Query 012025
Match_columns 472
No_of_seqs 127 out of 159
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 07:49:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012025.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012025hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03468 XS: XS domain; Inter 100.0 6.8E-46 1.5E-50 325.2 7.8 114 324-444 1-114 (116)
2 PF03470 zf-XS: XS zinc finger 99.4 3.1E-14 6.8E-19 106.4 1.8 36 254-292 1-43 (43)
3 PF14259 RRM_6: RNA recognitio 87.3 2.7 5.8E-05 32.2 6.6 58 334-401 1-60 (70)
4 PF00076 RRM_1: RNA recognitio 83.3 3.5 7.7E-05 30.7 5.4 55 334-398 1-57 (70)
5 PF03115 Astro_capsid: Astrovi 79.6 0.58 1.3E-05 53.8 0.0 22 253-278 734-755 (787)
6 PF05605 zf-Di19: Drought indu 78.6 1.1 2.4E-05 34.4 1.3 23 250-279 1-23 (54)
7 KOG0943 Predicted ubiquitin-pr 77.9 1.6 3.5E-05 52.5 2.8 14 56-69 1628-1641(3015)
8 KOG3130 Uncharacterized conser 77.0 1.7 3.6E-05 46.9 2.4 16 197-212 285-300 (514)
9 smart00362 RRM_2 RNA recogniti 75.7 8.4 0.00018 27.7 5.3 47 334-389 2-49 (72)
10 KOG1832 HIV-1 Vpr-binding prot 74.0 1.7 3.6E-05 51.0 1.6 9 99-107 1272-1280(1516)
11 PF04931 DNA_pol_phi: DNA poly 72.8 2.3 5.1E-05 48.4 2.4 6 54-59 512-517 (784)
12 PF04147 Nop14: Nop14-like fam 72.3 2.3 4.9E-05 49.3 2.1 10 249-258 419-428 (840)
13 PF03153 TFIIA: Transcription 70.9 1.5 3.2E-05 45.4 0.2 13 243-256 340-352 (375)
14 PF13894 zf-C2H2_4: C2H2-type 65.9 3.7 8E-05 25.1 1.2 20 252-277 1-20 (24)
15 KOG0943 Predicted ubiquitin-pr 65.5 3.6 7.7E-05 49.8 1.9 12 285-296 1891-1902(3015)
16 TIGR01661 ELAV_HUD_SF ELAV/HuD 64.6 11 0.00025 37.5 5.1 51 334-393 272-325 (352)
17 PHA03346 US22 family homolog; 59.2 17 0.00037 40.4 5.6 12 115-126 392-403 (520)
18 KOG1189 Global transcriptional 57.2 13 0.00028 43.2 4.4 11 149-159 865-875 (960)
19 PF14812 PBP1_TM: Transmembran 55.3 2.5 5.4E-05 36.2 -1.2 10 223-232 61-70 (81)
20 COG5406 Nucleosome binding fac 53.6 11 0.00024 43.1 3.1 9 148-156 916-924 (1001)
21 KOG1994 Predicted RNA binding 53.3 7.9 0.00017 39.2 1.7 27 249-281 237-263 (268)
22 TIGR00165 S18 ribosomal protei 52.5 22 0.00049 29.6 4.0 43 253-296 7-57 (70)
23 PLN03120 nucleic acid binding 51.8 31 0.00066 35.4 5.6 58 333-401 6-64 (260)
24 KOG3064 RNA-binding nuclear pr 51.3 8 0.00017 39.8 1.4 23 197-219 238-261 (303)
25 PF13912 zf-C2H2_6: C2H2-type 50.0 7.9 0.00017 25.2 0.8 22 251-278 1-22 (27)
26 PF00096 zf-C2H2: Zinc finger, 49.1 8.5 0.00018 24.1 0.8 20 252-277 1-20 (23)
27 KOG1824 TATA-binding protein-i 46.7 11 0.00023 44.9 1.7 13 267-279 394-406 (1233)
28 TIGR01661 ELAV_HUD_SF ELAV/HuD 45.3 38 0.00083 33.8 5.2 47 334-389 6-55 (352)
29 smart00017 OSTEO Osteopontin. 45.2 13 0.00028 38.0 1.8 12 249-260 120-131 (287)
30 PRK13401 30S ribosomal protein 45.1 32 0.0007 29.7 3.9 45 252-297 14-66 (82)
31 smart00360 RRM RNA recognition 45.0 42 0.00091 23.8 4.1 37 352-388 8-47 (71)
32 PLN03121 nucleic acid binding 44.2 40 0.00086 34.3 5.0 58 332-399 6-63 (243)
33 PF04889 Cwf_Cwc_15: Cwf15/Cwc 43.1 22 0.00047 35.8 3.0 10 223-232 157-166 (244)
34 PRK00391 rpsR 30S ribosomal pr 42.6 39 0.00084 28.9 4.0 45 250-296 13-66 (79)
35 PLN03134 glycine-rich RNA-bind 41.3 63 0.0014 29.5 5.5 56 333-398 36-94 (144)
36 PF10058 DUF2296: Predicted in 40.1 23 0.00049 28.0 2.1 15 243-258 37-51 (54)
37 KOG3130 Uncharacterized conser 40.0 19 0.00041 39.2 2.2 11 84-94 169-179 (514)
38 TIGR01649 hnRNP-L_PTB hnRNP-L/ 37.8 61 0.0013 34.9 5.6 69 328-406 389-462 (481)
39 KOG0125 Ataxin 2-binding prote 37.7 53 0.0012 35.1 4.9 57 336-401 101-158 (376)
40 KOG0130 RNA-binding protein RB 37.1 38 0.00082 32.3 3.4 59 327-398 68-129 (170)
41 KOG0533 RRM motif-containing p 35.9 56 0.0012 33.2 4.6 64 334-407 86-151 (243)
42 COG0724 RNA-binding proteins ( 35.6 85 0.0018 28.1 5.3 61 331-400 115-178 (306)
43 PF12171 zf-C2H2_jaz: Zinc-fin 35.5 18 0.00039 23.9 0.8 23 251-279 1-23 (27)
44 KOG1991 Nuclear transport rece 35.3 21 0.00046 42.4 1.8 13 228-240 962-974 (1010)
45 PRK13400 30S ribosomal protein 33.8 55 0.0012 31.1 3.9 27 251-278 22-48 (147)
46 COG0238 RpsR Ribosomal protein 33.5 37 0.00081 28.9 2.5 28 250-279 14-41 (75)
47 KOG1991 Nuclear transport rece 31.0 30 0.00064 41.2 2.0 7 270-276 979-985 (1010)
48 PF04147 Nop14: Nop14-like fam 30.7 31 0.00067 40.2 2.2 14 323-336 557-570 (840)
49 KOG0717 Molecular chaperone (D 30.1 51 0.0011 36.6 3.5 39 252-298 293-331 (508)
50 PF13893 RRM_5: RNA recognitio 30.1 86 0.0019 23.2 3.8 40 357-403 1-41 (56)
51 KOG1824 TATA-binding protein-i 29.7 39 0.00084 40.5 2.7 13 286-298 435-447 (1233)
52 TIGR01628 PABP-1234 polyadenyl 29.0 89 0.0019 33.9 5.1 50 333-391 90-141 (562)
53 KOG3241 Uncharacterized conser 29.0 35 0.00075 33.7 1.8 7 1-7 1-7 (227)
54 KOG2817 Predicted E3 ubiquitin 28.6 25 0.00054 37.9 0.9 10 251-260 374-383 (394)
55 PF04194 PDCD2_C: Programmed c 27.8 66 0.0014 30.1 3.4 40 222-261 52-107 (164)
56 TIGR01642 U2AF_lg U2 snRNP aux 27.2 79 0.0017 33.4 4.3 57 333-389 411-474 (509)
57 PF04050 Upf2: Up-frameshift s 27.1 21 0.00045 33.6 0.0 16 286-301 64-79 (170)
58 KOG1999 RNA polymerase II tran 27.0 49 0.0011 39.5 2.9 6 430-435 424-429 (1024)
59 PRK00398 rpoP DNA-directed RNA 27.0 53 0.0011 24.4 2.1 11 250-260 20-30 (46)
60 PHA00616 hypothetical protein 26.6 20 0.00043 27.6 -0.2 22 251-278 1-22 (44)
61 CHL00077 rps18 ribosomal prote 26.5 94 0.002 27.1 3.8 41 253-297 19-68 (86)
62 TIGR01659 sex-lethal sex-letha 26.4 1.1E+02 0.0024 32.0 5.2 61 333-402 195-258 (346)
63 KOG2652 RNA polymerase II tran 26.3 47 0.001 35.4 2.4 7 249-255 318-324 (348)
64 KOG4364 Chromatin assembly fac 26.3 79 0.0017 36.6 4.2 59 270-340 610-671 (811)
65 COG5533 UBP5 Ubiquitin C-termi 25.9 40 0.00087 36.0 1.8 27 230-263 270-296 (415)
66 PF02724 CDC45: CDC45-like pro 25.9 39 0.00085 38.1 1.8 11 291-301 262-272 (622)
67 TIGR01659 sex-lethal sex-letha 25.8 1.2E+02 0.0026 31.9 5.2 54 334-397 110-166 (346)
68 KOG0107 Alternative splicing f 25.6 71 0.0015 31.5 3.3 36 353-391 23-59 (195)
69 PF11702 DUF3295: Protein of u 25.4 25 0.00055 39.0 0.2 7 270-276 348-354 (507)
70 PRK12495 hypothetical protein; 25.1 57 0.0012 32.9 2.6 42 212-259 4-50 (226)
71 KOG4212 RNA-binding protein hn 24.7 1.3E+02 0.0028 33.5 5.3 64 334-407 47-113 (608)
72 TIGR01645 half-pint poly-U bin 24.7 1.2E+02 0.0027 34.5 5.4 62 333-404 206-270 (612)
73 KOG3241 Uncharacterized conser 24.4 46 0.00099 32.9 1.7 10 211-220 214-223 (227)
74 cd00590 RRM RRM (RNA recogniti 24.1 1.7E+02 0.0036 20.9 4.4 38 352-389 11-50 (74)
75 TIGR00993 3a0901s04IAP86 chlor 24.1 75 0.0016 37.0 3.6 17 324-340 633-649 (763)
76 KOG0699 Serine/threonine prote 23.0 3.2E+02 0.007 30.1 7.7 16 249-265 349-364 (542)
77 TIGR01622 SF-CC1 splicing fact 22.8 1.6E+02 0.0034 30.8 5.5 47 333-388 188-237 (457)
78 PF03153 TFIIA: Transcription 22.1 33 0.00071 35.6 0.3 7 224-230 343-349 (375)
79 PF05285 SDA1: SDA1; InterPro 21.6 48 0.001 34.4 1.4 11 60-70 14-24 (324)
80 PF12253 CAF1A: Chromatin asse 21.2 1.2E+02 0.0026 25.8 3.4 10 145-154 11-20 (77)
81 PHA03249 DNA packaging tegumen 21.0 1.4E+03 0.029 26.8 13.4 31 29-59 35-67 (653)
82 smart00531 TFIIE Transcription 21.0 52 0.0011 30.2 1.4 12 249-260 121-132 (147)
83 smart00451 ZnF_U1 U1-like zinc 20.7 73 0.0016 21.6 1.7 25 250-280 2-26 (35)
84 PRK10144 formate-dependent nit 20.6 35 0.00075 31.5 0.1 11 250-260 39-49 (126)
85 PF00301 Rubredoxin: Rubredoxi 20.2 34 0.00075 26.4 0.0 13 249-261 32-44 (47)
86 PF05129 Elf1: Transcription e 20.2 42 0.0009 28.5 0.5 11 249-259 20-30 (81)
87 TIGR03655 anti_R_Lar restricti 20.1 45 0.00098 25.7 0.6 9 253-261 3-11 (53)
88 COG5109 Uncharacterized conser 20.1 46 0.00099 35.5 0.8 13 249-261 374-386 (396)
No 1
>PF03468 XS: XS domain; InterPro: IPR005380 The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Q9SBW2 from SWISSPROT and SGS3 Q9LDX1 from SWISSPROT. SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain containing proteins contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes [].; PDB: 4E8U_C.
Probab=100.00 E-value=6.8e-46 Score=325.23 Aligned_cols=114 Identities=39% Similarity=0.770 Sum_probs=85.4
Q ss_pred CCceeeeCceEEEeecccccCCCCcccccChHHHHHHhhccCcceeEeccCCCCCcceEEEEeCCCchhhHHHHHHHHHH
Q 012025 324 KDHEIVWPPMVIIMNTRLDKDENDKWTGMGNQELLEYFILYAAVRARHSYGPQGHRGMSVLIFESSAGGYLEAERLHKHF 403 (472)
Q Consensus 324 kDdliVWPWMGIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~KVr~lyg~~GH~G~aVVeF~kdwsGF~nA~rLekhF 403 (472)
+||+|||||||||+||+|+++++|+++|+|+++|+++|+.|+|++|++||+++||+|+|||+|++||+||+||++||+||
T Consensus 1 qdd~~VWPwmgIi~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~kv~~l~~~~gh~g~aiv~F~~~w~Gf~~A~~l~~~F 80 (116)
T PF03468_consen 1 QDDLIVWPWMGIIVNIPTEKDDDGRWVGMSNEELLDKLAEFNPLKVKPLYGKQGHTGFAIVEFNKDWSGFKNAMRLEKHF 80 (116)
T ss_dssp ---EEEES-EEEEE----EE-TTS-EE---SHHHHHHHHH---SEEEEEEETTEEEEEEEEE--SSHHHHHHHHHHHHHH
T ss_pred CCCcccCCCEEEEEcCccccCCCCceeccCHHHHHHHHHhcCCceeEECcCCCCCcEEEEEEECCChHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCChhhhhhhcccccccCCCcceeeeEecccccccccC
Q 012025 404 AEQGTDRDSWNNSNRRVLFHAGGKRQLYGFMALKEDLDVFN 444 (472)
Q Consensus 404 e~qg~GRkDW~~~~r~~~~~pG~~~~LYGWlAradDyds~n 444 (472)
+.++|||+||. +++. .+++||||||++|||++-+
T Consensus 81 ~~~~~Gr~dW~--~~~~-----~~~~lYGw~A~~dD~~~~~ 114 (116)
T PF03468_consen 81 EAQGHGRKDWE--RRRG-----GGSQLYGWVARADDYNSPG 114 (116)
T ss_dssp HHTT-SHHHHT---SSS--------S-EEEE-BHHHHHSSS
T ss_pred HHcCCCHHHHh--hccC-----CCCceeeeeCchhhccCCC
Confidence 99999999998 5443 4899999999999998744
No 2
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=99.44 E-value=3.1e-14 Score=106.42 Aligned_cols=36 Identities=42% Similarity=0.775 Sum_probs=34.2
Q ss_pred ccCCCCCCCCccccCCchHHhhhhcccC-------chhhhhHHHHH
Q 012025 254 CPACQGGPGAIDWYRGLQPLMTHAKTKG-------SKRVKLHRELA 292 (472)
Q Consensus 254 CP~C~gkkk~~D~Y~~lk~LLqHA~gvG-------ak~kalHrALa 292 (472)
||||+++|++ | |+ |++|||||+||| ++++++|||||
T Consensus 1 CP~C~~kkk~-~-Y~-~~~LlqHA~gvg~~~~~r~~k~ka~HrALa 43 (43)
T PF03470_consen 1 CPFCPGKKKQ-D-YK-YRELLQHASGVGASSSRRSAKEKANHRALA 43 (43)
T ss_pred CCCCCCCCCc-c-ee-hhHHHHHHHhhCcCcccchHHHHHhhhhhC
Confidence 9999999988 7 99 999999999999 79999999996
No 3
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=87.31 E-value=2.7 Score=32.21 Aligned_cols=58 Identities=24% Similarity=0.345 Sum_probs=41.9
Q ss_pred EEEeecccccCCCCcccccChHHHHHHhhccCcc-eeEeccCCCCC-cceEEEEeCCCchhhHHHHHHHH
Q 012025 334 VIIMNTRLDKDENDKWTGMGNQELLEYFILYAAV-RARHSYGPQGH-RGMSVLIFESSAGGYLEAERLHK 401 (472)
Q Consensus 334 GIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~-KVr~lyg~~GH-~G~aVVeF~kdwsGF~nA~rLek 401 (472)
+.|-|+|. ..+.++|++.|..|+++ +++.+.+++|. +|+|+|+|. +-.....|+.+.+
T Consensus 1 v~i~nlp~---------~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~-~~~~a~~al~~~~ 60 (70)
T PF14259_consen 1 VYISNLPP---------STTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFS-SEEDAKRALELLN 60 (70)
T ss_dssp EEEESSTT---------T--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEES-SHHHHHHHHHHHT
T ss_pred CEEeCCCC---------CCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeC-CHHHHHHHHHHCC
Confidence 45777764 24578899999998765 68888887765 899999996 5666666666653
No 4
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=83.28 E-value=3.5 Score=30.75 Aligned_cols=55 Identities=18% Similarity=0.304 Sum_probs=38.8
Q ss_pred EEEeecccccCCCCcccccChHHHHHHhhccCcc-eeEeccCCCC-CcceEEEEeCCCchhhHHHHH
Q 012025 334 VIIMNTRLDKDENDKWTGMGNQELLEYFILYAAV-RARHSYGPQG-HRGMSVLIFESSAGGYLEAER 398 (472)
Q Consensus 334 GIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~-KVr~lyg~~G-H~G~aVVeF~kdwsGF~nA~r 398 (472)
+.|-|+|. .++.++|++.|+.|.++ .+....+..+ +.|+++|+|.+ ...-..|+.
T Consensus 1 l~v~nlp~---------~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~-~~~a~~a~~ 57 (70)
T PF00076_consen 1 LYVGNLPP---------DVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFES-EEDAEKALE 57 (70)
T ss_dssp EEEESETT---------TSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESS-HHHHHHHHH
T ss_pred cEEcCCCC---------cCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcC-HHHHHHHHH
Confidence 35667764 24678999999999998 4556664444 58999999998 455555544
No 5
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=79.60 E-value=0.58 Score=53.75 Aligned_cols=22 Identities=9% Similarity=0.107 Sum_probs=0.0
Q ss_pred EccCCCCCCCCccccCCchHHhhhhc
Q 012025 253 HCPACQGGPGAIDWYRGLQPLMTHAK 278 (472)
Q Consensus 253 ~CP~C~gkkk~~D~Y~~lk~LLqHA~ 278 (472)
-||-|..+.+. ..|+ +||.=..
T Consensus 734 AfPT~aek~~r-~vy~---d~LaDGl 755 (787)
T PF03115_consen 734 AFPTLAEKERR-NVYM---DALADGL 755 (787)
T ss_dssp --------------------------
T ss_pred cCCCchhhhhh-hhHH---hhhccCC
Confidence 35666655443 4354 6664433
No 6
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=78.59 E-value=1.1 Score=34.37 Aligned_cols=23 Identities=22% Similarity=0.674 Sum_probs=16.6
Q ss_pred CeEEccCCCCCCCCccccCCchHHhhhhcc
Q 012025 250 RQWHCPACQGGPGAIDWYRGLQPLMTHAKT 279 (472)
Q Consensus 250 ~tf~CP~C~gkkk~~D~Y~~lk~LLqHA~g 279 (472)
.+|.||||.. . | +...|+.|-..
T Consensus 1 ~~f~CP~C~~---~---~-~~~~L~~H~~~ 23 (54)
T PF05605_consen 1 DSFTCPYCGK---G---F-SESSLVEHCED 23 (54)
T ss_pred CCcCCCCCCC---c---c-CHHHHHHHHHh
Confidence 3799999963 1 3 37799999654
No 7
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=77.95 E-value=1.6 Score=52.47 Aligned_cols=14 Identities=14% Similarity=0.188 Sum_probs=8.3
Q ss_pred EEEeeccCCCCCCC
Q 012025 56 VYVRKSKNKAGSGT 69 (472)
Q Consensus 56 ~~~~k~k~~~~~~~ 69 (472)
.|-|+||+-...++
T Consensus 1628 evlkrskkeeraia 1641 (3015)
T KOG0943|consen 1628 EVLKRSKKEERAIA 1641 (3015)
T ss_pred HHHhhhhhhhcccc
Confidence 34477776655553
No 8
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.04 E-value=1.7 Score=46.94 Aligned_cols=16 Identities=19% Similarity=0.252 Sum_probs=7.8
Q ss_pred CCCCCCCCccccCCCC
Q 012025 197 SNVSDDSDDELLSDEF 212 (472)
Q Consensus 197 ~~~~~d~dd~~~~dd~ 212 (472)
++..||++.|.+++++
T Consensus 285 eeN~ddd~~d~d~e~~ 300 (514)
T KOG3130|consen 285 EENIDDDDGDNDHEAL 300 (514)
T ss_pred hhcccccccccchhhh
Confidence 3445555555554444
No 9
>smart00362 RRM_2 RNA recognition motif.
Probab=75.73 E-value=8.4 Score=27.74 Aligned_cols=47 Identities=17% Similarity=0.328 Sum_probs=33.9
Q ss_pred EEEeecccccCCCCcccccChHHHHHHhhccCcc-eeEeccCCCCCcceEEEEeCCC
Q 012025 334 VIIMNTRLDKDENDKWTGMGNQELLEYFILYAAV-RARHSYGPQGHRGMSVLIFESS 389 (472)
Q Consensus 334 GIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~-KVr~lyg~~GH~G~aVVeF~kd 389 (472)
++|-|++. ..+..+|++.|..|.++ .++....+..++|+++|+|...
T Consensus 2 v~i~~l~~---------~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~ 49 (72)
T smart00362 2 LFVGNLPP---------DVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESE 49 (72)
T ss_pred EEEcCCCC---------cCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCH
Confidence 56677643 23567899999999986 4555655545689999999864
No 10
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=73.98 E-value=1.7 Score=51.03 Aligned_cols=9 Identities=0% Similarity=-0.067 Sum_probs=5.8
Q ss_pred CCCCCCCCc
Q 012025 99 SSGRAPAKT 107 (472)
Q Consensus 99 ~~~~~~~n~ 107 (472)
|..+++||-
T Consensus 1272 G~FHP~g~e 1280 (1516)
T KOG1832|consen 1272 GGFHPSGNE 1280 (1516)
T ss_pred ccccCCCce
Confidence 566666665
No 11
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=72.75 E-value=2.3 Score=48.43 Aligned_cols=6 Identities=17% Similarity=0.911 Sum_probs=2.8
Q ss_pred eeEEEe
Q 012025 54 WEVYVR 59 (472)
Q Consensus 54 w~~~~~ 59 (472)
|..+.+
T Consensus 512 ~~~~~~ 517 (784)
T PF04931_consen 512 WKTLKK 517 (784)
T ss_pred HHHHHH
Confidence 555443
No 12
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=72.26 E-value=2.3 Score=49.26 Aligned_cols=10 Identities=20% Similarity=0.703 Sum_probs=6.8
Q ss_pred CCeEEccCCC
Q 012025 249 ARQWHCPACQ 258 (472)
Q Consensus 249 ~~tf~CP~C~ 258 (472)
--||-||-+.
T Consensus 419 Pftf~~P~s~ 428 (840)
T PF04147_consen 419 PFTFPCPSSH 428 (840)
T ss_pred CceecCCCCH
Confidence 3578888763
No 13
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=70.87 E-value=1.5 Score=45.37 Aligned_cols=13 Identities=15% Similarity=0.608 Sum_probs=7.3
Q ss_pred eeecCCCCeEEccC
Q 012025 243 EEINEPARQWHCPA 256 (472)
Q Consensus 243 kvkn~~~~tf~CP~ 256 (472)
||... ...|+|-+
T Consensus 340 kv~r~-k~~wk~~l 352 (375)
T PF03153_consen 340 KVTRV-KNKWKCTL 352 (375)
T ss_dssp EEEEE-TTEEEEEE
T ss_pred ccccc-cceeEEEe
Confidence 34444 56677754
No 14
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=65.91 E-value=3.7 Score=25.10 Aligned_cols=20 Identities=30% Similarity=0.805 Sum_probs=14.1
Q ss_pred EEccCCCCCCCCccccCCchHHhhhh
Q 012025 252 WHCPACQGGPGAIDWYRGLQPLMTHA 277 (472)
Q Consensus 252 f~CP~C~gkkk~~D~Y~~lk~LLqHA 277 (472)
|.|++|+.. |....+|.+|-
T Consensus 1 ~~C~~C~~~------~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKS------FRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-E------ESSHHHHHHHH
T ss_pred CCCcCCCCc------CCcHHHHHHHH
Confidence 789999632 66688898884
No 15
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=65.49 E-value=3.6 Score=49.79 Aligned_cols=12 Identities=25% Similarity=0.221 Sum_probs=5.7
Q ss_pred hhhHHHHHHHHH
Q 012025 285 VKLHRELAELLD 296 (472)
Q Consensus 285 kalHrALa~lLe 296 (472)
.+.-|||-.|-.
T Consensus 1891 aaRaralealaa 1902 (3015)
T KOG0943|consen 1891 AARARALEALAA 1902 (3015)
T ss_pred HHHHHHHHHHHh
Confidence 344455554443
No 16
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=64.65 E-value=11 Score=37.48 Aligned_cols=51 Identities=14% Similarity=0.187 Sum_probs=39.3
Q ss_pred EEEeecccccCCCCcccccChHHHHHHhhccCcc-eeEeccCC--CCCcceEEEEeCCCchhh
Q 012025 334 VIIMNTRLDKDENDKWTGMGNQELLEYFILYAAV-RARHSYGP--QGHRGMSVLIFESSAGGY 393 (472)
Q Consensus 334 GIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~-KVr~lyg~--~GH~G~aVVeF~kdwsGF 393 (472)
++|-|++... +.++|++.|+.|.++ .|++++.+ ....|+++|.|.+--...
T Consensus 272 lfV~NL~~~~---------~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~ 325 (352)
T TIGR01661 272 IFVYNLSPDT---------DETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAA 325 (352)
T ss_pred EEEeCCCCCC---------CHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHH
Confidence 7789987533 467899999999997 68888876 345899999998755443
No 17
>PHA03346 US22 family homolog; Provisional
Probab=59.19 E-value=17 Score=40.43 Aligned_cols=12 Identities=17% Similarity=0.315 Sum_probs=6.2
Q ss_pred CCCCCCCcCCCC
Q 012025 115 SKIPAGRVNARP 126 (472)
Q Consensus 115 ~~~~~~~~~~~~ 126 (472)
.+||++....++
T Consensus 392 ~~r~~~~~~~~~ 403 (520)
T PHA03346 392 RRRPRGPPENED 403 (520)
T ss_pred hccCCCCCCccc
Confidence 455655554443
No 18
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=57.16 E-value=13 Score=43.18 Aligned_cols=11 Identities=18% Similarity=0.737 Sum_probs=8.5
Q ss_pred CCCCcccccCC
Q 012025 149 EHGWNWQSRAG 159 (472)
Q Consensus 149 ~~g~~w~~~~~ 159 (472)
++||....-.+
T Consensus 865 ~GgW~fL~~~~ 875 (960)
T KOG1189|consen 865 DGGWSFLNVES 875 (960)
T ss_pred cCCeeeecCCC
Confidence 78999887554
No 19
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=55.34 E-value=2.5 Score=36.24 Aligned_cols=10 Identities=50% Similarity=0.876 Sum_probs=0.0
Q ss_pred hhhhhhHHHH
Q 012025 223 TRKKSRWFKK 232 (472)
Q Consensus 223 ~~k~~k~f~K 232 (472)
.+||..||=-
T Consensus 61 ~rkKrrwlwL 70 (81)
T PF14812_consen 61 PRKKRRWLWL 70 (81)
T ss_dssp ----------
T ss_pred ccccchhHHH
Confidence 3466666643
No 20
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=53.55 E-value=11 Score=43.05 Aligned_cols=9 Identities=22% Similarity=0.771 Sum_probs=6.8
Q ss_pred CCCCCcccc
Q 012025 148 LEHGWNWQS 156 (472)
Q Consensus 148 ~~~g~~w~~ 156 (472)
+++||+...
T Consensus 916 edGgW~fL~ 924 (1001)
T COG5406 916 EDGGWSFLM 924 (1001)
T ss_pred hcCcceeee
Confidence 578888765
No 21
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=53.30 E-value=7.9 Score=39.22 Aligned_cols=27 Identities=19% Similarity=0.402 Sum_probs=22.7
Q ss_pred CCeEEccCCCCCCCCccccCCchHHhhhhcccC
Q 012025 249 ARQWHCPACQGGPGAIDWYRGLQPLMTHAKTKG 281 (472)
Q Consensus 249 ~~tf~CP~C~gkkk~~D~Y~~lk~LLqHA~gvG 281 (472)
.+-|+|.||+- . |++--+|+.|--||-
T Consensus 237 ~eh~YC~fCG~-----~-y~~~edl~ehCPGvn 263 (268)
T KOG1994|consen 237 SEHYYCFFCGI-----K-YKDEEDLYEHCPGVN 263 (268)
T ss_pred ccceEEEEecc-----c-cCCHHHHHHhCCCCC
Confidence 57899999974 3 888999999988763
No 22
>TIGR00165 S18 ribosomal protein S18. This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically.
Probab=52.50 E-value=22 Score=29.63 Aligned_cols=43 Identities=28% Similarity=0.444 Sum_probs=25.6
Q ss_pred EccCCCCCCCCccccCCchHHhhhhcccC---c-----hhhhhHHHHHHHHH
Q 012025 253 HCPACQGGPGAIDWYRGLQPLMTHAKTKG---S-----KRVKLHRELAELLD 296 (472)
Q Consensus 253 ~CP~C~gkkk~~D~Y~~lk~LLqHA~gvG---a-----k~kalHrALa~lLe 296 (472)
.||+|..+...+| |++..-|-+=-+..| . --...||.|++.+.
T Consensus 7 ~c~~~~~~~~~iD-YKnv~lL~~Fis~~GkIlpRriTgl~~k~Qr~l~~aIK 57 (70)
T TIGR00165 7 YCRFTAEGIQFID-YKDLDLLKKFISERGKILPRRITGTSAKYQRRLARAIK 57 (70)
T ss_pred CCCccCCCCCcCC-ccCHHHHHHhcCCCCeEcCCccCCcCHHHHHHHHHHHH
Confidence 4999987666789 996655544433334 1 12345566655554
No 23
>PLN03120 nucleic acid binding protein; Provisional
Probab=51.84 E-value=31 Score=35.37 Aligned_cols=58 Identities=16% Similarity=0.232 Sum_probs=41.3
Q ss_pred eEEEeecccccCCCCcccccChHHHHHHhhccCcce-eEeccCCCCCcceEEEEeCCCchhhHHHHHHHH
Q 012025 333 MVIIMNTRLDKDENDKWTGMGNQELLEYFILYAAVR-ARHSYGPQGHRGMSVLIFESSAGGYLEAERLHK 401 (472)
Q Consensus 333 MGIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~K-Vr~lyg~~GH~G~aVVeF~kdwsGF~nA~rLek 401 (472)
.+.|-|++.. .+.++|+++|+.|+.+. ++..... ..+|++.|.|... .....|+.|..
T Consensus 6 tVfVgNLs~~---------tTE~dLrefFS~~G~I~~V~I~~d~-~~~GfAFVtF~d~-eaAe~AllLnG 64 (260)
T PLN03120 6 TVKVSNVSLK---------ATERDIKEFFSFSGDIEYVEMQSEN-ERSQIAYVTFKDP-QGAETALLLSG 64 (260)
T ss_pred EEEEeCCCCC---------CCHHHHHHHHHhcCCeEEEEEeecC-CCCCEEEEEeCcH-HHHHHHHHhcC
Confidence 3668888643 35678999999998874 5554433 3689999999654 66788886543
No 24
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=51.26 E-value=8 Score=39.79 Aligned_cols=23 Identities=48% Similarity=0.560 Sum_probs=10.1
Q ss_pred CCCCCCCCccccCC-CCCchhhhh
Q 012025 197 SNVSDDSDDELLSD-EFDSDTSQK 219 (472)
Q Consensus 197 ~~~~~d~dd~~~~d-d~Dsd~se~ 219 (472)
++..+|||+|-+|| ++|+|+-|+
T Consensus 238 ~~~~~~s~~d~d~e~esd~de~Ee 261 (303)
T KOG3064|consen 238 SDESDDSDEDSDSEDESDSDEIEE 261 (303)
T ss_pred hhhhhhcccccccccCCchhhHHH
Confidence 34445555553333 334444444
No 25
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=49.98 E-value=7.9 Score=25.19 Aligned_cols=22 Identities=23% Similarity=0.671 Sum_probs=17.5
Q ss_pred eEEccCCCCCCCCccccCCchHHhhhhc
Q 012025 251 QWHCPACQGGPGAIDWYRGLQPLMTHAK 278 (472)
Q Consensus 251 tf~CP~C~gkkk~~D~Y~~lk~LLqHA~ 278 (472)
.|.|..|.. . |..+..|++|-.
T Consensus 1 ~~~C~~C~~-----~-F~~~~~l~~H~~ 22 (27)
T PF13912_consen 1 PFECDECGK-----T-FSSLSALREHKR 22 (27)
T ss_dssp SEEETTTTE-----E-ESSHHHHHHHHC
T ss_pred CCCCCccCC-----c-cCChhHHHHHhH
Confidence 489999953 3 888999999953
No 26
>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=49.07 E-value=8.5 Score=24.09 Aligned_cols=20 Identities=25% Similarity=0.718 Sum_probs=15.1
Q ss_pred EEccCCCCCCCCccccCCchHHhhhh
Q 012025 252 WHCPACQGGPGAIDWYRGLQPLMTHA 277 (472)
Q Consensus 252 f~CP~C~gkkk~~D~Y~~lk~LLqHA 277 (472)
|.||.|.. . |.....|.+|-
T Consensus 1 y~C~~C~~-----~-f~~~~~l~~H~ 20 (23)
T PF00096_consen 1 YKCPICGK-----S-FSSKSNLKRHM 20 (23)
T ss_dssp EEETTTTE-----E-ESSHHHHHHHH
T ss_pred CCCCCCCC-----c-cCCHHHHHHHH
Confidence 78999963 2 66678888884
No 27
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=46.68 E-value=11 Score=44.92 Aligned_cols=13 Identities=8% Similarity=0.414 Sum_probs=7.7
Q ss_pred cCCchHHhhhhcc
Q 012025 267 YRGLQPLMTHAKT 279 (472)
Q Consensus 267 Y~~lk~LLqHA~g 279 (472)
|.-|..||.|...
T Consensus 394 f~~yi~ll~qt~~ 406 (1233)
T KOG1824|consen 394 FHAYIALLKQTRP 406 (1233)
T ss_pred HHHHHHHHHcCCC
Confidence 3345677777654
No 28
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=45.32 E-value=38 Score=33.81 Aligned_cols=47 Identities=13% Similarity=0.204 Sum_probs=36.0
Q ss_pred EEEeecccccCCCCcccccChHHHHHHhhccCcc-eeEeccCCC-C-CcceEEEEeCCC
Q 012025 334 VIIMNTRLDKDENDKWTGMGNQELLEYFILYAAV-RARHSYGPQ-G-HRGMSVLIFESS 389 (472)
Q Consensus 334 GIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~-KVr~lyg~~-G-H~G~aVVeF~kd 389 (472)
+.|-|+|.. .+..+|++.|+.|+++ .|+++..+. | ++|++.|+|...
T Consensus 6 l~V~nLp~~---------~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~ 55 (352)
T TIGR01661 6 LIVNYLPQT---------MTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRP 55 (352)
T ss_pred EEEeCCCCC---------CCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcH
Confidence 567787642 3568899999999997 577877653 4 589999999764
No 29
>smart00017 OSTEO Osteopontin. Osteopontin is an acidic phosphorylated glycoprotein of about 40 Kd which is abundant in the mineral matrix of bones and which binds tightly to hydroxyapatite [1,2,3]. It is suggested that osteopontin might function as a cell attachment factor and could play a key role in the adhesion of osteoclasts to the mineral matrix of bone
Probab=45.23 E-value=13 Score=38.03 Aligned_cols=12 Identities=17% Similarity=0.019 Sum_probs=7.3
Q ss_pred CCeEEccCCCCC
Q 012025 249 ARQWHCPACQGG 260 (472)
Q Consensus 249 ~~tf~CP~C~gk 260 (472)
....--||-+.+
T Consensus 120 ~~~vfTP~vpt~ 131 (287)
T smart00017 120 ATDVFTPFVPTV 131 (287)
T ss_pred ccceeccccccC
Confidence 445566777753
No 30
>PRK13401 30S ribosomal protein S18; Provisional
Probab=45.13 E-value=32 Score=29.66 Aligned_cols=45 Identities=22% Similarity=0.257 Sum_probs=27.4
Q ss_pred EEccCCCCCCCCccccCCchHHhhhhcccC---c-----hhhhhHHHHHHHHHH
Q 012025 252 WHCPACQGGPGAIDWYRGLQPLMTHAKTKG---S-----KRVKLHRELAELLDE 297 (472)
Q Consensus 252 f~CP~C~gkkk~~D~Y~~lk~LLqHA~gvG---a-----k~kalHrALa~lLe~ 297 (472)
=.||||..+-..+| |++..-|-+--+..| . --...||.|++-++.
T Consensus 14 k~c~~~~~~~~~iD-YKnv~lL~~Fis~~GkIlpRR~TGl~~k~QR~l~~AIKr 66 (82)
T PRK13401 14 KKNLLDSLGIESVD-YKDTALLRTFISDRGKIRSRRVTGLTVQQQRQVATAIKN 66 (82)
T ss_pred CCCCcccCCCCcCC-ccCHHHHHHhcCCCccCcCcccCCcCHHHHHHHHHHHHH
Confidence 35999987655579 996665544444444 1 223566666666553
No 31
>smart00360 RRM RNA recognition motif.
Probab=44.97 E-value=42 Score=23.83 Aligned_cols=37 Identities=24% Similarity=0.403 Sum_probs=27.7
Q ss_pred cChHHHHHHhhccCcc-eeEeccCC--CCCcceEEEEeCC
Q 012025 352 MGNQELLEYFILYAAV-RARHSYGP--QGHRGMSVLIFES 388 (472)
Q Consensus 352 ~S~~eLkd~fsgF~P~-KVr~lyg~--~GH~G~aVVeF~k 388 (472)
.+..+|++.|..|+++ .++....+ .-++|+++|+|..
T Consensus 8 ~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~ 47 (71)
T smart00360 8 VTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFES 47 (71)
T ss_pred cCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCC
Confidence 4678899999999976 45555544 3458899999964
No 32
>PLN03121 nucleic acid binding protein; Provisional
Probab=44.16 E-value=40 Score=34.31 Aligned_cols=58 Identities=10% Similarity=0.079 Sum_probs=40.6
Q ss_pred ceEEEeecccccCCCCcccccChHHHHHHhhccCcceeEeccCCCCCcceEEEEeCCCchhhHHHHHH
Q 012025 332 PMVIIMNTRLDKDENDKWTGMGNQELLEYFILYAAVRARHSYGPQGHRGMSVLIFESSAGGYLEAERL 399 (472)
Q Consensus 332 WMGIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~KVr~lyg~~GH~G~aVVeF~kdwsGF~nA~rL 399 (472)
|++.|-|++..- +.+.|++.|+.|+.+.-..+....+..+++.|+|..- .+...|+.|
T Consensus 6 ~TV~V~NLS~~t---------TE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~-~aaetAllL 63 (243)
T PLN03121 6 YTAEVTNLSPKA---------TEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDA-YALETAVLL 63 (243)
T ss_pred eEEEEecCCCCC---------CHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCH-HHHHHHHhc
Confidence 678999986533 4678999999999975444444455668999999753 333666654
No 33
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=43.08 E-value=22 Score=35.84 Aligned_cols=10 Identities=40% Similarity=0.199 Sum_probs=4.4
Q ss_pred hhhhhhHHHH
Q 012025 223 TRKKSRWFKK 232 (472)
Q Consensus 223 ~~k~~k~f~K 232 (472)
.-|+.+..++
T Consensus 157 kIKkER~ee~ 166 (244)
T PF04889_consen 157 KIKKERAEEK 166 (244)
T ss_pred HHHHHHHHHH
Confidence 3344444443
No 34
>PRK00391 rpsR 30S ribosomal protein S18; Reviewed
Probab=42.58 E-value=39 Score=28.86 Aligned_cols=45 Identities=27% Similarity=0.499 Sum_probs=26.3
Q ss_pred CeEEccCCCCCCCCccccCCchHHhhhhcc-cC---c-----hhhhhHHHHHHHHH
Q 012025 250 RQWHCPACQGGPGAIDWYRGLQPLMTHAKT-KG---S-----KRVKLHRELAELLD 296 (472)
Q Consensus 250 ~tf~CP~C~gkkk~~D~Y~~lk~LLqHA~g-vG---a-----k~kalHrALa~lLe 296 (472)
+.-.||+|..+-..+| |++.. ||++=.+ .| . --...||.|++-++
T Consensus 13 r~k~c~~c~~~~~~iD-YKnv~-lL~~Fis~~GkIlprriTG~~~k~Qr~l~~aIk 66 (79)
T PRK00391 13 RKKVCRFCAEKIEYID-YKDVE-LLKKFISERGKILPRRITGTSAKHQRQLATAIK 66 (79)
T ss_pred CCCCCcccCCCCCcCC-ccCHH-HHHHhcCCCceEcCcccCCcCHHHHHHHHHHHH
Confidence 4446999987755589 99654 5555333 34 1 22355666665554
No 35
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=41.35 E-value=63 Score=29.54 Aligned_cols=56 Identities=18% Similarity=0.235 Sum_probs=39.0
Q ss_pred eEEEeecccccCCCCcccccChHHHHHHhhccCcce-eEeccCCC--CCcceEEEEeCCCchhhHHHHH
Q 012025 333 MVIIMNTRLDKDENDKWTGMGNQELLEYFILYAAVR-ARHSYGPQ--GHRGMSVLIFESSAGGYLEAER 398 (472)
Q Consensus 333 MGIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~K-Vr~lyg~~--GH~G~aVVeF~kdwsGF~nA~r 398 (472)
.+.|-|++.. .+.++|++.|..|.++. +++...+. -+.|+++|+|... ..-..|++
T Consensus 36 ~lfVgnL~~~---------~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~-e~A~~Al~ 94 (144)
T PLN03134 36 KLFIGGLSWG---------TDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDE-GAATAAIS 94 (144)
T ss_pred EEEEeCCCCC---------CCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCH-HHHHHHHH
Confidence 3567888642 46788999999998864 55555542 3589999999854 44455543
No 36
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=40.14 E-value=23 Score=28.05 Aligned_cols=15 Identities=40% Similarity=0.778 Sum_probs=10.1
Q ss_pred eeecCCCCeEEccCCC
Q 012025 243 EEINEPARQWHCPACQ 258 (472)
Q Consensus 243 kvkn~~~~tf~CP~C~ 258 (472)
++..+ .-+|+||+|+
T Consensus 37 ~~~~~-~i~y~C~~Cg 51 (54)
T PF10058_consen 37 KEEFE-EIQYRCPYCG 51 (54)
T ss_pred cccCC-ceEEEcCCCC
Confidence 44444 5588899885
No 37
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.98 E-value=19 Score=39.22 Aligned_cols=11 Identities=18% Similarity=-0.067 Sum_probs=5.6
Q ss_pred CCCCCCCCCCC
Q 012025 84 GHLDSTQKPGM 94 (472)
Q Consensus 84 g~~~~~~~~~~ 94 (472)
-..++.++.+|
T Consensus 169 ~~~d~~~~dvl 179 (514)
T KOG3130|consen 169 IANDVKSKDVL 179 (514)
T ss_pred hhcchhhhhcc
Confidence 34455555554
No 38
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=37.83 E-value=61 Score=34.87 Aligned_cols=69 Identities=20% Similarity=0.234 Sum_probs=44.4
Q ss_pred eeeCce--EEEeecccccCCCCcccccChHHHHHHhhccCc---ceeEeccCCCCCcceEEEEeCCCchhhHHHHHHHHH
Q 012025 328 IVWPPM--VIIMNTRLDKDENDKWTGMGNQELLEYFILYAA---VRARHSYGPQGHRGMSVLIFESSAGGYLEAERLHKH 402 (472)
Q Consensus 328 iVWPWM--GIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P---~KVr~lyg~~GH~G~aVVeF~kdwsGF~nA~rLekh 402 (472)
.+.||. +.|-|++.+ .+.++|++.|+.|.. ..++.+-...+.+|+++|+|..--.. .+|+..-++
T Consensus 389 ~~~~ps~~L~v~NLp~~---------~tee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A-~~Al~~ln~ 458 (481)
T TIGR01649 389 NIQPPSATLHLSNIPLS---------VSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDA-VEALIALNH 458 (481)
T ss_pred ccCCCCcEEEEecCCCC---------CCHHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHH-HHHHHHhcC
Confidence 457884 556688743 356789999998875 34555444445579999999984333 355554344
Q ss_pred Hhhc
Q 012025 403 FAEQ 406 (472)
Q Consensus 403 Fe~q 406 (472)
+...
T Consensus 459 ~~l~ 462 (481)
T TIGR01649 459 HQLN 462 (481)
T ss_pred CccC
Confidence 4443
No 39
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=37.72 E-value=53 Score=35.09 Aligned_cols=57 Identities=18% Similarity=0.321 Sum_probs=44.3
Q ss_pred EeecccccCCCCcccccChHHHHHHhhccCcc-eeEeccCCCCCcceEEEEeCCCchhhHHHHHHHH
Q 012025 336 IMNTRLDKDENDKWTGMGNQELLEYFILYAAV-RARHSYGPQGHRGMSVLIFESSAGGYLEAERLHK 401 (472)
Q Consensus 336 IvNt~te~dddgk~~G~S~~eLkd~fsgF~P~-KVr~lyg~~GH~G~aVVeF~kdwsGF~nA~rLek 401 (472)
|-|||...-| ..|+..|-.|.++ .|-+++|.+|.-||..|.|++..+.=+-=.+||.
T Consensus 101 VSNIPFrFRd---------pDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHg 158 (376)
T KOG0125|consen 101 VSNIPFRFRD---------PDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHG 158 (376)
T ss_pred eecCCccccC---------ccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhc
Confidence 6788776654 3488889999995 8999999999999999999998755444444443
No 40
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=37.09 E-value=38 Score=32.35 Aligned_cols=59 Identities=15% Similarity=0.280 Sum_probs=40.9
Q ss_pred eeeeCceEEEeecccccCCCCcccccChHHHHHHhhccCcceeEeccCC--CCC-cceEEEEeCCCchhhHHHHH
Q 012025 327 EIVWPPMVIIMNTRLDKDENDKWTGMGNQELLEYFILYAAVRARHSYGP--QGH-RGMSVLIFESSAGGYLEAER 398 (472)
Q Consensus 327 liVWPWMGIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~KVr~lyg~--~GH-~G~aVVeF~kdwsGF~nA~r 398 (472)
.-|=-|+++|.++--|-. .+.+.+.|+.|.++|-.+|--. -|. .|||+|+++. +++|.+
T Consensus 68 rSVEGwIi~VtgvHeEat---------Eedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet----~keAq~ 129 (170)
T KOG0130|consen 68 RSVEGWIIFVTGVHEEAT---------EEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYET----LKEAQA 129 (170)
T ss_pred cceeeEEEEEeccCcchh---------HHHHHHHHhhcccccceeeccccccccccceeeeehHh----HHHHHH
Confidence 345568899988854443 3567899999999997775332 354 6899999864 455543
No 41
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=35.91 E-value=56 Score=33.15 Aligned_cols=64 Identities=20% Similarity=0.291 Sum_probs=48.7
Q ss_pred EEEeecccccCCCCcccccChHHHHHHhhcc-CcceeEeccCCCCC-cceEEEEeCCCchhhHHHHHHHHHHhhcC
Q 012025 334 VIIMNTRLDKDENDKWTGMGNQELLEYFILY-AAVRARHSYGPQGH-RGMSVLIFESSAGGYLEAERLHKHFAEQG 407 (472)
Q Consensus 334 GIIvNt~te~dddgk~~G~S~~eLkd~fsgF-~P~KVr~lyg~~GH-~G~aVVeF~kdwsGF~nA~rLekhFe~qg 407 (472)
++|-|.++ |+....|++-|..| .+.+|-.-|++.|- .|++-|.|...-..+.--..|+. |..++
T Consensus 86 v~v~NL~~---------~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~g-v~ldG 151 (243)
T KOG0533|consen 86 VNVSNLPY---------GVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNG-VALDG 151 (243)
T ss_pred eeeecCCc---------CcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcC-cccCC
Confidence 56777654 45677788889988 77788889999986 79999999998766666666666 55443
No 42
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=35.58 E-value=85 Score=28.06 Aligned_cols=61 Identities=25% Similarity=0.340 Sum_probs=44.8
Q ss_pred CceEEEeecccccCCCCcccccChHHHHHHhhccCcc-eeEeccCC--CCCcceEEEEeCCCchhhHHHHHHH
Q 012025 331 PPMVIIMNTRLDKDENDKWTGMGNQELLEYFILYAAV-RARHSYGP--QGHRGMSVLIFESSAGGYLEAERLH 400 (472)
Q Consensus 331 PWMGIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~-KVr~lyg~--~GH~G~aVVeF~kdwsGF~nA~rLe 400 (472)
.-.+.|-|++.. ...++|.+.|..|.++ .++..+.. .-.+|++.|+|...-....-...|.
T Consensus 115 ~~~l~v~nL~~~---------~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~ 178 (306)
T COG0724 115 NNTLFVGNLPYD---------VTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELN 178 (306)
T ss_pred CceEEEeCCCCC---------CCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcC
Confidence 677889998742 3568899999999997 67777764 3469999999998765544444443
No 43
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=35.51 E-value=18 Score=23.95 Aligned_cols=23 Identities=30% Similarity=0.600 Sum_probs=17.5
Q ss_pred eEEccCCCCCCCCccccCCchHHhhhhcc
Q 012025 251 QWHCPACQGGPGAIDWYRGLQPLMTHAKT 279 (472)
Q Consensus 251 tf~CP~C~gkkk~~D~Y~~lk~LLqHA~g 279 (472)
+|.|.+|.. . |.+-..|.+|=.+
T Consensus 1 q~~C~~C~k-----~-f~~~~~~~~H~~s 23 (27)
T PF12171_consen 1 QFYCDACDK-----Y-FSSENQLKQHMKS 23 (27)
T ss_dssp -CBBTTTTB-----B-BSSHHHHHCCTTS
T ss_pred CCCcccCCC-----C-cCCHHHHHHHHcc
Confidence 589999952 3 7888899999655
No 44
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=35.29 E-value=21 Score=42.39 Aligned_cols=13 Identities=31% Similarity=0.450 Sum_probs=8.4
Q ss_pred hHHHHHHHHhccc
Q 012025 228 RWFKKFFESLESL 240 (472)
Q Consensus 228 k~f~K~ye~Lk~g 240 (472)
+.|..++..|.++
T Consensus 962 ~~f~~~i~~lq~~ 974 (1010)
T KOG1991|consen 962 QLFKEAITNLQSS 974 (1010)
T ss_pred HHHHHHHHhhhcc
Confidence 5666666666665
No 45
>PRK13400 30S ribosomal protein S18; Provisional
Probab=33.82 E-value=55 Score=31.09 Aligned_cols=27 Identities=22% Similarity=0.364 Sum_probs=18.7
Q ss_pred eEEccCCCCCCCCccccCCchHHhhhhc
Q 012025 251 QWHCPACQGGPGAIDWYRGLQPLMTHAK 278 (472)
Q Consensus 251 tf~CP~C~gkkk~~D~Y~~lk~LLqHA~ 278 (472)
.-.||+|..+...+| |++..-|-+--+
T Consensus 22 rK~C~~c~~~~~~ID-YKNv~lL~~FIS 48 (147)
T PRK13400 22 RKICSFCAEKVSRID-YKDSAKLARYIS 48 (147)
T ss_pred CCCCCccCCCCCccC-CcCHHHHHHhcC
Confidence 346999997767789 996655444333
No 46
>COG0238 RpsR Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=33.54 E-value=37 Score=28.94 Aligned_cols=28 Identities=25% Similarity=0.429 Sum_probs=19.9
Q ss_pred CeEEccCCCCCCCCccccCCchHHhhhhcc
Q 012025 250 RQWHCPACQGGPGAIDWYRGLQPLMTHAKT 279 (472)
Q Consensus 250 ~tf~CP~C~gkkk~~D~Y~~lk~LLqHA~g 279 (472)
+.=.||||..+-..+| |+|+ +||.+-.+
T Consensus 14 rrk~c~~~~~~~~~iD-YKd~-~~L~rfis 41 (75)
T COG0238 14 RRKVCRFTAEGIEEID-YKDV-ELLKRFIS 41 (75)
T ss_pred cccccccccccCCccC-ccCH-HHHHHHhc
Confidence 4457999998655789 8855 56666554
No 47
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=31.03 E-value=30 Score=41.24 Aligned_cols=7 Identities=29% Similarity=0.467 Sum_probs=3.4
Q ss_pred chHHhhh
Q 012025 270 LQPLMTH 276 (472)
Q Consensus 270 lk~LLqH 276 (472)
|+.|++|
T Consensus 979 yq~l~~~ 985 (1010)
T KOG1991|consen 979 YQKLIST 985 (1010)
T ss_pred HHHHHhc
Confidence 3355554
No 48
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=30.69 E-value=31 Score=40.24 Aligned_cols=14 Identities=21% Similarity=0.605 Sum_probs=6.1
Q ss_pred CCCceeeeCceEEE
Q 012025 323 EKDHEIVWPPMVII 336 (472)
Q Consensus 323 ~kDdliVWPWMGII 336 (472)
..-+.+|=|=|+.|
T Consensus 557 D~~HpVVTPalllm 570 (840)
T PF04147_consen 557 DFRHPVVTPALLLM 570 (840)
T ss_pred cccCcchhHHHHHH
Confidence 33345554444433
No 49
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=30.14 E-value=51 Score=36.60 Aligned_cols=39 Identities=26% Similarity=0.486 Sum_probs=29.7
Q ss_pred EEccCCCCCCCCccccCCchHHhhhhcccCchhhhhHHHHHHHHHHh
Q 012025 252 WHCPACQGGPGAIDWYRGLQPLMTHAKTKGSKRVKLHRELAELLDEE 298 (472)
Q Consensus 252 f~CP~C~gkkk~~D~Y~~lk~LLqHA~gvGak~kalHrALa~lLe~D 298 (472)
+.|++|-. . |+.-+.|.+|--.+ +|+.+=..|+.-|+++
T Consensus 293 lyC~vCnK---s---FKseKq~kNHEnSK--KHkenv~eLrqemEEE 331 (508)
T KOG0717|consen 293 LYCVVCNK---S---FKSEKQLKNHENSK--KHKENVAELRQEMEEE 331 (508)
T ss_pred eEEeeccc---c---ccchHHHHhhHHHH--HHHHHHHHHHHHHHHh
Confidence 99999952 2 77789999996543 5666667788888877
No 50
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=30.10 E-value=86 Score=23.20 Aligned_cols=40 Identities=20% Similarity=0.352 Sum_probs=26.1
Q ss_pred HHHHhhccCcce-eEeccCCCCCcceEEEEeCCCchhhHHHHHHHHHH
Q 012025 357 LLEYFILYAAVR-ARHSYGPQGHRGMSVLIFESSAGGYLEAERLHKHF 403 (472)
Q Consensus 357 Lkd~fsgF~P~K-Vr~lyg~~GH~G~aVVeF~kdwsGF~nA~rLekhF 403 (472)
|.+.|+.|+.++ ++..... ++++.|+|.+ -.+|...-+++
T Consensus 1 L~~~f~~fG~V~~i~~~~~~---~~~a~V~f~~----~~~A~~a~~~l 41 (56)
T PF13893_consen 1 LYKLFSKFGEVKKIKIFKKK---RGFAFVEFAS----VEDAQKAIEQL 41 (56)
T ss_dssp HHHHHTTTS-EEEEEEETTS---TTEEEEEESS----HHHHHHHHHHH
T ss_pred ChHHhCCcccEEEEEEEeCC---CCEEEEEECC----HHHHHHHHHHh
Confidence 567899999875 4444433 7899999974 34555555544
No 51
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=29.74 E-value=39 Score=40.52 Aligned_cols=13 Identities=15% Similarity=0.312 Sum_probs=6.9
Q ss_pred hhHHHHHHHHHHh
Q 012025 286 KLHRELAELLDEE 298 (472)
Q Consensus 286 alHrALa~lLe~D 298 (472)
..=+||.+.|..+
T Consensus 435 ~iVkai~~qlr~k 447 (1233)
T KOG1824|consen 435 LIVKAIQKQLREK 447 (1233)
T ss_pred HHHHHHHHHHhhc
Confidence 4445556666644
No 52
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=28.98 E-value=89 Score=33.91 Aligned_cols=50 Identities=18% Similarity=0.394 Sum_probs=38.0
Q ss_pred eEEEeecccccCCCCcccccChHHHHHHhhccCcc-eeEeccCCCC-CcceEEEEeCCCch
Q 012025 333 MVIIMNTRLDKDENDKWTGMGNQELLEYFILYAAV-RARHSYGPQG-HRGMSVLIFESSAG 391 (472)
Q Consensus 333 MGIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~-KVr~lyg~~G-H~G~aVVeF~kdws 391 (472)
.+.|-|++.. ...++|.+.|+.|..+ .++......| +.|++.|+|.+.-+
T Consensus 90 ~vfV~nLp~~---------~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~ 141 (562)
T TIGR01628 90 NIFVKNLDKS---------VDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEES 141 (562)
T ss_pred ceEEcCCCcc---------CCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHH
Confidence 3667887542 3577899999999875 4677777777 68999999998654
No 53
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.96 E-value=35 Score=33.74 Aligned_cols=7 Identities=43% Similarity=0.838 Sum_probs=5.5
Q ss_pred CCCcCCC
Q 012025 1 MSARRGG 7 (472)
Q Consensus 1 ~~~~~~~ 7 (472)
|||++|.
T Consensus 1 MsSq~GN 7 (227)
T KOG3241|consen 1 MSSQQGN 7 (227)
T ss_pred CCcccCc
Confidence 8888874
No 54
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.60 E-value=25 Score=37.93 Aligned_cols=10 Identities=30% Similarity=0.949 Sum_probs=8.7
Q ss_pred eEEccCCCCC
Q 012025 251 QWHCPACQGG 260 (472)
Q Consensus 251 tf~CP~C~gk 260 (472)
+|.|||||..
T Consensus 374 sfKCPYCP~e 383 (394)
T KOG2817|consen 374 SFKCPYCPVE 383 (394)
T ss_pred eeeCCCCCcc
Confidence 6999999964
No 55
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=27.80 E-value=66 Score=30.13 Aligned_cols=40 Identities=15% Similarity=0.211 Sum_probs=25.9
Q ss_pred hhhhhhhHHHHHHHHhcccCceeecC-----------CCC-----eEEccCCCCCC
Q 012025 222 DTRKKSRWFKKFFESLESLTVEEINE-----------PAR-----QWHCPACQGGP 261 (472)
Q Consensus 222 e~~k~~k~f~K~ye~Lk~g~~kvkn~-----------~~~-----tf~CP~C~gkk 261 (472)
.....-+.|.+|.+.|..-.-.++.. ... .=+|+.|++.+
T Consensus 52 ~~~~~D~~f~~F~~rl~~~P~QvlRY~~gG~PLw~s~~~~~~~~~ip~C~~Cg~~R 107 (164)
T PF04194_consen 52 EEDEVDKAFLKFQKRLSRNPEQVLRYCRGGKPLWISSTPIPPESDIPKCENCGSPR 107 (164)
T ss_pred cccccCHHHHHHHHHHhcCCCeEEEECCCCeEEEecCCCCCccccCCCCccCCCcc
Confidence 44566788999999998765444332 111 23799998654
No 56
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=27.19 E-value=79 Score=33.43 Aligned_cols=57 Identities=14% Similarity=0.063 Sum_probs=35.1
Q ss_pred eEEEeecccccC-CCCcccccChHHHHHHhhccCcce-eEeccCCCC-----CcceEEEEeCCC
Q 012025 333 MVIIMNTRLDKD-ENDKWTGMGNQELLEYFILYAAVR-ARHSYGPQG-----HRGMSVLIFESS 389 (472)
Q Consensus 333 MGIIvNt~te~d-ddgk~~G~S~~eLkd~fsgF~P~K-Vr~lyg~~G-----H~G~aVVeF~kd 389 (472)
+++|.|+.+..+ -+....-+-.+.|+++|..|..+. |++.....+ ..|++.|+|..-
T Consensus 411 v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~ 474 (509)
T TIGR01642 411 VVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADV 474 (509)
T ss_pred EEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCH
Confidence 567888875332 112223334567888899999974 555443222 258999999875
No 57
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=27.11 E-value=21 Score=33.61 Aligned_cols=16 Identities=25% Similarity=0.574 Sum_probs=10.8
Q ss_pred hhHHHHHHHHHHhhhc
Q 012025 286 KLHRELAELLDEELRR 301 (472)
Q Consensus 286 alHrALa~lLe~Dla~ 301 (472)
-+=++|+++|-.-+..
T Consensus 64 dFeref~kmm~eS~~s 79 (170)
T PF04050_consen 64 DFEREFQKMMAESLES 79 (170)
T ss_dssp HHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHh
Confidence 3447888888876644
No 58
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=27.03 E-value=49 Score=39.50 Aligned_cols=6 Identities=33% Similarity=0.379 Sum_probs=2.7
Q ss_pred eeeEec
Q 012025 430 LYGFMA 435 (472)
Q Consensus 430 LYGWlA 435 (472)
|=||+-
T Consensus 424 lkG~ve 429 (1024)
T KOG1999|consen 424 LKGKVE 429 (1024)
T ss_pred ceeEEE
Confidence 444543
No 59
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=26.95 E-value=53 Score=24.44 Aligned_cols=11 Identities=27% Similarity=0.582 Sum_probs=8.8
Q ss_pred CeEEccCCCCC
Q 012025 250 RQWHCPACQGG 260 (472)
Q Consensus 250 ~tf~CP~C~gk 260 (472)
..++||+|+..
T Consensus 20 ~~~~Cp~CG~~ 30 (46)
T PRK00398 20 TGVRCPYCGYR 30 (46)
T ss_pred CceECCCCCCe
Confidence 37999999753
No 60
>PHA00616 hypothetical protein
Probab=26.57 E-value=20 Score=27.60 Aligned_cols=22 Identities=23% Similarity=0.606 Sum_probs=16.5
Q ss_pred eEEccCCCCCCCCccccCCchHHhhhhc
Q 012025 251 QWHCPACQGGPGAIDWYRGLQPLMTHAK 278 (472)
Q Consensus 251 tf~CP~C~gkkk~~D~Y~~lk~LLqHA~ 278 (472)
.|.||-|+.. |...++|.+|-.
T Consensus 1 pYqC~~CG~~------F~~~s~l~~H~r 22 (44)
T PHA00616 1 MYQCLRCGGI------FRKKKEVIEHLL 22 (44)
T ss_pred CCccchhhHH------HhhHHHHHHHHH
Confidence 3789999743 555889999954
No 61
>CHL00077 rps18 ribosomal protein S18
Probab=26.48 E-value=94 Score=27.14 Aligned_cols=41 Identities=24% Similarity=0.466 Sum_probs=25.0
Q ss_pred EccCCCCCCCCccccCCchHHhhhhcc-cC---c-----hhhhhHHHHHHHHHH
Q 012025 253 HCPACQGGPGAIDWYRGLQPLMTHAKT-KG---S-----KRVKLHRELAELLDE 297 (472)
Q Consensus 253 ~CP~C~gkkk~~D~Y~~lk~LLqHA~g-vG---a-----k~kalHrALa~lLe~ 297 (472)
.||+|.+. .+| |++.. ||+.=.+ .| . --...||.|++-++.
T Consensus 19 ~~~~~~~~--~iD-YKnv~-lL~~Fis~~GkIlpRriTGl~~K~QR~l~~aIKr 68 (86)
T CHL00077 19 LPPIQSGD--RID-YKNMS-LLSRFISEQGKILSRRVTRLTLKQQRLITKAIKQ 68 (86)
T ss_pred CCCCCCCC--cCC-ccCHH-HHHHhcCCCCeEcCcccCCcCHHHHHHHHHHHHH
Confidence 49999974 579 99664 5555333 34 1 233566777666653
No 62
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=26.42 E-value=1.1e+02 Score=32.03 Aligned_cols=61 Identities=15% Similarity=0.191 Sum_probs=41.4
Q ss_pred eEEEeecccccCCCCcccccChHHHHHHhhccCcce-eEeccCC-CCC-cceEEEEeCCCchhhHHHHHHHHH
Q 012025 333 MVIIMNTRLDKDENDKWTGMGNQELLEYFILYAAVR-ARHSYGP-QGH-RGMSVLIFESSAGGYLEAERLHKH 402 (472)
Q Consensus 333 MGIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~K-Vr~lyg~-~GH-~G~aVVeF~kdwsGF~nA~rLekh 402 (472)
.++|-|++.. .+.++|++.|+.|..+. ++++..+ .|. +|++.|+|..--.--.-..+|...
T Consensus 195 ~lfV~nLp~~---------vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~ 258 (346)
T TIGR01659 195 NLYVTNLPRT---------ITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNV 258 (346)
T ss_pred eeEEeCCCCc---------ccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence 5778898753 35678999999998864 5666554 343 699999998765544444445443
No 63
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=26.33 E-value=47 Score=35.35 Aligned_cols=7 Identities=29% Similarity=1.170 Sum_probs=3.0
Q ss_pred CCeEEcc
Q 012025 249 ARQWHCP 255 (472)
Q Consensus 249 ~~tf~CP 255 (472)
...|+|-
T Consensus 318 KnKWKc~ 324 (348)
T KOG2652|consen 318 KNKWKCY 324 (348)
T ss_pred cceeeEE
Confidence 3444443
No 64
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=26.28 E-value=79 Score=36.63 Aligned_cols=59 Identities=22% Similarity=0.133 Sum_probs=31.2
Q ss_pred chHHhhhhcccCchhhhhHHHHHHHHHHhhhcCCcccCCCCcccccccCCCCCCCCc---eeeeCceEEEeecc
Q 012025 270 LQPLMTHAKTKGSKRVKLHRELAELLDEELRRRGTSVIPAGEVFGKWKGLKDTEKDH---EIVWPPMVIIMNTR 340 (472)
Q Consensus 270 lk~LLqHA~gvGak~kalHrALa~lLe~Dla~~~~sv~p~~e~~~~~k~L~~~~kDd---liVWPWMGIIvNt~ 340 (472)
+++|+.||... -|.++...|+....+++++....|.. .. +..-++ ..+-||.--++|..
T Consensus 610 ~~A~~ah~a~d----------~ak~~~~~la~ep~~lpa~~dqtp~q-pv-e~~~d~alm~ql~pl~hgn~ns~ 671 (811)
T KOG4364|consen 610 LQALTAHAAKD----------TAKLIICNLAHEPVSLPAAKDQTPTQ-PV-EQICDRALMVQLFPLSHGNENSI 671 (811)
T ss_pred HHHHHHHHhhh----------hHHHhhhhhccCCCCCchhhccCCCc-ch-HHHHHHHHHHHHhhhhcccccch
Confidence 56888887653 33555556777666666654332211 00 001111 12478888777753
No 65
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=25.89 E-value=40 Score=35.97 Aligned_cols=27 Identities=26% Similarity=0.746 Sum_probs=17.9
Q ss_pred HHHHHHHhcccCceeecCCCCeEEccCCCCCCCC
Q 012025 230 FKKFFESLESLTVEEINEPARQWHCPACQGGPGA 263 (472)
Q Consensus 230 f~K~ye~Lk~g~~kvkn~~~~tf~CP~C~gkkk~ 263 (472)
+++||+.-+- .-+.+|+||.|..+..+
T Consensus 270 ~~~f~~~e~L-------~g~d~W~CpkC~~k~ss 296 (415)
T COG5533 270 IDRFYEEEKL-------EGKDAWRCPKCGRKESS 296 (415)
T ss_pred HHHhhhHHhh-------cCcccccCchhcccccc
Confidence 6677764322 22789999999866444
No 66
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=25.88 E-value=39 Score=38.13 Aligned_cols=11 Identities=36% Similarity=0.640 Sum_probs=5.3
Q ss_pred HHHHHHHhhhc
Q 012025 291 LAELLDEELRR 301 (472)
Q Consensus 291 La~lLe~Dla~ 301 (472)
+..+|..++.+
T Consensus 262 ~~~~L~~eV~r 272 (622)
T PF02724_consen 262 YVPLLQDEVSR 272 (622)
T ss_pred HHHHHHHHHHh
Confidence 34455555444
No 67
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=25.80 E-value=1.2e+02 Score=31.88 Aligned_cols=54 Identities=22% Similarity=0.250 Sum_probs=37.0
Q ss_pred EEEeecccccCCCCcccccChHHHHHHhhccCcce-eEeccCCC-C-CcceEEEEeCCCchhhHHHH
Q 012025 334 VIIMNTRLDKDENDKWTGMGNQELLEYFILYAAVR-ARHSYGPQ-G-HRGMSVLIFESSAGGYLEAE 397 (472)
Q Consensus 334 GIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~K-Vr~lyg~~-G-H~G~aVVeF~kdwsGF~nA~ 397 (472)
++|-|++.. ++.++|++.|+.|.++. |+++.... | +.|++.|+|.. ...-..|+
T Consensus 110 LfVgnLp~~---------~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~-~e~A~~Ai 166 (346)
T TIGR01659 110 LIVNYLPQD---------MTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGS-EADSQRAI 166 (346)
T ss_pred EEEeCCCCC---------CCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEcc-HHHHHHHH
Confidence 568888753 35678999999999874 66655432 3 57999999954 34444444
No 68
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=25.63 E-value=71 Score=31.54 Aligned_cols=36 Identities=25% Similarity=0.422 Sum_probs=26.8
Q ss_pred ChHHHHHHhhccCcce-eEeccCCCCCcceEEEEeCCCch
Q 012025 353 GNQELLEYFILYAAVR-ARHSYGPQGHRGMSVLIFESSAG 391 (472)
Q Consensus 353 S~~eLkd~fsgF~P~K-Vr~lyg~~GH~G~aVVeF~kdws 391 (472)
+-.+|+..|..|.|++ |=+..++. |||.|+|+.-=.
T Consensus 23 ~k~eLE~~F~~yG~lrsvWvArnPP---GfAFVEFed~RD 59 (195)
T KOG0107|consen 23 TKRELERAFSKYGPLRSVWVARNPP---GFAFVEFEDPRD 59 (195)
T ss_pred chHHHHHHHHhcCcceeEEEeecCC---CceEEeccCccc
Confidence 4678999999999875 44555555 599999987543
No 69
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=25.38 E-value=25 Score=39.04 Aligned_cols=7 Identities=57% Similarity=0.738 Sum_probs=3.6
Q ss_pred chHHhhh
Q 012025 270 LQPLMTH 276 (472)
Q Consensus 270 lk~LLqH 276 (472)
|--||.|
T Consensus 348 llT~ml~ 354 (507)
T PF11702_consen 348 LLTLMLH 354 (507)
T ss_pred HHHHHhh
Confidence 4455555
No 70
>PRK12495 hypothetical protein; Provisional
Probab=25.13 E-value=57 Score=32.91 Aligned_cols=42 Identities=21% Similarity=0.355 Sum_probs=26.4
Q ss_pred CCchhh-----hhhhhhhhhhhHHHHHHHHhcccCceeecCCCCeEEccCCCC
Q 012025 212 FDSDTS-----QKSHDTRKKSRWFKKFFESLESLTVEEINEPARQWHCPACQG 259 (472)
Q Consensus 212 ~Dsd~s-----e~s~e~~k~~k~f~K~ye~Lk~g~~kvkn~~~~tf~CP~C~g 259 (472)
||-++. |||-....|.+--++.-++|..|.- -..++|+.|+.
T Consensus 4 FDkEaEREkLREKye~d~~~R~~~~~ma~lL~~gat------msa~hC~~CG~ 50 (226)
T PRK12495 4 FDKEAEREKLREKYEQDEQKREATERMSELLLQGAT------MTNAHCDECGD 50 (226)
T ss_pred hhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhcc------cchhhcccccC
Confidence 665553 5565666677777777788877632 24566666653
No 71
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=24.75 E-value=1.3e+02 Score=33.52 Aligned_cols=64 Identities=23% Similarity=0.389 Sum_probs=41.0
Q ss_pred EEEeecccccCCCCcccccChHHHHHHhhccCc-ce-eEeccCCCCC-cceEEEEeCCCchhhHHHHHHHHHHhhcC
Q 012025 334 VIIMNTRLDKDENDKWTGMGNQELLEYFILYAA-VR-ARHSYGPQGH-RGMSVLIFESSAGGYLEAERLHKHFAEQG 407 (472)
Q Consensus 334 GIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P-~K-Vr~lyg~~GH-~G~aVVeF~kdwsGF~nA~rLekhFe~qg 407 (472)
|.|.|||.+. +| +.|++.++.-.. +. |..|....|- +|.+||+|.-- .+.+-|+.--+-|+..+
T Consensus 47 vfItNIpyd~----rW-----qdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~-E~~qKa~E~lnk~~~~G 113 (608)
T KOG4212|consen 47 VFITNIPYDY----RW-----QDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDP-ENVQKALEKLNKYEVNG 113 (608)
T ss_pred EEEecCcchh----hh-----HhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCH-HHHHHHHHHhhhccccC
Confidence 7799999733 33 458887774333 33 5567777885 89999999654 44444544444455443
No 72
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=24.73 E-value=1.2e+02 Score=34.53 Aligned_cols=62 Identities=15% Similarity=0.341 Sum_probs=41.9
Q ss_pred eEEEeecccccCCCCcccccChHHHHHHhhccCcc-eeEeccCCCC--CcceEEEEeCCCchhhHHHHHHHHHHh
Q 012025 333 MVIIMNTRLDKDENDKWTGMGNQELLEYFILYAAV-RARHSYGPQG--HRGMSVLIFESSAGGYLEAERLHKHFA 404 (472)
Q Consensus 333 MGIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~-KVr~lyg~~G--H~G~aVVeF~kdwsGF~nA~rLekhFe 404 (472)
.+.|-|++.. .+.++|++.|+.|.++ .++...++.+ ++|++.|+|.+- .--..|+.--+.|+
T Consensus 206 rLfVgnLp~~---------vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~-e~A~kAI~amNg~e 270 (612)
T TIGR01645 206 RIYVASVHPD---------LSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNL-QSQSEAIASMNLFD 270 (612)
T ss_pred eEEeecCCCC---------CCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCH-HHHHHHHHHhCCCe
Confidence 4667777532 3578899999999997 5677776653 689999999973 22334444334443
No 73
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.42 E-value=46 Score=32.94 Aligned_cols=10 Identities=40% Similarity=0.371 Sum_probs=5.4
Q ss_pred CCCchhhhhh
Q 012025 211 EFDSDTSQKS 220 (472)
Q Consensus 211 d~Dsd~se~s 220 (472)
+.|||+.+++
T Consensus 214 ~edsde~~q~ 223 (227)
T KOG3241|consen 214 LEDSDENEQS 223 (227)
T ss_pred cccccccccc
Confidence 3456655554
No 74
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=24.14 E-value=1.7e+02 Score=20.91 Aligned_cols=38 Identities=21% Similarity=0.388 Sum_probs=27.3
Q ss_pred cChHHHHHHhhccCcc-eeEeccCCCC-CcceEEEEeCCC
Q 012025 352 MGNQELLEYFILYAAV-RARHSYGPQG-HRGMSVLIFESS 389 (472)
Q Consensus 352 ~S~~eLkd~fsgF~P~-KVr~lyg~~G-H~G~aVVeF~kd 389 (472)
.+.++|++.|+.|.++ ++.....+.+ ..|++.|+|.+-
T Consensus 11 ~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~ 50 (74)
T cd00590 11 VTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDE 50 (74)
T ss_pred cCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCH
Confidence 4678899999988765 4555554432 478999999954
No 75
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.
Probab=24.13 E-value=75 Score=37.04 Aligned_cols=17 Identities=18% Similarity=0.215 Sum_probs=10.9
Q ss_pred CCceeeeCceEEEeecc
Q 012025 324 KDHEIVWPPMVIIMNTR 340 (472)
Q Consensus 324 kDdliVWPWMGIIvNt~ 340 (472)
.|...|=+.+.+|+|+-
T Consensus 633 Ed~~~~gkr~~lv~~~G 649 (763)
T TIGR00993 633 EDQIALGKRLVLVGSTG 649 (763)
T ss_pred hheeeeccceEEEEecc
Confidence 45666667777777753
No 76
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=22.96 E-value=3.2e+02 Score=30.09 Aligned_cols=16 Identities=31% Similarity=0.549 Sum_probs=12.2
Q ss_pred CCeEEccCCCCCCCCcc
Q 012025 249 ARQWHCPACQGGPGAID 265 (472)
Q Consensus 249 ~~tf~CP~C~gkkk~~D 265 (472)
.+.-||..|..++ ++|
T Consensus 349 AGDSRcV~sr~Gk-Avd 364 (542)
T KOG0699|consen 349 AGDSRCVLSRNGK-AVD 364 (542)
T ss_pred CCCcceEEecCCc-eee
Confidence 5888999998764 555
No 77
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=22.76 E-value=1.6e+02 Score=30.83 Aligned_cols=47 Identities=17% Similarity=0.342 Sum_probs=0.0
Q ss_pred eEEEeecccccCCCCcccccChHHHHHHhhccCcc-eeEeccCCCC--CcceEEEEeCC
Q 012025 333 MVIIMNTRLDKDENDKWTGMGNQELLEYFILYAAV-RARHSYGPQG--HRGMSVLIFES 388 (472)
Q Consensus 333 MGIIvNt~te~dddgk~~G~S~~eLkd~fsgF~P~-KVr~lyg~~G--H~G~aVVeF~k 388 (472)
.+.|-|++ ...+.++|++.|..|..+ .|+.+....+ ..|++.|+|..
T Consensus 188 ~l~v~nl~---------~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~ 237 (457)
T TIGR01622 188 KLYVGNLH---------FNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHD 237 (457)
T ss_pred EEEEcCCC---------CCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECC
No 78
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=22.06 E-value=33 Score=35.58 Aligned_cols=7 Identities=43% Similarity=0.985 Sum_probs=3.4
Q ss_pred hhhhhHH
Q 012025 224 RKKSRWF 230 (472)
Q Consensus 224 ~k~~k~f 230 (472)
|-|+||.
T Consensus 343 r~k~~wk 349 (375)
T PF03153_consen 343 RVKNKWK 349 (375)
T ss_dssp EETTEEE
T ss_pred cccceeE
Confidence 4455553
No 79
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=21.64 E-value=48 Score=34.42 Aligned_cols=11 Identities=36% Similarity=0.229 Sum_probs=4.1
Q ss_pred eccCCCCCCCc
Q 012025 60 KSKNKAGSGTT 70 (472)
Q Consensus 60 k~k~~~~~~~~ 70 (472)
++|+|+-+.|+
T Consensus 14 ~~k~K~V~~Aa 24 (324)
T PF05285_consen 14 KSKDKGVMMAA 24 (324)
T ss_pred hhhhhHHHHHH
Confidence 33333333333
No 80
>PF12253 CAF1A: Chromatin assembly factor 1 subunit A; InterPro: IPR022043 The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A []. The A domain is uniquely required for the progression of S phase in mouse cells [], independent of its ability to promote histone deposition [] but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints [].
Probab=21.20 E-value=1.2e+02 Score=25.84 Aligned_cols=10 Identities=40% Similarity=0.863 Sum_probs=4.9
Q ss_pred CCCCCCCCcc
Q 012025 145 RPPLEHGWNW 154 (472)
Q Consensus 145 ~~p~~~g~~w 154 (472)
|||.-+=|.-
T Consensus 11 RPpY~GT~~k 20 (77)
T PF12253_consen 11 RPPYYGTWTK 20 (77)
T ss_pred CCCEeeEEcc
Confidence 5555554443
No 81
>PHA03249 DNA packaging tegument protein UL25; Provisional
Probab=21.04 E-value=1.4e+03 Score=26.78 Aligned_cols=31 Identities=23% Similarity=0.280 Sum_probs=19.5
Q ss_pred ccccccccccccccccCCCcCCC--CCeeEEEe
Q 012025 29 SNSQVDHLSGSVADISLDSAQDD--GGWEVYVR 59 (472)
Q Consensus 29 ~~~~~~~l~~~~~~~~~~~~~~~--g~w~~~~~ 59 (472)
+....|.|-.--|++.--|++.| ...|+|+-
T Consensus 35 ~r~~~~~ld~meagl~~~s~~sd~~ssfe~v~e 67 (653)
T PHA03249 35 PRAPTEDLDRMEAGLSSYSSSSDNKSSFEVVSE 67 (653)
T ss_pred CCCchhhhHHHhcccccccccCCCccceeeeec
Confidence 34556777776666666666655 45788843
No 82
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.98 E-value=52 Score=30.15 Aligned_cols=12 Identities=25% Similarity=0.816 Sum_probs=9.7
Q ss_pred CCeEEccCCCCC
Q 012025 249 ARQWHCPACQGG 260 (472)
Q Consensus 249 ~~tf~CP~C~gk 260 (472)
++.|.||.|++.
T Consensus 121 ~~~f~Cp~Cg~~ 132 (147)
T smart00531 121 DGTFTCPRCGEE 132 (147)
T ss_pred CCcEECCCCCCE
Confidence 577999999763
No 83
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=20.67 E-value=73 Score=21.60 Aligned_cols=25 Identities=20% Similarity=0.344 Sum_probs=19.0
Q ss_pred CeEEccCCCCCCCCccccCCchHHhhhhccc
Q 012025 250 RQWHCPACQGGPGAIDWYRGLQPLMTHAKTK 280 (472)
Q Consensus 250 ~tf~CP~C~gkkk~~D~Y~~lk~LLqHA~gv 280 (472)
+.|.|.+|.- +|.+...|.+|-.+.
T Consensus 2 ~~~~C~~C~~------~~~~~~~~~~H~~gk 26 (35)
T smart00451 2 GGFYCKLCNV------TFTDEISVEAHLKGK 26 (35)
T ss_pred cCeEccccCC------ccCCHHHHHHHHChH
Confidence 4699999952 267788999997663
No 84
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=20.61 E-value=35 Score=31.53 Aligned_cols=11 Identities=45% Similarity=1.057 Sum_probs=9.4
Q ss_pred CeEEccCCCCC
Q 012025 250 RQWHCPACQGG 260 (472)
Q Consensus 250 ~tf~CP~C~gk 260 (472)
..+|||.|++-
T Consensus 39 ~~LRC~vCqnq 49 (126)
T PRK10144 39 SQLRCPQCQNQ 49 (126)
T ss_pred HcCCCCCCCCC
Confidence 57899999975
No 85
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=20.18 E-value=34 Score=26.42 Aligned_cols=13 Identities=31% Similarity=1.053 Sum_probs=7.9
Q ss_pred CCeEEccCCCCCC
Q 012025 249 ARQWHCPACQGGP 261 (472)
Q Consensus 249 ~~tf~CP~C~gkk 261 (472)
-..|+||.|...|
T Consensus 32 p~~w~CP~C~a~K 44 (47)
T PF00301_consen 32 PDDWVCPVCGAPK 44 (47)
T ss_dssp -TT-B-TTTSSBG
T ss_pred CCCCcCcCCCCcc
Confidence 3679999998753
No 86
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=20.17 E-value=42 Score=28.46 Aligned_cols=11 Identities=27% Similarity=1.002 Sum_probs=4.4
Q ss_pred CCeEEccCCCC
Q 012025 249 ARQWHCPACQG 259 (472)
Q Consensus 249 ~~tf~CP~C~g 259 (472)
...|.||||..
T Consensus 20 ~~~F~CPfC~~ 30 (81)
T PF05129_consen 20 PKVFDCPFCNH 30 (81)
T ss_dssp SS----TTT--
T ss_pred CceEcCCcCCC
Confidence 58999999984
No 87
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=20.09 E-value=45 Score=25.66 Aligned_cols=9 Identities=44% Similarity=1.206 Sum_probs=7.2
Q ss_pred EccCCCCCC
Q 012025 253 HCPACQGGP 261 (472)
Q Consensus 253 ~CP~C~gkk 261 (472)
.||||+++.
T Consensus 3 PCPfCGg~~ 11 (53)
T TIGR03655 3 PCPFCGGAD 11 (53)
T ss_pred CCCCCCCcc
Confidence 599998763
No 88
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=20.07 E-value=46 Score=35.47 Aligned_cols=13 Identities=23% Similarity=0.682 Sum_probs=10.3
Q ss_pred CCeEEccCCCCCC
Q 012025 249 ARQWHCPACQGGP 261 (472)
Q Consensus 249 ~~tf~CP~C~gkk 261 (472)
.-+|.|||||..-
T Consensus 374 ~~~FKCPYCP~~~ 386 (396)
T COG5109 374 VLSFKCPYCPEMS 386 (396)
T ss_pred cEEeeCCCCCcch
Confidence 4589999999753
Done!