Query 042575
Match_columns 169
No_of_seqs 151 out of 432
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 07:31:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042575.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042575hhsearch_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 5.1E-45 1.1E-49 294.5 8.9 149 6-169 15-167 (167)
2 PF01754 zf-A20: A20-like zinc 99.5 2.4E-15 5.3E-20 87.6 1.9 25 6-30 1-25 (25)
3 smart00154 ZnF_AN1 AN1-like Zi 99.5 3.1E-15 6.6E-20 95.0 2.3 38 109-146 1-39 (39)
4 smart00259 ZnF_A20 A20-like zi 99.5 1.1E-14 2.3E-19 85.6 1.2 25 6-30 1-26 (26)
5 PF01428 zf-AN1: AN1-like Zinc 99.1 3.3E-11 7.2E-16 77.4 1.3 38 109-147 1-41 (43)
6 COG3582 Predicted nucleic acid 96.8 0.0006 1.3E-08 55.6 1.7 37 109-146 100-137 (162)
7 KOG3183 Predicted Zn-finger pr 96.1 0.0021 4.5E-08 55.5 0.8 41 106-147 8-51 (250)
8 PF01363 FYVE: FYVE zinc finge 92.8 0.054 1.2E-06 36.8 1.3 29 106-134 9-40 (69)
9 cd00065 FYVE FYVE domain; Zinc 92.5 0.051 1.1E-06 35.4 0.8 29 106-134 2-33 (57)
10 KOG3183 Predicted Zn-finger pr 91.6 0.037 8E-07 47.9 -0.9 38 106-143 98-139 (250)
11 smart00064 FYVE Protein presen 91.6 0.081 1.8E-06 35.8 0.9 29 106-134 10-41 (68)
12 KOG1818 Membrane trafficking a 87.9 0.19 4.2E-06 48.7 0.6 43 106-148 165-221 (634)
13 PF10571 UPF0547: Uncharacteri 87.6 0.28 6.1E-06 28.6 1.0 22 108-129 2-24 (26)
14 PF00130 C1_1: Phorbol esters/ 85.2 0.48 1E-05 30.5 1.2 23 106-128 11-37 (53)
15 PF02148 zf-UBP: Zn-finger in 74.1 1.7 3.7E-05 29.3 1.1 23 109-132 1-24 (63)
16 PF15135 UPF0515: Uncharacteri 68.2 2.4 5.3E-05 37.3 1.0 26 106-131 132-167 (278)
17 KOG1729 FYVE finger containing 62.9 1.9 4.1E-05 38.2 -0.7 32 106-138 168-203 (288)
18 cd00029 C1 Protein kinase C co 62.7 3.8 8.3E-05 25.3 0.9 23 106-128 11-37 (50)
19 smart00109 C1 Protein kinase C 62.0 4.1 8.9E-05 24.9 0.9 23 106-128 11-36 (49)
20 PHA02768 hypothetical protein; 60.8 3.6 7.7E-05 28.1 0.5 15 117-131 2-17 (55)
21 COG1996 RPC10 DNA-directed RNA 59.1 4.3 9.3E-05 27.2 0.7 24 106-129 6-34 (49)
22 PF08882 Acetone_carb_G: Aceto 53.0 7 0.00015 30.3 1.1 35 110-146 16-50 (112)
23 PF13978 DUF4223: Protein of u 52.8 6.4 0.00014 26.9 0.7 18 129-146 19-36 (56)
24 PF03604 DNA_RNApol_7kD: DNA d 52.6 6.6 0.00014 23.9 0.7 20 108-127 2-25 (32)
25 KOG1819 FYVE finger-containing 52.1 4.3 9.3E-05 39.4 -0.3 28 106-133 901-931 (990)
26 PHA00626 hypothetical protein 50.8 8.2 0.00018 26.8 1.0 24 106-131 11-35 (59)
27 PF03107 C1_2: C1 domain; Int 50.7 11 0.00024 22.0 1.4 20 108-127 2-23 (30)
28 PF07649 C1_3: C1-like domain; 50.7 7 0.00015 22.7 0.6 22 108-129 2-25 (30)
29 smart00659 RPOLCX RNA polymera 49.9 8.4 0.00018 24.8 0.9 21 107-127 3-27 (44)
30 smart00290 ZnF_UBP Ubiquitin C 49.6 5.4 0.00012 25.2 -0.0 24 108-133 1-25 (50)
31 PTZ00303 phosphatidylinositol 47.8 9.7 0.00021 38.8 1.4 27 107-133 461-495 (1374)
32 PF05207 zf-CSL: CSL zinc fing 47.4 8.4 0.00018 25.8 0.6 14 118-131 16-29 (55)
33 PF01194 RNA_pol_N: RNA polyme 47.4 9.4 0.0002 26.5 0.9 13 106-118 4-16 (60)
34 PF14471 DUF4428: Domain of un 45.5 10 0.00022 25.1 0.8 22 108-129 1-30 (51)
35 PRK04016 DNA-directed RNA poly 44.7 8.2 0.00018 27.0 0.3 13 106-118 4-16 (62)
36 PF07975 C1_4: TFIIH C1-like d 44.4 9.6 0.00021 25.6 0.5 34 109-142 2-47 (51)
37 PRK00398 rpoP DNA-directed RNA 44.3 13 0.00028 23.6 1.1 29 106-134 3-36 (46)
38 COG1571 Predicted DNA-binding 43.9 10 0.00022 35.4 0.9 54 106-161 350-409 (421)
39 PF13842 Tnp_zf-ribbon_2: DDE_ 42.6 18 0.0004 21.7 1.5 26 108-133 2-30 (32)
40 PLN00032 DNA-directed RNA poly 42.5 9.7 0.00021 27.4 0.4 13 106-118 4-16 (71)
41 KOG2807 RNA polymerase II tran 42.5 12 0.00026 34.2 1.1 27 106-132 330-358 (378)
42 PF13240 zinc_ribbon_2: zinc-r 40.9 15 0.00033 20.5 0.9 20 108-127 1-21 (23)
43 PF02928 zf-C5HC2: C5HC2 zinc 40.6 14 0.0003 24.4 0.9 27 109-135 1-29 (54)
44 KOG1812 Predicted E3 ubiquitin 40.6 16 0.00036 33.2 1.6 29 106-134 306-338 (384)
45 COG1997 RPL43A Ribosomal prote 40.4 17 0.00037 27.2 1.4 30 106-136 35-70 (89)
46 PF02318 FYVE_2: FYVE-type zin 40.0 18 0.0004 27.2 1.6 31 106-136 54-88 (118)
47 KOG3497 DNA-directed RNA polym 39.4 11 0.00023 26.7 0.2 13 106-118 4-16 (69)
48 smart00647 IBR In Between Ring 39.2 20 0.00044 23.0 1.5 18 119-136 39-57 (64)
49 PRK08402 replication factor A; 38.8 13 0.00028 33.7 0.7 29 106-135 212-245 (355)
50 PRK04136 rpl40e 50S ribosomal 38.4 16 0.00035 24.4 0.9 22 106-127 14-36 (48)
51 cd04476 RPA1_DBD_C RPA1_DBD_C: 38.0 14 0.0003 28.9 0.7 31 106-136 34-69 (166)
52 PF13717 zinc_ribbon_4: zinc-r 36.7 19 0.0004 22.1 0.9 9 121-129 26-35 (36)
53 PF01780 Ribosomal_L37ae: Ribo 34.9 18 0.00039 27.0 0.8 31 106-137 35-71 (90)
54 PF06750 DiS_P_DiS: Bacterial 34.6 21 0.00046 26.2 1.1 13 106-118 33-45 (92)
55 KOG3507 DNA-directed RNA polym 34.6 18 0.00039 25.4 0.7 22 106-127 20-45 (62)
56 PF01485 IBR: IBR domain; Int 34.3 18 0.00039 23.2 0.6 16 121-136 41-57 (64)
57 KOG1074 Transcriptional repres 33.9 28 0.0006 35.5 2.1 40 106-145 605-672 (958)
58 PF15549 PGC7_Stella: PGC7/Ste 33.9 22 0.00047 29.2 1.2 19 120-140 123-141 (160)
59 PF09723 Zn-ribbon_8: Zinc rib 33.1 27 0.00059 21.8 1.3 20 118-137 3-23 (42)
60 COG1644 RPB10 DNA-directed RNA 33.0 15 0.00032 25.9 0.1 13 106-118 4-16 (63)
61 PF10367 Vps39_2: Vacuolar sor 31.8 32 0.00069 24.3 1.6 24 106-129 78-102 (109)
62 KOG0193 Serine/threonine prote 31.5 17 0.00038 35.7 0.3 49 107-161 190-243 (678)
63 PF13248 zf-ribbon_3: zinc-rib 30.7 29 0.00062 19.6 1.0 21 107-127 3-24 (26)
64 PF00096 zf-C2H2: Zinc finger, 30.7 21 0.00046 18.7 0.4 9 121-129 1-10 (23)
65 PRK07218 replication factor A; 29.8 24 0.00052 32.8 0.9 21 106-128 297-318 (423)
66 COG3582 Predicted nucleic acid 29.2 30 0.00065 28.4 1.3 35 125-159 19-53 (162)
67 PF08600 Rsm1: Rsm1-like; Int 28.8 21 0.00047 26.0 0.3 17 106-122 19-35 (91)
68 PF09538 FYDLN_acid: Protein o 28.1 34 0.00075 26.0 1.3 25 106-130 9-37 (108)
69 PF08073 CHDNT: CHDNT (NUC034) 28.1 26 0.00056 24.0 0.6 20 147-166 21-40 (55)
70 PF04438 zf-HIT: HIT zinc fing 27.8 21 0.00046 21.2 0.1 23 107-132 3-26 (30)
71 PF10122 Mu-like_Com: Mu-like 27.1 23 0.00049 24.0 0.2 24 106-129 4-34 (51)
72 KOG1842 FYVE finger-containing 26.5 17 0.00037 34.5 -0.7 26 106-131 180-208 (505)
73 COG3357 Predicted transcriptio 26.0 25 0.00054 26.6 0.2 16 116-131 54-70 (97)
74 PF13465 zf-H2C2_2: Zinc-finge 25.7 37 0.00081 19.0 0.9 10 120-129 14-24 (26)
75 PF11781 RRN7: RNA polymerase 25.1 33 0.00072 21.1 0.6 22 107-128 9-34 (36)
76 smart00834 CxxC_CXXC_SSSS Puta 25.0 36 0.00078 20.3 0.8 14 119-132 4-18 (41)
77 PF12662 cEGF: Complement Clr- 24.4 67 0.0015 18.3 1.8 20 120-142 1-20 (24)
78 PF14634 zf-RING_5: zinc-RING 24.2 42 0.00091 20.8 1.0 29 108-136 1-31 (44)
79 PF00412 LIM: LIM domain; Int 24.1 33 0.00072 21.7 0.5 28 106-133 26-53 (58)
80 PRK12366 replication factor A; 23.8 32 0.0007 33.3 0.6 29 106-135 532-563 (637)
81 COG1773 Rubredoxin [Energy pro 22.2 37 0.0008 23.2 0.5 13 120-132 3-16 (55)
82 PF13923 zf-C3HC4_2: Zinc fing 22.1 43 0.00093 20.1 0.7 23 109-131 1-23 (39)
83 PTZ00218 40S ribosomal protein 21.8 50 0.0011 22.5 1.1 13 22-34 34-46 (54)
84 COG1552 RPL40A Ribosomal prote 21.0 27 0.00058 23.6 -0.4 23 106-128 14-37 (50)
85 PF14446 Prok-RING_1: Prokaryo 20.9 56 0.0012 22.2 1.2 24 106-129 5-31 (54)
86 PF14835 zf-RING_6: zf-RING of 20.6 55 0.0012 23.1 1.1 28 106-133 7-34 (65)
87 PF11722 zf-TRM13_CCCH: CCCH z 20.3 44 0.00095 20.1 0.5 10 125-134 21-30 (31)
No 1
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=5.1e-45 Score=294.48 Aligned_cols=149 Identities=40% Similarity=0.827 Sum_probs=99.3
Q ss_pred ccccccCCCCCCcccCCCchhhhhhHHHHHHHHhh-hhhhhhhhhccCCCCCCCCCCccCCCCCch-hhhhcccccCCcc
Q 042575 6 VTMCMKGCGFYGSKENKNMCSKCYDDYLKAELIAK-SSKLLDAAKKSIGPTNAPNPSVLDKSWPPQ-WIISAAKTTNTSN 83 (169)
Q Consensus 6 p~lC~n~CGFfGs~at~n~CSkCyr~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 83 (169)
++||.|||||||+|+|+||||+||++++.++++.. ..+.. +...+. ++. .+....++. .... .+..
T Consensus 15 ~~lc~~gCGf~G~p~~~n~CSkC~~e~~~~~~~~~~~~~~~--~~~~~~-~~~----s~~~~~~~~~~~~~-----~~~~ 82 (167)
T KOG3173|consen 15 DLLCVNGCGFYGSPATENLCSKCYRDHLLRQQQKQARASPP--VESSLS-SPR----SVPSRDPPAVSLES-----TTES 82 (167)
T ss_pred ccccccCccccCChhhccHHHHHHHHHHHHhhhccccccCc--cccccc-Ccc----ccCccccccccccc-----cccc
Confidence 58999999999999999999999999998887652 21111 101100 000 000000000 0000 0000
Q ss_pred ccCCcccCCCccc--cccCCCCCcccccccccccccccceeeecCcccccCCCCCCCCCCcccchhhhHHHHHHhCCccc
Q 042575 84 AVDSRASNQTTST--IESGAGSSVKRRCEICNKKVGLIEFRCRCGHLYCGTHRYPKEHACTFDFKKFDREMLVKDNPLIR 161 (169)
Q Consensus 84 ~~~~~~~~~~~~~--~~~~~~~~~~~rC~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk~~gr~~l~k~np~v~ 161 (169)
+.......+++ .........++||+.|+|||||+||.||||++||+.|||||.|+|+||||.+||+.|+++||+|+
T Consensus 83 --~~~~~~~~~s~~~~~~~~~~~~~~rC~~C~kk~gltgf~CrCG~~fC~~HRy~e~H~C~fDyK~~gr~~i~k~nP~v~ 160 (167)
T KOG3173|consen 83 --ELKLVSDTPSTEEEDEESKPKKKKRCFKCRKKVGLTGFKCRCGNTFCGTHRYPEQHDCSFDYKQAGREKIAKANPVVK 160 (167)
T ss_pred --cccccccCCcccccccccccccchhhhhhhhhhcccccccccCCcccccccCCccccccccHHHHHHHHHHHhCCeee
Confidence 00000000000 01111122278999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCC
Q 042575 162 ADKLEGRI 169 (169)
Q Consensus 162 ~~Kl~~KI 169 (169)
++||+ ||
T Consensus 161 a~k~~-ki 167 (167)
T KOG3173|consen 161 ADKLQ-KI 167 (167)
T ss_pred ccccc-cC
Confidence 99999 98
No 2
>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=99.54 E-value=2.4e-15 Score=87.59 Aligned_cols=25 Identities=52% Similarity=1.360 Sum_probs=21.0
Q ss_pred ccccccCCCCCCcccCCCchhhhhh
Q 042575 6 VTMCMKGCGFYGSKENKNMCSKCYD 30 (169)
Q Consensus 6 p~lC~n~CGFfGs~at~n~CSkCyr 30 (169)
|+||++|||||||++|+||||+|||
T Consensus 1 ~~~C~~gCgf~Gs~~~~~~Cs~C~~ 25 (25)
T PF01754_consen 1 PSLCANGCGFYGSPATNGLCSKCYR 25 (25)
T ss_dssp SSB-TTTSSSB-BGGGTTS-HHHHH
T ss_pred CCcccCCCCCcccccccCcchhhcC
Confidence 6799999999999999999999997
No 3
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.53 E-value=3.1e-15 Score=95.04 Aligned_cols=38 Identities=58% Similarity=1.430 Sum_probs=36.9
Q ss_pred cccccccccccceeee-cCcccccCCCCCCCCCCcccch
Q 042575 109 CEICNKKVGLIEFRCR-CGHLYCGTHRYPKEHACTFDFK 146 (169)
Q Consensus 109 C~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 146 (169)
|+.|+++++|++|+|+ |+++||..|||||+|+|++|||
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 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=99.47 E-value=1.1e-14 Score=85.59 Aligned_cols=25 Identities=40% Similarity=1.172 Sum_probs=23.6
Q ss_pred ccccc-cCCCCCCcccCCCchhhhhh
Q 042575 6 VTMCM-KGCGFYGSKENKNMCSKCYD 30 (169)
Q Consensus 6 p~lC~-n~CGFfGs~at~n~CSkCyr 30 (169)
|++|. +|||||||++|+||||||||
T Consensus 1 ~~~C~~~~CgF~G~~~t~~~CskCy~ 26 (26)
T smart00259 1 PIKCRRPGCGFFGNPATEGLCSKCFK 26 (26)
T ss_pred CCccccCCCCCcCChhhcccCHhhcC
Confidence 46899 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=3.3e-11 Score=77.43 Aligned_cols=38 Identities=42% Similarity=1.015 Sum_probs=28.1
Q ss_pred ccc--ccccccccceeee-cCcccccCCCCCCCCCCcccchh
Q 042575 109 CEI--CNKKVGLIEFRCR-CGHLYCGTHRYPKEHACTFDFKK 147 (169)
Q Consensus 109 C~~--C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 147 (169)
|.. |++++. ++|.|+ |+..||..|||||.|+|+++++.
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 455 899888 699999 99999999999999999999974
No 6
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=96.80 E-value=0.0006 Score=55.58 Aligned_cols=37 Identities=27% Similarity=0.546 Sum_probs=29.9
Q ss_pred cccccccccccceeee-cCcccccCCCCCCCCCCcccch
Q 042575 109 CEICNKKVGLIEFRCR-CGHLYCGTHRYPKEHACTFDFK 146 (169)
Q Consensus 109 C~~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk 146 (169)
|..|++..+| .++|- |++.||+.||+++.|+|.+...
T Consensus 100 ~~~~g~~s~l-~~~c~~c~g~fc~~h~lp~nhdc~~L~s 137 (162)
T COG3582 100 PQCTGKGSTL-AGKCNYCTGYFCAEHRLPENHDCNGLGS 137 (162)
T ss_pred ceeccCCccc-cccccCCCCcceeceecccccccccHHH
Confidence 3444454444 78999 9999999999999999998875
No 7
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=96.09 E-value=0.0021 Score=55.52 Aligned_cols=41 Identities=24% Similarity=0.835 Sum_probs=35.8
Q ss_pred ccccc--cccccccccceeee-cCcccccCCCCCCCCCCcccchh
Q 042575 106 KRRCE--ICNKKVGLIEFRCR-CGHLYCGTHRYPKEHACTFDFKK 147 (169)
Q Consensus 106 ~~rC~--~C~kkvgl~gf~Cr-Cg~~FC~~HRy~e~H~C~fDyk~ 147 (169)
...|. .|+. +.++.|+|- |+.+||..||.-+.|.|.+-+..
T Consensus 8 GkHCs~~~Ckq-lDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~ 51 (250)
T KOG3183|consen 8 GKHCSVPYCKQ-LDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRI 51 (250)
T ss_pred ccccCcchhhh-ccccceeeCCccchhhhccchHhhcCCCccccc
Confidence 45677 7765 688999999 99999999999999999998863
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=92.85 E-value=0.054 Score=36.83 Aligned_cols=29 Identities=38% Similarity=0.981 Sum_probs=17.4
Q ss_pred cccccccccccccc--ceeee-cCcccccCCC
Q 042575 106 KRRCEICNKKVGLI--EFRCR-CGHLYCGTHR 134 (169)
Q Consensus 106 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HR 134 (169)
...|..|+++.+|+ -..|| ||.+||+.+-
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs 40 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCS 40 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EEECCCS
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEECCchh
Confidence 57999999999995 47999 9999997653
No 9
>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=92.51 E-value=0.051 Score=35.44 Aligned_cols=29 Identities=31% Similarity=0.865 Sum_probs=24.3
Q ss_pred cccccccccccccc--ceeee-cCcccccCCC
Q 042575 106 KRRCEICNKKVGLI--EFRCR-CGHLYCGTHR 134 (169)
Q Consensus 106 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HR 134 (169)
...|..|+++.++. ...|| ||.+||..+-
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~ 33 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCS 33 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHHc
Confidence 35799999999994 68999 9999998543
No 10
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=91.64 E-value=0.037 Score=47.94 Aligned_cols=38 Identities=34% Similarity=0.920 Sum_probs=32.3
Q ss_pred ccccc--ccccccccc-ceeee-cCcccccCCCCCCCCCCcc
Q 042575 106 KRRCE--ICNKKVGLI-EFRCR-CGHLYCGTHRYPKEHACTF 143 (169)
Q Consensus 106 ~~rC~--~C~kkvgl~-gf~Cr-Cg~~FC~~HRy~e~H~C~f 143 (169)
.++|. .|+|++-+. .+.|+ ||..||-+||++-.|.|.-
T Consensus 98 t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~~ 139 (250)
T KOG3183|consen 98 TNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCNK 139 (250)
T ss_pred cccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhhh
Confidence 56676 688887773 69999 9999999999999999983
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=87.90 E-value=0.19 Score=48.65 Aligned_cols=43 Identities=28% Similarity=0.756 Sum_probs=34.4
Q ss_pred ccccccccccccccc--eeee-cCcccccCCC-----------CCCCCCCcccchhh
Q 042575 106 KRRCEICNKKVGLIE--FRCR-CGHLYCGTHR-----------YPKEHACTFDFKKF 148 (169)
Q Consensus 106 ~~rC~~C~kkvgl~g--f~Cr-Cg~~FC~~HR-----------y~e~H~C~fDyk~~ 148 (169)
...|..|+.+.|+++ ..|| ||.+||+.|- |-+.--|..||...
T Consensus 165 ~~~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l 221 (634)
T KOG1818|consen 165 SEECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELL 221 (634)
T ss_pred ccccceeeeeeeeccccccccccchhhccCccccccCcccccccccceehhhhHHHh
Confidence 579999999999975 6899 9999999874 34556677777533
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=87.60 E-value=0.28 Score=28.57 Aligned_cols=22 Identities=27% Similarity=0.593 Sum_probs=20.2
Q ss_pred ccccccccccccceeee-cCccc
Q 042575 108 RCEICNKKVGLIEFRCR-CGHLY 129 (169)
Q Consensus 108 rC~~C~kkvgl~gf~Cr-Cg~~F 129 (169)
+|-.|++.|.+..-.|- ||+.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 68999999999999999 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=85.20 E-value=0.48 Score=30.46 Aligned_cols=23 Identities=35% Similarity=1.021 Sum_probs=18.5
Q ss_pred ccccccccccc---cccceeee-cCcc
Q 042575 106 KRRCEICNKKV---GLIEFRCR-CGHL 128 (169)
Q Consensus 106 ~~rC~~C~kkv---gl~gf~Cr-Cg~~ 128 (169)
+..|..|++.| ++.|++|+ |+.+
T Consensus 11 ~~~C~~C~~~i~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 11 PTYCDVCGKFIWGLGKQGYRCSWCGLV 37 (53)
T ss_dssp TEB-TTSSSBECSSSSCEEEETTTT-E
T ss_pred CCCCcccCcccCCCCCCeEEECCCCCh
Confidence 78999999999 66899999 8765
No 15
>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=74.12 E-value=1.7 Score=29.34 Aligned_cols=23 Identities=30% Similarity=0.896 Sum_probs=15.8
Q ss_pred cccccccccccceeee-cCcccccC
Q 042575 109 CEICNKKVGLIEFRCR-CGHLYCGT 132 (169)
Q Consensus 109 C~~C~kkvgl~gf~Cr-Cg~~FC~~ 132 (169)
|..|+.. +-.-+.|- ||.++|+.
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 5677765 44567788 99999994
No 16
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=68.17 E-value=2.4 Score=37.27 Aligned_cols=26 Identities=42% Similarity=1.039 Sum_probs=22.0
Q ss_pred cccccccccc---------ccccceeee-cCccccc
Q 042575 106 KRRCEICNKK---------VGLIEFRCR-CGHLYCG 131 (169)
Q Consensus 106 ~~rC~~C~kk---------vgl~gf~Cr-Cg~~FC~ 131 (169)
.+||..|+|| .|+--|.|. |+++|=+
T Consensus 132 VSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 132 VSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRG 167 (278)
T ss_pred cccccccccccCCCccccccceeeeecccccccchh
Confidence 6899999998 677789995 9999954
No 17
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=62.90 E-value=1.9 Score=38.16 Aligned_cols=32 Identities=25% Similarity=0.712 Sum_probs=25.9
Q ss_pred ccccccccc-ccccc--ceeee-cCcccccCCCCCCC
Q 042575 106 KRRCEICNK-KVGLI--EFRCR-CGHLYCGTHRYPKE 138 (169)
Q Consensus 106 ~~rC~~C~k-kvgl~--gf~Cr-Cg~~FC~~HRy~e~ 138 (169)
.++|..|.+ .-.|. --.|| ||.+||. |.....
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~-~Cs~n~ 203 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCA-PCSRNR 203 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhh-hhhcCc
Confidence 689999999 77774 35899 9999999 876543
No 18
>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=62.70 E-value=3.8 Score=25.34 Aligned_cols=23 Identities=26% Similarity=0.648 Sum_probs=19.1
Q ss_pred ccccccccccccc---cceeee-cCcc
Q 042575 106 KRRCEICNKKVGL---IEFRCR-CGHL 128 (169)
Q Consensus 106 ~~rC~~C~kkvgl---~gf~Cr-Cg~~ 128 (169)
+..|..|++.+.. .|++|+ |+.+
T Consensus 11 ~~~C~~C~~~i~~~~~~~~~C~~C~~~ 37 (50)
T cd00029 11 PTFCDVCRKSIWGLFKQGLRCSWCKVK 37 (50)
T ss_pred CCChhhcchhhhccccceeEcCCCCCc
Confidence 6789999999884 799999 7654
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=62.04 E-value=4.1 Score=24.88 Aligned_cols=23 Identities=26% Similarity=0.651 Sum_probs=18.7
Q ss_pred ccccccccccccc--cceeee-cCcc
Q 042575 106 KRRCEICNKKVGL--IEFRCR-CGHL 128 (169)
Q Consensus 106 ~~rC~~C~kkvgl--~gf~Cr-Cg~~ 128 (169)
+..|..|++.+.. .|++|+ |+.+
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~ 36 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVK 36 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCch
Confidence 6789999999887 489998 7543
No 20
>PHA02768 hypothetical protein; Provisional
Probab=60.81 E-value=3.6 Score=28.12 Aligned_cols=15 Identities=33% Similarity=1.099 Sum_probs=11.3
Q ss_pred cccceeee-cCccccc
Q 042575 117 GLIEFRCR-CGHLYCG 131 (169)
Q Consensus 117 gl~gf~Cr-Cg~~FC~ 131 (169)
.|+||.|- ||..|=.
T Consensus 2 ~~~~y~C~~CGK~Fs~ 17 (55)
T PHA02768 2 ALLGYECPICGEIYIK 17 (55)
T ss_pred cccccCcchhCCeecc
Confidence 46788888 8888754
No 21
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=59.07 E-value=4.3 Score=27.16 Aligned_cols=24 Identities=33% Similarity=0.856 Sum_probs=19.6
Q ss_pred ccccccccccccc----cceeee-cCccc
Q 042575 106 KRRCEICNKKVGL----IEFRCR-CGHLY 129 (169)
Q Consensus 106 ~~rC~~C~kkvgl----~gf~Cr-Cg~~F 129 (169)
..+|..|++++.+ .+..|. ||+-.
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcEE
Confidence 6899999999985 478999 87543
No 22
>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=53.00 E-value=7 Score=30.35 Aligned_cols=35 Identities=29% Similarity=0.444 Sum_probs=26.1
Q ss_pred ccccccccccceeeecCcccccCCCCCCCCCCcccch
Q 042575 110 EICNKKVGLIEFRCRCGHLYCGTHRYPKEHACTFDFK 146 (169)
Q Consensus 110 ~~C~kkvgl~gf~CrCg~~FC~~HRy~e~H~C~fDyk 146 (169)
+.|+++- .-.+|+||+.||+-+.-=..|.--++-.
T Consensus 16 ~i~~~~~--k~vkc~CGh~f~d~r~NwK~~alv~vRd 50 (112)
T PF08882_consen 16 WIVQKKD--KVVKCDCGHEFCDARENWKLGALVYVRD 50 (112)
T ss_pred EEEEecC--ceeeccCCCeecChhcChhhCcEEEecC
Confidence 5666655 2789999999999988777776555443
No 23
>PF13978 DUF4223: Protein of unknown function (DUF4223)
Probab=52.80 E-value=6.4 Score=26.92 Aligned_cols=18 Identities=33% Similarity=0.748 Sum_probs=16.0
Q ss_pred cccCCCCCCCCCCcccch
Q 042575 129 YCGTHRYPKEHACTFDFK 146 (169)
Q Consensus 129 FC~~HRy~e~H~C~fDyk 146 (169)
-|--|-|-.+.+|+|||-
T Consensus 19 ~CTG~v~Nk~knCsYDYl 36 (56)
T PF13978_consen 19 ACTGHVENKEKNCSYDYL 36 (56)
T ss_pred hccceeeccCCCCcceee
Confidence 477899999999999996
No 24
>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=52.57 E-value=6.6 Score=23.87 Aligned_cols=20 Identities=45% Similarity=1.016 Sum_probs=12.1
Q ss_pred ccccccccccc---cceeee-cCc
Q 042575 108 RCEICNKKVGL---IEFRCR-CGH 127 (169)
Q Consensus 108 rC~~C~kkvgl---~gf~Cr-Cg~ 127 (169)
.|..|+..+.| ...+|+ ||+
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeEcCCCCcEECCcCCC
Confidence 46777777777 346777 654
No 25
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=52.05 E-value=4.3 Score=39.39 Aligned_cols=28 Identities=29% Similarity=0.903 Sum_probs=20.7
Q ss_pred ccccccccccccc--cceeee-cCcccccCC
Q 042575 106 KRRCEICNKKVGL--IEFRCR-CGHLYCGTH 133 (169)
Q Consensus 106 ~~rC~~C~kkvgl--~gf~Cr-Cg~~FC~~H 133 (169)
.-+|..|.-.... .--.|| ||++||++-
T Consensus 901 a~~cmacq~pf~afrrrhhcrncggifcg~c 931 (990)
T KOG1819|consen 901 AEQCMACQMPFNAFRRRHHCRNCGGIFCGKC 931 (990)
T ss_pred chhhhhccCcHHHHHHhhhhcccCceeeccc
Confidence 4689999765443 234899 999999864
No 26
>PHA00626 hypothetical protein
Probab=50.76 E-value=8.2 Score=26.79 Aligned_cols=24 Identities=13% Similarity=0.166 Sum_probs=16.4
Q ss_pred ccccccccccccccceeee-cCccccc
Q 042575 106 KRRCEICNKKVGLIEFRCR-CGHLYCG 131 (169)
Q Consensus 106 ~~rC~~C~kkvgl~gf~Cr-Cg~~FC~ 131 (169)
-.||.+|++-. +-|+|. ||+.|-.
T Consensus 11 Ivrcg~cr~~s--nrYkCkdCGY~ft~ 35 (59)
T PHA00626 11 IAKEKTMRGWS--DDYVCCDCGYNDSK 35 (59)
T ss_pred eeeeceecccC--cceEcCCCCCeech
Confidence 34777777732 458998 8887753
No 27
>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=50.72 E-value=11 Score=22.03 Aligned_cols=20 Identities=25% Similarity=0.928 Sum_probs=16.6
Q ss_pred cccccccccccc-ceeee-cCc
Q 042575 108 RCEICNKKVGLI-EFRCR-CGH 127 (169)
Q Consensus 108 rC~~C~kkvgl~-gf~Cr-Cg~ 127 (169)
.|..|++++.-. .|.|. |+.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f 23 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCF 23 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCC
Confidence 589999999888 89997 653
No 28
>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=50.72 E-value=7 Score=22.70 Aligned_cols=22 Identities=32% Similarity=0.822 Sum_probs=8.8
Q ss_pred ccccccccccc-cceeee-cCccc
Q 042575 108 RCEICNKKVGL-IEFRCR-CGHLY 129 (169)
Q Consensus 108 rC~~C~kkvgl-~gf~Cr-Cg~~F 129 (169)
+|..|++.+.. ..|.|. |...+
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 68999999888 789998 76654
No 29
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=49.88 E-value=8.4 Score=24.84 Aligned_cols=21 Identities=33% Similarity=0.830 Sum_probs=16.2
Q ss_pred ccccccccccccc---ceeee-cCc
Q 042575 107 RRCEICNKKVGLI---EFRCR-CGH 127 (169)
Q Consensus 107 ~rC~~C~kkvgl~---gf~Cr-Cg~ 127 (169)
.+|..|+..+.+. +.+|+ ||+
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCc
Confidence 5799999988883 67887 754
No 30
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=49.65 E-value=5.4 Score=25.16 Aligned_cols=24 Identities=33% Similarity=0.952 Sum_probs=18.0
Q ss_pred ccccccccccccceeee-cCcccccCC
Q 042575 108 RCEICNKKVGLIEFRCR-CGHLYCGTH 133 (169)
Q Consensus 108 rC~~C~kkvgl~gf~Cr-Cg~~FC~~H 133 (169)
||..|..... -+.|- |+.++|+..
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 46776 999999764
No 31
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=47.76 E-value=9.7 Score=38.82 Aligned_cols=27 Identities=26% Similarity=0.607 Sum_probs=20.9
Q ss_pred cccccccccccc-------cceeee-cCcccccCC
Q 042575 107 RRCEICNKKVGL-------IEFRCR-CGHLYCGTH 133 (169)
Q Consensus 107 ~rC~~C~kkvgl-------~gf~Cr-Cg~~FC~~H 133 (169)
..|..|+++-+. .--.|| ||.+||+..
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~C 495 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFC 495 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccc
Confidence 579999999863 234599 999998754
No 32
>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=47.43 E-value=8.4 Score=25.80 Aligned_cols=14 Identities=29% Similarity=0.790 Sum_probs=10.8
Q ss_pred ccceeeecCccccc
Q 042575 118 LIEFRCRCGHLYCG 131 (169)
Q Consensus 118 l~gf~CrCg~~FC~ 131 (169)
...+.||||..|--
T Consensus 16 ~~~y~CRCG~~f~i 29 (55)
T PF05207_consen 16 VYSYPCRCGGEFEI 29 (55)
T ss_dssp EEEEEETTSSEEEE
T ss_pred EEEEcCCCCCEEEE
Confidence 35789999998753
No 33
>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=47.43 E-value=9.4 Score=26.54 Aligned_cols=13 Identities=38% Similarity=0.749 Sum_probs=10.2
Q ss_pred ccccccccccccc
Q 042575 106 KRRCEICNKKVGL 118 (169)
Q Consensus 106 ~~rC~~C~kkvgl 118 (169)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvi~~ 16 (60)
T PF01194_consen 4 PVRCFTCGKVIGN 16 (60)
T ss_dssp SSS-STTTSBTCG
T ss_pred ceecCCCCCChhH
Confidence 6799999998874
No 34
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=45.50 E-value=10 Score=25.14 Aligned_cols=22 Identities=41% Similarity=1.103 Sum_probs=16.2
Q ss_pred cccccccccccc-------ceeee-cCccc
Q 042575 108 RCEICNKKVGLI-------EFRCR-CGHLY 129 (169)
Q Consensus 108 rC~~C~kkvgl~-------gf~Cr-Cg~~F 129 (169)
+|..|++++||+ ||-|. |-...
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 599999999994 46677 64333
No 35
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=44.67 E-value=8.2 Score=27.03 Aligned_cols=13 Identities=31% Similarity=0.598 Sum_probs=11.2
Q ss_pred ccccccccccccc
Q 042575 106 KRRCEICNKKVGL 118 (169)
Q Consensus 106 ~~rC~~C~kkvgl 118 (169)
|-||++|+|-+|-
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 6799999998764
No 36
>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=44.35 E-value=9.6 Score=25.59 Aligned_cols=34 Identities=26% Similarity=0.588 Sum_probs=15.5
Q ss_pred ccccccccccc--------ceeee-cCcccccC---CCCCCCCCCc
Q 042575 109 CEICNKKVGLI--------EFRCR-CGHLYCGT---HRYPKEHACT 142 (169)
Q Consensus 109 C~~C~kkvgl~--------gf~Cr-Cg~~FC~~---HRy~e~H~C~ 142 (169)
|+.|.+.+.-. .|.|. |+..||.. --+-.-|+|.
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 66666666553 58887 99999852 2223456664
No 37
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=44.29 E-value=13 Score=23.55 Aligned_cols=29 Identities=31% Similarity=0.679 Sum_probs=20.7
Q ss_pred ccccccccccccc----cceeee-cCcccccCCC
Q 042575 106 KRRCEICNKKVGL----IEFRCR-CGHLYCGTHR 134 (169)
Q Consensus 106 ~~rC~~C~kkvgl----~gf~Cr-Cg~~FC~~HR 134 (169)
..+|..|+..+.+ ..+.|. ||..+--.+|
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 4689999998755 368898 8776655554
No 38
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.93 E-value=10 Score=35.36 Aligned_cols=54 Identities=24% Similarity=0.406 Sum_probs=33.3
Q ss_pred ccccccccccccc---cceeee-cCcccccCCCCCC--CCCCcccchhhhHHHHHHhCCccc
Q 042575 106 KRRCEICNKKVGL---IEFRCR-CGHLYCGTHRYPK--EHACTFDFKKFDREMLVKDNPLIR 161 (169)
Q Consensus 106 ~~rC~~C~kkvgl---~gf~Cr-Cg~~FC~~HRy~e--~H~C~fDyk~~gr~~l~k~np~v~ 161 (169)
.-+|..|++++-- .||+|+ ||..+=..-+-.= .-.=.+++-..+|..|.| |.+-
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~~~~~~v~r~l~~g~evp~~arRHLsk--P~~~ 409 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARETLIKEVPRDLEPGVEVPPVARRHLSK--PLVL 409 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCcccccccccccCCCCcCCchhhhhccC--Ccch
Confidence 3599999998755 489999 9887644322211 111223455667777766 5543
No 39
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=42.59 E-value=18 Score=21.71 Aligned_cols=26 Identities=31% Similarity=0.810 Sum_probs=18.8
Q ss_pred ccccccccccc--cceeee-cCcccccCC
Q 042575 108 RCEICNKKVGL--IEFRCR-CGHLYCGTH 133 (169)
Q Consensus 108 rC~~C~kkvgl--~gf~Cr-Cg~~FC~~H 133 (169)
||..|.++--. +.|.|. |+...|..|
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 67778775222 679998 887777766
No 40
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=42.53 E-value=9.7 Score=27.38 Aligned_cols=13 Identities=38% Similarity=0.749 Sum_probs=11.1
Q ss_pred ccccccccccccc
Q 042575 106 KRRCEICNKKVGL 118 (169)
Q Consensus 106 ~~rC~~C~kkvgl 118 (169)
|-||++|+|-+|-
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 6799999998764
No 41
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=42.48 E-value=12 Score=34.22 Aligned_cols=27 Identities=26% Similarity=0.774 Sum_probs=22.7
Q ss_pred ccccccc-cccccccceeee-cCcccccC
Q 042575 106 KRRCEIC-NKKVGLIEFRCR-CGHLYCGT 132 (169)
Q Consensus 106 ~~rC~~C-~kkvgl~gf~Cr-Cg~~FC~~ 132 (169)
.++|+.| .+.++-..|.|+ |-++||..
T Consensus 330 ~~~Cf~C~~~~~~~~~y~C~~Ck~~FCld 358 (378)
T KOG2807|consen 330 SRFCFACQGELLSSGRYRCESCKNVFCLD 358 (378)
T ss_pred CcceeeeccccCCCCcEEchhccceeecc
Confidence 6789999 666677789999 99999963
No 42
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=40.89 E-value=15 Score=20.52 Aligned_cols=20 Identities=25% Similarity=0.592 Sum_probs=11.0
Q ss_pred ccccccccccccceeee-cCc
Q 042575 108 RCEICNKKVGLIEFRCR-CGH 127 (169)
Q Consensus 108 rC~~C~kkvgl~gf~Cr-Cg~ 127 (169)
+|..|++++.-..-.|. ||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 35666666655444455 543
No 43
>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=40.61 E-value=14 Score=24.44 Aligned_cols=27 Identities=30% Similarity=0.716 Sum_probs=22.2
Q ss_pred cccccccccccceeeec--CcccccCCCC
Q 042575 109 CEICNKKVGLIEFRCRC--GHLYCGTHRY 135 (169)
Q Consensus 109 C~~C~kkvgl~gf~CrC--g~~FC~~HRy 135 (169)
|..|+.-.=|..+.|.| +.++|-.|--
T Consensus 1 C~~Ck~~~yLS~v~C~C~~~~~~CL~H~~ 29 (54)
T PF02928_consen 1 CSICKAYCYLSAVTCSCKPDKVVCLRHAK 29 (54)
T ss_pred CcccCCchhhcccccCCCCCcEEccccch
Confidence 67788877788899997 8999999853
No 44
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.57 E-value=16 Score=33.21 Aligned_cols=29 Identities=34% Similarity=0.849 Sum_probs=24.3
Q ss_pred cccccccccccccc----ceeeecCcccccCCC
Q 042575 106 KRRCEICNKKVGLI----EFRCRCGHLYCGTHR 134 (169)
Q Consensus 106 ~~rC~~C~kkvgl~----gf~CrCg~~FC~~HR 134 (169)
-.+|..|+-.+.|. -++||||+-||..=.
T Consensus 306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~ 338 (384)
T KOG1812|consen 306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCG 338 (384)
T ss_pred cCcCcccceeeeecCCcceEEeeccccchhhcC
Confidence 57899999988883 489999999997655
No 45
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=40.43 E-value=17 Score=27.16 Aligned_cols=30 Identities=30% Similarity=0.885 Sum_probs=23.8
Q ss_pred ccccccccccccc----cc-eeee-cCcccccCCCCC
Q 042575 106 KRRCEICNKKVGL----IE-FRCR-CGHLYCGTHRYP 136 (169)
Q Consensus 106 ~~rC~~C~kkvgl----~g-f~Cr-Cg~~FC~~HRy~ 136 (169)
+..|..|+++ .+ +| ..|+ ||.+|=+---.|
T Consensus 35 ~~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 35 KHVCPFCGRT-TVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred CCcCCCCCCc-ceeeeccCeEEcCCCCCeeccccccc
Confidence 7899999998 33 34 6999 999998876665
No 46
>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=40.00 E-value=18 Score=27.24 Aligned_cols=31 Identities=29% Similarity=0.669 Sum_probs=23.9
Q ss_pred cccccccccccccc---ceeee-cCcccccCCCCC
Q 042575 106 KRRCEICNKKVGLI---EFRCR-CGHLYCGTHRYP 136 (169)
Q Consensus 106 ~~rC~~C~kkvgl~---gf~Cr-Cg~~FC~~HRy~ 136 (169)
...|..|.+.+|++ |..|. |...+|..=+.-
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc
Confidence 57999999999984 78999 999999875543
No 47
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=39.38 E-value=11 Score=26.75 Aligned_cols=13 Identities=38% Similarity=0.713 Sum_probs=11.2
Q ss_pred ccccccccccccc
Q 042575 106 KRRCEICNKKVGL 118 (169)
Q Consensus 106 ~~rC~~C~kkvgl 118 (169)
|-||++|+|-+|-
T Consensus 4 PiRCFtCGKvig~ 16 (69)
T KOG3497|consen 4 PIRCFTCGKVIGD 16 (69)
T ss_pred eeEeeeccccccc
Confidence 6799999998874
No 48
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=39.15 E-value=20 Score=23.03 Aligned_cols=18 Identities=28% Similarity=0.864 Sum_probs=14.9
Q ss_pred cceee-ecCcccccCCCCC
Q 042575 119 IEFRC-RCGHLYCGTHRYP 136 (169)
Q Consensus 119 ~gf~C-rCg~~FC~~HRy~ 136 (169)
..+.| .||..||..++.+
T Consensus 39 ~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 39 NRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred CeeECCCCCCeECCCCCCc
Confidence 45789 7999999998865
No 49
>PRK08402 replication factor A; Reviewed
Probab=38.80 E-value=13 Score=33.68 Aligned_cols=29 Identities=21% Similarity=0.367 Sum_probs=19.2
Q ss_pred ccccccccccccc----cceeee-cCcccccCCCC
Q 042575 106 KRRCEICNKKVGL----IEFRCR-CGHLYCGTHRY 135 (169)
Q Consensus 106 ~~rC~~C~kkvgl----~gf~Cr-Cg~~FC~~HRy 135 (169)
-.+|..|+|||-. ..+.|. ||.+-+ .|||
T Consensus 212 y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p-~~ry 245 (355)
T PRK08402 212 YDACPECRRKVDYDPATDTWICPEHGEVEP-IKIT 245 (355)
T ss_pred EecCCCCCeEEEEecCCCCEeCCCCCCcCc-ceeE
Confidence 3699999999963 347777 554433 4553
No 50
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=38.36 E-value=16 Score=24.40 Aligned_cols=22 Identities=36% Similarity=0.816 Sum_probs=19.5
Q ss_pred ccccccccccccccceeee-cCc
Q 042575 106 KRRCEICNKKVGLIEFRCR-CGH 127 (169)
Q Consensus 106 ~~rC~~C~kkvgl~gf~Cr-Cg~ 127 (169)
..-|..|.-+.....-.|| ||+
T Consensus 14 k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 14 KKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred ccchhcccCCCCccccccccCCC
Confidence 6689999999999999999 876
No 51
>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=37.99 E-value=14 Score=28.91 Aligned_cols=31 Identities=35% Similarity=0.584 Sum_probs=22.5
Q ss_pred cccccccccccccc---ceeee-cCccc-ccCCCCC
Q 042575 106 KRRCEICNKKVGLI---EFRCR-CGHLY-CGTHRYP 136 (169)
Q Consensus 106 ~~rC~~C~kkvgl~---gf~Cr-Cg~~F-C~~HRy~ 136 (169)
=..|..|+|||-.. .|.|. |+..+ =-.+||-
T Consensus 34 Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~ 69 (166)
T cd04476 34 YPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYI 69 (166)
T ss_pred EccccccCcccEeCCCCcEECCCCCCcCCCccEEEE
Confidence 56789999998775 48888 87765 4455663
No 52
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=36.66 E-value=19 Score=22.09 Aligned_cols=9 Identities=56% Similarity=1.741 Sum_probs=5.1
Q ss_pred eeee-cCccc
Q 042575 121 FRCR-CGHLY 129 (169)
Q Consensus 121 f~Cr-Cg~~F 129 (169)
.+|. ||.+|
T Consensus 26 v~C~~C~~~f 35 (36)
T PF13717_consen 26 VRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEe
Confidence 4555 66554
No 53
>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=34.87 E-value=18 Score=27.00 Aligned_cols=31 Identities=29% Similarity=0.851 Sum_probs=22.1
Q ss_pred ccccccccccccc----cc-eeee-cCcccccCCCCCC
Q 042575 106 KRRCEICNKKVGL----IE-FRCR-CGHLYCGTHRYPK 137 (169)
Q Consensus 106 ~~rC~~C~kkvgl----~g-f~Cr-Cg~~FC~~HRy~e 137 (169)
...|..|+|.. + +| .+|+ ||.+|-+-=..|+
T Consensus 35 ky~Cp~Cgk~~-vkR~a~GIW~C~~C~~~~AGGAy~~~ 71 (90)
T PF01780_consen 35 KYTCPFCGKTS-VKRVATGIWKCKKCGKKFAGGAYTPS 71 (90)
T ss_dssp -BEESSSSSSE-EEEEETTEEEETTTTEEEE-BSSSSS
T ss_pred CCcCCCCCCce-eEEeeeEEeecCCCCCEEeCCCcccc
Confidence 78999999874 3 34 7999 9999987654443
No 54
>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=34.65 E-value=21 Score=26.16 Aligned_cols=13 Identities=15% Similarity=0.649 Sum_probs=11.5
Q ss_pred ccccccccccccc
Q 042575 106 KRRCEICNKKVGL 118 (169)
Q Consensus 106 ~~rC~~C~kkvgl 118 (169)
+++|..|++++..
T Consensus 33 rS~C~~C~~~L~~ 45 (92)
T PF06750_consen 33 RSHCPHCGHPLSW 45 (92)
T ss_pred CCcCcCCCCcCcc
Confidence 7899999999876
No 55
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=34.64 E-value=18 Score=25.35 Aligned_cols=22 Identities=36% Similarity=0.727 Sum_probs=18.6
Q ss_pred ccccccccccccc---cceeee-cCc
Q 042575 106 KRRCEICNKKVGL---IEFRCR-CGH 127 (169)
Q Consensus 106 ~~rC~~C~kkvgl---~gf~Cr-Cg~ 127 (169)
..-|.-|+.+..| ..+.|| ||+
T Consensus 20 iYiCgdC~~en~lk~~D~irCReCG~ 45 (62)
T KOG3507|consen 20 IYICGDCGQENTLKRGDVIRCRECGY 45 (62)
T ss_pred EEEeccccccccccCCCcEehhhcch
Confidence 6889999999888 369999 875
No 56
>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=34.31 E-value=18 Score=23.20 Aligned_cols=16 Identities=31% Similarity=0.825 Sum_probs=14.1
Q ss_pred eeee-cCcccccCCCCC
Q 042575 121 FRCR-CGHLYCGTHRYP 136 (169)
Q Consensus 121 f~Cr-Cg~~FC~~HRy~ 136 (169)
+.|. |+..||..++-+
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 7899 999999998854
No 57
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=33.88 E-value=28 Score=35.49 Aligned_cols=40 Identities=28% Similarity=0.779 Sum_probs=29.2
Q ss_pred ccccccccccc--------------cccceeee-cCccccc---------CCC----CCCCCCCcccc
Q 042575 106 KRRCEICNKKV--------------GLIEFRCR-CGHLYCG---------THR----YPKEHACTFDF 145 (169)
Q Consensus 106 ~~rC~~C~kkv--------------gl~gf~Cr-Cg~~FC~---------~HR----y~e~H~C~fDy 145 (169)
+|.|-+|.|-| |-..|+|+ ||+-|-- .|| +.-.|.|.+-|
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R~q~ScP~~~ 672 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPARVQFSCPSTF 672 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCccccccccCCchh
Confidence 89999998754 34679999 9999963 344 33577888554
No 58
>PF15549 PGC7_Stella: PGC7/Stella/Dppa3 domain
Probab=33.87 E-value=22 Score=29.22 Aligned_cols=19 Identities=53% Similarity=1.281 Sum_probs=15.6
Q ss_pred ceeeecCcccccCCCCCCCCC
Q 042575 120 EFRCRCGHLYCGTHRYPKEHA 140 (169)
Q Consensus 120 gf~CrCg~~FC~~HRy~e~H~ 140 (169)
-|+|.| .||-.||.|.+-+
T Consensus 123 ~FrC~C--~yC~~~~~~~~~n 141 (160)
T PF15549_consen 123 RFRCEC--HYCQSHRNPGERN 141 (160)
T ss_pred ceeeee--eeecccCCCcccc
Confidence 589998 7999999776666
No 59
>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=33.13 E-value=27 Score=21.85 Aligned_cols=20 Identities=30% Similarity=0.801 Sum_probs=15.9
Q ss_pred ccceeee-cCcccccCCCCCC
Q 042575 118 LIEFRCR-CGHLYCGTHRYPK 137 (169)
Q Consensus 118 l~gf~Cr-Cg~~FC~~HRy~e 137 (169)
+-.|+|. ||..|=-.+...+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISE 23 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCC
Confidence 4468898 9999988877776
No 60
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=32.99 E-value=15 Score=25.89 Aligned_cols=13 Identities=38% Similarity=0.746 Sum_probs=11.0
Q ss_pred ccccccccccccc
Q 042575 106 KRRCEICNKKVGL 118 (169)
Q Consensus 106 ~~rC~~C~kkvgl 118 (169)
|-||++|+|-+|-
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 6799999998764
No 61
>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=31.82 E-value=32 Score=24.27 Aligned_cols=24 Identities=33% Similarity=0.836 Sum_probs=16.9
Q ss_pred ccccccccccccccceeee-cCccc
Q 042575 106 KRRCEICNKKVGLIEFRCR-CGHLY 129 (169)
Q Consensus 106 ~~rC~~C~kkvgl~gf~Cr-Cg~~F 129 (169)
...|..|+|++|...|.=- ||.+|
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~~~v~ 102 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPCGHVV 102 (109)
T ss_pred CCCccCcCCcCCCceEEEeCCCeEE
Confidence 5689999999998555332 55544
No 62
>KOG0193 consensus Serine/threonine protein kinase RAF [Signal transduction mechanisms]
Probab=31.53 E-value=17 Score=35.73 Aligned_cols=49 Identities=33% Similarity=0.757 Sum_probs=33.1
Q ss_pred cccccccccccccceeee-cCccc---ccCCCCCCCCCCc-ccchhhhHHHHHHhCCccc
Q 042575 107 RRCEICNKKVGLIEFRCR-CGHLY---CGTHRYPKEHACT-FDFKKFDREMLVKDNPLIR 161 (169)
Q Consensus 107 ~rC~~C~kkvgl~gf~Cr-Cg~~F---C~~HRy~e~H~C~-fDyk~~gr~~l~k~np~v~ 161 (169)
--|..|.+++=.+||+|+ ||+.| |+.|- |. .|. +|. .|+.+...+|-+.
T Consensus 190 ~fC~~~~~~~l~~gfrC~~C~~KfHq~Cs~~v-p~--~C~~~~~---~~~~~~~~~~~~~ 243 (678)
T KOG0193|consen 190 AFCDSCCNKFLFTGFRCQTCGYKFHQSCSPRV-PT--SCVNPDH---LRQLLVFEFPAVG 243 (678)
T ss_pred hhhhhhcchhhhcccccCCCCCccccccCCCC-CC--CCCCcch---Hhhhhhhcccccc
Confidence 457778888888999999 99976 54443 22 343 333 4667777777664
No 63
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=30.72 E-value=29 Score=19.62 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=13.1
Q ss_pred cccccccccccccceeee-cCc
Q 042575 107 RRCEICNKKVGLIEFRCR-CGH 127 (169)
Q Consensus 107 ~rC~~C~kkvgl~gf~Cr-Cg~ 127 (169)
..|..|++.+.-..-.|. ||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 467777776655555665 553
No 64
>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=30.67 E-value=21 Score=18.73 Aligned_cols=9 Identities=33% Similarity=1.483 Sum_probs=4.6
Q ss_pred eeee-cCccc
Q 042575 121 FRCR-CGHLY 129 (169)
Q Consensus 121 f~Cr-Cg~~F 129 (169)
|.|. ||..|
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 4455 55555
No 65
>PRK07218 replication factor A; Provisional
Probab=29.76 E-value=24 Score=32.77 Aligned_cols=21 Identities=29% Similarity=0.683 Sum_probs=16.5
Q ss_pred ccccccccccccccceeee-cCcc
Q 042575 106 KRRCEICNKKVGLIEFRCR-CGHL 128 (169)
Q Consensus 106 ~~rC~~C~kkvgl~gf~Cr-Cg~~ 128 (169)
-.||..|+|+|.. ..|+ ||.+
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 4899999999854 7788 6654
No 66
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=29.18 E-value=30 Score=28.38 Aligned_cols=35 Identities=11% Similarity=0.091 Sum_probs=21.3
Q ss_pred cCcccccCCCCCCCCCCcccchhhhHHHHHHhCCc
Q 042575 125 CGHLYCGTHRYPKEHACTFDFKKFDREMLVKDNPL 159 (169)
Q Consensus 125 Cg~~FC~~HRy~e~H~C~fDyk~~gr~~l~k~np~ 159 (169)
|+.+||..|+.+-.|.|.+--..-.|-.|++.-|.
T Consensus 19 ~~kv~s~~~~~~~~~~f~~~i~~~~r~~i~k~~~~ 53 (162)
T COG3582 19 TAKVSSTDNSLTLFSPFKLFIQLCDRKKIKKPDPG 53 (162)
T ss_pred eeeeccCccccccccccchhhhhhhhhccccCCCc
Confidence 44567777777777777776444445555544443
No 67
>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=28.83 E-value=21 Score=25.98 Aligned_cols=17 Identities=29% Similarity=0.757 Sum_probs=14.0
Q ss_pred cccccccccccccccee
Q 042575 106 KRRCEICNKKVGLIEFR 122 (169)
Q Consensus 106 ~~rC~~C~kkvgl~gf~ 122 (169)
--.|..|.+||||=.|+
T Consensus 19 ~~~C~~C~Rr~GLW~f~ 35 (91)
T PF08600_consen 19 LLSCSYCFRRLGLWMFK 35 (91)
T ss_pred eEEccccCcEeeeeecc
Confidence 45899999999996654
No 68
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=28.13 E-value=34 Score=26.02 Aligned_cols=25 Identities=32% Similarity=0.720 Sum_probs=17.9
Q ss_pred cccccccccc---ccccceeee-cCcccc
Q 042575 106 KRRCEICNKK---VGLIEFRCR-CGHLYC 130 (169)
Q Consensus 106 ~~rC~~C~kk---vgl~gf~Cr-Cg~~FC 130 (169)
+..|..|++| |+.....|- ||..|=
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGTEFP 37 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCCccC
Confidence 6789999998 444567777 666653
No 69
>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=28.08 E-value=26 Score=23.98 Aligned_cols=20 Identities=35% Similarity=0.419 Sum_probs=16.0
Q ss_pred hhhHHHHHHhCCcccccccc
Q 042575 147 KFDREMLVKDNPLIRADKLE 166 (169)
Q Consensus 147 ~~gr~~l~k~np~v~~~Kl~ 166 (169)
..=|-.|+++||++.-.||.
T Consensus 21 q~vRP~l~~~NPk~~~sKl~ 40 (55)
T PF08073_consen 21 QHVRPLLAKANPKAPMSKLM 40 (55)
T ss_pred HHHHHHHHHHCCCCcHHHHH
Confidence 34478899999999888874
No 70
>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=27.82 E-value=21 Score=21.20 Aligned_cols=23 Identities=35% Similarity=1.158 Sum_probs=14.8
Q ss_pred cccccccccccccceeee-cCcccccC
Q 042575 107 RRCEICNKKVGLIEFRCR-CGHLYCGT 132 (169)
Q Consensus 107 ~rC~~C~kkvgl~gf~Cr-Cg~~FC~~ 132 (169)
..|..|+. .--++|. |+..||++
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 3458887 88889875
No 71
>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=27.06 E-value=23 Score=23.97 Aligned_cols=24 Identities=33% Similarity=0.844 Sum_probs=17.6
Q ss_pred ccccccccccccc------cceeee-cCccc
Q 042575 106 KRRCEICNKKVGL------IEFRCR-CGHLY 129 (169)
Q Consensus 106 ~~rC~~C~kkvgl------~gf~Cr-Cg~~F 129 (169)
.-||..|+|.|.. ...+|- ||.++
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 4699999998776 245775 77654
No 72
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=26.52 E-value=17 Score=34.50 Aligned_cols=26 Identities=35% Similarity=0.961 Sum_probs=22.3
Q ss_pred cccccccccccccc--ceeee-cCccccc
Q 042575 106 KRRCEICNKKVGLI--EFRCR-CGHLYCG 131 (169)
Q Consensus 106 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~ 131 (169)
.--|..|.++.||+ --.|| ||.+.|.
T Consensus 180 V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~ 208 (505)
T KOG1842|consen 180 VQFCPECANSFGLTRRRHHCRLCGRVMCR 208 (505)
T ss_pred ccccccccchhhhHHHhhhhhhcchHHHH
Confidence 35899999999996 57999 9999884
No 73
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=26.03 E-value=25 Score=26.65 Aligned_cols=16 Identities=25% Similarity=0.648 Sum_probs=10.5
Q ss_pred ccccceeee-cCccccc
Q 042575 116 VGLIEFRCR-CGHLYCG 131 (169)
Q Consensus 116 vgl~gf~Cr-Cg~~FC~ 131 (169)
+-+..-.|| ||++|=.
T Consensus 54 Llv~Pa~CkkCGfef~~ 70 (97)
T COG3357 54 LLVRPARCKKCGFEFRD 70 (97)
T ss_pred EEecChhhcccCccccc
Confidence 334566787 8888754
No 74
>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=25.65 E-value=37 Score=18.96 Aligned_cols=10 Identities=30% Similarity=1.318 Sum_probs=5.3
Q ss_pred ceeee-cCccc
Q 042575 120 EFRCR-CGHLY 129 (169)
Q Consensus 120 gf~Cr-Cg~~F 129 (169)
.|+|. |+..|
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 45555 55544
No 75
>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=25.06 E-value=33 Score=21.15 Aligned_cols=22 Identities=32% Similarity=0.907 Sum_probs=17.1
Q ss_pred ccccccccccccc--c-eee-ecCcc
Q 042575 107 RRCEICNKKVGLI--E-FRC-RCGHL 128 (169)
Q Consensus 107 ~rC~~C~kkvgl~--g-f~C-rCg~~ 128 (169)
-+|..|+-+.... | |.| +||.+
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 4699999996663 4 789 79875
No 76
>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=24.99 E-value=36 Score=20.30 Aligned_cols=14 Identities=43% Similarity=1.068 Sum_probs=7.5
Q ss_pred cceeee-cCcccccC
Q 042575 119 IEFRCR-CGHLYCGT 132 (169)
Q Consensus 119 ~gf~Cr-Cg~~FC~~ 132 (169)
-.|+|. ||..|=..
T Consensus 4 Y~y~C~~Cg~~fe~~ 18 (41)
T smart00834 4 YEYRCEDCGHTFEVL 18 (41)
T ss_pred EEEEcCCCCCEEEEE
Confidence 345666 66655433
No 77
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=24.39 E-value=67 Score=18.26 Aligned_cols=20 Identities=25% Similarity=0.768 Sum_probs=12.9
Q ss_pred ceeeecCcccccCCCCCCCCCCc
Q 042575 120 EFRCRCGHLYCGTHRYPKEHACT 142 (169)
Q Consensus 120 gf~CrCg~~FC~~HRy~e~H~C~ 142 (169)
+|.|.|..-| ..-++.|.|.
T Consensus 1 sy~C~C~~Gy---~l~~d~~~C~ 20 (24)
T PF12662_consen 1 SYTCSCPPGY---QLSPDGRSCE 20 (24)
T ss_pred CEEeeCCCCC---cCCCCCCccc
Confidence 5888886544 3445777774
No 78
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=24.23 E-value=42 Score=20.76 Aligned_cols=29 Identities=28% Similarity=0.620 Sum_probs=19.7
Q ss_pred ccccccccccc--cceeeecCcccccCCCCC
Q 042575 108 RCEICNKKVGL--IEFRCRCGHLYCGTHRYP 136 (169)
Q Consensus 108 rC~~C~kkvgl--~gf~CrCg~~FC~~HRy~ 136 (169)
+|..|.++... ..+-=.||.+||..+...
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~ 31 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKK 31 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHh
Confidence 47778887722 344556999999876543
No 79
>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=24.10 E-value=33 Score=21.65 Aligned_cols=28 Identities=25% Similarity=0.485 Sum_probs=19.5
Q ss_pred ccccccccccccccceeeecCcccccCC
Q 042575 106 KRRCEICNKKVGLIEFRCRCGHLYCGTH 133 (169)
Q Consensus 106 ~~rC~~C~kkvgl~gf~CrCg~~FC~~H 133 (169)
=-+|..|++.|...+|.=+=|..||..|
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 3578889988887666555566666554
No 80
>PRK12366 replication factor A; Reviewed
Probab=23.82 E-value=32 Score=33.30 Aligned_cols=29 Identities=28% Similarity=0.636 Sum_probs=20.7
Q ss_pred cccccccccccccc--ceeee-cCcccccCCCC
Q 042575 106 KRRCEICNKKVGLI--EFRCR-CGHLYCGTHRY 135 (169)
Q Consensus 106 ~~rC~~C~kkvgl~--gf~Cr-Cg~~FC~~HRy 135 (169)
-.+|..|+|||-.. .|.|. ||.+ =..|||
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 47999999999653 37886 8877 234555
No 81
>COG1773 Rubredoxin [Energy production and conversion]
Probab=22.25 E-value=37 Score=23.23 Aligned_cols=13 Identities=38% Similarity=1.040 Sum_probs=9.0
Q ss_pred ceeee-cCcccccC
Q 042575 120 EFRCR-CGHLYCGT 132 (169)
Q Consensus 120 gf~Cr-Cg~~FC~~ 132 (169)
-++|+ ||++|=..
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 36788 88887443
No 82
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=22.08 E-value=43 Score=20.05 Aligned_cols=23 Identities=30% Similarity=0.749 Sum_probs=12.4
Q ss_pred cccccccccccceeeecCccccc
Q 042575 109 CEICNKKVGLIEFRCRCGHLYCG 131 (169)
Q Consensus 109 C~~C~kkvgl~gf~CrCg~~FC~ 131 (169)
|..|...+.-.-..-.||++||.
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~ 23 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCK 23 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEH
T ss_pred CCCCCCcccCcCEECCCCCchhH
Confidence 34454433332245569999985
No 83
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=21.79 E-value=50 Score=22.54 Aligned_cols=13 Identities=23% Similarity=0.864 Sum_probs=11.1
Q ss_pred CCchhhhhhHHHH
Q 042575 22 KNMCSKCYDDYLK 34 (169)
Q Consensus 22 ~n~CSkCyr~~~~ 34 (169)
.|||..|||+...
T Consensus 34 L~~CRqCFRe~A~ 46 (54)
T PTZ00218 34 LNVCRQCFRENAE 46 (54)
T ss_pred cchhhHHHHHhhH
Confidence 5799999999864
No 84
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=21.01 E-value=27 Score=23.57 Aligned_cols=23 Identities=30% Similarity=0.687 Sum_probs=18.4
Q ss_pred ccccccccccccccceeee-cCcc
Q 042575 106 KRRCEICNKKVGLIEFRCR-CGHL 128 (169)
Q Consensus 106 ~~rC~~C~kkvgl~gf~Cr-Cg~~ 128 (169)
..-|..|+-+-+...-+|| ||+.
T Consensus 14 kkIC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 14 KKICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred HHHHHHhcCCCCcchhHHhhccCC
Confidence 4568888889888889999 7653
No 85
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=20.92 E-value=56 Score=22.24 Aligned_cols=24 Identities=38% Similarity=0.826 Sum_probs=18.7
Q ss_pred ccccccccccc--cccceeee-cCccc
Q 042575 106 KRRCEICNKKV--GLIEFRCR-CGHLY 129 (169)
Q Consensus 106 ~~rC~~C~kkv--gl~gf~Cr-Cg~~F 129 (169)
..+|..|++++ +-....|- ||-.+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcc
Confidence 57999999999 55567888 77664
No 86
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=20.63 E-value=55 Score=23.14 Aligned_cols=28 Identities=25% Similarity=0.560 Sum_probs=11.3
Q ss_pred ccccccccccccccceeeecCcccccCC
Q 042575 106 KRRCEICNKKVGLIEFRCRCGHLYCGTH 133 (169)
Q Consensus 106 ~~rC~~C~kkvgl~gf~CrCg~~FC~~H 133 (169)
--||+.|.--+..----=.|+++||+.-
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~C 34 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSC 34 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTT
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHH
Confidence 4588888776444222335889999863
No 87
>PF11722 zf-TRM13_CCCH: CCCH zinc finger in TRM13 protein; InterPro: IPR021721 This domain is found at the N terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain. ; GO: 0008168 methyltransferase activity
Probab=20.33 E-value=44 Score=20.11 Aligned_cols=10 Identities=40% Similarity=0.949 Sum_probs=8.0
Q ss_pred cCcccccCCC
Q 042575 125 CGHLYCGTHR 134 (169)
Q Consensus 125 Cg~~FC~~HR 134 (169)
=|..||+.|.
T Consensus 21 ~g~~fC~~H~ 30 (31)
T PF11722_consen 21 PGSRFCGEHM 30 (31)
T ss_pred CcCCccccCC
Confidence 3778999985
Done!