
Q ss_pred ccccccccCcCc--c-eEeeCCeeeeHHHHHHHh
Q 034188 36 KCSHCKGTLKLS--N-YSSMEGVLYCKPHFEQLF 66 (102)
Q Consensus 36 ~C~~C~~~l~~~--~-~~~~~~~~~C~~~~~~~~ 66 (102)
+|..|....... . +.-.+-.++|..|+..+|
T Consensus 138 kC~QC~~~~~~~~~~~~~~F~~~lFC~~ClFPLF 171 (173)
T PF11077_consen 138 KCVQCSQKCENVGAKIFTYFNFNLFCKNCLFPLF 171 (173)
T ss_pred ccCcCCCCcccccceeEEecChhhcccccCcccc
Confidence 455555543322 2 555688999998887665
No 68
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=23.41 E-value=35 Score=21.84 Aligned_cols=36 Identities=14% Similarity=0.420 Sum_probs=21.6
Q ss_pred ccccccccceeecCceEEecC------ccccccCcccccccc
Q 034188 7 QQKCKVCEKTVYPVEQLSADG------IVYHKSCFKCSHCKG 42 (102)
Q Consensus 7 ~~~C~~C~~~i~~~~~~~~~~------~~~h~~Cf~C~~C~~ 42 (102)
..+|..||..+.....-.+.+ ...+.+.+.|..|++
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgk 138 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGK 138 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcc
Confidence 458999999875433211111 123566778888865
No 69
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=23.10 E-value=69 Score=15.93 Aligned_cols=10 Identities=10% Similarity=0.228 Sum_probs=6.1
Q ss_pred eeeeHHHHHH
Q 034188 55 VLYCKPHFEQ 64 (102)
Q Consensus 55 ~~~C~~~~~~ 64 (102)
--+|..||..
T Consensus 26 ~DlC~~C~~~ 35 (48)
T cd02341 26 FDLCQDCVVK 35 (48)
T ss_pred CccCHHHHhC
Confidence 3457777754
No 70
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=22.32 E-value=41 Score=17.07 Aligned_cols=6 Identities=33% Similarity=1.054 Sum_probs=2.5
Q ss_pred cccccc
Q 034188 10 CKVCEK 15 (102)
Q Consensus 10 C~~C~~ 15 (102)
|.+|+.
T Consensus 22 CPrCG~ 27 (51)
T COG1998 22 CPRCGP 27 (51)
T ss_pred CCCCCC
Confidence 444443
No 71
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=22.28 E-value=46 Score=14.31 Aligned_cols=6 Identities=33% Similarity=1.425 Sum_probs=3.1
Q ss_pred cccccc
Q 034188 9 KCKVCE 14 (102)
Q Consensus 9 ~C~~C~ 14 (102)
+|+.|+
T Consensus 18 rCa~C~ 23 (25)
T PF06943_consen 18 RCACCH 23 (25)
T ss_pred ECCccC
Confidence 455554
No 72
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=21.63 E-value=59 Score=20.00 Aligned_cols=13 Identities=31% Similarity=0.884 Sum_probs=9.3
Q ss_pred cccccccceeecC
Q 034188 8 QKCKVCEKTVYPV 20 (102)
Q Consensus 8 ~~C~~C~~~i~~~ 20 (102)
.+|..||..+...
T Consensus 92 sRC~~CN~~L~~v 104 (147)
T PF01927_consen 92 SRCPKCNGPLRPV 104 (147)
T ss_pred CccCCCCcEeeec
Confidence 4888898876543
No 73
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=21.11 E-value=25 Score=17.02 Aligned_cols=10 Identities=30% Similarity=0.913 Sum_probs=3.5
Q ss_pred cccccceeec
Q 034188 10 CKVCEKTVYP 19 (102)
Q Consensus 10 C~~C~~~i~~ 19 (102)
|..|++.+..
T Consensus 1 C~~C~~iv~~ 10 (43)
T PF08746_consen 1 CEACKEIVTQ 10 (43)
T ss_dssp -TTT-SB-SS
T ss_pred CcccchhHee
Confidence 4455555543
No 74
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=20.61 E-value=61 Score=15.13 Aligned_cols=11 Identities=18% Similarity=0.537 Sum_probs=8.7
Q ss_pred ccccccceeec
Q 034188 9 KCKVCEKTVYP 19 (102)
Q Consensus 9 ~C~~C~~~i~~ 19 (102)
.|..|++.+..
T Consensus 34 ~C~~CGE~~~~ 44 (46)
T TIGR03831 34 VCPQCGEEYLD 44 (46)
T ss_pred ccccCCCEeeC
Confidence 69999988754
No 75
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=20.39 E-value=50 Score=13.93 Aligned_cols=10 Identities=20% Similarity=0.531 Sum_probs=7.0
Q ss_pred ccccccceee
Q 034188 9 KCKVCEKTVY 18 (102)
Q Consensus 9 ~C~~C~~~i~ 18 (102)
.|..|++.+.
T Consensus 4 ~Cp~Cg~~~~ 13 (26)
T PF13248_consen 4 FCPNCGAEID 13 (26)
T ss_pred CCcccCCcCC
Confidence 6777877653
Done!