Query 030404
Match_columns 178
No_of_seqs 162 out of 435
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 13:13:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030404.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030404hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3173 Predicted Zn-finger pr 100.0 1.2E-45 2.7E-50 300.7 8.5 164 1-178 1-167 (167)
2 smart00154 ZnF_AN1 AN1-like Zi 99.5 2.3E-15 4.9E-20 96.5 2.3 38 119-156 1-39 (39)
3 PF01754 zf-A20: A20-like zinc 99.5 9.4E-15 2E-19 86.0 1.8 24 19-42 2-25 (25)
4 smart00259 ZnF_A20 A20-like zi 99.4 3.3E-14 7.1E-19 84.3 1.2 24 19-42 2-26 (26)
5 PF01428 zf-AN1: AN1-like Zinc 99.1 3.4E-11 7.4E-16 78.1 1.2 38 119-157 1-41 (43)
6 COG3582 Predicted nucleic acid 96.8 0.00056 1.2E-08 56.3 1.6 38 118-156 99-137 (162)
7 KOG3183 Predicted Zn-finger pr 96.5 0.001 2.2E-08 57.9 1.0 40 117-157 9-51 (250)
8 PF01363 FYVE: FYVE zinc finge 94.7 0.019 4.1E-07 39.5 1.6 29 115-143 8-39 (69)
9 KOG3183 Predicted Zn-finger pr 93.4 0.018 3.8E-07 50.3 -0.6 41 112-152 94-138 (250)
10 cd00065 FYVE FYVE domain; Zinc 92.6 0.052 1.1E-06 35.7 0.9 27 117-143 3-32 (57)
11 smart00064 FYVE Protein presen 92.0 0.078 1.7E-06 36.3 1.2 29 116-144 10-41 (68)
12 KOG1818 Membrane trafficking a 89.7 0.13 2.8E-06 50.3 0.8 47 114-160 163-223 (634)
13 PF10571 UPF0547: Uncharacteri 85.7 0.41 8.9E-06 28.2 1.0 22 118-139 2-24 (26)
14 PF00130 C1_1: Phorbol esters/ 83.9 0.63 1.4E-05 30.2 1.4 24 115-138 10-37 (53)
15 PF10122 Mu-like_Com: Mu-like 76.1 0.95 2.1E-05 30.9 0.2 24 116-139 4-34 (51)
16 PF15135 UPF0515: Uncharacteri 73.9 1.7 3.7E-05 38.6 1.3 28 114-141 130-167 (278)
17 KOG1729 FYVE finger containing 70.2 1.1 2.4E-05 40.0 -0.7 32 115-147 167-202 (288)
18 PF02148 zf-UBP: Zn-finger in 67.7 3.1 6.7E-05 28.4 1.2 23 119-142 1-24 (63)
19 smart00109 C1 Protein kinase C 58.9 5 0.00011 24.7 0.9 24 115-138 10-36 (49)
20 cd00029 C1 Protein kinase C co 58.6 5.1 0.00011 25.0 0.9 24 115-138 10-37 (50)
21 PHA02768 hypothetical protein; 56.2 4.7 0.0001 27.8 0.5 15 127-141 2-17 (55)
22 PF01194 RNA_pol_N: RNA polyme 55.4 6.1 0.00013 27.8 1.0 13 116-128 4-16 (60)
23 PF13978 DUF4223: Protein of u 53.5 6.3 0.00014 27.3 0.8 18 139-156 19-36 (56)
24 PF08882 Acetone_carb_G: Aceto 52.5 6.9 0.00015 30.7 0.9 33 120-154 16-48 (112)
25 KOG1812 Predicted E3 ubiquitin 52.3 8.8 0.00019 35.3 1.8 31 114-144 304-338 (384)
26 PRK04016 DNA-directed RNA poly 51.0 5.8 0.00013 28.1 0.3 14 115-128 3-16 (62)
27 COG1996 RPC10 DNA-directed RNA 50.9 6.7 0.00014 26.5 0.6 23 116-138 6-33 (49)
28 KOG1819 FYVE finger-containing 50.2 4.6 0.0001 39.6 -0.4 30 115-144 900-932 (990)
29 PTZ00303 phosphatidylinositol 50.2 8.3 0.00018 39.7 1.3 27 117-143 461-495 (1374)
30 PF05207 zf-CSL: CSL zinc fing 49.9 7.1 0.00015 26.4 0.6 12 129-140 17-28 (55)
31 PLN00032 DNA-directed RNA poly 49.7 6.6 0.00014 28.5 0.4 13 116-128 4-16 (71)
32 KOG2807 RNA polymerase II tran 48.3 9.9 0.00021 35.1 1.4 28 115-142 329-358 (378)
33 PF11781 RRN7: RNA polymerase 48.3 8.5 0.00018 24.1 0.7 22 117-138 9-34 (36)
34 PF07649 C1_3: C1-like domain; 48.2 7.9 0.00017 22.7 0.5 22 118-139 2-25 (30)
35 PF03107 C1_2: C1 domain; Int 46.3 14 0.00031 21.8 1.5 20 118-137 2-23 (30)
36 PF13717 zinc_ribbon_4: zinc-r 44.7 11 0.00024 23.4 0.8 9 131-139 26-35 (36)
37 KOG3497 DNA-directed RNA polym 44.6 7.8 0.00017 27.7 0.1 13 116-128 4-16 (69)
38 smart00290 ZnF_UBP Ubiquitin C 44.1 8.2 0.00018 24.6 0.2 24 118-143 1-25 (50)
39 PF14471 DUF4428: Domain of un 42.8 12 0.00026 25.0 0.8 22 118-139 1-30 (51)
40 smart00659 RPOLCX RNA polymera 42.6 13 0.00027 24.3 0.9 21 117-137 3-27 (44)
41 PRK08402 replication factor A; 42.6 12 0.00025 34.3 1.0 28 117-145 213-245 (355)
42 PHA00626 hypothetical protein 42.4 13 0.00028 26.1 1.0 23 117-141 12-35 (59)
43 PF03604 DNA_RNApol_7kD: DNA d 41.2 12 0.00027 22.9 0.6 19 118-136 2-24 (32)
44 PF06750 DiS_P_DiS: Bacterial 40.2 16 0.00035 27.1 1.3 15 115-129 32-46 (92)
45 cd04476 RPA1_DBD_C RPA1_DBD_C: 40.0 13 0.00028 29.4 0.8 32 115-146 33-69 (166)
46 COG1644 RPB10 DNA-directed RNA 39.7 10 0.00022 27.0 0.1 12 116-127 4-15 (63)
47 PF07975 C1_4: TFIIH C1-like d 39.6 12 0.00026 25.4 0.4 34 119-152 2-47 (51)
48 PF02318 FYVE_2: FYVE-type zin 39.6 21 0.00045 27.2 1.8 32 115-146 53-88 (118)
49 PRK00398 rpoP DNA-directed RNA 39.6 18 0.00039 23.1 1.3 28 117-144 4-36 (46)
50 PF13240 zinc_ribbon_2: zinc-r 39.0 17 0.00037 20.5 1.0 20 118-137 1-21 (23)
51 PF02928 zf-C5HC2: C5HC2 zinc 38.8 15 0.00033 24.5 0.9 26 119-144 1-28 (54)
52 COG1997 RPL43A Ribosomal prote 37.2 20 0.00044 27.1 1.4 35 112-146 31-70 (89)
53 smart00647 IBR In Between Ring 35.9 24 0.00051 22.9 1.4 17 130-146 40-57 (64)
54 PF15549 PGC7_Stella: PGC7/Ste 35.8 19 0.00042 29.8 1.2 18 131-150 124-141 (160)
55 COG2888 Predicted Zn-ribbon RN 35.8 13 0.00029 26.2 0.2 20 116-137 38-58 (61)
56 PRK04136 rpl40e 50S ribosomal 35.4 19 0.00042 24.3 0.9 23 115-137 13-36 (48)
57 COG1571 Predicted DNA-binding 34.9 18 0.00038 34.2 0.9 26 116-141 350-379 (421)
58 PF09723 Zn-ribbon_8: Zinc rib 34.5 24 0.00052 22.4 1.2 20 128-147 3-23 (42)
59 PF13842 Tnp_zf-ribbon_2: DDE_ 33.8 31 0.00068 20.9 1.6 26 118-143 2-30 (32)
60 KOG1842 FYVE finger-containing 33.3 11 0.00023 36.2 -0.8 26 116-141 180-208 (505)
61 PF04438 zf-HIT: HIT zinc fing 32.0 17 0.00036 21.9 0.2 23 117-142 3-26 (30)
62 PF13248 zf-ribbon_3: zinc-rib 32.0 27 0.00059 20.0 1.1 21 117-137 3-24 (26)
63 PF01485 IBR: IBR domain; Int 31.5 20 0.00042 23.3 0.5 16 131-146 41-57 (64)
64 PRK07218 replication factor A; 30.6 23 0.00049 33.3 0.9 21 116-138 297-318 (423)
65 PF10367 Vps39_2: Vacuolar sor 29.5 37 0.0008 24.1 1.7 24 116-139 78-102 (109)
66 KOG3507 DNA-directed RNA polym 29.3 25 0.00055 24.9 0.7 23 115-137 19-45 (62)
67 KOG0193 Serine/threonine prote 29.0 20 0.00043 35.7 0.2 50 117-171 190-243 (678)
68 PHA00616 hypothetical protein 27.9 16 0.00035 24.1 -0.4 11 131-141 2-13 (44)
69 PF00096 zf-C2H2: Zinc finger, 27.6 26 0.00055 18.6 0.4 9 131-139 1-10 (23)
70 PF00412 LIM: LIM domain; Int 26.7 30 0.00064 22.1 0.7 28 116-143 26-53 (58)
71 PF08073 CHDNT: CHDNT (NUC034) 26.7 23 0.0005 24.5 0.2 20 157-176 21-40 (55)
72 PF14634 zf-RING_5: zinc-RING 26.6 23 0.00051 22.2 0.2 29 118-146 1-31 (44)
73 PRK12366 replication factor A; 25.8 29 0.00062 34.0 0.7 29 116-145 532-563 (637)
74 PF01780 Ribosomal_L37ae: Ribo 25.8 29 0.00063 26.2 0.6 33 113-146 32-70 (90)
75 PF08600 Rsm1: Rsm1-like; Int 25.7 26 0.00057 25.8 0.3 18 116-133 19-36 (91)
76 KOG1074 Transcriptional repres 24.6 32 0.00069 35.4 0.8 45 112-156 601-673 (958)
77 smart00834 CxxC_CXXC_SSSS Puta 23.5 38 0.00083 20.4 0.7 12 129-140 4-16 (41)
78 PF14835 zf-RING_6: zf-RING of 23.0 46 0.00099 23.8 1.1 27 116-142 7-33 (65)
79 smart00396 ZnF_UBR1 Putative z 21.7 50 0.0011 23.2 1.1 13 131-143 51-70 (71)
80 smart00508 PostSET Cysteine-ri 21.1 50 0.0011 19.5 0.8 11 131-141 3-13 (26)
81 COG3357 Predicted transcriptio 20.9 35 0.00077 26.1 0.2 18 124-141 52-70 (97)
82 PF01927 Mut7-C: Mut7-C RNAse 20.7 50 0.0011 26.0 1.0 11 116-126 91-101 (147)
83 PF13465 zf-H2C2_2: Zinc-finge 20.4 56 0.0012 18.4 0.9 10 130-139 14-24 (26)
84 PF07282 OrfB_Zn_ribbon: Putat 20.4 67 0.0015 21.6 1.5 24 115-138 27-55 (69)
85 PRK08197 threonine synthase; V 20.3 46 0.001 30.1 0.8 31 116-146 7-39 (394)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.2e-45 Score=300.68 Aligned_cols=164 Identities=39% Similarity=0.757 Sum_probs=107.6
Q ss_pred CCccccccccccCCCcccccccccCCCcCCccCCCchhhhhhhhhhhhccc-ccCC-CCCCCCCCCCCcccccccccccc
Q 030404 1 MAQKTEKEETEFKVPETLTLCVNNCGFTGNPATNNMCQKCFNATATTTASA-VAGS-STGGGGGGGSGVAIIKFSSEKSL 78 (178)
Q Consensus 1 Ma~~~~~~~pe~~~p~~~~lC~ngCGFfGs~at~n~CSkCyr~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 78 (178)
|+++.....+. ++.+.||.|||||||+|+|+||||+||++++.++++. ...+ .+...+. ++ ...+..+...
T Consensus 1 M~~e~~~~~~~---~~~~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~~~~~~~-~~---~s~~~~~~~~ 73 (167)
T KOG3173|consen 1 MASETNGSQTP---PSQDLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPPVESSLS-SP---RSVPSRDPPA 73 (167)
T ss_pred CcccccCCCCC---CccccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCccccccc-Cc---cccCcccccc
Confidence 77765553322 2245899999999999999999999999999877665 2211 1111100 00 0001000000
Q ss_pred ccccccccCCCC-CCCCCCcccchhhhhhhhhhhccccCCccccccccccccceeeecCccccccCCCCCCCCCCccchH
Q 030404 79 RSRPIIRSGSSD-AAGTTGQNQELTDRREKEANVEKRVVNRCSGCRRKVGLTGFRCRCGELFCGEHRYSDRHDCSYDYKS 157 (178)
Q Consensus 79 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~rC~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk~ 157 (178)
.........+ ...... +.. ...........++||+.|+|||||+||.||||++||+.|||||.|+|+||||.
T Consensus 74 --~~~~~~~~~~~~~~~~~---~s~--~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~ 146 (167)
T KOG3173|consen 74 --VSLESTTESELKLVSDT---PST--EEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQ 146 (167)
T ss_pred --ccccccccccccccccC---Ccc--cccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHH
Confidence 0000000000 000000 000 01112233456789999999999999999999999999999999999999999
Q ss_pred hhHHHHHHhCCcccccccccC
Q 030404 158 AGRDAIARENPVIKAAKIVRV 178 (178)
Q Consensus 158 ~~r~~l~k~NP~v~~~Kl~ki 178 (178)
+||+.|+++||+|+++||.||
T Consensus 147 ~gr~~i~k~nP~v~a~k~~ki 167 (167)
T KOG3173|consen 147 AGREKIAKANPVVKADKLQKI 167 (167)
T ss_pred HHHHHHHHhCCeeeccccccC
Confidence 999999999999999999998
No 2
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.54 E-value=2.3e-15 Score=96.52 Aligned_cols=38 Identities=71% Similarity=1.547 Sum_probs=36.8
Q ss_pred cccccccccccceeee-cCccccccCCCCCCCCCCccch
Q 030404 119 CSGCRRKVGLTGFRCR-CGELFCGEHRYSDRHDCSYDYK 156 (178)
Q Consensus 119 C~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 156 (178)
|+.|+++++|++|+|+ |+++||..|||||.|+|++|||
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~HR~~e~H~C~~~~k 39 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39 (39)
T ss_pred CcccCCcccccCeECCccCCccccccCCccccCCccccC
Confidence 7899999999999999 9999999999999999999996
No 3
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 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 the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=99.49 E-value=9.4e-15 Score=85.97 Aligned_cols=24 Identities=58% Similarity=1.432 Sum_probs=20.2
Q ss_pred ccccccCCCcCCccCCCchhhhhh
Q 030404 19 TLCVNNCGFTGNPATNNMCQKCFN 42 (178)
Q Consensus 19 ~lC~ngCGFfGs~at~n~CSkCyr 42 (178)
.+|++|||||||++|+||||+|||
T Consensus 2 ~~C~~gCgf~Gs~~~~~~Cs~C~~ 25 (25)
T PF01754_consen 2 SLCANGCGFYGSPATNGLCSKCYR 25 (25)
T ss_dssp SB-TTTSSSB-BGGGTTS-HHHHH
T ss_pred CcccCCCCCcccccccCcchhhcC
Confidence 789999999999999999999997
No 4
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=99.43 E-value=3.3e-14 Score=84.31 Aligned_cols=24 Identities=54% Similarity=1.254 Sum_probs=23.0
Q ss_pred cccc-ccCCCcCCccCCCchhhhhh
Q 030404 19 TLCV-NNCGFTGNPATNNMCQKCFN 42 (178)
Q Consensus 19 ~lC~-ngCGFfGs~at~n~CSkCyr 42 (178)
++|. +||||||||+|+||||||||
T Consensus 2 ~~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 2 IKCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred CccccCCCCCcCChhhcccCHhhcC
Confidence 6899 99999999999999999996
No 5
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.08 E-value=3.4e-11 Score=78.07 Aligned_cols=38 Identities=42% Similarity=0.919 Sum_probs=28.0
Q ss_pred ccc--ccccccccceeee-cCccccccCCCCCCCCCCccchH
Q 030404 119 CSG--CRRKVGLTGFRCR-CGELFCGEHRYSDRHDCSYDYKS 157 (178)
Q Consensus 119 C~~--C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 157 (178)
|.. |++++. ++|.|+ |+..||..||||+.|+|+++++.
T Consensus 1 C~~~~C~~~~~-~~~~C~~C~~~FC~~Hr~~e~H~C~~~~~~ 41 (43)
T PF01428_consen 1 CSFPGCKKKDF-LPFKCKHCGKSFCLKHRLPEDHNCSKLQKK 41 (43)
T ss_dssp -SSTTT--BCT-SHEE-TTTS-EE-TTTHSTTTCT-SSTTSC
T ss_pred CccCcCcCccC-CCeECCCCCcccCccccCccccCCcchhhc
Confidence 444 998887 789999 99999999999999999999874
No 6
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.82 E-value=0.00056 Score=56.32 Aligned_cols=38 Identities=29% Similarity=0.565 Sum_probs=30.7
Q ss_pred ccccccccccccceeee-cCccccccCCCCCCCCCCccch
Q 030404 118 RCSGCRRKVGLTGFRCR-CGELFCGEHRYSDRHDCSYDYK 156 (178)
Q Consensus 118 rC~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 156 (178)
+|..|++..+|. ++|- |++.||+.||+++.|+|.+...
T Consensus 99 ~~~~~g~~s~l~-~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 99 TPQCTGKGSTLA-GKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred cceeccCCcccc-ccccCCCCcceeceecccccccccHHH
Confidence 444556655555 8997 9999999999999999998854
No 7
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=96.47 E-value=0.001 Score=57.92 Aligned_cols=40 Identities=33% Similarity=0.890 Sum_probs=34.8
Q ss_pred Cccc--cccccccccceeee-cCccccccCCCCCCCCCCccchH
Q 030404 117 NRCS--GCRRKVGLTGFRCR-CGELFCGEHRYSDRHDCSYDYKS 157 (178)
Q Consensus 117 ~rC~--~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 157 (178)
..|. .|+ ++.++.|+|- |+.+||..||-.+.|.|.+.|..
T Consensus 9 kHCs~~~Ck-qlDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~ 51 (250)
T KOG3183|consen 9 KHCSVPYCK-QLDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRI 51 (250)
T ss_pred cccCcchhh-hccccceeeCCccchhhhccchHhhcCCCccccc
Confidence 4677 776 6778999996 99999999999999999998764
No 8
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=94.66 E-value=0.019 Score=39.48 Aligned_cols=29 Identities=31% Similarity=0.811 Sum_probs=17.5
Q ss_pred cCCcccccccccccc--ceeee-cCccccccC
Q 030404 115 VVNRCSGCRRKVGLT--GFRCR-CGELFCGEH 143 (178)
Q Consensus 115 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 143 (178)
....|..|+++.+|+ -..|| ||.+||+.+
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EEECCC
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEECCch
Confidence 357999999999996 49999 999999754
No 9
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=93.39 E-value=0.018 Score=50.34 Aligned_cols=41 Identities=34% Similarity=0.867 Sum_probs=34.5
Q ss_pred ccccCCccc--ccccccccc-ceeee-cCccccccCCCCCCCCCC
Q 030404 112 EKRVVNRCS--GCRRKVGLT-GFRCR-CGELFCGEHRYSDRHDCS 152 (178)
Q Consensus 112 ~~~~~~rC~--~C~kkvgl~-gf~Cr-Cg~~FC~~HRy~e~H~C~ 152 (178)
.+...++|. .|++++-+. .+.|+ ||..||-+||++-.|.|.
T Consensus 94 ~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~ 138 (250)
T KOG3183|consen 94 RKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCN 138 (250)
T ss_pred cccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhh
Confidence 345567776 688888775 69998 999999999999999998
No 10
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=92.65 E-value=0.052 Score=35.74 Aligned_cols=27 Identities=41% Similarity=1.126 Sum_probs=23.5
Q ss_pred Ccccccccccccc--ceeee-cCccccccC
Q 030404 117 NRCSGCRRKVGLT--GFRCR-CGELFCGEH 143 (178)
Q Consensus 117 ~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~H 143 (178)
..|..|+++.++. ...|| ||.+||+.+
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKC 32 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHH
Confidence 5799999999996 69998 999999854
No 11
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=89.75 E-value=0.13 Score=50.33 Aligned_cols=47 Identities=36% Similarity=0.756 Sum_probs=36.4
Q ss_pred ccCCccccccccccccc--eeee-cCccccccCC-----------CCCCCCCCccchHhhH
Q 030404 114 RVVNRCSGCRRKVGLTG--FRCR-CGELFCGEHR-----------YSDRHDCSYDYKSAGR 160 (178)
Q Consensus 114 ~~~~rC~~C~kkvgl~g--f~Cr-Cg~~FC~~HR-----------y~e~H~C~fDyk~~~r 160 (178)
.....|..|+.+.|+++ ..|| ||.+||+.|= |-+.--|..||...-|
T Consensus 163 ~D~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l~~ 223 (634)
T KOG1818|consen 163 IDSEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELLTR 223 (634)
T ss_pred ccccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHhhh
Confidence 34679999999999985 8999 9999999874 3455667777764433
No 13
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=85.71 E-value=0.41 Score=28.18 Aligned_cols=22 Identities=32% Similarity=0.690 Sum_probs=19.8
Q ss_pred ccccccccccccceeee-cCccc
Q 030404 118 RCSGCRRKVGLTGFRCR-CGELF 139 (178)
Q Consensus 118 rC~~C~kkvgl~gf~Cr-Cg~~F 139 (178)
+|-.|++.|.+.--.|- ||+.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 68999999999989997 99887
No 14
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=83.94 E-value=0.63 Score=30.18 Aligned_cols=24 Identities=33% Similarity=0.919 Sum_probs=18.6
Q ss_pred cCCccccccccc---cccceeee-cCcc
Q 030404 115 VVNRCSGCRRKV---GLTGFRCR-CGEL 138 (178)
Q Consensus 115 ~~~rC~~C~kkv---gl~gf~Cr-Cg~~ 138 (178)
.+..|..|++.+ ++.|++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLV 37 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-E
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCCh
Confidence 567999999999 56799998 8765
No 15
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=76.09 E-value=0.95 Score=30.94 Aligned_cols=24 Identities=25% Similarity=0.733 Sum_probs=18.5
Q ss_pred CCcccccccccccc------ceee-ecCccc
Q 030404 116 VNRCSGCRRKVGLT------GFRC-RCGELF 139 (178)
Q Consensus 116 ~~rC~~C~kkvgl~------gf~C-rCg~~F 139 (178)
.-||..|+|.|... -++| |||.++
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 46999999998774 3788 688664
No 16
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=73.85 E-value=1.7 Score=38.62 Aligned_cols=28 Identities=39% Similarity=1.062 Sum_probs=22.4
Q ss_pred ccCCcccccccc---------ccccceee-ecCccccc
Q 030404 114 RVVNRCSGCRRK---------VGLTGFRC-RCGELFCG 141 (178)
Q Consensus 114 ~~~~rC~~C~kk---------vgl~gf~C-rCg~~FC~ 141 (178)
+..+||..|+|| .|+.-|.| .|+.+|=+
T Consensus 130 KeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 130 KEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccccccccccccCCCccccccceeeeecccccccchh
Confidence 456899999998 56666999 59999954
No 17
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=70.24 E-value=1.1 Score=39.97 Aligned_cols=32 Identities=25% Similarity=0.709 Sum_probs=26.4
Q ss_pred cCCccccccc-ccccc--ceeee-cCccccccCCCCC
Q 030404 115 VVNRCSGCRR-KVGLT--GFRCR-CGELFCGEHRYSD 147 (178)
Q Consensus 115 ~~~rC~~C~k-kvgl~--gf~Cr-Cg~~FC~~HRy~e 147 (178)
..++|..|.+ .-.|+ --.|| ||.+||. |.-..
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~-~Cs~n 202 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIVCA-PCSRN 202 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHhhh-hhhcC
Confidence 4689999999 77775 48899 9999999 87544
No 18
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=67.68 E-value=3.1 Score=28.37 Aligned_cols=23 Identities=35% Similarity=0.817 Sum_probs=15.0
Q ss_pred cccccccccccceeee-cCcccccc
Q 030404 119 CSGCRRKVGLTGFRCR-CGELFCGE 142 (178)
Q Consensus 119 C~~C~kkvgl~gf~Cr-Cg~~FC~~ 142 (178)
|..|+.. +-.-+.|- ||.++|+.
T Consensus 1 C~~C~~~-~~~lw~CL~Cg~~~C~~ 24 (63)
T PF02148_consen 1 CSVCGST-NSNLWLCLTCGYVGCGR 24 (63)
T ss_dssp -SSSHTC-SSSEEEETTTS-EEETT
T ss_pred CCCCCCc-CCceEEeCCCCcccccC
Confidence 5667755 33447886 99999994
No 19
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=58.86 E-value=5 Score=24.73 Aligned_cols=24 Identities=29% Similarity=0.753 Sum_probs=18.8
Q ss_pred cCCcccccccccccc--ceeee-cCcc
Q 030404 115 VVNRCSGCRRKVGLT--GFRCR-CGEL 138 (178)
Q Consensus 115 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~ 138 (178)
.+..|..|++.+... |++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~ 36 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVK 36 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCch
Confidence 367899999999873 89998 7543
No 20
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=58.59 E-value=5.1 Score=25.01 Aligned_cols=24 Identities=29% Similarity=0.656 Sum_probs=19.2
Q ss_pred cCCccccccccccc---cceeee-cCcc
Q 030404 115 VVNRCSGCRRKVGL---TGFRCR-CGEL 138 (178)
Q Consensus 115 ~~~rC~~C~kkvgl---~gf~Cr-Cg~~ 138 (178)
.+..|..|++.+.. .|++|+ |+.+
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCc
Confidence 36789999999985 689998 7654
No 21
>PHA02768 hypothetical protein; Provisional
Probab=56.16 E-value=4.7 Score=27.83 Aligned_cols=15 Identities=40% Similarity=1.183 Sum_probs=11.8
Q ss_pred cccceeee-cCccccc
Q 030404 127 GLTGFRCR-CGELFCG 141 (178)
Q Consensus 127 gl~gf~Cr-Cg~~FC~ 141 (178)
.|+||.|- ||..|-.
T Consensus 2 ~~~~y~C~~CGK~Fs~ 17 (55)
T PHA02768 2 ALLGYECPICGEIYIK 17 (55)
T ss_pred cccccCcchhCCeecc
Confidence 47889996 9888864
No 22
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=55.42 E-value=6.1 Score=27.78 Aligned_cols=13 Identities=31% Similarity=0.680 Sum_probs=10.0
Q ss_pred CCccccccccccc
Q 030404 116 VNRCSGCRRKVGL 128 (178)
Q Consensus 116 ~~rC~~C~kkvgl 128 (178)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvi~~ 16 (60)
T PF01194_consen 4 PVRCFTCGKVIGN 16 (60)
T ss_dssp SSS-STTTSBTCG
T ss_pred ceecCCCCCChhH
Confidence 6799999998863
No 23
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=53.48 E-value=6.3 Score=27.27 Aligned_cols=18 Identities=39% Similarity=0.835 Sum_probs=16.1
Q ss_pred ccccCCCCCCCCCCccch
Q 030404 139 FCGEHRYSDRHDCSYDYK 156 (178)
Q Consensus 139 FC~~HRy~e~H~C~fDyk 156 (178)
-|--|-|-.+.+|+|||-
T Consensus 19 ~CTG~v~Nk~knCsYDYl 36 (56)
T PF13978_consen 19 ACTGHVENKEKNCSYDYL 36 (56)
T ss_pred hccceeeccCCCCcceee
Confidence 477899999999999995
No 24
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=52.49 E-value=6.9 Score=30.72 Aligned_cols=33 Identities=21% Similarity=0.364 Sum_probs=24.1
Q ss_pred ccccccccccceeeecCccccccCCCCCCCCCCcc
Q 030404 120 SGCRRKVGLTGFRCRCGELFCGEHRYSDRHDCSYD 154 (178)
Q Consensus 120 ~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fD 154 (178)
+.|+++-. -.+|+||+.||+-+.--..|.--++
T Consensus 16 ~i~~~~~k--~vkc~CGh~f~d~r~NwK~~alv~v 48 (112)
T PF08882_consen 16 WIVQKKDK--VVKCDCGHEFCDARENWKLGALVYV 48 (112)
T ss_pred EEEEecCc--eeeccCCCeecChhcChhhCcEEEe
Confidence 55665542 5899999999999887777765444
No 25
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.34 E-value=8.8 Score=35.30 Aligned_cols=31 Identities=29% Similarity=0.774 Sum_probs=25.9
Q ss_pred ccCCccccccccccccc----eeeecCccccccCC
Q 030404 114 RVVNRCSGCRRKVGLTG----FRCRCGELFCGEHR 144 (178)
Q Consensus 114 ~~~~rC~~C~kkvgl~g----f~CrCg~~FC~~HR 144 (178)
+.-.+|..|+-.+-|.+ ++||||.-||..=.
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 45689999999988863 99999999997655
No 26
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=51.01 E-value=5.8 Score=28.07 Aligned_cols=14 Identities=21% Similarity=0.565 Sum_probs=11.3
Q ss_pred cCCccccccccccc
Q 030404 115 VVNRCSGCRRKVGL 128 (178)
Q Consensus 115 ~~~rC~~C~kkvgl 128 (178)
.|-||++|+|-+|-
T Consensus 3 iPvRCFTCGkvi~~ 16 (62)
T PRK04016 3 IPVRCFTCGKVIAE 16 (62)
T ss_pred CCeEecCCCCChHH
Confidence 36799999998864
No 27
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=50.88 E-value=6.7 Score=26.54 Aligned_cols=23 Identities=43% Similarity=1.057 Sum_probs=18.3
Q ss_pred CCcccccccccccc----ceeee-cCcc
Q 030404 116 VNRCSGCRRKVGLT----GFRCR-CGEL 138 (178)
Q Consensus 116 ~~rC~~C~kkvgl~----gf~Cr-Cg~~ 138 (178)
..+|..|++++-++ +..|. ||+-
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 47899999999853 79997 7654
No 28
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=50.23 E-value=4.6 Score=39.57 Aligned_cols=30 Identities=30% Similarity=0.873 Sum_probs=22.0
Q ss_pred cCCcccccccccccc--ceeee-cCccccccCC
Q 030404 115 VVNRCSGCRRKVGLT--GFRCR-CGELFCGEHR 144 (178)
Q Consensus 115 ~~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HR 144 (178)
..-+|..|....... -..|| ||++||++--
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncggifcg~cs 932 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCS 932 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCceeecccc
Confidence 457899998654442 36899 9999998743
No 29
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=50.17 E-value=8.3 Score=39.65 Aligned_cols=27 Identities=30% Similarity=0.714 Sum_probs=21.1
Q ss_pred Cccccccccccc-------cceeee-cCccccccC
Q 030404 117 NRCSGCRRKVGL-------TGFRCR-CGELFCGEH 143 (178)
Q Consensus 117 ~rC~~C~kkvgl-------~gf~Cr-Cg~~FC~~H 143 (178)
..|..|+++-+. .--.|| ||.+||+..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~C 495 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFC 495 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccc
Confidence 579999999864 246699 999998653
No 30
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=49.85 E-value=7.1 Score=26.43 Aligned_cols=12 Identities=42% Similarity=1.038 Sum_probs=9.8
Q ss_pred cceeeecCcccc
Q 030404 129 TGFRCRCGELFC 140 (178)
Q Consensus 129 ~gf~CrCg~~FC 140 (178)
.-+.||||..|-
T Consensus 17 ~~y~CRCG~~f~ 28 (55)
T PF05207_consen 17 YSYPCRCGGEFE 28 (55)
T ss_dssp EEEEETTSSEEE
T ss_pred EEEcCCCCCEEE
Confidence 458999999875
No 31
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=49.68 E-value=6.6 Score=28.54 Aligned_cols=13 Identities=31% Similarity=0.680 Sum_probs=10.9
Q ss_pred CCccccccccccc
Q 030404 116 VNRCSGCRRKVGL 128 (178)
Q Consensus 116 ~~rC~~C~kkvgl 128 (178)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 6799999998764
No 32
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=48.34 E-value=9.9 Score=35.14 Aligned_cols=28 Identities=25% Similarity=0.719 Sum_probs=22.9
Q ss_pred cCCccccc-cccccccceeee-cCcccccc
Q 030404 115 VVNRCSGC-RRKVGLTGFRCR-CGELFCGE 142 (178)
Q Consensus 115 ~~~rC~~C-~kkvgl~gf~Cr-Cg~~FC~~ 142 (178)
..++|+.| .+.++-..|.|+ |-++||-.
T Consensus 329 ~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCld 358 (378)
T KOG2807|consen 329 GSRFCFACQGELLSSGRYRCESCKNVFCLD 358 (378)
T ss_pred CCcceeeeccccCCCCcEEchhccceeecc
Confidence 46789999 666666789998 99999964
No 33
>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=48.29 E-value=8.5 Score=24.09 Aligned_cols=22 Identities=32% Similarity=0.883 Sum_probs=17.6
Q ss_pred Ccccccccccccc--c-eee-ecCcc
Q 030404 117 NRCSGCRRKVGLT--G-FRC-RCGEL 138 (178)
Q Consensus 117 ~rC~~C~kkvgl~--g-f~C-rCg~~ 138 (178)
-+|..|+-+...+ | |.| +||.+
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 4699999997775 3 899 89875
No 34
>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=48.22 E-value=7.9 Score=22.71 Aligned_cols=22 Identities=27% Similarity=0.708 Sum_probs=8.7
Q ss_pred ccccccccccc-cceeee-cCccc
Q 030404 118 RCSGCRRKVGL-TGFRCR-CGELF 139 (178)
Q Consensus 118 rC~~C~kkvgl-~gf~Cr-Cg~~F 139 (178)
+|..|++.+.. ..|.|. |...+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDL 25 (30)
T ss_dssp --TTTS----S--EEE-TTT----
T ss_pred cCCcCCCcCCCCceEECccCCCcc
Confidence 68999999988 779997 76654
No 35
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=46.29 E-value=14 Score=21.75 Aligned_cols=20 Identities=35% Similarity=0.753 Sum_probs=16.5
Q ss_pred cccccccccccc-ceeee-cCc
Q 030404 118 RCSGCRRKVGLT-GFRCR-CGE 137 (178)
Q Consensus 118 rC~~C~kkvgl~-gf~Cr-Cg~ 137 (178)
.|..|++++.-. .|.|. |+.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f 23 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCF 23 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCC
Confidence 489999999888 89996 653
No 36
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=44.72 E-value=11 Score=23.35 Aligned_cols=9 Identities=56% Similarity=1.604 Sum_probs=5.2
Q ss_pred eeee-cCccc
Q 030404 131 FRCR-CGELF 139 (178)
Q Consensus 131 f~Cr-Cg~~F 139 (178)
.+|. ||.+|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 5664 66655
No 37
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=44.57 E-value=7.8 Score=27.72 Aligned_cols=13 Identities=31% Similarity=0.639 Sum_probs=10.9
Q ss_pred CCccccccccccc
Q 030404 116 VNRCSGCRRKVGL 128 (178)
Q Consensus 116 ~~rC~~C~kkvgl 128 (178)
|-||++|+|-+|-
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 6799999998764
No 38
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=44.10 E-value=8.2 Score=24.56 Aligned_cols=24 Identities=38% Similarity=0.844 Sum_probs=17.6
Q ss_pred ccccccccccccceeee-cCccccccC
Q 030404 118 RCSGCRRKVGLTGFRCR-CGELFCGEH 143 (178)
Q Consensus 118 rC~~C~kkvgl~gf~Cr-Cg~~FC~~H 143 (178)
||..|..... -+.|- |+.++|+..
T Consensus 1 ~C~~C~~~~~--l~~CL~C~~~~c~~~ 25 (50)
T smart00290 1 RCSVCGTIEN--LWLCLTCGQVGCGRY 25 (50)
T ss_pred CcccCCCcCC--eEEecCCCCcccCCC
Confidence 6888886554 36775 999999764
No 39
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=42.85 E-value=12 Score=25.05 Aligned_cols=22 Identities=36% Similarity=1.065 Sum_probs=16.3
Q ss_pred cccccccccccc-------ceeee-cCccc
Q 030404 118 RCSGCRRKVGLT-------GFRCR-CGELF 139 (178)
Q Consensus 118 rC~~C~kkvgl~-------gf~Cr-Cg~~F 139 (178)
+|..|++++||+ ||-|. |-...
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHh
Confidence 599999999996 46776 64333
No 40
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=42.63 E-value=13 Score=24.27 Aligned_cols=21 Identities=38% Similarity=0.899 Sum_probs=15.4
Q ss_pred Ccccccccccccc---ceeee-cCc
Q 030404 117 NRCSGCRRKVGLT---GFRCR-CGE 137 (178)
Q Consensus 117 ~rC~~C~kkvgl~---gf~Cr-Cg~ 137 (178)
.+|..|+..+.+. +.+|+ ||+
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCc
Confidence 4788888888875 47786 654
No 41
>PRK08402 replication factor A; Reviewed
Probab=42.60 E-value=12 Score=34.30 Aligned_cols=28 Identities=32% Similarity=0.576 Sum_probs=19.0
Q ss_pred Cccccccccccc----cceeee-cCccccccCCC
Q 030404 117 NRCSGCRRKVGL----TGFRCR-CGELFCGEHRY 145 (178)
Q Consensus 117 ~rC~~C~kkvgl----~gf~Cr-Cg~~FC~~HRy 145 (178)
.+|..|+|||-. -.+.|. ||.+-+ .|||
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p-~~ry 245 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGEVEP-IKIT 245 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCCcCc-ceeE
Confidence 699999999963 247776 654433 4554
No 42
>PHA00626 hypothetical protein
Probab=42.39 E-value=13 Score=26.11 Aligned_cols=23 Identities=17% Similarity=0.235 Sum_probs=14.8
Q ss_pred Cccccccccccccceeee-cCccccc
Q 030404 117 NRCSGCRRKVGLTGFRCR-CGELFCG 141 (178)
Q Consensus 117 ~rC~~C~kkvgl~gf~Cr-Cg~~FC~ 141 (178)
.||.+|++.. .-|+|. ||+.|-.
T Consensus 12 vrcg~cr~~s--nrYkCkdCGY~ft~ 35 (59)
T PHA00626 12 AKEKTMRGWS--DDYVCCDCGYNDSK 35 (59)
T ss_pred eeeceecccC--cceEcCCCCCeech
Confidence 4777777522 238886 8877753
No 43
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=41.24 E-value=12 Score=22.92 Aligned_cols=19 Identities=42% Similarity=1.039 Sum_probs=10.4
Q ss_pred cccccccccccc---ceeee-cC
Q 030404 118 RCSGCRRKVGLT---GFRCR-CG 136 (178)
Q Consensus 118 rC~~C~kkvgl~---gf~Cr-Cg 136 (178)
.|..|+..+.|. ..+|+ ||
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCcCCCeeEcCCCCcEECCcCC
Confidence 356666666663 35666 54
No 44
>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=40.19 E-value=16 Score=27.06 Aligned_cols=15 Identities=13% Similarity=0.373 Sum_probs=12.7
Q ss_pred cCCcccccccccccc
Q 030404 115 VVNRCSGCRRKVGLT 129 (178)
Q Consensus 115 ~~~rC~~C~kkvgl~ 129 (178)
.+++|..|++++...
T Consensus 32 ~rS~C~~C~~~L~~~ 46 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWW 46 (92)
T ss_pred CCCcCcCCCCcCccc
Confidence 468999999999864
No 45
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=39.97 E-value=13 Score=29.38 Aligned_cols=32 Identities=38% Similarity=0.795 Sum_probs=23.2
Q ss_pred cCCccccccccccccc---eeee-cCccc-cccCCCC
Q 030404 115 VVNRCSGCRRKVGLTG---FRCR-CGELF-CGEHRYS 146 (178)
Q Consensus 115 ~~~rC~~C~kkvgl~g---f~Cr-Cg~~F-C~~HRy~ 146 (178)
.=..|..|+|||-..+ |.|. |+..+ =-.+||-
T Consensus 33 ~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~ 69 (166)
T cd04476 33 WYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYI 69 (166)
T ss_pred EEccccccCcccEeCCCCcEECCCCCCcCCCccEEEE
Confidence 3467889999997653 8886 87765 4566774
No 46
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=39.66 E-value=10 Score=27.01 Aligned_cols=12 Identities=33% Similarity=0.861 Sum_probs=10.4
Q ss_pred CCcccccccccc
Q 030404 116 VNRCSGCRRKVG 127 (178)
Q Consensus 116 ~~rC~~C~kkvg 127 (178)
|-||++|+|-+|
T Consensus 4 PiRCFsCGkvi~ 15 (63)
T COG1644 4 PVRCFSCGKVIG 15 (63)
T ss_pred ceEeecCCCCHH
Confidence 679999999875
No 47
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=39.65 E-value=12 Score=25.41 Aligned_cols=34 Identities=29% Similarity=0.810 Sum_probs=14.9
Q ss_pred ccccccccccc--------ceeee-cCcccccc---CCCCCCCCCC
Q 030404 119 CSGCRRKVGLT--------GFRCR-CGELFCGE---HRYSDRHDCS 152 (178)
Q Consensus 119 C~~C~kkvgl~--------gf~Cr-Cg~~FC~~---HRy~e~H~C~ 152 (178)
|+.|.+.+.-. .|.|. |+..||.. -=+-.-|+|+
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CP 47 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCP 47 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSS
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCc
Confidence 56666666553 48894 99999853 2222356654
No 48
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=39.62 E-value=21 Score=27.22 Aligned_cols=32 Identities=22% Similarity=0.555 Sum_probs=24.8
Q ss_pred cCCcccccccccccc---ceeee-cCccccccCCCC
Q 030404 115 VVNRCSGCRRKVGLT---GFRCR-CGELFCGEHRYS 146 (178)
Q Consensus 115 ~~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~~HRy~ 146 (178)
....|..|.+.+|++ |..|. |...+|..=+.-
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 467999999999986 68998 999999876654
No 49
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=39.57 E-value=18 Score=23.08 Aligned_cols=28 Identities=39% Similarity=0.853 Sum_probs=19.0
Q ss_pred Ccccccccccccc----ceeee-cCccccccCC
Q 030404 117 NRCSGCRRKVGLT----GFRCR-CGELFCGEHR 144 (178)
Q Consensus 117 ~rC~~C~kkvgl~----gf~Cr-Cg~~FC~~HR 144 (178)
.+|..|+..+-+. .++|. ||..+--.+|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 5788888887552 48886 7766554444
No 50
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=39.03 E-value=17 Score=20.55 Aligned_cols=20 Identities=25% Similarity=0.708 Sum_probs=11.3
Q ss_pred ccccccccccccceeee-cCc
Q 030404 118 RCSGCRRKVGLTGFRCR-CGE 137 (178)
Q Consensus 118 rC~~C~kkvgl~gf~Cr-Cg~ 137 (178)
+|..|++++.-..-.|. ||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 36666666655544454 553
No 51
>PF02928 zf-C5HC2: C5HC2 zinc finger; InterPro: IPR004198 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji [], and may have a DNA binding function. The mouse jumonji protein is required for neural tube formation, and is essential for normal heart development. It also plays a role in the down-regulation of cell proliferation signalling. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005634 nucleus
Probab=38.75 E-value=15 Score=24.47 Aligned_cols=26 Identities=31% Similarity=0.788 Sum_probs=22.1
Q ss_pred cccccccccccceeeec--CccccccCC
Q 030404 119 CSGCRRKVGLTGFRCRC--GELFCGEHR 144 (178)
Q Consensus 119 C~~C~kkvgl~gf~CrC--g~~FC~~HR 144 (178)
|..|+.-.=|..+.|.| +.++|=.|-
T Consensus 1 C~~Ck~~~yLS~v~C~C~~~~~~CL~H~ 28 (54)
T PF02928_consen 1 CSICKAYCYLSAVTCSCKPDKVVCLRHA 28 (54)
T ss_pred CcccCCchhhcccccCCCCCcEEccccc
Confidence 67788888888999997 899998884
No 52
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=37.20 E-value=20 Score=27.09 Aligned_cols=35 Identities=34% Similarity=0.751 Sum_probs=25.7
Q ss_pred ccccCCccccccccccc---cc-eeee-cCccccccCCCC
Q 030404 112 EKRVVNRCSGCRRKVGL---TG-FRCR-CGELFCGEHRYS 146 (178)
Q Consensus 112 ~~~~~~rC~~C~kkvgl---~g-f~Cr-Cg~~FC~~HRy~ 146 (178)
.+..+-.|..|+++.-. +| ..|+ ||.+|=+---.|
T Consensus 31 ~~~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 31 QQRAKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred HHhcCCcCCCCCCcceeeeccCeEEcCCCCCeeccccccc
Confidence 35578899999987322 23 8998 999998776665
No 53
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=35.92 E-value=24 Score=22.92 Aligned_cols=17 Identities=29% Similarity=0.776 Sum_probs=14.7
Q ss_pred ceee-ecCccccccCCCC
Q 030404 130 GFRC-RCGELFCGEHRYS 146 (178)
Q Consensus 130 gf~C-rCg~~FC~~HRy~ 146 (178)
...| .||..||..++.+
T Consensus 40 ~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 40 RVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred eeECCCCCCeECCCCCCc
Confidence 4899 8999999998865
No 54
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=35.79 E-value=19 Score=29.80 Aligned_cols=18 Identities=39% Similarity=1.147 Sum_probs=15.2
Q ss_pred eeeecCccccccCCCCCCCC
Q 030404 131 FRCRCGELFCGEHRYSDRHD 150 (178)
Q Consensus 131 f~CrCg~~FC~~HRy~e~H~ 150 (178)
|+|.| .||-.||.|.+-+
T Consensus 124 FrC~C--~yC~~~~~~~~~n 141 (160)
T PF15549_consen 124 FRCEC--HYCQSHRNPGERN 141 (160)
T ss_pred eeeee--eeecccCCCcccc
Confidence 89998 7999999776665
No 55
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=35.78 E-value=13 Score=26.25 Aligned_cols=20 Identities=45% Similarity=1.311 Sum_probs=12.2
Q ss_pred CCccccccccccccceee-ecCc
Q 030404 116 VNRCSGCRRKVGLTGFRC-RCGE 137 (178)
Q Consensus 116 ~~rC~~C~kkvgl~gf~C-rCg~ 137 (178)
-.||..||| +|. .|+| .||.
T Consensus 38 I~Rc~~CRk-~g~-~Y~Cp~CGF 58 (61)
T COG2888 38 IYRCAKCRK-LGN-PYRCPKCGF 58 (61)
T ss_pred eehhhhHHH-cCC-ceECCCcCc
Confidence 467777774 333 3777 5764
No 56
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=35.39 E-value=19 Score=24.32 Aligned_cols=23 Identities=26% Similarity=0.658 Sum_probs=19.9
Q ss_pred cCCccccccccccccceeee-cCc
Q 030404 115 VVNRCSGCRRKVGLTGFRCR-CGE 137 (178)
Q Consensus 115 ~~~rC~~C~kkvgl~gf~Cr-Cg~ 137 (178)
...-|..|+-++....-.|| ||+
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 46789999999999999998 875
No 57
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=34.87 E-value=18 Score=34.22 Aligned_cols=26 Identities=31% Similarity=0.769 Sum_probs=20.2
Q ss_pred CCcccccccccccc---ceeee-cCccccc
Q 030404 116 VNRCSGCRRKVGLT---GFRCR-CGELFCG 141 (178)
Q Consensus 116 ~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~ 141 (178)
.-+|-.|++++.-. ||+|+ ||..+=.
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCc
Confidence 35999999988653 79998 9876643
No 58
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=34.46 E-value=24 Score=22.36 Aligned_cols=20 Identities=30% Similarity=0.677 Sum_probs=16.2
Q ss_pred ccceeee-cCccccccCCCCC
Q 030404 128 LTGFRCR-CGELFCGEHRYSD 147 (178)
Q Consensus 128 l~gf~Cr-Cg~~FC~~HRy~e 147 (178)
+-.|+|. ||..|=-.+.+.+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISE 23 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCC
Confidence 4569997 9999988887776
No 59
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=33.76 E-value=31 Score=20.90 Aligned_cols=26 Identities=35% Similarity=0.791 Sum_probs=18.4
Q ss_pred cccccccccc-c-cceeee-cCccccccC
Q 030404 118 RCSGCRRKVG-L-TGFRCR-CGELFCGEH 143 (178)
Q Consensus 118 rC~~C~kkvg-l-~gf~Cr-Cg~~FC~~H 143 (178)
||..|.++-- - +-|.|. |+..+|..|
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~v~lC~~~ 30 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCDVPLCVEP 30 (32)
T ss_pred CCeECCcCCccceeEEEccCCCCcccCCC
Confidence 6777776432 2 679997 988888776
No 60
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=33.30 E-value=11 Score=36.20 Aligned_cols=26 Identities=42% Similarity=1.083 Sum_probs=22.6
Q ss_pred CCcccccccccccc--ceeee-cCccccc
Q 030404 116 VNRCSGCRRKVGLT--GFRCR-CGELFCG 141 (178)
Q Consensus 116 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~ 141 (178)
..-|..|.++.||+ --.|| ||.+.|.
T Consensus 180 V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~ 208 (505)
T KOG1842|consen 180 VQFCPECANSFGLTRRRHHCRLCGRVMCR 208 (505)
T ss_pred ccccccccchhhhHHHhhhhhhcchHHHH
Confidence 35799999999997 58999 9999884
No 61
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=31.97 E-value=17 Score=21.89 Aligned_cols=23 Identities=35% Similarity=0.977 Sum_probs=15.3
Q ss_pred Cccccccccccccceeee-cCcccccc
Q 030404 117 NRCSGCRRKVGLTGFRCR-CGELFCGE 142 (178)
Q Consensus 117 ~rC~~C~kkvgl~gf~Cr-Cg~~FC~~ 142 (178)
..|..|+. ..-++|. |+..||+.
T Consensus 3 ~~C~vC~~---~~kY~Cp~C~~~~CSl 26 (30)
T PF04438_consen 3 KLCSVCGN---PAKYRCPRCGARYCSL 26 (30)
T ss_dssp EEETSSSS---EESEE-TTT--EESSH
T ss_pred CCCccCcC---CCEEECCCcCCceeCc
Confidence 46888887 4568994 99999985
No 62
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=31.95 E-value=27 Score=19.95 Aligned_cols=21 Identities=24% Similarity=0.661 Sum_probs=13.1
Q ss_pred Cccccccccccccceeee-cCc
Q 030404 117 NRCSGCRRKVGLTGFRCR-CGE 137 (178)
Q Consensus 117 ~rC~~C~kkvgl~gf~Cr-Cg~ 137 (178)
..|..|++.+....-.|. ||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 467778776655555665 554
No 63
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=31.55 E-value=20 Score=23.26 Aligned_cols=16 Identities=31% Similarity=0.742 Sum_probs=14.0
Q ss_pred eeee-cCccccccCCCC
Q 030404 131 FRCR-CGELFCGEHRYS 146 (178)
Q Consensus 131 f~Cr-Cg~~FC~~HRy~ 146 (178)
+.|. |+..||..++-+
T Consensus 41 ~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 41 VTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp CCTTSCCSEECSSSTSE
T ss_pred eECCCCCCcCccccCcc
Confidence 7898 999999998864
No 64
>PRK07218 replication factor A; Provisional
Probab=30.56 E-value=23 Score=33.28 Aligned_cols=21 Identities=33% Similarity=0.839 Sum_probs=16.1
Q ss_pred CCccccccccccccceeee-cCcc
Q 030404 116 VNRCSGCRRKVGLTGFRCR-CGEL 138 (178)
Q Consensus 116 ~~rC~~C~kkvgl~gf~Cr-Cg~~ 138 (178)
-.||..|+|+|.. +.|+ ||.+
T Consensus 297 i~rCP~C~r~v~~--~~C~~hG~v 318 (423)
T PRK07218 297 IERCPECGRVIQK--GQCRSHGAV 318 (423)
T ss_pred eecCcCccccccC--CcCCCCCCc
Confidence 3799999999954 6787 6644
No 65
>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=29.48 E-value=37 Score=24.14 Aligned_cols=24 Identities=29% Similarity=0.708 Sum_probs=16.8
Q ss_pred CCccccccccccccceeee-cCccc
Q 030404 116 VNRCSGCRRKVGLTGFRCR-CGELF 139 (178)
Q Consensus 116 ~~rC~~C~kkvgl~gf~Cr-Cg~~F 139 (178)
...|..|+|++|..-|.=- ||.+|
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~ 102 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVV 102 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEE
Confidence 4789999999998654332 55544
No 66
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=29.33 E-value=25 Score=24.89 Aligned_cols=23 Identities=35% Similarity=0.882 Sum_probs=18.1
Q ss_pred cCCcccccccccccc---ceeee-cCc
Q 030404 115 VVNRCSGCRRKVGLT---GFRCR-CGE 137 (178)
Q Consensus 115 ~~~rC~~C~kkvgl~---gf~Cr-Cg~ 137 (178)
-..-|.-|+-+.-|. .+.|| ||+
T Consensus 19 miYiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 19 MIYICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred EEEEeccccccccccCCCcEehhhcch
Confidence 357899999988884 39999 864
No 67
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=29.01 E-value=20 Score=35.67 Aligned_cols=50 Identities=32% Similarity=0.697 Sum_probs=31.9
Q ss_pred Cccccccccccccceeee-cCccc---cccCCCCCCCCCCccchHhhHHHHHHhCCccc
Q 030404 117 NRCSGCRRKVGLTGFRCR-CGELF---CGEHRYSDRHDCSYDYKSAGRDAIARENPVIK 171 (178)
Q Consensus 117 ~rC~~C~kkvgl~gf~Cr-Cg~~F---C~~HRy~e~H~C~fDyk~~~r~~l~k~NP~v~ 171 (178)
--|..|.+++=.+||+|+ ||+.| |+.| -|. .|. +|. -.|+.+...+|-+.
T Consensus 190 ~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~-vp~--~C~-~~~-~~~~~~~~~~~~~~ 243 (678)
T KOG0193|consen 190 AFCDSCCNKFLFTGFRCQTCGYKFHQSCSPR-VPT--SCV-NPD-HLRQLLVFEFPAVG 243 (678)
T ss_pred hhhhhhcchhhhcccccCCCCCccccccCCC-CCC--CCC-Ccc-hHhhhhhhcccccc
Confidence 457777788878999999 99876 4443 222 343 332 34566666666553
No 68
>PHA00616 hypothetical protein
Probab=27.85 E-value=16 Score=24.10 Aligned_cols=11 Identities=45% Similarity=1.410 Sum_probs=7.9
Q ss_pred eee-ecCccccc
Q 030404 131 FRC-RCGELFCG 141 (178)
Q Consensus 131 f~C-rCg~~FC~ 141 (178)
|+| |||.+|..
T Consensus 2 YqC~~CG~~F~~ 13 (44)
T PHA00616 2 YQCLRCGGIFRK 13 (44)
T ss_pred CccchhhHHHhh
Confidence 567 58888864
No 69
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=27.62 E-value=26 Score=18.59 Aligned_cols=9 Identities=44% Similarity=1.575 Sum_probs=4.9
Q ss_pred eeee-cCccc
Q 030404 131 FRCR-CGELF 139 (178)
Q Consensus 131 f~Cr-Cg~~F 139 (178)
|.|. ||..|
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 4554 65555
No 70
>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=26.73 E-value=30 Score=22.10 Aligned_cols=28 Identities=21% Similarity=0.549 Sum_probs=19.6
Q ss_pred CCccccccccccccceeeecCccccccC
Q 030404 116 VNRCSGCRRKVGLTGFRCRCGELFCGEH 143 (178)
Q Consensus 116 ~~rC~~C~kkvgl~gf~CrCg~~FC~~H 143 (178)
=-+|..|++.|...+|.=+=|..||..|
T Consensus 26 Cf~C~~C~~~l~~~~~~~~~~~~~C~~c 53 (58)
T PF00412_consen 26 CFKCSKCGKPLNDGDFYEKDGKPYCKDC 53 (58)
T ss_dssp TSBETTTTCBTTTSSEEEETTEEEEHHH
T ss_pred ccccCCCCCccCCCeeEeECCEEECHHH
Confidence 3678888888877766656666666554
No 71
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=26.68 E-value=23 Score=24.48 Aligned_cols=20 Identities=25% Similarity=0.386 Sum_probs=16.5
Q ss_pred HhhHHHHHHhCCcccccccc
Q 030404 157 SAGRDAIARENPVIKAAKIV 176 (178)
Q Consensus 157 ~~~r~~l~k~NP~v~~~Kl~ 176 (178)
..=|-.|+++||++.-.||-
T Consensus 21 q~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHH
Confidence 34588899999999888874
No 72
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=26.64 E-value=23 Score=22.18 Aligned_cols=29 Identities=24% Similarity=0.503 Sum_probs=19.4
Q ss_pred ccccccccccc--cceeeecCccccccCCCC
Q 030404 118 RCSGCRRKVGL--TGFRCRCGELFCGEHRYS 146 (178)
Q Consensus 118 rC~~C~kkvgl--~gf~CrCg~~FC~~HRy~ 146 (178)
+|..|.++... ..+.=.||.+||..+-..
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~ 31 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKK 31 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHh
Confidence 47778877722 234456999999876543
No 73
>PRK12366 replication factor A; Reviewed
Probab=25.83 E-value=29 Score=33.99 Aligned_cols=29 Identities=28% Similarity=0.732 Sum_probs=21.0
Q ss_pred CCcccccccccccc--ceeee-cCccccccCCC
Q 030404 116 VNRCSGCRRKVGLT--GFRCR-CGELFCGEHRY 145 (178)
Q Consensus 116 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HRy 145 (178)
-.+|..|+|||-.. .|.|. ||.+ =..|||
T Consensus 532 y~aCp~CnkKv~~~~g~~~C~~c~~~-~p~~~~ 563 (637)
T PRK12366 532 LYLCPNCRKRVEEVDGEYICEFCGEV-EPNELL 563 (637)
T ss_pred EecccccCeEeEcCCCcEECCCCCCC-CCcEEE
Confidence 37999999999653 28895 8877 335665
No 74
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=25.83 E-value=29 Score=26.18 Aligned_cols=33 Identities=27% Similarity=0.765 Sum_probs=22.9
Q ss_pred cccCCccccccccccc----cc-eeee-cCccccccCCCC
Q 030404 113 KRVVNRCSGCRRKVGL----TG-FRCR-CGELFCGEHRYS 146 (178)
Q Consensus 113 ~~~~~rC~~C~kkvgl----~g-f~Cr-Cg~~FC~~HRy~ 146 (178)
+.....|..|++.. + +| .+|+ ||.+|-+-=-.|
T Consensus 32 q~~ky~Cp~Cgk~~-vkR~a~GIW~C~~C~~~~AGGAy~~ 70 (90)
T PF01780_consen 32 QHAKYTCPFCGKTS-VKRVATGIWKCKKCGKKFAGGAYTP 70 (90)
T ss_dssp HHS-BEESSSSSSE-EEEEETTEEEETTTTEEEE-BSSSS
T ss_pred HhCCCcCCCCCCce-eEEeeeEEeecCCCCCEEeCCCccc
Confidence 44678999999865 3 13 8998 999998765443
No 75
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=25.67 E-value=26 Score=25.78 Aligned_cols=18 Identities=39% Similarity=0.726 Sum_probs=14.8
Q ss_pred CCccccccccccccceee
Q 030404 116 VNRCSGCRRKVGLTGFRC 133 (178)
Q Consensus 116 ~~rC~~C~kkvgl~gf~C 133 (178)
.-.|..|.+||||=.|+=
T Consensus 19 ~~~C~~C~Rr~GLW~f~~ 36 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFKS 36 (91)
T ss_pred eEEccccCcEeeeeeccc
Confidence 468999999999976654
No 76
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=24.63 E-value=32 Score=35.41 Aligned_cols=45 Identities=27% Similarity=0.659 Sum_probs=30.8
Q ss_pred ccccCCccccccccc--------------cccceeee-cCccccc---------cCCCC----CCCCCCccch
Q 030404 112 EKRVVNRCSGCRRKV--------------GLTGFRCR-CGELFCG---------EHRYS----DRHDCSYDYK 156 (178)
Q Consensus 112 ~~~~~~rC~~C~kkv--------------gl~gf~Cr-Cg~~FC~---------~HRy~----e~H~C~fDyk 156 (178)
+...+|.|..|.|-| |-..|+|+ ||.-|-- .||-. -.|.|.+-|-
T Consensus 601 ~~TdPNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~i 673 (958)
T KOG1074|consen 601 KRTDPNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTFI 673 (958)
T ss_pred ccCCccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchhh
Confidence 345789999998744 33359999 9999963 34432 5677875543
No 77
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=23.52 E-value=38 Score=20.39 Aligned_cols=12 Identities=42% Similarity=1.115 Sum_probs=6.9
Q ss_pred cceeee-cCcccc
Q 030404 129 TGFRCR-CGELFC 140 (178)
Q Consensus 129 ~gf~Cr-Cg~~FC 140 (178)
-.|+|. ||..|=
T Consensus 4 Y~y~C~~Cg~~fe 16 (41)
T smart00834 4 YEYRCEDCGHTFE 16 (41)
T ss_pred EEEEcCCCCCEEE
Confidence 346665 666554
No 78
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=23.00 E-value=46 Score=23.81 Aligned_cols=27 Identities=26% Similarity=0.498 Sum_probs=11.3
Q ss_pred CCccccccccccccceeeecCcccccc
Q 030404 116 VNRCSGCRRKVGLTGFRCRCGELFCGE 142 (178)
Q Consensus 116 ~~rC~~C~kkvgl~gf~CrCg~~FC~~ 142 (178)
--||..|.--+...--.=.|+++||+.
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~ 33 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSS 33 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TT
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHH
Confidence 468898887654433334689999985
No 79
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=21.67 E-value=50 Score=23.24 Aligned_cols=13 Identities=38% Similarity=0.907 Sum_probs=11.4
Q ss_pred eeeecCcc-------ccccC
Q 030404 131 FRCRCGEL-------FCGEH 143 (178)
Q Consensus 131 f~CrCg~~-------FC~~H 143 (178)
|.|-||.. ||..|
T Consensus 51 ~~CDCG~~~~~~~~~~C~~h 70 (71)
T smart00396 51 GICDCGDKEAWNEDLKCKAH 70 (71)
T ss_pred EEECCCChhccCCCcccccc
Confidence 89999988 88887
No 80
>smart00508 PostSET Cysteine-rich motif following a subset of SET domains.
Probab=21.08 E-value=50 Score=19.54 Aligned_cols=11 Identities=36% Similarity=0.878 Sum_probs=9.8
Q ss_pred eeeecCccccc
Q 030404 131 FRCRCGELFCG 141 (178)
Q Consensus 131 f~CrCg~~FC~ 141 (178)
|.|+||...|-
T Consensus 3 ~~C~CGs~~CR 13 (26)
T smart00508 3 QPCLCGAPNCR 13 (26)
T ss_pred eeeeCCCcccc
Confidence 78999999886
No 81
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=20.91 E-value=35 Score=26.11 Aligned_cols=18 Identities=28% Similarity=0.661 Sum_probs=11.5
Q ss_pred ccccccceeee-cCccccc
Q 030404 124 RKVGLTGFRCR-CGELFCG 141 (178)
Q Consensus 124 kkvgl~gf~Cr-Cg~~FC~ 141 (178)
++|=+..-.|| ||++|=.
T Consensus 52 ~~Llv~Pa~CkkCGfef~~ 70 (97)
T COG3357 52 KRLLVRPARCKKCGFEFRD 70 (97)
T ss_pred ceEEecChhhcccCccccc
Confidence 34444467887 8888754
No 82
>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=20.74 E-value=50 Score=25.98 Aligned_cols=11 Identities=27% Similarity=0.863 Sum_probs=9.1
Q ss_pred CCccccccccc
Q 030404 116 VNRCSGCRRKV 126 (178)
Q Consensus 116 ~~rC~~C~kkv 126 (178)
-.||..||..+
T Consensus 91 ~sRC~~CN~~L 101 (147)
T PF01927_consen 91 FSRCPKCNGPL 101 (147)
T ss_pred CCccCCCCcEe
Confidence 58999999766
No 83
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=20.38 E-value=56 Score=18.42 Aligned_cols=10 Identities=40% Similarity=1.364 Sum_probs=5.4
Q ss_pred ceeee-cCccc
Q 030404 130 GFRCR-CGELF 139 (178)
Q Consensus 130 gf~Cr-Cg~~F 139 (178)
.|.|. |+..|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 36665 55554
No 84
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.37 E-value=67 Score=21.63 Aligned_cols=24 Identities=25% Similarity=0.636 Sum_probs=17.2
Q ss_pred cCCccccccccccc--c--ceeee-cCcc
Q 030404 115 VVNRCSGCRRKVGL--T--GFRCR-CGEL 138 (178)
Q Consensus 115 ~~~rC~~C~kkvgl--~--gf~Cr-Cg~~ 138 (178)
....|..|+.++.- . .|.|. ||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 45679999988776 2 48887 7665
No 85
>PRK08197 threonine synthase; Validated
Probab=20.35 E-value=46 Score=30.12 Aligned_cols=31 Identities=19% Similarity=0.399 Sum_probs=23.7
Q ss_pred CCccccccccccccc--eeeecCccccccCCCC
Q 030404 116 VNRCSGCRRKVGLTG--FRCRCGELFCGEHRYS 146 (178)
Q Consensus 116 ~~rC~~C~kkvgl~g--f~CrCg~~FC~~HRy~ 146 (178)
.-+|..|++...+.. +.|+||..+=-.+.|+
T Consensus 7 ~~~C~~Cg~~~~~~~~~~~C~cg~~l~~~~d~~ 39 (394)
T PRK08197 7 HLECSKCGETYDADQVHNLCKCGKPLLVRYDLE 39 (394)
T ss_pred EEEECCCCCCCCCCCcceecCCCCeeEEEechh
Confidence 469999999998864 6899987765555543
Done!