Query 019781
Match_columns 336
No_of_seqs 259 out of 328
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 04:29:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019781.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019781hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0227 Splicing factor 3a, su 100.0 5.7E-94 1.2E-98 646.7 14.0 216 1-216 3-218 (222)
2 COG5246 PRP11 Splicing factor 100.0 4.9E-67 1.1E-71 469.8 12.7 211 2-214 4-220 (222)
3 KOG1924 RhoA GTPase effector D 99.6 4.5E-16 9.8E-21 163.5 4.0 59 121-181 442-500 (1102)
4 PF09732 CactinC_cactus: Cactu 99.4 1.5E-13 3.3E-18 117.9 6.3 84 122-213 35-121 (125)
5 KOG1924 RhoA GTPase effector D 98.8 2.1E-08 4.6E-13 106.7 9.9 34 272-310 570-603 (1102)
6 KOG3671 Actin regulatory prote 98.3 1.1E-05 2.4E-10 82.9 14.1 27 7-33 58-84 (569)
7 smart00451 ZnF_U1 U1-like zinc 98.0 1.6E-06 3.5E-11 57.6 0.9 34 49-82 1-34 (35)
8 KOG4727 U1-like Zn-finger prot 97.7 1.1E-05 2.3E-10 73.5 1.2 39 43-81 67-105 (193)
9 PF12874 zf-met: Zinc-finger o 97.5 2E-05 4.4E-10 48.9 0.0 25 52-76 1-25 (25)
10 PF12171 zf-C2H2_jaz: Zinc-fin 96.4 0.0012 2.5E-08 42.1 0.5 27 51-77 1-27 (27)
11 KOG0132 RNA polymerase II C-te 96.3 0.074 1.6E-06 58.0 13.5 14 192-205 500-513 (894)
12 KOG3671 Actin regulatory prote 95.7 0.13 2.9E-06 53.8 11.8 14 198-211 285-298 (569)
13 PF06220 zf-U1: U1 zinc finger 95.4 0.0076 1.7E-07 42.1 1.4 34 50-83 2-37 (38)
14 KOG2370 Cactin [Signal transdu 95.4 0.011 2.4E-07 61.4 2.8 75 127-212 538-618 (623)
15 KOG0150 Spliceosomal protein F 92.3 0.067 1.5E-06 53.0 1.6 36 49-84 8-44 (336)
16 KOG3032 Uncharacterized conser 92.2 0.14 3E-06 49.1 3.5 48 34-82 17-65 (264)
17 PLN02748 tRNA dimethylallyltra 91.3 0.093 2E-06 54.5 1.4 39 49-87 416-455 (468)
18 KOG3454 U1 snRNP-specific prot 91.1 0.076 1.6E-06 48.3 0.5 31 51-81 3-35 (165)
19 KOG4722 Zn-finger protein [Gen 90.5 0.19 4E-06 52.1 2.6 33 52-84 494-526 (672)
20 KOG4672 Uncharacterized conser 90.3 2.3 5.1E-05 43.9 10.2 23 32-54 39-65 (487)
21 PHA03247 large tegument protei 90.2 4.2 9.2E-05 50.1 13.4 30 38-68 2317-2347(3151)
22 PHA03247 large tegument protei 89.5 5.9 0.00013 49.0 13.9 12 39-50 2450-2461(3151)
23 KOG1830 Wiskott Aldrich syndro 89.0 4.2 9.1E-05 42.3 10.9 10 203-212 246-255 (518)
24 KOG1923 Rac1 GTPase effector F 85.7 4.5 9.8E-05 44.7 9.4 25 58-82 100-124 (830)
25 PF05477 SURF2: Surfeit locus 83.3 1.1 2.3E-05 43.3 3.2 65 23-87 46-116 (244)
26 KOG1830 Wiskott Aldrich syndro 80.6 32 0.00068 36.2 12.6 12 65-76 154-165 (518)
27 KOG0132 RNA polymerase II C-te 75.6 49 0.0011 37.1 12.9 16 196-211 531-546 (894)
28 PF13912 zf-C2H2_6: C2H2-type 71.4 1.1 2.3E-05 27.9 -0.4 21 52-72 2-22 (27)
29 PF00096 zf-C2H2: Zinc finger, 70.8 1 2.2E-05 26.9 -0.5 21 52-72 1-21 (23)
30 smart00355 ZnF_C2H2 zinc finge 65.9 1.3 2.8E-05 25.9 -0.8 21 52-72 1-21 (26)
31 PTZ00448 hypothetical protein; 65.3 2.8 6.2E-05 42.6 1.0 36 50-85 313-348 (373)
32 KOG1074 Transcriptional repres 64.1 2.9 6.2E-05 46.6 0.8 31 44-74 624-656 (958)
33 PF08799 PRP4: pre-mRNA proces 61.2 6.5 0.00014 26.5 1.8 15 17-31 15-29 (30)
34 smart00500 SFM Splicing Factor 60.2 7.1 0.00015 28.4 2.0 24 15-38 18-41 (44)
35 KOG3576 Ovo and related transc 59.5 3.4 7.5E-05 39.5 0.4 48 35-85 158-210 (267)
36 COG5136 U1 snRNP-specific prot 59.1 2 4.3E-05 39.4 -1.2 32 50-81 2-35 (188)
37 KOG4672 Uncharacterized conser 58.0 49 0.0011 34.7 8.2 14 76-89 104-117 (487)
38 PF13894 zf-C2H2_4: C2H2-type 57.3 2.7 5.8E-05 24.5 -0.5 21 52-72 1-21 (24)
39 KOG1923 Rac1 GTPase effector F 55.6 66 0.0014 36.0 9.1 12 200-211 241-252 (830)
40 PHA03378 EBNA-3B; Provisional 55.5 2.1E+02 0.0046 32.2 12.7 9 112-120 481-489 (991)
41 KOG2893 Zn finger protein [Gen 53.0 1.5E+02 0.0032 29.4 10.1 7 52-58 35-41 (341)
42 PF13909 zf-H2C2_5: C2H2-type 52.2 3.2 6.9E-05 25.2 -0.8 21 52-73 1-21 (24)
43 PF12756 zf-C2H2_2: C2H2 type 51.4 3.7 8.1E-05 31.7 -0.7 31 51-81 50-80 (100)
44 KOG3408 U1-like Zn-finger-cont 48.5 6.9 0.00015 34.4 0.4 34 48-81 54-87 (129)
45 PF11281 DUF3083: Protein of u 47.8 18 0.0004 36.1 3.3 28 187-214 243-270 (316)
46 KOG0717 Molecular chaperone (D 46.7 14 0.00031 38.9 2.4 32 52-83 293-324 (508)
47 KOG4849 mRNA cleavage factor I 44.7 1.4E+02 0.003 31.0 8.9 12 153-164 115-126 (498)
48 PF12756 zf-C2H2_2: C2H2 type 41.6 8.7 0.00019 29.6 0.0 30 53-83 1-30 (100)
49 PF04959 ARS2: Arsenite-resist 39.2 15 0.00032 34.8 1.1 35 47-82 73-107 (214)
50 KOG3623 Homeobox transcription 38.9 14 0.0003 41.2 0.9 32 46-77 302-335 (1007)
51 KOG3608 Zn finger proteins [Ge 37.9 7.7 0.00017 39.8 -1.0 30 45-74 257-286 (467)
52 PF02892 zf-BED: BED zinc fing 37.0 13 0.00028 25.7 0.3 23 49-71 14-40 (45)
53 PF13465 zf-H2C2_2: Zinc-finge 35.8 12 0.00026 23.6 -0.0 14 46-59 7-22 (26)
54 COG2871 NqrF Na+-transporting 33.3 44 0.00096 33.8 3.4 30 162-199 165-196 (410)
55 KOG4849 mRNA cleavage factor I 33.2 5.9E+02 0.013 26.6 12.3 11 59-69 89-99 (498)
56 PF12013 DUF3505: Protein of u 32.2 33 0.00072 28.2 2.0 39 49-88 9-48 (109)
57 COG5188 PRP9 Splicing factor 3 31.5 15 0.00033 37.7 -0.1 37 48-84 235-271 (470)
58 PHA03233 DNA packaging protein 30.8 74 0.0016 34.1 4.7 47 16-63 270-326 (518)
59 KOG0703 Predicted GTPase-activ 30.4 50 0.0011 32.8 3.2 48 19-66 7-60 (287)
60 COG5112 UFD2 U1-like Zn-finger 30.3 19 0.0004 31.3 0.3 38 48-90 52-89 (126)
61 COG5178 PRP8 U5 snRNP spliceos 27.4 54 0.0012 38.8 3.2 28 244-273 3-30 (2365)
62 PF03194 LUC7: LUC7 N_terminus 27.4 51 0.0011 31.8 2.7 36 49-84 188-226 (254)
63 PF12940 RAG1: Recombination-a 25.6 33 0.00071 35.5 1.1 33 51-83 216-249 (442)
64 PF04988 AKAP95: A-kinase anch 24.6 29 0.00064 31.8 0.5 31 52-82 1-31 (165)
65 PF08864 UPF0302: UPF0302 doma 24.2 68 0.0015 27.1 2.5 63 141-213 31-98 (106)
66 PLN03131 hypothetical protein; 21.9 1.8E+02 0.0039 32.2 5.6 41 25-66 11-58 (705)
67 KOG2837 Protein containing a U 21.7 30 0.00065 34.3 -0.0 31 51-81 25-55 (309)
68 KOG1994 Predicted RNA binding 21.6 72 0.0016 31.1 2.4 25 49-73 237-261 (268)
69 KOG3277 Uncharacterized conser 21.3 47 0.001 30.5 1.1 16 51-66 79-94 (165)
70 PF14968 CCDC84: Coiled coil p 21.2 53 0.0011 33.2 1.6 25 54-81 2-26 (336)
71 PHA00626 hypothetical protein 20.9 49 0.0011 25.6 0.9 22 43-64 15-36 (59)
72 PF14445 Prok-RING_2: Prokaryo 20.5 22 0.00048 27.1 -1.0 16 50-65 6-21 (57)
No 1
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=100.00 E-value=5.7e-94 Score=646.74 Aligned_cols=216 Identities=69% Similarity=1.101 Sum_probs=209.3
Q ss_pred CCCCCCCCCCCccccchhhhHHHHHHHHHHHhhhhcCCCCCcceeeccCCceeeeccccccCCccccccccchhhHHHHH
Q 019781 1 MDREWGSKPGSGGAASAQNEAIDRRERLRRLALETIDLAKDPYFMRNHLGSYECKLCLTLHNNEGNYLAHTQGKRHQTNL 80 (336)
Q Consensus 1 ~~~~~GsK~G~Gg~As~~~~n~~rrerl~~L~~e~id~~~dPy~~rNh~G~yeC~LClt~h~~e~syl~H~qGkkHq~nL 80 (336)
|.+|+|||+|||||||+||.|+|||||||+||+|+|||++||||||||+|+|||+||+|+|+||+||++||||||||+||
T Consensus 3 ~~~r~GsK~G~ggvAS~se~n~~RrerlrqLaletidl~kDPy~mkNh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nl 82 (222)
T KOG0227|consen 3 YQNRAGSKTGSGGVASESEFNRDRRERLRQLALETIDLNKDPYFMKNHLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNL 82 (222)
T ss_pred cccccCccCCCCcccchhhhhHHHHHHHHHHHHhhcccccCchhhhccCcceeehhhhhhhcchhhhhhhhccchhhHHH
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCCCcccccccccceecCCCceeEEEeeCCCcCccceEEEEecccccccCCcccccccchhhccccc
Q 019781 81 AKRAAREAKDAPAQPQPHKRKVNVRKTVKIGRPGYRVTKQFDPETKQRSLLFQIEYPEIEDLSKPRHRFMSSFEQRVQPF 160 (336)
Q Consensus 81 ~rR~a~~~k~~~~~~~~~~~~~~~r~~vkigrPgykVtk~rDPet~q~gllfqIdyp~i~d~~~P~~RiMSa~EqKvEel 160 (336)
+||+|+|+|++....++.+..+++|++||||||||||||||||+.+|++|+|||||++|+++++|+|||||++||++|..
T Consensus 83 arraa~e~k~s~~~~~~~k~~v~vk~~vkigrpgykvtk~r~~~~gq~~L~fQv~Yp~i~~~~~Pr~rfmssyeq~ve~~ 162 (222)
T KOG0227|consen 83 ARRAAKEAKESPDLPQPQKIIVEVKKFVKIGRPGYKVTKQRDPENGQQGLLFQVNYPEIEEGIMPRHRFMSSYEQKVEPP 162 (222)
T ss_pred HHHHHHHhhcCccccccccchhhhhhhhhcCCCcceeeeeecCccCceeeEEEecchhhhhccCCcchhhhhhHhhcCCc
Confidence 99999999999877777666789999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccceeeeeecccccccccccCcccccCCCcccccccCCCceEEEEEeeccCCCC
Q 019781 161 DKRYQYLMFAAEPYEIIAFKVPSTEIDKSTPKFFSHWDPDSKMFTLQLYFKSKPVE 216 (336)
Q Consensus 161 dkk~qyLliA~EPyEtIa~kIPn~eId~~~~~~~~~WD~d~K~f~lQf~Fk~~~~e 216 (336)
|+++|||+||+||||+|+|||||+|||++++|||||||.+||+||||||||....+
T Consensus 163 dk~~qyLvfaaePyE~Iafk~p~~Eid~se~Kf~t~wd~~tk~y~lqF~fk~~~~~ 218 (222)
T KOG0227|consen 163 DKSWQYLVFAAEPYENIAFKVPSREIDKSEGKFWTHWDAETKQYTLQFFFKQAEPE 218 (222)
T ss_pred cccceEEEEEeccccceeeecCchhhhhccCceeeeecCCCceEEEEEEecccCcc
Confidence 99999999999999999999999999999999999999999999999999976554
No 2
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=100.00 E-value=4.9e-67 Score=469.81 Aligned_cols=211 Identities=35% Similarity=0.623 Sum_probs=190.3
Q ss_pred CCCCCCCCCCccccchhhhHHHHHHHHHHHhhhhcCCCCCcceeeccCCceeeeccccccCCccccccccchhhHHHHHH
Q 019781 2 DREWGSKPGSGGAASAQNEAIDRRERLRRLALETIDLAKDPYFMRNHLGSYECKLCLTLHNNEGNYLAHTQGKRHQTNLA 81 (336)
Q Consensus 2 ~~~~GsK~G~Gg~As~~~~n~~rrerl~~L~~e~id~~~dPy~~rNh~G~yeC~LClt~h~~e~syl~H~qGkkHq~nL~ 81 (336)
-+|+|||+|+|||||+++.|.+||+|++.|+++++|+.+|||+||||+|.|+|+||+|+|.+|+||++|++||||++|++
T Consensus 4 ~~r~Gsk~Gggg~Ase~~~n~~rR~r~~~L~~~gqDl~dDPyl~knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~ 83 (222)
T COG5246 4 GGRGGSKTGGGGTASEIKKNKKRRSRQLLLEAYGQDLMDDPYLSKNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSS 83 (222)
T ss_pred ccccccccCCCcchhHHHhhHHHHHHHHHHHhcCcccccCcchhhcCCCcEEeeeeccccccHHHHHHhhccchhhhhHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCC-CCCC----cccccccccc-eecCCCceeEEEeeCCCcCccceEEEEecccccccCCcccccccchhh
Q 019781 82 KRAAREAKDAPA-QPQP----HKRKVNVRKT-VKIGRPGYRVTKQFDPETKQRSLLFQIEYPEIEDLSKPRHRFMSSFEQ 155 (336)
Q Consensus 82 rR~a~~~k~~~~-~~~~----~~~~~~~r~~-vkigrPgykVtk~rDPet~q~gllfqIdyp~i~d~~~P~~RiMSa~Eq 155 (336)
||.+.+.+.+.. +.+. ++.-+++|+. +++|+|+|||.++++|+.+.+||.|||+|+.++...+|++||||+|||
T Consensus 84 rrs~eksslgrEnqtthdfrqqQkiieaKqSlk~~GiP~ykv~~~~epk~G~~Gl~iqvnY~Dd~a~~~P~yRivs~lEq 163 (222)
T COG5246 84 RRSEEKSSLGRENQTTHDFRQQQKIIEAKQSLKRSGIPSYKVRSLVEPKGGRRGLGIQVNYEDDLAEEMPQYRIVSSLEQ 163 (222)
T ss_pred HHHHHhhcccccCCchhhhhhHHHHHHHHHHHHhcCCCceeEEEeecCCCCceeeEEEEeccchhhccCcceehhhhhhh
Confidence 997655543322 2211 1222555554 588999999999999999999999999999988889999999999999
Q ss_pred cccccccccceeeeeecccccccccccCcccccCCCcccccccCCCceEEEEEeeccCC
Q 019781 156 RVQPFDKRYQYLMFAAEPYEIIAFKVPSTEIDKSTPKFFSHWDPDSKMFTLQLYFKSKP 214 (336)
Q Consensus 156 KvEeldkk~qyLliA~EPyEtIa~kIPn~eId~~~~~~~~~WD~d~K~f~lQf~Fk~~~ 214 (336)
++|+.|++++||+|||||||+|+|||++.|||.. +.|++||..|++|+|||||+...
T Consensus 164 ~ve~~d~~f~yLV~a~ePyEnIafk~~~~ei~f~--s~~~~wDa~~~tYt~qFff~~a~ 220 (222)
T COG5246 164 NVEEYDESFRYLVFACEPYENIAFKFENKEIDFL--SIYEDWDAETGTYTLQFFFLEAG 220 (222)
T ss_pred cchhhcccceEEEEEeccccceeeecCCCccchh--hhcccccccCceEEEEEeeeccc
Confidence 9999999999999999999999999999999976 36789999999999999998644
No 3
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=99.59 E-value=4.5e-16 Score=163.52 Aligned_cols=59 Identities=20% Similarity=0.255 Sum_probs=52.9
Q ss_pred eCCCcCccceEEEEecccccccCCcccccccchhhcccccccccceeeeeecccccccccc
Q 019781 121 FDPETKQRSLLFQIEYPEIEDLSKPRHRFMSSFEQRVQPFDKRYQYLMFAAEPYEIIAFKV 181 (336)
Q Consensus 121 rDPet~q~gllfqIdyp~i~d~~~P~~RiMSa~EqKvEeldkk~qyLliA~EPyEtIa~kI 181 (336)
.||++.++-+ |+||+.+|+|.++++.+. .+.||++.+++++++.++.++++.+....|.
T Consensus 442 ~DPdf~yr~~-l~id~~~liD~~vdkak~-eeseqkA~e~~kk~~ke~ta~qe~qael~k~ 500 (1102)
T KOG1924|consen 442 MDPDFKYRFR-LDIDLTELIDKMVDKAKA-EESEQKAAELEKKFDKELTARQEAQAELQKH 500 (1102)
T ss_pred CCCCcchhhc-ccCcHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 5899988774 899999999999999997 8999999999999999999999998777655
No 4
>PF09732 CactinC_cactus: Cactus-binding C-terminus of cactin protein; InterPro: IPR019134 This entry represents the C-terminal 200 residues of the cactin protein which is necessary for the association of cactin with IkappaB-cactus, as one of the intracellular members of the Rel complex. The Rel (NF-kappaB) pathway is conserved in invertebrates and vertebrates. In mammals, it controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development and in the establishment of dorsal-ventral polarity in the early embryo []. Most members of the family also have the conserved mid region of cactin (IPR018816 from INTERPRO) further upstream.
Probab=99.44 E-value=1.5e-13 Score=117.89 Aligned_cols=84 Identities=31% Similarity=0.474 Sum_probs=71.7
Q ss_pred CCCcCccceEEEEecccccc-cCCcccccccchhhcccccccccceeeee-ecccccccccccCcccccCCC-ccccccc
Q 019781 122 DPETKQRSLLFQIEYPEIED-LSKPRHRFMSSFEQRVQPFDKRYQYLMFA-AEPYEIIAFKVPSTEIDKSTP-KFFSHWD 198 (336)
Q Consensus 122 DPet~q~gllfqIdyp~i~d-~~~P~~RiMSa~EqKvEeldkk~qyLliA-~EPyEtIa~kIPn~eId~~~~-~~~~~WD 198 (336)
.|-...+|+.|+|.|++|++ +..|.+|||+ +++ ++++++|+++ .+|||+|||||.|+|+|.+.+ .|+++||
T Consensus 35 pPPK~vqGYkFnIfYPdL~d~~~~P~y~i~~-----~~~-~~~~~~L~F~AgpPYeDIAFkIvnrEWd~s~k~Gfr~~Fd 108 (125)
T PF09732_consen 35 PPPKIVQGYKFNIFYPDLIDKSKTPRYRIEP-----DED-NPDFCILRFHAGPPYEDIAFKIVNREWDYSHKRGFRCSFD 108 (125)
T ss_pred CCCceeeeeEEEEECCcccCCCCCCcEEEEE-----CCC-CCCEEEEEEeCCCCCcCEEEEEecCeeecCCCCCceEEee
Confidence 34455689999999999986 6889999988 333 7788899985 689999999999999999988 7888998
Q ss_pred CCCceEEEEEeeccC
Q 019781 199 PDSKMFTLQLYFKSK 213 (336)
Q Consensus 199 ~d~K~f~lQf~Fk~~ 213 (336)
. ++|.|+|+||..
T Consensus 109 ~--gilqL~F~FKr~ 121 (125)
T PF09732_consen 109 R--GILQLYFNFKRY 121 (125)
T ss_pred C--CEEEEEEEEEhh
Confidence 6 699999999964
No 5
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=98.79 E-value=2.1e-08 Score=106.72 Aligned_cols=34 Identities=50% Similarity=1.003 Sum_probs=15.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 019781 272 GPRPMPPGGAPPAPPPPPGGSGTMANFTPGTQVGRPPTM 310 (336)
Q Consensus 272 ~p~pp~p~g~p~~pp~pp~~~g~~~~~~~~~ppp~ppp~ 310 (336)
||||||++|+.++|||||++ | |..|.||||++.|
T Consensus 570 PPpPppppg~~gppPPPpp~-g----~~Gg~ppPP~~gm 603 (1102)
T KOG1924|consen 570 PPPPPPPPGGGGPPPPPPPG-G----FLGGPPPPPPPGM 603 (1102)
T ss_pred CCccCCCCCCCCCCCcCCCC-C----CCCCCCCCCCCCc
Confidence 33444444444444333332 2 4556666666544
No 6
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=98.31 E-value=1.1e-05 Score=82.95 Aligned_cols=27 Identities=26% Similarity=0.305 Sum_probs=22.4
Q ss_pred CCCCCccccchhhhHHHHHHHHHHHhh
Q 019781 7 SKPGSGGAASAQNEAIDRRERLRRLAL 33 (336)
Q Consensus 7 sK~G~Gg~As~~~~n~~rrerl~~L~~ 33 (336)
.|+|..|+.+...+|.+|-..||-+.+
T Consensus 58 ~~~~~~Gal~lVkD~~~rsyFlrl~di 84 (569)
T KOG3671|consen 58 NKTGLCGALCLVKDNAQRSYFLRLVDI 84 (569)
T ss_pred ccccCceeEEEeeccccceeeeEEeee
Confidence 589999999999999999888865543
No 7
>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=98.03 E-value=1.6e-06 Score=57.56 Aligned_cols=34 Identities=38% Similarity=0.684 Sum_probs=31.6
Q ss_pred CCceeeeccccccCCccccccccchhhHHHHHHH
Q 019781 49 LGSYECKLCLTLHNNEGNYLAHTQGKRHQTNLAK 82 (336)
Q Consensus 49 ~G~yeC~LClt~h~~e~syl~H~qGkkHq~nL~r 82 (336)
.|.|.|.||++..++..++..|+.||+|+.+|++
T Consensus 1 ~~~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 1 TGGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CcCeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 3679999999999999999999999999999875
No 8
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=97.73 E-value=1.1e-05 Score=73.45 Aligned_cols=39 Identities=36% Similarity=0.663 Sum_probs=35.6
Q ss_pred ceeeccCCceeeeccccccCCccccccccchhhHHHHHH
Q 019781 43 YFMRNHLGSYECKLCLTLHNNEGNYLAHTQGKRHQTNLA 81 (336)
Q Consensus 43 y~~rNh~G~yeC~LClt~h~~e~syl~H~qGkkHq~nL~ 81 (336)
.+-+-..|.|.|.+|+++...-.+||.|+.||+||.||.
T Consensus 67 ~tp~sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlg 105 (193)
T KOG4727|consen 67 STPRSQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLG 105 (193)
T ss_pred CCcccccCceeeeecceeehhhHHHHHHhccHHHHHHHh
Confidence 455666899999999999999999999999999999997
No 9
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.52 E-value=2e-05 Score=48.86 Aligned_cols=25 Identities=24% Similarity=0.619 Sum_probs=24.4
Q ss_pred eeeeccccccCCccccccccchhhH
Q 019781 52 YECKLCLTLHNNEGNYLAHTQGKRH 76 (336)
Q Consensus 52 yeC~LClt~h~~e~syl~H~qGkkH 76 (336)
|.|++|++..+++.+|..|++|+||
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 7899999999999999999999998
No 10
>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=96.36 E-value=0.0012 Score=42.14 Aligned_cols=27 Identities=22% Similarity=0.566 Sum_probs=25.1
Q ss_pred ceeeeccccccCCccccccccchhhHH
Q 019781 51 SYECKLCLTLHNNEGNYLAHTQGKRHQ 77 (336)
Q Consensus 51 ~yeC~LClt~h~~e~syl~H~qGkkHq 77 (336)
.|.|.+|+..-+++..|..|+.+|+|+
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence 378999999999999999999999996
No 11
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=96.26 E-value=0.074 Score=57.99 Aligned_cols=14 Identities=14% Similarity=0.368 Sum_probs=11.4
Q ss_pred cccccccCCCceEE
Q 019781 192 KFFSHWDPDSKMFT 205 (336)
Q Consensus 192 ~~~~~WD~d~K~f~ 205 (336)
.|++|||.++.+-|
T Consensus 500 e~k~~wD~~lGVt~ 513 (894)
T KOG0132|consen 500 EYKDYWDVELGVTY 513 (894)
T ss_pred hhhhhhhcccCeeE
Confidence 57889999888766
No 12
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=95.66 E-value=0.13 Score=53.78 Aligned_cols=14 Identities=21% Similarity=0.344 Sum_probs=6.3
Q ss_pred cCCCceEEEEEeec
Q 019781 198 DPDSKMFTLQLYFK 211 (336)
Q Consensus 198 D~d~K~f~lQf~Fk 211 (336)
|.||+.|..-|.=|
T Consensus 285 ~~~t~~fi~~fi~k 298 (569)
T KOG3671|consen 285 ERDTMKFIYDFIQK 298 (569)
T ss_pred chhhccccccchhc
Confidence 34455554444433
No 13
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=95.43 E-value=0.0076 Score=42.13 Aligned_cols=34 Identities=21% Similarity=0.467 Sum_probs=19.9
Q ss_pred CceeeeccccccCCcc--ccccccchhhHHHHHHHH
Q 019781 50 GSYECKLCLTLHNNEG--NYLAHTQGKRHQTNLAKR 83 (336)
Q Consensus 50 G~yeC~LClt~h~~e~--syl~H~qGkkHq~nL~rR 83 (336)
-+|-|+.|.++.++.. +-..|..|.||+.|+++.
T Consensus 2 ~ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~ 37 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY 37 (38)
T ss_dssp -S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred cCeecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence 3689999999995554 448999999999999864
No 14
>KOG2370 consensus Cactin [Signal transduction mechanisms]
Probab=95.35 E-value=0.011 Score=61.38 Aligned_cols=75 Identities=28% Similarity=0.410 Sum_probs=54.7
Q ss_pred ccceEEEEecccccc-cCCcccccccchhhccccccccccee---eeeecccccccccccCcccccCC--CcccccccCC
Q 019781 127 QRSLLFQIEYPEIED-LSKPRHRFMSSFEQRVQPFDKRYQYL---MFAAEPYEIIAFKVPSTEIDKST--PKFFSHWDPD 200 (336)
Q Consensus 127 q~gllfqIdyp~i~d-~~~P~~RiMSa~EqKvEeldkk~qyL---liA~EPyEtIa~kIPn~eId~~~--~~~~~~WD~d 200 (336)
.+|.-|.|-|+.|++ +..|.|+|-++ ..+.+++ +.|..|||.|||+|=|+|-+.+- |..|+| +
T Consensus 538 VQGYkFNIFYPDLidk~~aP~y~ie~~--------~d~~d~ciIRF~aGpPYeDIAFkIVnkeWeyshKrGfKcqF---~ 606 (623)
T KOG2370|consen 538 VQGYKFNIFYPDLIDKGRAPTYRIERC--------RDKNDFCIIRFHAGPPYEDIAFKIVNKEWEYSHKRGFKCQF---D 606 (623)
T ss_pred hcceeecccchhhhccccCCeeeeeec--------CCCCceEEEEeccCCcchhhhhhhhcchhhhhhhcCcccee---e
Confidence 478999999999864 47899997322 2222333 45788999999999999987753 333443 5
Q ss_pred CceEEEEEeecc
Q 019781 201 SKMFTLQLYFKS 212 (336)
Q Consensus 201 ~K~f~lQf~Fk~ 212 (336)
+.+|.|-|.||.
T Consensus 607 ngvlqL~F~FKk 618 (623)
T KOG2370|consen 607 NGVLQLWFRFKK 618 (623)
T ss_pred CCeeeeeehhhh
Confidence 688999999985
No 15
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=92.30 E-value=0.067 Score=52.97 Aligned_cols=36 Identities=31% Similarity=0.491 Sum_probs=32.4
Q ss_pred CCceeeeccccccCCc-cccccccchhhHHHHHHHHH
Q 019781 49 LGSYECKLCLTLHNNE-GNYLAHTQGKRHQTNLAKRA 84 (336)
Q Consensus 49 ~G~yeC~LClt~h~~e-~syl~H~qGkkHq~nL~rR~ 84 (336)
.|.+-|+.|-++..+. -|...|-+||+|+.||++|.
T Consensus 8 ~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~Kri 44 (336)
T KOG0150|consen 8 QPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAKRI 44 (336)
T ss_pred ccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHHHH
Confidence 4889999999988766 89999999999999999885
No 16
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.17 E-value=0.14 Score=49.10 Aligned_cols=48 Identities=21% Similarity=0.378 Sum_probs=38.5
Q ss_pred hhcCCCCC-cceeeccCCceeeeccccccCCccccccccchhhHHHHHHH
Q 019781 34 ETIDLAKD-PYFMRNHLGSYECKLCLTLHNNEGNYLAHTQGKRHQTNLAK 82 (336)
Q Consensus 34 e~id~~~d-Py~~rNh~G~yeC~LClt~h~~e~syl~H~qGkkHq~nL~r 82 (336)
.+-+...| |+..-|.+|.+.|.+|++-.. +.-...|..||||..++..
T Consensus 17 kk~~~ri~splakyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~ 65 (264)
T KOG3032|consen 17 KKKDTRIDSPLAKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDS 65 (264)
T ss_pred cCcccccccHhhccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHH
Confidence 34444333 455668899999999999888 9999999999999998874
No 17
>PLN02748 tRNA dimethylallyltransferase
Probab=91.33 E-value=0.093 Score=54.47 Aligned_cols=39 Identities=18% Similarity=0.475 Sum_probs=32.8
Q ss_pred CCceeeecccc-ccCCccccccccchhhHHHHHHHHHHHH
Q 019781 49 LGSYECKLCLT-LHNNEGNYLAHTQGKRHQTNLAKRAARE 87 (336)
Q Consensus 49 ~G~yeC~LClt-~h~~e~syl~H~qGkkHq~nL~rR~a~~ 87 (336)
.-.|+|.+|.. ..+.+-....|++|++|..++++...+.
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~~ 455 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQKQ 455 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhhh
Confidence 34589999998 7999999999999999999998654433
No 18
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=91.15 E-value=0.076 Score=48.26 Aligned_cols=31 Identities=26% Similarity=0.576 Sum_probs=27.0
Q ss_pred ceeeeccccccCCc--cccccccchhhHHHHHH
Q 019781 51 SYECKLCLTLHNNE--GNYLAHTQGKRHQTNLA 81 (336)
Q Consensus 51 ~yeC~LClt~h~~e--~syl~H~qGkkHq~nL~ 81 (336)
+|.|..|+|+++++ ++=..|..|+||..|.+
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk 35 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVK 35 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHH
Confidence 69999999877766 67788999999999987
No 19
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=90.47 E-value=0.19 Score=52.08 Aligned_cols=33 Identities=30% Similarity=0.593 Sum_probs=29.6
Q ss_pred eeeeccccccCCccccccccchhhHHHHHHHHH
Q 019781 52 YECKLCLTLHNNEGNYLAHTQGKRHQTNLAKRA 84 (336)
Q Consensus 52 yeC~LClt~h~~e~syl~H~qGkkHq~nL~rR~ 84 (336)
-.|.||+++-.++.-+.+|..|+|||..|..-.
T Consensus 494 kqcslcnvlissevylfshvkgrkhqqal~e~~ 526 (672)
T KOG4722|consen 494 KQCSLCNVLISSEVYLFSHVKGRKHQQALNELL 526 (672)
T ss_pred hccchhhhhhhhhhhhhhhhcchhHHHHHHHHh
Confidence 379999999999999999999999999887543
No 20
>KOG4672 consensus Uncharacterized conserved low complexity protein [Function unknown]
Probab=90.32 E-value=2.3 Score=43.95 Aligned_cols=23 Identities=17% Similarity=-0.087 Sum_probs=10.8
Q ss_pred hhhhcCCCCCc----ceeeccCCceee
Q 019781 32 ALETIDLAKDP----YFMRNHLGSYEC 54 (336)
Q Consensus 32 ~~e~id~~~dP----y~~rNh~G~yeC 54 (336)
.++.+-..||| |-|+.|.+.-.|
T Consensus 39 VR~a~lk~KDp~qi~~~m~kldem~~~ 65 (487)
T KOG4672|consen 39 VRAAVLKYKDPDQITSKMEKLDEMEYN 65 (487)
T ss_pred HHHhhhccCCHHHHHHHHHhhcccccC
Confidence 33444445666 445554443333
No 21
>PHA03247 large tegument protein UL36; Provisional
Probab=90.18 E-value=4.2 Score=50.15 Aligned_cols=30 Identities=27% Similarity=0.284 Sum_probs=16.5
Q ss_pred CCCCcceeeccCCceee-eccccccCCccccc
Q 019781 38 LAKDPYFMRNHLGSYEC-KLCLTLHNNEGNYL 68 (336)
Q Consensus 38 ~~~dPy~~rNh~G~yeC-~LClt~h~~e~syl 68 (336)
.+.+.-|.+| +|.--| +||+..+.+.+.++
T Consensus 2317 ~E~~~~fS~~-SgL~Lc~~LFDSR~g~~d~~l 2347 (3151)
T PHA03247 2317 LRSDPAFSRG-SELELCVTLFDSRARGADAAL 2347 (3151)
T ss_pred ecCccccCCC-CcceehhhhhcCCCCCcccch
Confidence 3555556555 465445 56666666655544
No 22
>PHA03247 large tegument protein UL36; Provisional
Probab=89.53 E-value=5.9 Score=49.00 Aligned_cols=12 Identities=50% Similarity=0.996 Sum_probs=7.1
Q ss_pred CCCcceeeccCC
Q 019781 39 AKDPYFMRNHLG 50 (336)
Q Consensus 39 ~~dPy~~rNh~G 50 (336)
..||+|.|+=+|
T Consensus 2450 ~~dp~~~~~i~g 2461 (3151)
T PHA03247 2450 DGDPFFARTILG 2461 (3151)
T ss_pred CCCCchhheecC
Confidence 356666666555
No 23
>KOG1830 consensus Wiskott Aldrich syndrome proteins [Cytoskeleton]
Probab=89.02 E-value=4.2 Score=42.33 Aligned_cols=10 Identities=20% Similarity=-0.034 Sum_probs=5.3
Q ss_pred eEEEEEeecc
Q 019781 203 MFTLQLYFKS 212 (336)
Q Consensus 203 ~f~lQf~Fk~ 212 (336)
.+.|++-|+.
T Consensus 246 ~~~lp~~~~n 255 (518)
T KOG1830|consen 246 YSSLPPNPKN 255 (518)
T ss_pred hhccCCCccc
Confidence 3445665554
No 24
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=85.66 E-value=4.5 Score=44.66 Aligned_cols=25 Identities=20% Similarity=0.222 Sum_probs=17.8
Q ss_pred ccccCCccccccccchhhHHHHHHH
Q 019781 58 LTLHNNEGNYLAHTQGKRHQTNLAK 82 (336)
Q Consensus 58 lt~h~~e~syl~H~qGkkHq~nL~r 82 (336)
+.+|....+|..|.|.+--+.-|.+
T Consensus 100 ifv~v~d~n~rvhlQye~t~lgld~ 124 (830)
T KOG1923|consen 100 VFVGVPDENFRVHLQYEATHLGLDK 124 (830)
T ss_pred HHhcchhhhhHHHhhhHHHHHhhhh
Confidence 4455577999999999766555553
No 25
>PF05477 SURF2: Surfeit locus protein 2 (SURF2); InterPro: IPR008833 Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown [].
Probab=83.31 E-value=1.1 Score=43.26 Aligned_cols=65 Identities=25% Similarity=0.303 Sum_probs=47.1
Q ss_pred HHHHHHHHHh--hhhcCC-CCCcceee--ccCCceeeeccccccCCc-cccccccchhhHHHHHHHHHHHH
Q 019781 23 DRRERLRRLA--LETIDL-AKDPYFMR--NHLGSYECKLCLTLHNNE-GNYLAHTQGKRHQTNLAKRAARE 87 (336)
Q Consensus 23 ~rrerl~~L~--~e~id~-~~dPy~~r--Nh~G~yeC~LClt~h~~e-~syl~H~qGkkHq~nL~rR~a~~ 87 (336)
-|-++.++|+ ...+|+ .=.|||.- ++-..|-|+|=++..|.. ..+++|++|||.|..|.+-....
T Consensus 46 ~~gKKy~~l~~~~~~~d~~~yeP~ivps~~~~~~LfCkLT~~~iNk~pe~V~rHv~GKRf~kaLek~ee~~ 116 (244)
T PF05477_consen 46 IRGKKYQRLIRAKPEFDFSKYEPHIVPSTKNPHKLFCKLTGRHINKSPEHVERHVNGKRFQKALEKYEECQ 116 (244)
T ss_pred hccHHHHHHHhcccCCChHhcCCccccccCCCceeEEechHhHhccCHHHHHHHhhhHHHHHHHHHHHHHH
Confidence 3445566663 334665 45777663 456679999988888766 89999999999999999665433
No 26
>KOG1830 consensus Wiskott Aldrich syndrome proteins [Cytoskeleton]
Probab=80.57 E-value=32 Score=36.16 Aligned_cols=12 Identities=8% Similarity=0.132 Sum_probs=5.6
Q ss_pred cccccccchhhH
Q 019781 65 GNYLAHTQGKRH 76 (336)
Q Consensus 65 ~syl~H~qGkkH 76 (336)
=||.=-+|-+|-
T Consensus 154 PsyFFDLWKekm 165 (518)
T KOG1830|consen 154 PSYFFDLWKEKM 165 (518)
T ss_pred cHHHHHHHHHHH
Confidence 345445554443
No 27
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=75.56 E-value=49 Score=37.08 Aligned_cols=16 Identities=13% Similarity=-0.168 Sum_probs=10.1
Q ss_pred cccCCCceEEEEEeec
Q 019781 196 HWDPDSKMFTLQLYFK 211 (336)
Q Consensus 196 ~WD~d~K~f~lQf~Fk 211 (336)
-||.+|..-..-.+++
T Consensus 531 m~d~~t~~p~~kgi~~ 546 (894)
T KOG0132|consen 531 MLDGTTGPPEWKGIAK 546 (894)
T ss_pred eecCccCCcccccccc
Confidence 3887777665555555
No 28
>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=71.41 E-value=1.1 Score=27.90 Aligned_cols=21 Identities=19% Similarity=0.449 Sum_probs=19.7
Q ss_pred eeeeccccccCCccccccccc
Q 019781 52 YECKLCLTLHNNEGNYLAHTQ 72 (336)
Q Consensus 52 yeC~LClt~h~~e~syl~H~q 72 (336)
|+|..|...-.++..|+.|++
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHC
T ss_pred CCCCccCCccCChhHHHHHhH
Confidence 799999999999999999984
No 29
>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=70.85 E-value=1 Score=26.92 Aligned_cols=21 Identities=24% Similarity=0.621 Sum_probs=19.3
Q ss_pred eeeeccccccCCccccccccc
Q 019781 52 YECKLCLTLHNNEGNYLAHTQ 72 (336)
Q Consensus 52 yeC~LClt~h~~e~syl~H~q 72 (336)
|+|..|...-.+..+|.+|+.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 799999999999999999975
No 30
>smart00355 ZnF_C2H2 zinc finger.
Probab=65.87 E-value=1.3 Score=25.95 Aligned_cols=21 Identities=19% Similarity=0.524 Sum_probs=18.8
Q ss_pred eeeeccccccCCccccccccc
Q 019781 52 YECKLCLTLHNNEGNYLAHTQ 72 (336)
Q Consensus 52 yeC~LClt~h~~e~syl~H~q 72 (336)
|+|.+|...-.+..++..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 689999999999999998876
No 31
>PTZ00448 hypothetical protein; Provisional
Probab=65.33 E-value=2.8 Score=42.64 Aligned_cols=36 Identities=17% Similarity=0.283 Sum_probs=33.1
Q ss_pred CceeeeccccccCCccccccccchhhHHHHHHHHHH
Q 019781 50 GSYECKLCLTLHNNEGNYLAHTQGKRHQTNLAKRAA 85 (336)
Q Consensus 50 G~yeC~LClt~h~~e~syl~H~qGkkHq~nL~rR~a 85 (336)
+.|.|..|.+.-.+...+-.|..--=|..||+||.+
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl~ 348 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNAR 348 (373)
T ss_pred CCccccccccccCCHHHHHHHhhhhHHHHHHHHHhc
Confidence 568999999999889999999999999999999875
No 32
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=64.07 E-value=2.9 Score=46.59 Aligned_cols=31 Identities=32% Similarity=0.663 Sum_probs=28.8
Q ss_pred eeeccCCc--eeeeccccccCCccccccccchh
Q 019781 44 FMRNHLGS--YECKLCLTLHNNEGNYLAHTQGK 74 (336)
Q Consensus 44 ~~rNh~G~--yeC~LClt~h~~e~syl~H~qGk 74 (336)
-||.|.|- |.||+|.-.-++.||+.+|+.+-
T Consensus 624 HyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vH 656 (958)
T KOG1074|consen 624 HYRTHTGERPFKCKICGRAFTTKGNLKAHMSVH 656 (958)
T ss_pred hhhcccCcCccccccccchhccccchhhccccc
Confidence 68899997 99999999999999999999993
No 33
>PF08799 PRP4: pre-mRNA processing factor 4 (PRP4) like; InterPro: IPR014906 This small protein is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing. ; PDB: 1MZW_B 2DK4_A.
Probab=61.24 E-value=6.5 Score=26.48 Aligned_cols=15 Identities=60% Similarity=0.804 Sum_probs=11.5
Q ss_pred hhhhHHHHHHHHHHH
Q 019781 17 AQNEAIDRRERLRRL 31 (336)
Q Consensus 17 ~~~~n~~rrerl~~L 31 (336)
..|.+.+||+||++|
T Consensus 15 FGE~~~~R~~RLr~l 29 (30)
T PF08799_consen 15 FGETDADRRERLRRL 29 (30)
T ss_dssp TT--HHHHHHHHHHH
T ss_pred hCCChHHHHHHHHHh
Confidence 457899999999998
No 34
>smart00500 SFM Splicing Factor Motif, present in Prp18 and Pr04.
Probab=60.16 E-value=7.1 Score=28.39 Aligned_cols=24 Identities=29% Similarity=0.444 Sum_probs=18.2
Q ss_pred cchhhhHHHHHHHHHHHhhhhcCC
Q 019781 15 ASAQNEAIDRRERLRRLALETIDL 38 (336)
Q Consensus 15 As~~~~n~~rrerl~~L~~e~id~ 38 (336)
.-..|.+.+||+||++|..+.-++
T Consensus 18 ~lFGE~~~~Rr~RL~~ll~~~~e~ 41 (44)
T smart00500 18 TLFGEDDQERRQRLRQLLIVQDEL 41 (44)
T ss_pred eecCCChHHHHHHHHHHHHccccc
Confidence 345678899999999998765443
No 35
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=59.52 E-value=3.4 Score=39.49 Aligned_cols=48 Identities=33% Similarity=0.600 Sum_probs=34.9
Q ss_pred hcCCCCCcceeeccCCc--eeeeccccccCCcccccccc---chhhHHHHHHHHHH
Q 019781 35 TIDLAKDPYFMRNHLGS--YECKLCLTLHNNEGNYLAHT---QGKRHQTNLAKRAA 85 (336)
Q Consensus 35 ~id~~~dPy~~rNh~G~--yeC~LClt~h~~e~syl~H~---qGkkHq~nL~rR~a 85 (336)
|+||.. -+|.|.|- |.|.+|...-+---|+.+|+ -|-.||...+.|.+
T Consensus 158 tfdlkr---h~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~ 210 (267)
T KOG3576|consen 158 TFDLKR---HTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRA 210 (267)
T ss_pred hhhhhh---hhccccCccccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhh
Confidence 677753 37888886 99999997777666777665 46777777776544
No 36
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=59.06 E-value=2 Score=39.44 Aligned_cols=32 Identities=19% Similarity=0.362 Sum_probs=27.1
Q ss_pred CceeeeccccccCCc--cccccccchhhHHHHHH
Q 019781 50 GSYECKLCLTLHNNE--GNYLAHTQGKRHQTNLA 81 (336)
Q Consensus 50 G~yeC~LClt~h~~e--~syl~H~qGkkHq~nL~ 81 (336)
-+|-|..|..++++. +.-.+|..|++|..+.+
T Consensus 2 pRY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~ 35 (188)
T COG5136 2 PRYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRK 35 (188)
T ss_pred cchHHHHHHHHHhccHHHHHHHhhhhHHHHHHHH
Confidence 368999999888877 66778999999988776
No 37
>KOG4672 consensus Uncharacterized conserved low complexity protein [Function unknown]
Probab=57.99 E-value=49 Score=34.66 Aligned_cols=14 Identities=14% Similarity=0.200 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHhh
Q 019781 76 HQTNLAKRAAREAK 89 (336)
Q Consensus 76 Hq~nL~rR~a~~~k 89 (336)
|-..|.||....++
T Consensus 104 ~~~~L~r~eveye~ 117 (487)
T KOG4672|consen 104 MFSHLQRREVEYED 117 (487)
T ss_pred HHHHHHHHhhhhhh
Confidence 34445555544433
No 38
>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=57.30 E-value=2.7 Score=24.46 Aligned_cols=21 Identities=14% Similarity=0.536 Sum_probs=16.0
Q ss_pred eeeeccccccCCccccccccc
Q 019781 52 YECKLCLTLHNNEGNYLAHTQ 72 (336)
Q Consensus 52 yeC~LClt~h~~e~syl~H~q 72 (336)
|.|.+|...-.+...+..|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 789999999888888888764
No 39
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=55.60 E-value=66 Score=36.04 Aligned_cols=12 Identities=25% Similarity=0.257 Sum_probs=5.8
Q ss_pred CCceEEEEEeec
Q 019781 200 DSKMFTLQLYFK 211 (336)
Q Consensus 200 d~K~f~lQf~Fk 211 (336)
++|.=-+|..=+
T Consensus 241 ~~ki~emq~~ss 252 (830)
T KOG1923|consen 241 ETKIGEMQLASS 252 (830)
T ss_pred cCCccccccccc
Confidence 445555555443
No 40
>PHA03378 EBNA-3B; Provisional
Probab=55.53 E-value=2.1e+02 Score=32.16 Aligned_cols=9 Identities=33% Similarity=0.231 Sum_probs=4.5
Q ss_pred CCceeEEEe
Q 019781 112 RPGYRVTKQ 120 (336)
Q Consensus 112 rPgykVtk~ 120 (336)
.|.-+||-|
T Consensus 481 l~~~~~~~v 489 (991)
T PHA03378 481 LPHPQVTPV 489 (991)
T ss_pred CCCcceeee
Confidence 345555544
No 41
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=52.99 E-value=1.5e+02 Score=29.39 Aligned_cols=7 Identities=29% Similarity=1.464 Sum_probs=3.8
Q ss_pred eeeeccc
Q 019781 52 YECKLCL 58 (336)
Q Consensus 52 yeC~LCl 58 (336)
|.|-+|.
T Consensus 35 fkchich 41 (341)
T KOG2893|consen 35 FKCHICH 41 (341)
T ss_pred ceeeeeh
Confidence 5555554
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=52.17 E-value=3.2 Score=25.23 Aligned_cols=21 Identities=24% Similarity=0.507 Sum_probs=15.4
Q ss_pred eeeeccccccCCccccccccch
Q 019781 52 YECKLCLTLHNNEGNYLAHTQG 73 (336)
Q Consensus 52 yeC~LClt~h~~e~syl~H~qG 73 (336)
|.|.+|...-+ +..+..|++-
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~ 21 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKR 21 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHh
Confidence 78999997776 8888888764
No 43
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=51.39 E-value=3.7 Score=31.69 Aligned_cols=31 Identities=19% Similarity=0.450 Sum_probs=25.7
Q ss_pred ceeeeccccccCCccccccccchhhHHHHHH
Q 019781 51 SYECKLCLTLHNNEGNYLAHTQGKRHQTNLA 81 (336)
Q Consensus 51 ~yeC~LClt~h~~e~syl~H~qGkkHq~nL~ 81 (336)
.+.|.+|...-.+...+..|+..+.|+....
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 5999999999999999999999998877543
No 44
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=48.48 E-value=6.9 Score=34.43 Aligned_cols=34 Identities=18% Similarity=0.304 Sum_probs=30.2
Q ss_pred cCCceeeeccccccCCccccccccchhhHHHHHH
Q 019781 48 HLGSYECKLCLTLHNNEGNYLAHTQGKRHQTNLA 81 (336)
Q Consensus 48 h~G~yeC~LClt~h~~e~syl~H~qGkkHq~nL~ 81 (336)
-+|.+.|-+|--.-.++..+..|..+|.|...|+
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK 87 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTKVHKRRVK 87 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhccHHHHHHH
Confidence 3688999999999999999999999999976665
No 45
>PF11281 DUF3083: Protein of unknown function (DUF3083); InterPro: IPR021433 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=47.77 E-value=18 Score=36.07 Aligned_cols=28 Identities=25% Similarity=0.593 Sum_probs=23.3
Q ss_pred ccCCCcccccccCCCceEEEEEeeccCC
Q 019781 187 DKSTPKFFSHWDPDSKMFTLQLYFKSKP 214 (336)
Q Consensus 187 d~~~~~~~~~WD~d~K~f~lQf~Fk~~~ 214 (336)
+.++..+.+|||.|.-+=+|+|.|....
T Consensus 243 ~~~~~q~~~~w~~~kLVet~~fvi~A~~ 270 (316)
T PF11281_consen 243 NAEEPQFICHWDADKLVETVHFVIVAGK 270 (316)
T ss_pred ccCCcceeeeeccceeeeeEEEEEEecC
Confidence 4455689999999999999999998643
No 46
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=46.72 E-value=14 Score=38.94 Aligned_cols=32 Identities=25% Similarity=0.471 Sum_probs=30.5
Q ss_pred eeeeccccccCCccccccccchhhHHHHHHHH
Q 019781 52 YECKLCLTLHNNEGNYLAHTQGKRHQTNLAKR 83 (336)
Q Consensus 52 yeC~LClt~h~~e~syl~H~qGkkHq~nL~rR 83 (336)
|+|-.|+-.--++-....|.+-|||..||++-
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eL 324 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAEL 324 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHH
Confidence 99999999999999999999999999999963
No 47
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=44.71 E-value=1.4e+02 Score=31.00 Aligned_cols=12 Identities=42% Similarity=0.639 Sum_probs=4.9
Q ss_pred hhhccccccccc
Q 019781 153 FEQRVQPFDKRY 164 (336)
Q Consensus 153 ~EqKvEeldkk~ 164 (336)
||-+..--+|.|
T Consensus 115 FENR~NGQSKG~ 126 (498)
T KOG4849|consen 115 FENRTNGQSKGY 126 (498)
T ss_pred hhcccCCcccce
Confidence 444443333333
No 48
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=41.57 E-value=8.7 Score=29.61 Aligned_cols=30 Identities=20% Similarity=0.525 Sum_probs=0.0
Q ss_pred eeeccccccCCccccccccchhhHHHHHHHH
Q 019781 53 ECKLCLTLHNNEGNYLAHTQGKRHQTNLAKR 83 (336)
Q Consensus 53 eC~LClt~h~~e~syl~H~qGkkHq~nL~rR 83 (336)
+|.+|...-.+...++.|+. ++|..++..+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~-~~H~~~~~~~ 30 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMK-KKHGFDIPDQ 30 (100)
T ss_dssp -------------------------------
T ss_pred Cccccccccccccccccccc-cccccccccc
Confidence 69999999999999999996 6798887743
No 49
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=39.22 E-value=15 Score=34.84 Aligned_cols=35 Identities=20% Similarity=0.365 Sum_probs=25.5
Q ss_pred ccCCceeeeccccccCCccccccccchhhHHHHHHH
Q 019781 47 NHLGSYECKLCLTLHNNEGNYLAHTQGKRHQTNLAK 82 (336)
Q Consensus 47 Nh~G~yeC~LClt~h~~e~syl~H~qGkkHq~nL~r 82 (336)
..-.+|-|.||..+-.-..=+..|+.-| |...|..
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nK-H~e~ve~ 107 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNK-HPEKVEE 107 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH--HHHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhc-CHHHHHH
Confidence 3556899999998888888888899864 9888873
No 50
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=38.85 E-value=14 Score=41.18 Aligned_cols=32 Identities=31% Similarity=0.643 Sum_probs=27.4
Q ss_pred eccCCc--eeeeccccccCCccccccccchhhHH
Q 019781 46 RNHLGS--YECKLCLTLHNNEGNYLAHTQGKRHQ 77 (336)
Q Consensus 46 rNh~G~--yeC~LClt~h~~e~syl~H~qGkkHq 77 (336)
|-|.|- |||.-|...-.+-|||-+|+.-||-=
T Consensus 302 RIHSGEKPfeCpnCkKRFSHSGSySSHmSSKKCI 335 (1007)
T KOG3623|consen 302 RIHSGEKPFECPNCKKRFSHSGSYSSHMSSKKCI 335 (1007)
T ss_pred eeecCCCCcCCcccccccccCCcccccccccchh
Confidence 445554 99999999999999999999999754
No 51
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=37.92 E-value=7.7 Score=39.80 Aligned_cols=30 Identities=20% Similarity=0.494 Sum_probs=26.9
Q ss_pred eeccCCceeeeccccccCCccccccccchh
Q 019781 45 MRNHLGSYECKLCLTLHNNEGNYLAHTQGK 74 (336)
Q Consensus 45 ~rNh~G~yeC~LClt~h~~e~syl~H~qGk 74 (336)
++||+..|.|.||......-+|+..|+.-|
T Consensus 257 v~rHvn~ykCplCdmtc~~~ssL~~H~r~r 286 (467)
T KOG3608|consen 257 VVRHVNCYKCPLCDMTCSSASSLTTHIRYR 286 (467)
T ss_pred HHHhhhcccccccccCCCChHHHHHHHHhh
Confidence 578999999999999999999999998765
No 52
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=37.01 E-value=13 Score=25.71 Aligned_cols=23 Identities=22% Similarity=0.338 Sum_probs=12.9
Q ss_pred CCceeeeccccccCCc----ccccccc
Q 019781 49 LGSYECKLCLTLHNNE----GNYLAHT 71 (336)
Q Consensus 49 ~G~yeC~LClt~h~~e----~syl~H~ 71 (336)
.....|++|....... +++.+|+
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 5678999999665543 4455555
No 53
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=35.82 E-value=12 Score=23.58 Aligned_cols=14 Identities=43% Similarity=1.042 Sum_probs=9.7
Q ss_pred eccCCc--eeeecccc
Q 019781 46 RNHLGS--YECKLCLT 59 (336)
Q Consensus 46 rNh~G~--yeC~LClt 59 (336)
|.|.|. |.|.+|.-
T Consensus 7 ~~H~~~k~~~C~~C~k 22 (26)
T PF13465_consen 7 RTHTGEKPYKCPYCGK 22 (26)
T ss_dssp HHHSSSSSEEESSSSE
T ss_pred hhcCCCCCCCCCCCcC
Confidence 345554 99999973
No 54
>COG2871 NqrF Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF [Energy production and conversion]
Probab=33.30 E-value=44 Score=33.84 Aligned_cols=30 Identities=27% Similarity=0.739 Sum_probs=19.7
Q ss_pred cccceeeeeeccccc--ccccccCcccccCCCcccccccC
Q 019781 162 KRYQYLMFAAEPYEI--IAFKVPSTEIDKSTPKFFSHWDP 199 (336)
Q Consensus 162 kk~qyLliA~EPyEt--Ia~kIPn~eId~~~~~~~~~WD~ 199 (336)
+.+.|+.|.+.+|.+ .+|+|+ ..|+.+||.
T Consensus 165 raGGyiQie~pph~v~y~Dfdi~--------~eY~~DWdk 196 (410)
T COG2871 165 RAGGYIQIEAPPHTVNYKDFDIP--------PEYHEDWDK 196 (410)
T ss_pred CCCceEEEecCCccccccccCCC--------hhHhcchhh
Confidence 346689999988843 345543 357777875
No 55
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=33.16 E-value=5.9e+02 Score=26.64 Aligned_cols=11 Identities=9% Similarity=0.178 Sum_probs=5.0
Q ss_pred cccCCcccccc
Q 019781 59 TLHNNEGNYLA 69 (336)
Q Consensus 59 t~h~~e~syl~ 69 (336)
||.++...++.
T Consensus 89 ~W~TTD~DL~~ 99 (498)
T KOG4849|consen 89 LWYTTDADLLK 99 (498)
T ss_pred eEEeccHHHHH
Confidence 44444444443
No 56
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=32.18 E-value=33 Score=28.21 Aligned_cols=39 Identities=15% Similarity=0.244 Sum_probs=28.8
Q ss_pred CCceeeeccccccCCccccccccchhhHHH-HHHHHHHHHh
Q 019781 49 LGSYECKLCLTLHNNEGNYLAHTQGKRHQT-NLAKRAAREA 88 (336)
Q Consensus 49 ~G~yeC~LClt~h~~e~syl~H~qGkkHq~-nL~rR~a~~~ 88 (336)
..-+.|..|.+.... +++.+|+..+-|.. ...++...++
T Consensus 9 ~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~ 48 (109)
T PF12013_consen 9 YRVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEA 48 (109)
T ss_pred CCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHH
Confidence 345899999987776 99999999987776 4445544443
No 57
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=31.46 E-value=15 Score=37.71 Aligned_cols=37 Identities=19% Similarity=0.257 Sum_probs=31.8
Q ss_pred cCCceeeeccccccCCccccccccchhhHHHHHHHHH
Q 019781 48 HLGSYECKLCLTLHNNEGNYLAHTQGKRHQTNLAKRA 84 (336)
Q Consensus 48 h~G~yeC~LClt~h~~e~syl~H~qGkkHq~nL~rR~ 84 (336)
..-.+.|-.|.-+-....-|.+|+.||.|.++..+|.
T Consensus 235 ~~~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~ 271 (470)
T COG5188 235 WFPKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKE 271 (470)
T ss_pred hccceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhh
Confidence 3446899999999999999999999999999877654
No 58
>PHA03233 DNA packaging protein UL32; Provisional
Probab=30.77 E-value=74 Score=34.07 Aligned_cols=47 Identities=23% Similarity=0.455 Sum_probs=33.9
Q ss_pred chhhhHHHHHHHHHHHhhh--hcCCCCCc--------ceeeccCCceeeeccccccCC
Q 019781 16 SAQNEAIDRRERLRRLALE--TIDLAKDP--------YFMRNHLGSYECKLCLTLHNN 63 (336)
Q Consensus 16 s~~~~n~~rrerl~~L~~e--~id~~~dP--------y~~rNh~G~yeC~LClt~h~~ 63 (336)
+..+..+..|.++.++..+ .+|.+--| ...||++++ ||-||..+.++
T Consensus 270 ~~t~~a~~~r~~~~~~~~~~~~~d~s~GP~lLsp~~~~~~Kn~T~s-vClLCelLa~~ 326 (518)
T PHA03233 270 PLTDLAIKKHHRLKALYSRKSEIEKSVGPIYLSPVPVFITKNQTTT-VCLLCELMACS 326 (518)
T ss_pred chhHHHHHHHhhHHhhccCCCCcccccCCeeeecccchhccCCCcc-chHhhHhhccC
Confidence 4555667788888888653 55655555 457999998 99999976554
No 59
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=30.38 E-value=50 Score=32.78 Aligned_cols=48 Identities=29% Similarity=0.466 Sum_probs=38.9
Q ss_pred hhHHHHHHHHHHHhhhhcCC------CCCcceeeccCCceeeeccccccCCccc
Q 019781 19 NEAIDRRERLRRLALETIDL------AKDPYFMRNHLGSYECKLCLTLHNNEGN 66 (336)
Q Consensus 19 ~~n~~rrerl~~L~~e~id~------~~dPy~~rNh~G~yeC~LClt~h~~e~s 66 (336)
..+.+-+.||++|+.+..+- +++|=.---.+|-|.|--|-.+|-+-|-
T Consensus 7 ~~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~ 60 (287)
T KOG0703|consen 7 GSNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGV 60 (287)
T ss_pred cccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccc
Confidence 34566688999999987652 6788777777999999999999998883
No 60
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=30.33 E-value=19 Score=31.27 Aligned_cols=38 Identities=34% Similarity=0.574 Sum_probs=30.8
Q ss_pred cCCceeeeccccccCCccccccccchhhHHHHHHHHHHHHhhc
Q 019781 48 HLGSYECKLCLTLHNNEGNYLAHTQGKRHQTNLAKRAAREAKD 90 (336)
Q Consensus 48 h~G~yeC~LClt~h~~e~syl~H~qGkkHq~nL~rR~a~~~k~ 90 (336)
-+|.+.|--|.-..-++--++.|..||-| ||.++|-++
T Consensus 52 GlGqhYCieCaryf~t~~aL~~HkkgkvH-----kRR~KelRe 89 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKKGKVH-----KRRAKELRE 89 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhccchh-----HHHHHHHhc
Confidence 57899999999999999999999999976 444544444
No 61
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=27.44 E-value=54 Score=38.77 Aligned_cols=28 Identities=46% Similarity=1.025 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 019781 244 GVSAGNAPRAPPPPMTGTLPPPPPPMANGP 273 (336)
Q Consensus 244 ~~~~g~p~~~~p~~~~~~~~~pppp~~~~p 273 (336)
.+++|.|||||||+ |--||.-||+|++|
T Consensus 3 ~lppg~pppppppp--g~epps~pppPppP 30 (2365)
T COG5178 3 SLPPGNPPPPPPPP--GFEPPSQPPPPPPP 30 (2365)
T ss_pred CCCCCCCcccccCC--CCCCCCCCCCccCC
No 62
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=27.44 E-value=51 Score=31.75 Aligned_cols=36 Identities=22% Similarity=0.338 Sum_probs=26.5
Q ss_pred CCceeeecccccc---CCccccccccchhhHHHHHHHHH
Q 019781 49 LGSYECKLCLTLH---NNEGNYLAHTQGKRHQTNLAKRA 84 (336)
Q Consensus 49 ~G~yeC~LClt~h---~~e~syl~H~qGkkHq~nL~rR~ 84 (336)
-..-+|.+|+.+. -++.-+..|..||-|.--+.=|.
T Consensus 188 qkl~VCeVCGA~Ls~~D~d~RladH~~GK~HlGy~~IR~ 226 (254)
T PF03194_consen 188 QKLEVCEVCGAFLSVGDNDRRLADHFGGKQHLGYAKIRE 226 (254)
T ss_pred cCccchhhhhhHHhccchHHHHHHHhccchhhhHHHHHH
Confidence 3446999998655 34567899999999986666554
No 63
>PF12940 RAG1: Recombination-activation protein 1 (RAG1); InterPro: IPR024627 This entry represents recombination activating protein 1 (RAG1), which is the catalytic component of the RAG complex. The RAG complex is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination []. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) []. Many of the proteins recognised by this entry are fragments.; GO: 0043565 sequence-specific DNA binding, 0033151 V(D)J recombination
Probab=25.57 E-value=33 Score=35.54 Aligned_cols=33 Identities=27% Similarity=0.582 Sum_probs=25.1
Q ss_pred ceeeeccccccCCc-cccccccchhhHHHHHHHH
Q 019781 51 SYECKLCLTLHNNE-GNYLAHTQGKRHQTNLAKR 83 (336)
Q Consensus 51 ~yeC~LClt~h~~e-~syl~H~qGkkHq~nL~rR 83 (336)
.|.|.||+..-..- .+...|.=-+.|..||.|=
T Consensus 216 tYiCTLCdstraeAsqnmvlhsItrsh~Enlery 249 (442)
T PF12940_consen 216 TYICTLCDSTRAEASQNMVLHSITRSHEENLERY 249 (442)
T ss_pred eEEEeeccCcchhhhhccccccccCCchhhhhhc
Confidence 39999998654433 5667788888899999864
No 64
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=24.62 E-value=29 Score=31.83 Aligned_cols=31 Identities=23% Similarity=0.397 Sum_probs=28.1
Q ss_pred eeeeccccccCCccccccccchhhHHHHHHH
Q 019781 52 YECKLCLTLHNNEGNYLAHTQGKRHQTNLAK 82 (336)
Q Consensus 52 yeC~LClt~h~~e~syl~H~qGkkHq~nL~r 82 (336)
|.|.+|...--++.-...|++.+-|+..|..
T Consensus 1 F~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~ 31 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLESKFHKETLKY 31 (165)
T ss_pred CccceeeeecccHHHHHHHHccchHHHHHHH
Confidence 5799999999999999999999999987764
No 65
>PF08864 UPF0302: UPF0302 domain; InterPro: IPR014963 These proteins are functionally uncharacterised. ; PDB: 3DO9_A.
Probab=24.16 E-value=68 Score=27.11 Aligned_cols=63 Identities=21% Similarity=0.088 Sum_probs=33.3
Q ss_pred ccCCcccccccchhhcccccccccceeeeeeccccccccc--ccCcccccCCCc---ccccccCCCceEEEEEeeccC
Q 019781 141 DLSKPRHRFMSSFEQRVQPFDKRYQYLMFAAEPYEIIAFK--VPSTEIDKSTPK---FFSHWDPDSKMFTLQLYFKSK 213 (336)
Q Consensus 141 d~~~P~~RiMSa~EqKvEeldkk~qyLliA~EPyEtIa~k--IPn~eId~~~~~---~~~~WD~d~K~f~lQf~Fk~~ 213 (336)
+.+..+..| ||+..+.-..|+|+....+..+|. ..+......+.. +-.+||.+ ++||+.|+..
T Consensus 31 ~~lL~~vhF-------Ve~~~~~~~~L~iS~~~~~~~pf~f~k~~~~~~d~~~~fhdir~n~~e~---~yI~l~F~~~ 98 (106)
T PF08864_consen 31 DHLLERVHF-------VENAIKYPRGLEISATCSDGEPFRFYKNNQMTTDVEQAFHDIRLNPDEP---IYIQLNFPGK 98 (106)
T ss_dssp TTTTTTEEE--------S-GGGSTTEEEEEBSSS-S-SEEEEESS-EE--HHHHHHHHHHHTSS----EEEEEE-SSS
T ss_pred HHHHhheEe-------ecccccCCCEEEEEeccCCCCcEEEEeCCcEEcCHHHHHHHHHcCCCCC---EEEEEECCCc
Confidence 345566666 445555566788888877766654 444432222222 22567754 9999999863
No 66
>PLN03131 hypothetical protein; Provisional
Probab=21.87 E-value=1.8e+02 Score=32.18 Aligned_cols=41 Identities=17% Similarity=0.344 Sum_probs=28.9
Q ss_pred HHHHHHHhhhhcC-----C-CCCc-ceeeccCCceeeeccccccCCccc
Q 019781 25 RERLRRLALETID-----L-AKDP-YFMRNHLGSYECKLCLTLHNNEGN 66 (336)
Q Consensus 25 rerl~~L~~e~id-----~-~~dP-y~~rNh~G~yeC~LClt~h~~e~s 66 (336)
++.|++|....-+ - .++| |..-| +|-|.|.-|--+|..-++
T Consensus 11 ekiLreLlk~PgNk~CADCga~~P~WASiN-lGIFICi~CSGIHRsLgh 58 (705)
T PLN03131 11 EKIIRGLMKLPPNRRCINCNSLGPQFVCTN-FWTFICMTCSGIHREFTH 58 (705)
T ss_pred HHHHHHHhhCcCCCccccCCCCCCCeeEec-cceEEchhchhhhcccCc
Confidence 5568888764332 2 4666 55544 799999999999988654
No 67
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=21.73 E-value=30 Score=34.34 Aligned_cols=31 Identities=26% Similarity=0.596 Sum_probs=29.2
Q ss_pred ceeeeccccccCCccccccccchhhHHHHHH
Q 019781 51 SYECKLCLTLHNNEGNYLAHTQGKRHQTNLA 81 (336)
Q Consensus 51 ~yeC~LClt~h~~e~syl~H~qGkkHq~nL~ 81 (336)
+|.|.+|--.++++.-|.+|+.-.-||.+|.
T Consensus 25 RwyCqmCQkQcrDeNGFkCH~~SeSHqRql~ 55 (309)
T KOG2837|consen 25 RWYCQMCQKQCRDENGFKCHTMSESHQRQLL 55 (309)
T ss_pred HHHHHHHHHHhccccccccccCCHHHHHHHH
Confidence 5799999999999999999999999999887
No 68
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=21.59 E-value=72 Score=31.09 Aligned_cols=25 Identities=24% Similarity=0.458 Sum_probs=22.6
Q ss_pred CCceeeeccccccCCccccccccch
Q 019781 49 LGSYECKLCLTLHNNEGNYLAHTQG 73 (336)
Q Consensus 49 ~G~yeC~LClt~h~~e~syl~H~qG 73 (336)
.+.|.|..|+....+++-++.|--|
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehCPG 261 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHCPG 261 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhCCC
Confidence 4779999999999999999999877
No 69
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.26 E-value=47 Score=30.47 Aligned_cols=16 Identities=31% Similarity=0.656 Sum_probs=12.0
Q ss_pred ceeeeccccccCCccc
Q 019781 51 SYECKLCLTLHNNEGN 66 (336)
Q Consensus 51 ~yeC~LClt~h~~e~s 66 (336)
.|.|++|+|.-+.-.|
T Consensus 79 ~yTCkvCntRs~ktis 94 (165)
T KOG3277|consen 79 AYTCKVCNTRSTKTIS 94 (165)
T ss_pred EEEeeccCCccccccC
Confidence 5999999987665444
No 70
>PF14968 CCDC84: Coiled coil protein 84
Probab=21.20 E-value=53 Score=33.23 Aligned_cols=25 Identities=28% Similarity=0.591 Sum_probs=0.0
Q ss_pred eeccccccCCccccccccchhhHHHHHH
Q 019781 54 CKLCLTLHNNEGNYLAHTQGKRHQTNLA 81 (336)
Q Consensus 54 C~LClt~h~~e~syl~H~qGkkHq~nL~ 81 (336)
|.+|...|.. ..+|.=+++||.+|.
T Consensus 2 C~vCr~~h~~---gr~H~Y~~~Hq~~L~ 26 (336)
T PF14968_consen 2 CEVCRRNHDQ---GRRHVYSPKHQKSLS 26 (336)
T ss_pred cchhhCcccc---cCCCccCHHHHHHHH
No 71
>PHA00626 hypothetical protein
Probab=20.86 E-value=49 Score=25.62 Aligned_cols=22 Identities=23% Similarity=0.311 Sum_probs=17.1
Q ss_pred ceeeccCCceeeeccccccCCc
Q 019781 43 YFMRNHLGSYECKLCLTLHNNE 64 (336)
Q Consensus 43 y~~rNh~G~yeC~LClt~h~~e 64 (336)
-+.|.|...|+|+.|+...+..
T Consensus 15 g~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 15 KTMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred ceecccCcceEcCCCCCeechh
Confidence 3567888999999999666554
No 72
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=20.45 E-value=22 Score=27.06 Aligned_cols=16 Identities=31% Similarity=0.704 Sum_probs=12.5
Q ss_pred CceeeeccccccCCcc
Q 019781 50 GSYECKLCLTLHNNEG 65 (336)
Q Consensus 50 G~yeC~LClt~h~~e~ 65 (336)
..|.|+||++.|...+
T Consensus 6 sry~CDLCn~~~p~~~ 21 (57)
T PF14445_consen 6 SRYSCDLCNSSHPISE 21 (57)
T ss_pred hhHhHHhhcccCcHHH
Confidence 5799999998776544
Done!