Query 045687
Match_columns 212
No_of_seqs 121 out of 1184
Neff 8.8
Searched_HMMs 46136
Date Fri Mar 29 04:31:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045687.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045687hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14244 UBN2_3: gag-polypepti 99.6 7.2E-15 1.6E-19 111.0 7.7 95 4-102 36-141 (152)
2 PF14227 UBN2_2: gag-polypepti 99.0 6.2E-10 1.4E-14 80.5 4.5 59 52-110 1-67 (119)
3 PF14223 UBN2: gag-polypeptide 98.9 1.6E-09 3.4E-14 78.4 5.1 58 53-110 1-69 (119)
4 PF00098 zf-CCHC: Zinc knuckle 98.7 6.3E-09 1.4E-13 49.5 0.8 18 157-174 1-18 (18)
5 PF13696 zf-CCHC_2: Zinc knuck 97.9 4.5E-06 9.8E-11 45.2 0.9 19 156-174 8-26 (32)
6 smart00343 ZnF_C2HC zinc finge 96.9 0.00033 7.1E-09 36.4 0.8 19 158-176 1-19 (26)
7 PF13917 zf-CCHC_3: Zinc knuck 96.9 0.00044 9.5E-09 40.1 1.0 19 156-174 4-22 (42)
8 PF15288 zf-CCHC_6: Zinc knuck 96.6 0.002 4.4E-08 36.7 2.4 22 157-178 2-25 (40)
9 PF14392 zf-CCHC_4: Zinc knuck 96.5 0.00079 1.7E-08 40.6 0.3 19 156-174 31-49 (49)
10 PF14787 zf-CCHC_5: GAG-polypr 96.4 0.0011 2.3E-08 36.8 0.6 21 157-177 3-23 (36)
11 COG5082 AIR1 Arginine methyltr 95.8 0.0036 7.7E-08 48.3 1.0 19 155-173 59-77 (190)
12 COG5082 AIR1 Arginine methyltr 95.6 0.0054 1.2E-07 47.3 1.1 21 157-177 98-119 (190)
13 KOG0109 RNA-binding protein LA 95.3 0.0099 2.2E-07 48.7 1.8 22 156-177 160-181 (346)
14 PTZ00368 universal minicircle 95.3 0.0084 1.8E-07 44.8 1.3 17 158-174 105-121 (148)
15 COG5222 Uncharacterized conser 94.5 0.069 1.5E-06 44.0 4.8 22 156-177 176-197 (427)
16 PF03564 DUF1759: Protein of u 92.7 0.47 1E-05 35.0 6.3 79 30-108 27-119 (145)
17 PTZ00368 universal minicircle 91.7 0.077 1.7E-06 39.6 1.0 19 156-174 77-95 (148)
18 KOG4400 E3 ubiquitin ligase in 91.5 0.078 1.7E-06 43.5 0.9 19 157-175 144-162 (261)
19 KOG2560 RNA splicing factor - 88.0 0.15 3.3E-06 44.4 -0.0 25 154-178 110-134 (529)
20 PF12353 eIF3g: Eukaryotic tra 85.8 0.37 7.9E-06 35.2 1.0 22 154-176 104-125 (128)
21 KOG2044 5'-3' exonuclease HKE1 84.0 0.44 9.6E-06 44.4 0.9 29 82-110 123-151 (931)
22 PF03732 Retrotrans_gag: Retro 83.6 2.3 5E-05 28.3 4.2 44 56-100 30-79 (96)
23 KOG0341 DEAD-box protein abstr 83.5 0.46 1E-05 41.1 0.7 22 156-177 570-591 (610)
24 KOG0119 Splicing factor 1/bran 83.5 0.59 1.3E-05 41.3 1.4 19 157-175 286-304 (554)
25 COG5179 TAF1 Transcription ini 81.6 0.89 1.9E-05 41.5 1.8 23 155-177 936-960 (968)
26 KOG3116 Predicted C3H1-type Zn 79.8 0.36 7.8E-06 35.8 -1.0 22 156-177 27-48 (177)
27 KOG2673 Uncharacterized conser 79.3 0.93 2E-05 39.7 1.1 21 157-177 129-149 (485)
28 KOG4400 E3 ubiquitin ligase in 76.0 1.5 3.3E-05 35.9 1.4 22 156-177 164-185 (261)
29 KOG2893 Zn finger protein [Gen 71.6 2.1 4.6E-05 34.4 1.2 13 153-165 7-19 (341)
30 KOG3794 CBF1-interacting corep 68.9 2.4 5.1E-05 36.5 1.0 23 155-177 123-147 (453)
31 KOG3497 DNA-directed RNA polym 61.4 3.5 7.5E-05 25.7 0.5 10 156-165 4-13 (69)
32 COG1644 RPB10 DNA-directed RNA 60.5 4.1 8.8E-05 25.6 0.7 10 156-165 4-13 (63)
33 PLN00032 DNA-directed RNA poly 58.2 4.1 8.9E-05 26.3 0.5 10 156-165 4-13 (71)
34 PF01194 RNA_pol_N: RNA polyme 55.7 4.2 9.1E-05 25.5 0.2 10 156-165 4-13 (60)
35 PRK04016 DNA-directed RNA poly 55.4 4.9 0.00011 25.3 0.4 10 156-165 4-13 (62)
36 COG4416 Com Mu-like prophage p 55.3 2.5 5.4E-05 25.7 -0.8 22 156-177 4-32 (60)
37 PF07904 Eaf7: Chromatin modif 52.3 19 0.00041 24.5 3.0 19 49-67 40-58 (91)
38 KOG0107 Alternative splicing f 50.8 7.1 0.00015 30.1 0.7 18 157-174 101-118 (195)
39 PF05741 zf-nanos: Nanos RNA b 47.2 5.7 0.00012 24.4 -0.2 20 156-175 33-55 (55)
40 PF14893 PNMA: PNMA 44.7 2E+02 0.0042 24.7 8.5 52 52-103 229-286 (331)
41 KOG4602 Nanos and related prot 43.8 11 0.00023 30.8 0.8 23 155-177 267-292 (318)
42 PHA00689 hypothetical protein 43.3 7.9 0.00017 23.1 0.0 12 156-167 17-28 (62)
43 COG1198 PriA Primosomal protei 41.9 14 0.0003 35.0 1.4 24 154-177 460-483 (730)
44 KOG4025 Putative apoptosis rel 39.4 1.3E+02 0.0028 23.1 5.9 68 29-96 100-167 (207)
45 KOG0314 Predicted E3 ubiquitin 39.1 21 0.00045 31.7 1.9 24 156-179 158-181 (448)
46 TIGR03859 PQQ_PqqD coenzyme PQ 38.9 1.1E+02 0.0024 20.1 5.0 29 40-68 31-59 (81)
47 KOG0119 Splicing factor 1/bran 38.1 15 0.00032 32.9 0.9 19 157-175 262-280 (554)
48 PRK09335 30S ribosomal protein 37.4 22 0.00048 24.4 1.4 12 153-164 17-28 (95)
49 PF11248 DUF3046: Protein of u 36.4 56 0.0012 20.7 3.1 37 33-69 23-60 (63)
50 PF13821 DUF4187: Domain of un 35.7 20 0.00043 22.0 0.9 21 156-176 27-51 (55)
51 PTZ00172 40S ribosomal protein 34.4 26 0.00056 24.6 1.4 12 153-164 17-28 (108)
52 PF05310 Tenui_NS3: Tenuivirus 34.1 13 0.00029 28.5 0.0 20 157-176 99-118 (186)
53 PLN00186 ribosomal protein S26 32.0 30 0.00065 24.3 1.4 12 153-164 17-28 (109)
54 PF09779 Ima1_N: Ima1 N-termin 31.2 29 0.00064 25.3 1.4 15 157-171 1-15 (131)
55 smart00647 IBR In Between Ring 30.2 26 0.00056 21.4 0.8 17 156-172 48-64 (64)
56 PF05369 MtmB: Monomethylamine 30.1 1.2E+02 0.0025 26.9 4.9 61 44-105 387-457 (457)
57 PF13395 HNH_4: HNH endonuclea 29.9 19 0.00042 21.7 0.2 7 159-165 1-7 (54)
58 PF05402 PqqD: Coenzyme PQQ sy 29.6 1.4E+02 0.003 18.3 5.8 31 37-67 14-44 (68)
59 KOG0122 Translation initiation 28.9 30 0.00064 28.2 1.1 21 156-177 119-139 (270)
60 cd03154 TM4SF3_like_LEL Tetras 27.7 83 0.0018 21.0 3.1 36 32-67 10-45 (100)
61 PF13376 OmdA: Bacteriocin-pro 24.7 60 0.0013 20.1 1.8 27 41-67 6-32 (63)
62 PF06689 zf-C4_ClpX: ClpX C4-t 24.5 20 0.00044 20.4 -0.4 10 157-166 2-11 (41)
63 smart00400 ZnF_CHCC zinc finge 24.1 39 0.00084 20.3 0.8 13 156-168 23-35 (55)
64 cd03155 CD151_like_LEL Tetrasp 23.6 1.4E+02 0.003 20.3 3.7 35 33-67 7-43 (110)
65 PRK14063 exodeoxyribonuclease 23.1 90 0.002 20.4 2.5 32 79-110 2-33 (76)
66 PRK00114 hslO Hsp33-like chape 22.7 27 0.00059 29.2 -0.1 16 156-171 268-283 (293)
67 PHA03230 nuclear protein UL55; 22.0 25 0.00054 27.1 -0.4 18 157-174 136-153 (180)
68 PF15056 NRN1: Neuritin protei 21.8 69 0.0015 21.7 1.7 15 53-67 55-69 (89)
69 cd03160 CD37_CD82_like_LEL Tet 21.1 1.5E+02 0.0032 20.5 3.5 36 32-67 7-44 (117)
70 cd03159 TM4SF9_like_LEL Tetras 21.0 1.5E+02 0.0033 20.6 3.6 34 33-67 7-40 (121)
71 PRK11582 flagella biosynthesis 21.0 3.8E+02 0.0082 20.3 5.6 26 81-106 104-129 (169)
72 TIGR00595 priA primosomal prot 20.3 51 0.0011 29.8 1.1 23 155-177 239-261 (505)
73 PF08844 DUF1815: Domain of un 20.3 53 0.0011 22.5 0.9 17 154-170 30-48 (105)
74 PRK01402 hslO Hsp33-like chape 20.1 32 0.00069 29.3 -0.2 15 156-170 308-322 (328)
No 1
>PF14244 UBN2_3: gag-polypeptide of LTR copia-type
Probab=99.57 E-value=7.2e-15 Score=111.03 Aligned_cols=95 Identities=19% Similarity=0.348 Sum_probs=77.2
Q ss_pred cccccc-CCCCCCCcchHHHHHHHHHHHHHHHHHHHhhccHHHHHhhcccccHHHHHHHHHHHHhhcccccccc------
Q 045687 4 AEFLTE-PPPDSDSENYEVLLQNWIKANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNF------ 76 (212)
Q Consensus 4 ~~vl~e-~~P~~~~~~~~~~~~~W~~~d~~a~~~I~~sl~~~i~~~i~~~~tA~~lW~~L~~~y~~~~~~~~~~------ 76 (212)
+||.++ ++|.+.++ +++.|.+.|.++++||+++|+++++..|..++||+++|++|+++|+..++..+.+
T Consensus 36 ~~i~g~~~~P~~~~~----~~~~W~~~d~~v~swl~~sis~~i~~~i~~~~tak~~W~~L~~~f~~~~~~~r~~~L~~~l 111 (152)
T PF14244_consen 36 GFIDGTIPKPPETDP----AYEKWERKDQLVLSWLLNSISPDILSTIIFCETAKEIWDALKERFSQKSNASRVFQLRNEL 111 (152)
T ss_pred ccccCccccccccch----hhhhHHHhhhHHHHHHHHhhcHHHHhhhHhhhhHHHHHHHHHHHhhcccHHHHHHHHHHHH
Confidence 344443 45544444 7999999999999999999999999999999999999999999999777455521
Q ss_pred --eecCCccHHHHHHHHHHHH--HHHHhCC
Q 045687 77 --KMAEDKEVTSQIHGFHMLI--NDLKNEN 102 (212)
Q Consensus 77 --~~~~~~sv~~~i~~~~~l~--~~L~~~~ 102 (212)
..+++++|.+|+.+|+.|+ .+|....
T Consensus 112 ~~~kq~~~sv~ey~~~lk~l~~~~el~~~~ 141 (152)
T PF14244_consen 112 HSLKQGDKSVTEYFNKLKSLWQEDELDEYR 141 (152)
T ss_pred HHHhhCCCcHHHHHHHHHHHhHHHHHhCcC
Confidence 1278999999999999999 5565543
No 2
>PF14227 UBN2_2: gag-polypeptide of LTR copia-type
Probab=98.97 E-value=6.2e-10 Score=80.48 Aligned_cols=59 Identities=31% Similarity=0.477 Sum_probs=55.4
Q ss_pred cccHHHHHHHHHHHHhhcccccc--------cceecCCccHHHHHHHHHHHHHHHHhCCCCCCcccc
Q 045687 52 HKFAYEIWAQLRKKYIIEDAGAQ--------NFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFM 110 (212)
Q Consensus 52 ~~tA~~lW~~L~~~y~~~~~~~~--------~~~~~~~~sv~~~i~~~~~l~~~L~~~~~~l~d~~~ 110 (212)
|+||++||++|+..|+..+...+ .++|.++.+|.+||.+|..|+++|..+|.+|+|+++
T Consensus 1 ~~ta~~~W~~L~~~y~~~~~~~~~~l~~kl~~~k~~~~~~v~~hi~~~~~l~~~L~~~g~~i~d~~~ 67 (119)
T PF14227_consen 1 CKTAKEMWDKLKKKYEKKSFANKIYLLRKLYSLKMDEGGSVRDHINEFRSLVNQLKSLGVPIDDEDK 67 (119)
T ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhHhccchhHHHHHHHHHHHHHhhccccccchHHHH
Confidence 68999999999999998887765 788999999999999999999999999999999988
No 3
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=98.92 E-value=1.6e-09 Score=78.36 Aligned_cols=58 Identities=22% Similarity=0.393 Sum_probs=53.1
Q ss_pred ccHHHHHHHHHHHHhhccc---ccc--------cceecCCccHHHHHHHHHHHHHHHHhCCCCCCcccc
Q 045687 53 KFAYEIWAQLRKKYIIEDA---GAQ--------NFKMAEDKEVTSQIHGFHMLINDLKNENIILPESFM 110 (212)
Q Consensus 53 ~tA~~lW~~L~~~y~~~~~---~~~--------~~~~~~~~sv~~~i~~~~~l~~~L~~~~~~l~d~~~ 110 (212)
+||+++|++|+..|++.+. ... .++|.++.+|.+|+.+|..|+++|..+|.+++|..+
T Consensus 1 ~tA~e~W~~L~~~y~~~~~~~~~~~~~L~~~l~~~k~~~~~sv~~y~~~~~~i~~~L~~~g~~i~d~~~ 69 (119)
T PF14223_consen 1 KTAKEAWDALKKRYEGQSKVKQARVQQLKSQLENLKMKDGESVDEYISRLKEIVDELRAIGKPISDEDL 69 (119)
T ss_pred ChHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHhhhhhhhcCCcccchhH
Confidence 5899999999999998887 332 788899999999999999999999999999999988
No 4
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.67 E-value=6.3e-09 Score=49.47 Aligned_cols=18 Identities=44% Similarity=1.228 Sum_probs=16.4
Q ss_pred cceeecCCCccccccCcC
Q 045687 157 GNCYVCGKPGHFANKCRY 174 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~C~~ 174 (212)
+.||+||+.||++++||+
T Consensus 1 ~~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCPK 18 (18)
T ss_dssp SBCTTTSCSSSCGCTSSS
T ss_pred CcCcCCCCcCcccccCcc
Confidence 369999999999999985
No 5
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=97.88 E-value=4.5e-06 Score=45.24 Aligned_cols=19 Identities=32% Similarity=0.777 Sum_probs=17.6
Q ss_pred CcceeecCCCccccccCcC
Q 045687 156 KGNCYVCGKPGHFANKCRY 174 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~ 174 (212)
.-.|+.|++.||++++||.
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCEeecCCCCCccHhHCCC
Confidence 3679999999999999998
No 6
>smart00343 ZnF_C2HC zinc finger.
Probab=96.95 E-value=0.00033 Score=36.39 Aligned_cols=19 Identities=47% Similarity=1.104 Sum_probs=16.4
Q ss_pred ceeecCCCccccccCcCcc
Q 045687 158 NCYVCGKPGHFANKCRYRK 176 (212)
Q Consensus 158 ~C~~Cgk~GH~~~~C~~~~ 176 (212)
.|++||+.||++++||...
T Consensus 1 ~C~~CG~~GH~~~~C~~~~ 19 (26)
T smart00343 1 KCYNCGKEGHIARDCPKXX 19 (26)
T ss_pred CCccCCCCCcchhhCCccc
Confidence 4999999999999998443
No 7
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=96.87 E-value=0.00044 Score=40.14 Aligned_cols=19 Identities=32% Similarity=0.922 Sum_probs=17.5
Q ss_pred CcceeecCCCccccccCcC
Q 045687 156 KGNCYVCGKPGHFANKCRY 174 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~ 174 (212)
...|..|++.||+..+|+.
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4789999999999999996
No 8
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=96.60 E-value=0.002 Score=36.74 Aligned_cols=22 Identities=27% Similarity=0.576 Sum_probs=19.0
Q ss_pred cceeecCCCcccc--ccCcCccCC
Q 045687 157 GNCYVCGKPGHFA--NKCRYRKGD 178 (212)
Q Consensus 157 ~~C~~Cgk~GH~~--~~C~~~~~~ 178 (212)
++|..||..||.+ +.||-+...
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~~ 25 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCWS 25 (40)
T ss_pred ccccccccccccccCccCCCCCCC
Confidence 6799999999998 779987763
No 9
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=96.49 E-value=0.00079 Score=40.64 Aligned_cols=19 Identities=32% Similarity=0.844 Sum_probs=17.3
Q ss_pred CcceeecCCCccccccCcC
Q 045687 156 KGNCYVCGKPGHFANKCRY 174 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~ 174 (212)
...|++||..||...+||+
T Consensus 31 p~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred ChhhcCCCCcCcCHhHcCC
Confidence 4779999999999999985
No 10
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=96.43 E-value=0.0011 Score=36.75 Aligned_cols=21 Identities=43% Similarity=0.885 Sum_probs=14.1
Q ss_pred cceeecCCCccccccCcCccC
Q 045687 157 GNCYVCGKPGHFANKCRYRKG 177 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~C~~~~~ 177 (212)
..|+.|+|..|++.+|+.+.+
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp -C-TTTSSSCS-TTT---TCC
T ss_pred ccCcccCCCcchhhhhhhhhc
Confidence 579999999999999998877
No 11
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=95.81 E-value=0.0036 Score=48.32 Aligned_cols=19 Identities=32% Similarity=0.994 Sum_probs=14.7
Q ss_pred CCcceeecCCCccccccCc
Q 045687 155 KKGNCYVCGKPGHFANKCR 173 (212)
Q Consensus 155 ~~~~C~~Cgk~GH~~~~C~ 173 (212)
....||+||+.||.++|||
T Consensus 59 ~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 59 ENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred cccccchhcccCcccccCC
Confidence 3467888888888888887
No 12
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=95.55 E-value=0.0054 Score=47.34 Aligned_cols=21 Identities=33% Similarity=1.009 Sum_probs=17.5
Q ss_pred cceeecCCCccccccC-cCccC
Q 045687 157 GNCYVCGKPGHFANKC-RYRKG 177 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~C-~~~~~ 177 (212)
.+|++||..||++++| |.+.+
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~~~ 119 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSKDQ 119 (190)
T ss_pred cccccccccCccccccCccccc
Confidence 6899999999999999 44333
No 13
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=95.29 E-value=0.0099 Score=48.73 Aligned_cols=22 Identities=36% Similarity=1.067 Sum_probs=19.8
Q ss_pred CcceeecCCCccccccCcCccC
Q 045687 156 KGNCYVCGKPGHFANKCRYRKG 177 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~~~~ 177 (212)
.-.|+-|||.|||.++||....
T Consensus 160 q~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 160 QSGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred HHHheeccccccccccCCccCC
Confidence 4569999999999999998877
No 14
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=95.26 E-value=0.0084 Score=44.85 Aligned_cols=17 Identities=41% Similarity=1.136 Sum_probs=8.6
Q ss_pred ceeecCCCccccccCcC
Q 045687 158 NCYVCGKPGHFANKCRY 174 (212)
Q Consensus 158 ~C~~Cgk~GH~~~~C~~ 174 (212)
.||.|+..||+.++||.
T Consensus 105 ~C~~Cg~~gH~~~~C~~ 121 (148)
T PTZ00368 105 ACYNCGGEGHISRDCPN 121 (148)
T ss_pred hhcccCcCCcchhcCCC
Confidence 45555555555555544
No 15
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.53 E-value=0.069 Score=44.05 Aligned_cols=22 Identities=32% Similarity=0.856 Sum_probs=19.4
Q ss_pred CcceeecCCCccccccCcCccC
Q 045687 156 KGNCYVCGKPGHFANKCRYRKG 177 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~~~~ 177 (212)
.-.||.||..|||...||.-.+
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred ceeEEecCCCCchhhcCCCCCC
Confidence 3679999999999999997666
No 16
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=92.73 E-value=0.47 Score=34.98 Aligned_cols=79 Identities=15% Similarity=0.110 Sum_probs=61.4
Q ss_pred HHHHHHHHHhhccHHHHHhhcccc----cHHHHHHHHHHHHhhcccccc-----c-----ceecCCccHHHHHHHHHHHH
Q 045687 30 NKVCRSTILSTLSNELYDVYSQHK----FAYEIWAQLRKKYIIEDAGAQ-----N-----FKMAEDKEVTSQIHGFHMLI 95 (212)
Q Consensus 30 d~~a~~~I~~sl~~~i~~~i~~~~----tA~~lW~~L~~~y~~~~~~~~-----~-----~~~~~~~sv~~~i~~~~~l~ 95 (212)
+..=+.+|.+.|..+....|.++. +=..+|+.|+++|+......+ . +...+...+...+..+..++
T Consensus 27 d~~K~~~L~~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~~i~~~~~~~l~~l~~~~~~d~~~L~~~~~~v~~~i 106 (145)
T PF03564_consen 27 DIEKLNYLRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPRRIIQALLEELRNLPPISNDDPEALRSLVDKVNNCI 106 (145)
T ss_pred HHHHHHHHHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCchHHHHHHHHHHhccccccchhHHHHHHHHHHHHHHH
Confidence 455567899999999999888763 238899999999997665443 2 22345667889999999999
Q ss_pred HHHHhCCCCCCcc
Q 045687 96 NDLKNENIILPES 108 (212)
Q Consensus 96 ~~L~~~~~~l~d~ 108 (212)
..|..+|..+++.
T Consensus 107 ~~L~~lg~~~~~~ 119 (145)
T PF03564_consen 107 RALKALGVNVDDP 119 (145)
T ss_pred HHHHHcCCCCCCH
Confidence 9999999888843
No 17
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=91.72 E-value=0.077 Score=39.62 Aligned_cols=19 Identities=37% Similarity=1.078 Sum_probs=14.3
Q ss_pred CcceeecCCCccccccCcC
Q 045687 156 KGNCYVCGKPGHFANKCRY 174 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~ 174 (212)
...|+.|++.||+.++|+.
T Consensus 77 ~~~C~~Cg~~GH~~~~C~~ 95 (148)
T PTZ00368 77 PRSCYNCGQTGHISRECPN 95 (148)
T ss_pred CcccCcCCCCCcccccCCC
Confidence 3568888888888888864
No 18
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=91.46 E-value=0.078 Score=43.49 Aligned_cols=19 Identities=37% Similarity=1.127 Sum_probs=17.3
Q ss_pred cceeecCCCccccccCcCc
Q 045687 157 GNCYVCGKPGHFANKCRYR 175 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~C~~~ 175 (212)
..||.||+.||+..+|+..
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred CccCCCCcCCcchhhCCCC
Confidence 6799999999999999965
No 19
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=87.95 E-value=0.15 Score=44.40 Aligned_cols=25 Identities=32% Similarity=0.610 Sum_probs=21.9
Q ss_pred cCCcceeecCCCccccccCcCccCC
Q 045687 154 KKKGNCYVCGKPGHFANKCRYRKGD 178 (212)
Q Consensus 154 ~~~~~C~~Cgk~GH~~~~C~~~~~~ 178 (212)
-+.+-|.+||-.||..++|..++++
T Consensus 110 yRKGACeNCGAmtHk~KDCmERPRK 134 (529)
T KOG2560|consen 110 YRKGACENCGAMTHKVKDCMERPRK 134 (529)
T ss_pred HhhhhhhhhhhhhcchHHHhhcchh
Confidence 3468899999999999999988884
No 20
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=85.78 E-value=0.37 Score=35.20 Aligned_cols=22 Identities=36% Similarity=0.933 Sum_probs=18.4
Q ss_pred cCCcceeecCCCccccccCcCcc
Q 045687 154 KKKGNCYVCGKPGHFANKCRYRK 176 (212)
Q Consensus 154 ~~~~~C~~Cgk~GH~~~~C~~~~ 176 (212)
...+.|.+|+ ..||...||.+-
T Consensus 104 ~~~v~CR~Ck-GdH~T~~CPyKd 125 (128)
T PF12353_consen 104 KSKVKCRICK-GDHWTSKCPYKD 125 (128)
T ss_pred CceEEeCCCC-CCcccccCCccc
Confidence 3458899996 999999999763
No 21
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=84.03 E-value=0.44 Score=44.43 Aligned_cols=29 Identities=21% Similarity=0.295 Sum_probs=22.2
Q ss_pred ccHHHHHHHHHHHHHHHHhCCCCCCcccc
Q 045687 82 KEVTSQIHGFHMLINDLKNENIILPESFM 110 (212)
Q Consensus 82 ~sv~~~i~~~~~l~~~L~~~~~~l~d~~~ 110 (212)
...++--.+..++..++...|..|++...
T Consensus 123 Keaae~~~e~e~~ree~~~~G~~lpp~~~ 151 (931)
T KOG2044|consen 123 KEAAEKEAEIERLREEFEAEGKFLPPKVK 151 (931)
T ss_pred hHHHHHHHHHHHHHHHHHhcCCcCCchhh
Confidence 33456667778888999999999988755
No 22
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=83.61 E-value=2.3 Score=28.30 Aligned_cols=44 Identities=18% Similarity=0.287 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhhcccccc------cceecCCccHHHHHHHHHHHHHHHHh
Q 045687 56 YEIWAQLRKKYIIEDAGAQ------NFKMAEDKEVTSQIHGFHMLINDLKN 100 (212)
Q Consensus 56 ~~lW~~L~~~y~~~~~~~~------~~~~~~~~sv~~~i~~~~~l~~~L~~ 100 (212)
.++=..|...|........ .++. ++++|.+|+.+|..|+..+..
T Consensus 30 ~~~~~~~~~~f~~~~~~~~~~~~l~~l~Q-~~esv~~y~~rf~~l~~~~~~ 79 (96)
T PF03732_consen 30 EEFKDAFRKRFFPPDRKEQARQELNSLRQ-GNESVREYVNRFRELARRAPP 79 (96)
T ss_pred HHHHHHHHHHHhhhhccccchhhhhhhhc-cCCcHHHHHHHHHHHHHHCCC
Confidence 3444445555554333222 3444 799999999999999998764
No 23
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=83.54 E-value=0.46 Score=41.10 Aligned_cols=22 Identities=27% Similarity=0.622 Sum_probs=19.9
Q ss_pred CcceeecCCCccccccCcCccC
Q 045687 156 KGNCYVCGKPGHFANKCRYRKG 177 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~~~~ 177 (212)
..-|.|||-.||...+||++..
T Consensus 570 ~kGCayCgGLGHRItdCPKle~ 591 (610)
T KOG0341|consen 570 EKGCAYCGGLGHRITDCPKLEA 591 (610)
T ss_pred ccccccccCCCcccccCchhhh
Confidence 3569999999999999999877
No 24
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=83.50 E-value=0.59 Score=41.28 Aligned_cols=19 Identities=32% Similarity=0.906 Sum_probs=17.6
Q ss_pred cceeecCCCccccccCcCc
Q 045687 157 GNCYVCGKPGHFANKCRYR 175 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~C~~~ 175 (212)
..|++||-.||+..+|+..
T Consensus 286 n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 286 NVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccCCcccccccCCCc
Confidence 4899999999999999877
No 25
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=81.57 E-value=0.89 Score=41.45 Aligned_cols=23 Identities=26% Similarity=0.621 Sum_probs=19.6
Q ss_pred CCcceeecCCCcccc--ccCcCccC
Q 045687 155 KKGNCYVCGKPGHFA--NKCRYRKG 177 (212)
Q Consensus 155 ~~~~C~~Cgk~GH~~--~~C~~~~~ 177 (212)
...+|-+||..||++ +.||....
T Consensus 936 Ttr~C~nCGQvGHmkTNK~CP~f~s 960 (968)
T COG5179 936 TTRTCGNCGQVGHMKTNKACPKFSS 960 (968)
T ss_pred cceecccccccccccccccCccccC
Confidence 357899999999987 56998887
No 26
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=79.79 E-value=0.36 Score=35.76 Aligned_cols=22 Identities=23% Similarity=0.782 Sum_probs=18.9
Q ss_pred CcceeecCCCccccccCcCccC
Q 045687 156 KGNCYVCGKPGHFANKCRYRKG 177 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~~~~ 177 (212)
.+.|+.|-..|||..+|..+..
T Consensus 27 ~~rCQKClq~GHWtYECk~kRk 48 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKNKRK 48 (177)
T ss_pred chhHHHHHhhccceeeecCcee
Confidence 4789999999999999976554
No 27
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=79.32 E-value=0.93 Score=39.68 Aligned_cols=21 Identities=24% Similarity=0.581 Sum_probs=19.1
Q ss_pred cceeecCCCccccccCcCccC
Q 045687 157 GNCYVCGKPGHFANKCRYRKG 177 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~C~~~~~ 177 (212)
..||+||-.-|-.++||.+.+
T Consensus 129 ~~CFNC~g~~hsLrdC~rp~d 149 (485)
T KOG2673|consen 129 DPCFNCGGTPHSLRDCPRPFD 149 (485)
T ss_pred ccccccCCCCCccccCCCccc
Confidence 449999999999999999888
No 28
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=76.01 E-value=1.5 Score=35.91 Aligned_cols=22 Identities=36% Similarity=0.927 Sum_probs=20.3
Q ss_pred CcceeecCCCccccccCcCccC
Q 045687 156 KGNCYVCGKPGHFANKCRYRKG 177 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~~~~ 177 (212)
.+.|+.|++.||...+||....
T Consensus 164 ~~~c~~c~~~~h~~~~C~~~~~ 185 (261)
T KOG4400|consen 164 GGTCFRCGKVGHGSRDCPSKQK 185 (261)
T ss_pred CCccccCCCcceecccCCcccc
Confidence 6889999999999999998777
No 29
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=71.58 E-value=2.1 Score=34.42 Aligned_cols=13 Identities=31% Similarity=0.733 Sum_probs=9.7
Q ss_pred ccCCcceeecCCC
Q 045687 153 KKKKGNCYVCGKP 165 (212)
Q Consensus 153 ~~~~~~C~~Cgk~ 165 (212)
+..+.+||||++.
T Consensus 7 k~~kpwcwycnre 19 (341)
T KOG2893|consen 7 KVDKPWCWYCNRE 19 (341)
T ss_pred ccCCceeeecccc
Confidence 4456899999853
No 30
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=68.87 E-value=2.4 Score=36.54 Aligned_cols=23 Identities=26% Similarity=0.560 Sum_probs=18.5
Q ss_pred CCcceeecCCCcccc--ccCcCccC
Q 045687 155 KKGNCYVCGKPGHFA--NKCRYRKG 177 (212)
Q Consensus 155 ~~~~C~~Cgk~GH~~--~~C~~~~~ 177 (212)
+.+.|+.|++.||+- ++||-+..
T Consensus 123 RNVrC~kChkwGH~n~DreCplf~~ 147 (453)
T KOG3794|consen 123 RNVRCLKCHKWGHINTDRECPLFGK 147 (453)
T ss_pred eeeeEEeecccccccCCccCcchhh
Confidence 358899999999975 66986655
No 31
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=61.44 E-value=3.5 Score=25.72 Aligned_cols=10 Identities=40% Similarity=1.042 Sum_probs=8.0
Q ss_pred CcceeecCCC
Q 045687 156 KGNCYVCGKP 165 (212)
Q Consensus 156 ~~~C~~Cgk~ 165 (212)
+++||.|||.
T Consensus 4 PiRCFtCGKv 13 (69)
T KOG3497|consen 4 PIRCFTCGKV 13 (69)
T ss_pred eeEeeecccc
Confidence 3679999975
No 32
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=60.48 E-value=4.1 Score=25.55 Aligned_cols=10 Identities=40% Similarity=1.049 Sum_probs=8.3
Q ss_pred CcceeecCCC
Q 045687 156 KGNCYVCGKP 165 (212)
Q Consensus 156 ~~~C~~Cgk~ 165 (212)
+++||.||+.
T Consensus 4 PiRCFsCGkv 13 (63)
T COG1644 4 PVRCFSCGKV 13 (63)
T ss_pred ceEeecCCCC
Confidence 4789999985
No 33
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=58.24 E-value=4.1 Score=26.33 Aligned_cols=10 Identities=40% Similarity=1.082 Sum_probs=8.3
Q ss_pred CcceeecCCC
Q 045687 156 KGNCYVCGKP 165 (212)
Q Consensus 156 ~~~C~~Cgk~ 165 (212)
+++||.|||.
T Consensus 4 PVRCFTCGkv 13 (71)
T PLN00032 4 PVRCFTCGKV 13 (71)
T ss_pred ceeecCCCCC
Confidence 4789999985
No 34
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=55.73 E-value=4.2 Score=25.45 Aligned_cols=10 Identities=40% Similarity=1.082 Sum_probs=7.3
Q ss_pred CcceeecCCC
Q 045687 156 KGNCYVCGKP 165 (212)
Q Consensus 156 ~~~C~~Cgk~ 165 (212)
+++||.||+.
T Consensus 4 PVRCFTCGkv 13 (60)
T PF01194_consen 4 PVRCFTCGKV 13 (60)
T ss_dssp SSS-STTTSB
T ss_pred ceecCCCCCC
Confidence 4789999985
No 35
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=55.35 E-value=4.9 Score=25.31 Aligned_cols=10 Identities=40% Similarity=1.082 Sum_probs=8.3
Q ss_pred CcceeecCCC
Q 045687 156 KGNCYVCGKP 165 (212)
Q Consensus 156 ~~~C~~Cgk~ 165 (212)
+++||.|||.
T Consensus 4 PvRCFTCGkv 13 (62)
T PRK04016 4 PVRCFTCGKV 13 (62)
T ss_pred CeEecCCCCC
Confidence 4789999985
No 36
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=55.32 E-value=2.5 Score=25.69 Aligned_cols=22 Identities=27% Similarity=0.481 Sum_probs=18.1
Q ss_pred CcceeecCC-------CccccccCcCccC
Q 045687 156 KGNCYVCGK-------PGHFANKCRYRKG 177 (212)
Q Consensus 156 ~~~C~~Cgk-------~GH~~~~C~~~~~ 177 (212)
..+|.+|+| .||+...||.-+-
T Consensus 4 tiRC~~CnKlLa~a~~~~yle~KCPrCK~ 32 (60)
T COG4416 4 TIRCAKCNKLLAEAEGQAYLEKKCPRCKE 32 (60)
T ss_pred eeehHHHhHHHHhcccceeeeecCCccce
Confidence 467999987 4899999997665
No 37
>PF07904 Eaf7: Chromatin modification-related protein EAF7; InterPro: IPR012423 The Saccharomyces cerevisiae (Baker's yeast) member of this family P53911 from SWISSPROT is part of NuA4, the only essential histone acetyltransferase complex in S. cerevisiae involved in global histone acetylation []. ; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0043189 H4/H2A histone acetyltransferase complex
Probab=52.31 E-value=19 Score=24.53 Aligned_cols=19 Identities=32% Similarity=0.562 Sum_probs=16.7
Q ss_pred hcccccHHHHHHHHHHHHh
Q 045687 49 YSQHKFAYEIWAQLRKKYI 67 (212)
Q Consensus 49 i~~~~tA~~lW~~L~~~y~ 67 (212)
+....|+.+||++|...|.
T Consensus 40 ~~~~~t~~~IW~kL~~~Yd 58 (91)
T PF07904_consen 40 LNKHFTIDDIWKKLRTLYD 58 (91)
T ss_pred cCCcCCHHHHHHHHHHhcC
Confidence 4566899999999999997
No 38
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=50.78 E-value=7.1 Score=30.07 Aligned_cols=18 Identities=44% Similarity=1.217 Sum_probs=16.2
Q ss_pred cceeecCCCccccccCcC
Q 045687 157 GNCYVCGKPGHFANKCRY 174 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~C~~ 174 (212)
..|++||..||+...|..
T Consensus 101 ~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 101 GFCYRCGERGHIGRNCKD 118 (195)
T ss_pred cccccCCCcccccccccc
Confidence 559999999999999976
No 39
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=47.22 E-value=5.7 Score=24.44 Aligned_cols=20 Identities=30% Similarity=0.662 Sum_probs=7.4
Q ss_pred CcceeecCCC---ccccccCcCc
Q 045687 156 KGNCYVCGKP---GHFANKCRYR 175 (212)
Q Consensus 156 ~~~C~~Cgk~---GH~~~~C~~~ 175 (212)
...|-.||-+ .|+.+.||.+
T Consensus 33 ~y~Cp~CgAtGd~AHT~~yCP~k 55 (55)
T PF05741_consen 33 KYVCPICGATGDNAHTIKYCPKK 55 (55)
T ss_dssp G---TTT---GGG---GGG-TT-
T ss_pred cCcCCCCcCcCccccccccCcCC
Confidence 3678889884 5899999863
No 40
>PF14893 PNMA: PNMA
Probab=44.65 E-value=2e+02 Score=24.66 Aligned_cols=52 Identities=8% Similarity=0.118 Sum_probs=41.0
Q ss_pred cccHHHHHHHHHHHHhhcccccc------cceecCCccHHHHHHHHHHHHHHHHhCCC
Q 045687 52 HKFAYEIWAQLRKKYIIEDAGAQ------NFKMAEDKEVTSQIHGFHMLINDLKNENI 103 (212)
Q Consensus 52 ~~tA~~lW~~L~~~y~~~~~~~~------~~~~~~~~sv~~~i~~~~~l~~~L~~~~~ 103 (212)
..++.+.-+.|...|...+.... ......+++|.+|+.++..+......-+.
T Consensus 229 ~~t~~~~l~aL~~~Fg~~es~~~~~~kf~~~~Q~~~E~ls~yv~RlE~lLqkav~k~a 286 (331)
T PF14893_consen 229 KQTAQDCLKALGQVFGSSESRETLEAKFLNTFQEPGEKLSAYVKRLESLLQKAVEKGA 286 (331)
T ss_pred CCCHHHHHHHHHHhcCCcccHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHhcC
Confidence 45788999999999986665433 44567899999999999999998766553
No 41
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=43.76 E-value=11 Score=30.83 Aligned_cols=23 Identities=30% Similarity=0.688 Sum_probs=18.7
Q ss_pred CCcceeecCCCc---cccccCcCccC
Q 045687 155 KKGNCYVCGKPG---HFANKCRYRKG 177 (212)
Q Consensus 155 ~~~~C~~Cgk~G---H~~~~C~~~~~ 177 (212)
+.-.|-.||-.| |+.+.||....
T Consensus 267 R~YVCPiCGATgDnAHTiKyCPl~~~ 292 (318)
T KOG4602|consen 267 RSYVCPICGATGDNAHTIKYCPLAFG 292 (318)
T ss_pred hhhcCccccccCCcccceecccccCC
Confidence 346789998877 99999997766
No 42
>PHA00689 hypothetical protein
Probab=43.30 E-value=7.9 Score=23.08 Aligned_cols=12 Identities=42% Similarity=0.841 Sum_probs=10.1
Q ss_pred CcceeecCCCcc
Q 045687 156 KGNCYVCGKPGH 167 (212)
Q Consensus 156 ~~~C~~Cgk~GH 167 (212)
.+.|-.|||.|-
T Consensus 17 avtckrcgktgl 28 (62)
T PHA00689 17 AVTCKRCGKTGL 28 (62)
T ss_pred eeehhhccccCc
Confidence 478999999874
No 43
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=41.90 E-value=14 Score=34.96 Aligned_cols=24 Identities=17% Similarity=0.357 Sum_probs=21.2
Q ss_pred cCCcceeecCCCccccccCcCccC
Q 045687 154 KKKGNCYVCGKPGHFANKCRYRKG 177 (212)
Q Consensus 154 ~~~~~C~~Cgk~GH~~~~C~~~~~ 177 (212)
.....|+|||........||.-..
T Consensus 460 ~~~L~CH~Cg~~~~~p~~Cp~Cgs 483 (730)
T COG1198 460 TGQLRCHYCGYQEPIPQSCPECGS 483 (730)
T ss_pred CCeeEeCCCCCCCCCCCCCCCCCC
Confidence 356889999999999999998777
No 44
>KOG4025 consensus Putative apoptosis related protein [Function unknown]
Probab=39.42 E-value=1.3e+02 Score=23.08 Aligned_cols=68 Identities=15% Similarity=0.099 Sum_probs=46.3
Q ss_pred HHHHHHHHHHhhccHHHHHhhcccccHHHHHHHHHHHHhhcccccccceecCCccHHHHHHHHHHHHH
Q 045687 29 ANKVCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYIIEDAGAQNFKMAEDKEVTSQIHGFHMLIN 96 (212)
Q Consensus 29 ~d~~a~~~I~~sl~~~i~~~i~~~~tA~~lW~~L~~~y~~~~~~~~~~~~~~~~sv~~~i~~~~~l~~ 96 (212)
+.+.++-.|++-|+++|-.....+.|-++|-.+++.....-....+.+.+..-..|...-.+|-....
T Consensus 100 ~ka~aLk~iLSriPdEinDR~~FLeTIK~IASaIKkLLd~vN~v~~~~p~t~~~AvE~rKkEFVkYSK 167 (207)
T KOG4025|consen 100 KKAIALKRILSRIPDEINDRHAFLETIKLIASAIKKLLDAVNAVYRIVPLTAQPAVEKRKKEFVKYSK 167 (207)
T ss_pred HHHHHHHHHHHhCcHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHH
Confidence 34556778999999999999999888888888888777655555554444444455544444444433
No 45
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.05 E-value=21 Score=31.67 Aligned_cols=24 Identities=25% Similarity=0.606 Sum_probs=21.0
Q ss_pred CcceeecCCCccccccCcCccCCC
Q 045687 156 KGNCYVCGKPGHFANKCRYRKGDH 179 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~~~~~~ 179 (212)
...|..|+..|||.+.||....+.
T Consensus 158 sy~c~rc~~~g~wikacptv~~~~ 181 (448)
T KOG0314|consen 158 SYKCVKCPTPGPWIKACPTVSGSY 181 (448)
T ss_pred CcceecCCCCCccceeccccCCcc
Confidence 477999999999999999887754
No 46
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=38.87 E-value=1.1e+02 Score=20.07 Aligned_cols=29 Identities=14% Similarity=0.266 Sum_probs=23.1
Q ss_pred hccHHHHHhhcccccHHHHHHHHHHHHhh
Q 045687 40 TLSNELYDVYSQHKFAYEIWAQLRKKYII 68 (212)
Q Consensus 40 sl~~~i~~~i~~~~tA~~lW~~L~~~y~~ 68 (212)
.+...|+..+....|..+||..|...|..
T Consensus 31 ~~g~~Iw~lldg~~tv~eI~~~L~~~Y~~ 59 (81)
T TIGR03859 31 DSAGEILELCDGKRSLAEIIQELAQRFPA 59 (81)
T ss_pred hHHHHHHHHccCCCcHHHHHHHHHHHcCC
Confidence 34445667788888999999999999984
No 47
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=38.12 E-value=15 Score=32.87 Aligned_cols=19 Identities=37% Similarity=0.772 Sum_probs=17.6
Q ss_pred cceeecCCCccccccCcCc
Q 045687 157 GNCYVCGKPGHFANKCRYR 175 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~C~~~ 175 (212)
..|..||..||...+||..
T Consensus 262 ~~c~~cg~~~H~q~~cp~r 280 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGR 280 (554)
T ss_pred ccccccCCCccccccCCcc
Confidence 5799999999999999977
No 48
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=37.42 E-value=22 Score=24.39 Aligned_cols=12 Identities=25% Similarity=0.567 Sum_probs=9.1
Q ss_pred ccCCcceeecCC
Q 045687 153 KKKKGNCYVCGK 164 (212)
Q Consensus 153 ~~~~~~C~~Cgk 164 (212)
+-..+.|.+||.
T Consensus 17 hv~~V~C~nCgr 28 (95)
T PRK09335 17 HVGYVQCDNCGR 28 (95)
T ss_pred CCccEEeCCCCC
Confidence 345689999994
No 49
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=36.44 E-value=56 Score=20.68 Aligned_cols=37 Identities=16% Similarity=0.312 Sum_probs=28.1
Q ss_pred HHHHHHhhcc-HHHHHhhcccccHHHHHHHHHHHHhhc
Q 045687 33 CRSTILSTLS-NELYDVYSQHKFAYEIWAQLRKKYIIE 69 (212)
Q Consensus 33 a~~~I~~sl~-~~i~~~i~~~~tA~~lW~~L~~~y~~~ 69 (212)
+....+..|. ....+.|..=-.++++|.+|+..|...
T Consensus 23 a~dhvL~~LGgrT~~eAL~~G~dpr~VW~AlC~~~dVP 60 (63)
T PF11248_consen 23 ARDHVLSELGGRTAAEALEAGVDPRDVWRALCDAFDVP 60 (63)
T ss_pred HHhcchhhcCCcCHHHHHHcCCCHHHHHHHHHHHcCCC
Confidence 3444556666 677778888889999999999998643
No 50
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=35.68 E-value=20 Score=21.99 Aligned_cols=21 Identities=19% Similarity=0.477 Sum_probs=14.3
Q ss_pred CcceeecCCCcccc----ccCcCcc
Q 045687 156 KGNCYVCGKPGHFA----NKCRYRK 176 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~----~~C~~~~ 176 (212)
..-||+||-.---. ..||-..
T Consensus 27 ~~YC~~Cg~~Y~d~~dL~~~CPG~t 51 (55)
T PF13821_consen 27 HNYCFWCGTKYDDEEDLERNCPGPT 51 (55)
T ss_pred CceeeeeCCccCCHHHHHhCCCCCC
Confidence 46799999766555 5577543
No 51
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=34.40 E-value=26 Score=24.65 Aligned_cols=12 Identities=33% Similarity=0.742 Sum_probs=9.2
Q ss_pred ccCCcceeecCC
Q 045687 153 KKKKGNCYVCGK 164 (212)
Q Consensus 153 ~~~~~~C~~Cgk 164 (212)
.-..+.|.+||.
T Consensus 17 hv~~V~C~nCgr 28 (108)
T PTZ00172 17 HVKPVRCSNCGR 28 (108)
T ss_pred CCccEEeCCccc
Confidence 345689999994
No 52
>PF05310 Tenui_NS3: Tenuivirus movement protein; InterPro: IPR007974 This family of ssRNA negative-strand crop plant tenuivirus proteins appears to combine PV2 [], NS2 [], NS3, and PV3 proteins. Plant viruses encode specific proteins known as movement proteins (MPs) to control their spread through plasmodesmata (PD) in walls between cells as well as from leaf to leaf via vascular-dependent transport. During this movement process, the virally encoded MPs interact with viral genomes for transport from the viral replication sites to the PDs in the walls of infected cells along the cytoskeleton and/or endoplasmic reticulum (ER) network. The virus is then thought to move through the PDs in the form of MP-associated ribonucleoprotein complexes or as virions []. The NS3 protein appears to function as an RNA silencing suppressor [].; PDB: 3AJF_A.
Probab=34.05 E-value=13 Score=28.50 Aligned_cols=20 Identities=20% Similarity=0.413 Sum_probs=0.0
Q ss_pred cceeecCCCccccccCcCcc
Q 045687 157 GNCYVCGKPGHFANKCRYRK 176 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~C~~~~ 176 (212)
.+||.|.|+.|...+=-+..
T Consensus 99 tKCWlCdk~~~~~t~~L~~~ 118 (186)
T PF05310_consen 99 TKCWLCDKPSYQETDNLKFI 118 (186)
T ss_dssp --------------------
T ss_pred cceEEecchhhhccCCcceE
Confidence 67999999999887754333
No 53
>PLN00186 ribosomal protein S26; Provisional
Probab=32.00 E-value=30 Score=24.34 Aligned_cols=12 Identities=42% Similarity=0.814 Sum_probs=9.1
Q ss_pred ccCCcceeecCC
Q 045687 153 KKKKGNCYVCGK 164 (212)
Q Consensus 153 ~~~~~~C~~Cgk 164 (212)
.-..+.|.+||+
T Consensus 17 hv~~V~C~nCgr 28 (109)
T PLN00186 17 HVKRIRCSNCGK 28 (109)
T ss_pred CCcceeeCCCcc
Confidence 345689999994
No 54
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=31.19 E-value=29 Score=25.25 Aligned_cols=15 Identities=27% Similarity=0.787 Sum_probs=10.2
Q ss_pred cceeecCCCcccccc
Q 045687 157 GNCYVCGKPGHFANK 171 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~ 171 (212)
+.|||||+.-.....
T Consensus 1 v~C~fC~~~s~~~~~ 15 (131)
T PF09779_consen 1 VNCWFCGQNSKVPYD 15 (131)
T ss_pred CeeccCCCCCCCCCC
Confidence 358888877666544
No 55
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=30.15 E-value=26 Score=21.35 Aligned_cols=17 Identities=29% Similarity=0.663 Sum_probs=14.0
Q ss_pred CcceeecCCCccccccC
Q 045687 156 KGNCYVCGKPGHFANKC 172 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C 172 (212)
...||.|+...|.-..|
T Consensus 48 ~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 48 FSFCFRCKVPWHSPVSC 64 (64)
T ss_pred CeECCCCCCcCCCCCCC
Confidence 47799999999987665
No 56
>PF05369 MtmB: Monomethylamine methyltransferase MtmB; InterPro: IPR008031 Monomethylamine methyltransferase of the archaebacterium Methanosarcina barkeri contains a novel amino acid, pyrrolysine, encoded by the termination codon UAG []. The structure of the enzyme reveals a homohexamer comprised of individual subunits with a TIM barrel fold. MtmB initiates the metabolism of monomethylamine by catalysing the transfer of the methyl group from monomethylamine to the corrinoid cofactor of MtmC.; GO: 0008168 methyltransferase activity
Probab=30.09 E-value=1.2e+02 Score=26.87 Aligned_cols=61 Identities=8% Similarity=0.180 Sum_probs=43.0
Q ss_pred HHHHhhcc--cccHHHHHHHHHHHHhhcccccc--------cceecCCccHHHHHHHHHHHHHHHHhCCCCC
Q 045687 44 ELYDVYSQ--HKFAYEIWAQLRKKYIIEDAGAQ--------NFKMAEDKEVTSQIHGFHMLINDLKNENIIL 105 (212)
Q Consensus 44 ~i~~~i~~--~~tA~~lW~~L~~~y~~~~~~~~--------~~~~~~~~sv~~~i~~~~~l~~~L~~~~~~l 105 (212)
++.+.+.. +..|.+||+.|-.+|+ ....+. -|.+.--.+-.+|+.-...+..+|..+|+.+
T Consensus 387 Eva~a~a~~~lsevN~i~~~i~~~Ye-~~~~~~p~Gk~F~EcYdv~t~~Pt~EY~~~Y~~~~k~l~~~gl~~ 457 (457)
T PF05369_consen 387 EVARAVAGMDLSEVNDILDKIVAKYE-KNYSSAPKGKPFQECYDVNTMQPTDEYMNVYDKAKKELEDLGLVF 457 (457)
T ss_pred HHHHHHhcccHHHHHHHHHHHHHHhh-hccccCCCCCChHHHhcccccCCcHHHHHHHHHHHHHHHHhcccC
Confidence 33444443 3468999999999998 333322 3444556677899999999999999998753
No 57
>PF13395 HNH_4: HNH endonuclease
Probab=29.89 E-value=19 Score=21.71 Aligned_cols=7 Identities=71% Similarity=1.720 Sum_probs=5.3
Q ss_pred eeecCCC
Q 045687 159 CYVCGKP 165 (212)
Q Consensus 159 C~~Cgk~ 165 (212)
|+|||+.
T Consensus 1 C~Y~g~~ 7 (54)
T PF13395_consen 1 CPYCGKP 7 (54)
T ss_pred CCCCCCC
Confidence 7888864
No 58
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=29.56 E-value=1.4e+02 Score=18.33 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=20.2
Q ss_pred HHhhccHHHHHhhcccccHHHHHHHHHHHHh
Q 045687 37 ILSTLSNELYDVYSQHKFAYEIWAQLRKKYI 67 (212)
Q Consensus 37 I~~sl~~~i~~~i~~~~tA~~lW~~L~~~y~ 67 (212)
.++.....|+..+....|..+|-+.|...|.
T Consensus 14 ~Ln~~a~~Iw~~~~g~~t~~ei~~~l~~~y~ 44 (68)
T PF05402_consen 14 TLNETAAFIWELLDGPRTVEEIVDALAEEYD 44 (68)
T ss_dssp ---THHHHHHHH--SSS-HHHHHHHHHHHTT
T ss_pred cccHHHHHHHHHccCCCCHHHHHHHHHHHcC
Confidence 5555666777777777888999999999996
No 59
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=28.92 E-value=30 Score=28.18 Aligned_cols=21 Identities=29% Similarity=0.830 Sum_probs=18.1
Q ss_pred CcceeecCCCccccccCcCccC
Q 045687 156 KGNCYVCGKPGHFANKCRYRKG 177 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~C~~~~~ 177 (212)
...|.+| +..||.-.||.+.-
T Consensus 119 ~~~CR~C-~gdHwt~~CPyK~~ 139 (270)
T KOG0122|consen 119 IVACRIC-KGDHWTTNCPYKDT 139 (270)
T ss_pred eeeeeec-CCCeeeecCCchhh
Confidence 4779999 89999999997655
No 60
>cd03154 TM4SF3_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF3_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This subfamily contaions transmembrane 4 superfamily 3 (TM4SF3) or D6.1a and related proteins. D6.1a associates with alpha6beta4 integrin and supports cell motility, it has been ascribed a role in tumor progression and metastasis.
Probab=27.68 E-value=83 Score=21.04 Aligned_cols=36 Identities=8% Similarity=-0.032 Sum_probs=20.8
Q ss_pred HHHHHHHhhccHHHHHhhcccccHHHHHHHHHHHHh
Q 045687 32 VCRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYI 67 (212)
Q Consensus 32 ~a~~~I~~sl~~~i~~~i~~~~tA~~lW~~L~~~y~ 67 (212)
.+..+|...|...+............+|+.|...|.
T Consensus 10 ~i~~~i~~~~~~~i~~y~~~~~~~~~~~d~lQ~~l~ 45 (100)
T cd03154 10 KIENELKEKNTKLLSLLGQNAKSVKKSLEKFQKELK 45 (100)
T ss_pred HHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHcCC
Confidence 345566666655544432221234678998888775
No 61
>PF13376 OmdA: Bacteriocin-protection, YdeI or OmpD-Associated
Probab=24.73 E-value=60 Score=20.15 Aligned_cols=27 Identities=19% Similarity=0.261 Sum_probs=22.8
Q ss_pred ccHHHHHhhcccccHHHHHHHHHHHHh
Q 045687 41 LSNELYDVYSQHKFAYEIWAQLRKKYI 67 (212)
Q Consensus 41 l~~~i~~~i~~~~tA~~lW~~L~~~y~ 67 (212)
|++++...+..-..|.+.|+.|...|.
T Consensus 6 vP~dl~~aL~~~p~a~~~f~~l~~~~r 32 (63)
T PF13376_consen 6 VPEDLEAALEANPEAKEFFESLTPSYR 32 (63)
T ss_pred CCHHHHHHHHCCHHHHHHHHHCCHHHH
Confidence 677888888888899999998888776
No 62
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=24.53 E-value=20 Score=20.41 Aligned_cols=10 Identities=40% Similarity=1.215 Sum_probs=4.3
Q ss_pred cceeecCCCc
Q 045687 157 GNCYVCGKPG 166 (212)
Q Consensus 157 ~~C~~Cgk~G 166 (212)
..|.+||++.
T Consensus 2 ~~CSFCgr~~ 11 (41)
T PF06689_consen 2 KRCSFCGRPE 11 (41)
T ss_dssp -B-TTT--BT
T ss_pred CCccCCCCCH
Confidence 4699999653
No 63
>smart00400 ZnF_CHCC zinc finger.
Probab=24.13 E-value=39 Score=20.33 Aligned_cols=13 Identities=31% Similarity=0.769 Sum_probs=9.7
Q ss_pred CcceeecCCCccc
Q 045687 156 KGNCYVCGKPGHF 168 (212)
Q Consensus 156 ~~~C~~Cgk~GH~ 168 (212)
.-.||.||+.|=.
T Consensus 23 ~~~Cf~cg~gGd~ 35 (55)
T smart00400 23 FFHCFGCGAGGNV 35 (55)
T ss_pred EEEEeCCCCCCCH
Confidence 4679999987743
No 64
>cd03155 CD151_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), CD151_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". CD151strongly associates with integrins, especially alpha3beta1, alpha6beta1, alpha7beta1, and alpha6beta4; it may play roles in cell-cell adhesion, cell migration, platelet aggregation, and angiogenesis. For example, CD151 is is involved in regulation of migration of neutrophils, endothelial cells, and
Probab=23.59 E-value=1.4e+02 Score=20.30 Aligned_cols=35 Identities=11% Similarity=0.199 Sum_probs=20.3
Q ss_pred HHHHHHhhccHHHHHhhccc--ccHHHHHHHHHHHHh
Q 045687 33 CRSTILSTLSNELYDVYSQH--KFAYEIWAQLRKKYI 67 (212)
Q Consensus 33 a~~~I~~sl~~~i~~~i~~~--~tA~~lW~~L~~~y~ 67 (212)
+...|..+|...|...+..- .....+|+.|...|.
T Consensus 7 ~~~~i~~~l~~~i~~~y~~~~~~~~~~~~d~iQ~~l~ 43 (110)
T cd03155 7 LEDELKESLKRTMQENYGQSGEEALTLTVDELQQEFK 43 (110)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhCc
Confidence 44455555555555444322 345778888887765
No 65
>PRK14063 exodeoxyribonuclease VII small subunit; Provisional
Probab=23.06 E-value=90 Score=20.44 Aligned_cols=32 Identities=16% Similarity=0.288 Sum_probs=26.2
Q ss_pred cCCccHHHHHHHHHHHHHHHHhCCCCCCcccc
Q 045687 79 AEDKEVTSQIHGFHMLINDLKNENIILPESFM 110 (212)
Q Consensus 79 ~~~~sv~~~i~~~~~l~~~L~~~~~~l~d~~~ 110 (212)
....++.+-+.++..|+..|..-.++|++...
T Consensus 2 e~~~sfEeal~~LE~Iv~~LE~~~l~Leesl~ 33 (76)
T PRK14063 2 ENKLSFEEAISQLEHLVSKLEQGDVPLEEAIS 33 (76)
T ss_pred CcccCHHHHHHHHHHHHHHHHCCCCCHHHHHH
Confidence 34568899999999999999988887776655
No 66
>PRK00114 hslO Hsp33-like chaperonin; Reviewed
Probab=22.71 E-value=27 Score=29.16 Aligned_cols=16 Identities=25% Similarity=0.555 Sum_probs=13.5
Q ss_pred CcceeecCCCcccccc
Q 045687 156 KGNCYVCGKPGHFANK 171 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~~ 171 (212)
.+.|.||++..||.++
T Consensus 268 ev~C~FC~~~Y~f~~~ 283 (293)
T PRK00114 268 EMVCQFCGNKYLFDEE 283 (293)
T ss_pred EEEEeCCCCEEEeCHH
Confidence 4889999999998753
No 67
>PHA03230 nuclear protein UL55; Provisional
Probab=22.02 E-value=25 Score=27.11 Aligned_cols=18 Identities=33% Similarity=0.767 Sum_probs=16.1
Q ss_pred cceeecCCCccccccCcC
Q 045687 157 GNCYVCGKPGHFANKCRY 174 (212)
Q Consensus 157 ~~C~~Cgk~GH~~~~C~~ 174 (212)
+.||+|+=..=|..+||.
T Consensus 136 Gl~yHCHCk~PFS~eCW~ 153 (180)
T PHA03230 136 GLCYHCHCKNPFSLECWQ 153 (180)
T ss_pred EEEEeeccCCCCCHHHHH
Confidence 789999999999999985
No 68
>PF15056 NRN1: Neuritin protein family
Probab=21.85 E-value=69 Score=21.66 Aligned_cols=15 Identities=33% Similarity=0.512 Sum_probs=12.5
Q ss_pred ccHHHHHHHHHHHHh
Q 045687 53 KFAYEIWAQLRKKYI 67 (212)
Q Consensus 53 ~tA~~lW~~L~~~y~ 67 (212)
..|.+||+.|++.--
T Consensus 55 eeAa~iWEsLrqESr 69 (89)
T PF15056_consen 55 EEAAAIWESLRQESR 69 (89)
T ss_pred HHHHHHHHHHHHHHH
Confidence 679999999998653
No 69
>cd03160 CD37_CD82_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), CD37_CD82_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". CD37 is a leukocyte-specific protein, and its restricted expression pattern suggests a role in the immune system. A regulatory role in T-cell proliferation has been suggested. CD82 is a metastasis suppressor implicated in biological processes ranging from fusion, adhesion, and migration to apoptos
Probab=21.10 E-value=1.5e+02 Score=20.50 Aligned_cols=36 Identities=11% Similarity=0.134 Sum_probs=20.6
Q ss_pred HHHHHHHhhccHHHHHhhcc--cccHHHHHHHHHHHHh
Q 045687 32 VCRSTILSTLSNELYDVYSQ--HKFAYEIWAQLRKKYI 67 (212)
Q Consensus 32 ~a~~~I~~sl~~~i~~~i~~--~~tA~~lW~~L~~~y~ 67 (212)
++..+|...|...+...... -.....+|+.|...|.
T Consensus 7 ~v~~~i~~~l~~~i~~y~~~~~~~~~~~~~d~iQ~~l~ 44 (117)
T cd03160 7 KLKQEMGDIVEKVIQNYGGNPENKTAEEAWDYVQFQLQ 44 (117)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHhhCc
Confidence 35556666665554432211 2346778888887765
No 70
>cd03159 TM4SF9_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF9_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This subfamily contaions transmembrane 4 superfamily 9 (TM4SF9) or Tetraspanin-5 and related proteins. TM4SF9 is strongly expressed witin the central nervous system, and expression levels appear to correlate with differentiation status of particular neurons, hinting at a role in neuronal maturation.
Probab=21.03 E-value=1.5e+02 Score=20.62 Aligned_cols=34 Identities=12% Similarity=0.170 Sum_probs=20.3
Q ss_pred HHHHHHhhccHHHHHhhcccccHHHHHHHHHHHHh
Q 045687 33 CRSTILSTLSNELYDVYSQHKFAYEIWAQLRKKYI 67 (212)
Q Consensus 33 a~~~I~~sl~~~i~~~i~~~~tA~~lW~~L~~~y~ 67 (212)
+..+|...|...+.. +..-....++|+.|...|.
T Consensus 7 v~~~i~~~l~~~i~~-y~~~~~~~~~~D~iQ~~l~ 40 (121)
T cd03159 7 IKDQLTEFLNNNIRA-YRDDIDLQNLIDFLQEYWQ 40 (121)
T ss_pred HHHHHHHHHHHHHHH-hccCHHHHHHHHHHHHhcc
Confidence 445555555555443 3333455688988888775
No 71
>PRK11582 flagella biosynthesis protein FliZ; Provisional
Probab=21.03 E-value=3.8e+02 Score=20.34 Aligned_cols=26 Identities=23% Similarity=0.262 Sum_probs=21.8
Q ss_pred CccHHHHHHHHHHHHHHHHhCCCCCC
Q 045687 81 DKEVTSQIHGFHMLINDLKNENIILP 106 (212)
Q Consensus 81 ~~sv~~~i~~~~~l~~~L~~~~~~l~ 106 (212)
..+|.||+-+++.|=.-|.+-.++.+
T Consensus 104 hSTvrEYVVRLRRLd~lL~~~n~p~~ 129 (169)
T PRK11582 104 HSTVREYVVRLRRLDEHLHEQNIPLD 129 (169)
T ss_pred cccHHHHHHHHHHHHHHHhhccCCHH
Confidence 35899999999999998888777644
No 72
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.33 E-value=51 Score=29.82 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=18.9
Q ss_pred CCcceeecCCCccccccCcCccC
Q 045687 155 KKGNCYVCGKPGHFANKCRYRKG 177 (212)
Q Consensus 155 ~~~~C~~Cgk~GH~~~~C~~~~~ 177 (212)
....|++||..--+...||.-..
T Consensus 239 ~~l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 239 GKLRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred CeEEcCCCcCcCCCCCCCCCCCC
Confidence 35789999988888889997765
No 73
>PF08844 DUF1815: Domain of unknown function (DUF1815); InterPro: IPR014943 This entry is about 100 amino acids in length and is functionally uncharacterised.
Probab=20.25 E-value=53 Score=22.53 Aligned_cols=17 Identities=29% Similarity=0.661 Sum_probs=10.7
Q ss_pred cCCcceeec--CCCccccc
Q 045687 154 KKKGNCYVC--GKPGHFAN 170 (212)
Q Consensus 154 ~~~~~C~~C--gk~GH~~~ 170 (212)
+-...||.| |..+|-+.
T Consensus 30 G~~AsCYtC~dG~~~~~AS 48 (105)
T PF08844_consen 30 GYLASCYTCGDGRDMNSAS 48 (105)
T ss_pred CceeEEEecCCCCCCCcee
Confidence 345779999 55555443
No 74
>PRK01402 hslO Hsp33-like chaperonin; Reviewed
Probab=20.10 E-value=32 Score=29.31 Aligned_cols=15 Identities=20% Similarity=0.476 Sum_probs=12.9
Q ss_pred CcceeecCCCccccc
Q 045687 156 KGNCYVCGKPGHFAN 170 (212)
Q Consensus 156 ~~~C~~Cgk~GH~~~ 170 (212)
.+.|.|||+..||..
T Consensus 308 ev~CeFC~~~Y~f~~ 322 (328)
T PRK01402 308 SVTCEFCSRVYRFDP 322 (328)
T ss_pred EEEeeCCCCEEEeCH
Confidence 488999999999864
Done!