Query psy9880
Match_columns 280
No_of_seqs 108 out of 153
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 22:00:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9880.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9880hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0227|consensus 100.0 7E-105 2E-109 705.4 13.6 210 1-263 1-219 (222)
2 COG5246 PRP11 Splicing factor 100.0 9.1E-81 2E-85 549.7 12.6 213 1-261 1-221 (222)
3 PF09732 CactinC_cactus: Cactu 99.6 4.4E-15 9.5E-20 124.8 8.5 76 152-259 35-121 (125)
4 smart00451 ZnF_U1 U1-like zinc 98.0 1.3E-06 2.9E-11 56.3 -0.5 34 51-84 1-34 (35)
5 PF12874 zf-met: Zinc-finger o 97.4 1.9E-05 4.2E-10 47.8 -1.6 25 54-78 1-25 (25)
6 KOG2370|consensus 96.6 0.0017 3.6E-08 66.0 3.7 72 157-257 538-617 (623)
7 KOG0227|consensus 94.4 0.012 2.6E-07 54.0 0.3 26 175-200 147-184 (222)
8 KOG4727|consensus 93.6 0.025 5.3E-07 51.1 0.6 40 44-83 66-105 (193)
9 PF12171 zf-C2H2_jaz: Zinc-fin 93.5 0.011 2.4E-07 36.8 -1.3 27 53-79 1-27 (27)
10 PF06220 zf-U1: U1 zinc finger 90.1 0.083 1.8E-06 36.3 -0.1 33 53-85 3-37 (38)
11 KOG3032|consensus 89.0 0.15 3.3E-06 48.0 0.7 49 36-85 17-66 (264)
12 PLN02748 tRNA dimethylallyltra 85.9 0.26 5.6E-06 49.7 0.3 36 52-87 417-453 (468)
13 KOG0150|consensus 77.9 0.62 1.3E-05 45.5 -0.4 36 51-86 8-44 (336)
14 KOG3454|consensus 69.8 1.1 2.4E-05 40.1 -0.8 32 53-84 3-36 (165)
15 KOG4722|consensus 66.8 1.7 3.7E-05 44.6 -0.2 32 54-85 494-525 (672)
16 smart00500 SFM Splicing Factor 61.1 6.8 0.00015 28.0 2.0 25 17-41 18-42 (44)
17 COG5246 PRP11 Splicing factor 61.0 4.1 9E-05 37.6 1.1 36 175-210 153-202 (222)
18 PF08799 PRP4: pre-mRNA proces 58.7 8.4 0.00018 25.7 2.0 16 19-34 15-30 (30)
19 PF12756 zf-C2H2_2: C2H2 type 38.9 10 0.00022 28.1 0.0 31 55-86 1-31 (100)
20 smart00355 ZnF_C2H2 zinc finge 37.5 3.5 7.5E-05 23.3 -2.2 21 54-74 1-21 (26)
21 PF15470 DUF4637: Domain of un 36.5 10 0.00023 33.9 -0.3 19 53-72 139-157 (173)
22 PF13912 zf-C2H2_6: C2H2-type 36.5 4.9 0.00011 24.3 -1.7 20 54-73 2-21 (27)
23 PF12756 zf-C2H2_2: C2H2 type 34.6 5.9 0.00013 29.4 -1.9 35 48-82 44-79 (100)
24 PF05477 SURF2: Surfeit locus 33.7 19 0.00041 34.0 0.9 65 26-90 47-117 (244)
25 PF00096 zf-C2H2: Zinc finger, 33.4 5.5 0.00012 23.2 -1.8 21 54-74 1-21 (23)
26 PF12013 DUF3505: Protein of u 31.0 19 0.00041 28.7 0.4 40 50-90 8-48 (109)
27 PRK01175 phosphoribosylformylg 29.5 59 0.0013 30.4 3.4 34 45-78 121-167 (261)
28 PF13507 GATase_5: CobB/CobQ-l 28.0 43 0.00093 31.4 2.2 25 40-65 117-141 (259)
29 PHA00626 hypothetical protein 25.5 31 0.00066 26.4 0.6 21 46-66 16-36 (59)
30 PF11520 Cren7: Chromatin prot 25.5 55 0.0012 25.2 2.0 24 134-157 24-49 (60)
31 PF09034 TRADD_N: TRADD, N-ter 24.0 20 0.00044 30.4 -0.6 38 140-184 4-41 (111)
32 COG5136 U1 snRNP-specific prot 23.1 8.3 0.00018 35.0 -3.2 32 53-84 3-36 (188)
33 PRK07080 hypothetical protein; 22.5 80 0.0017 31.1 3.0 31 18-49 186-225 (317)
34 KOG3608|consensus 22.0 16 0.00035 36.9 -1.8 34 40-73 233-283 (467)
35 KOG1280|consensus 20.3 25 0.00055 35.2 -0.9 22 53-74 79-100 (381)
36 PF14445 Prok-RING_2: Prokaryo 20.2 21 0.00046 27.0 -1.1 14 52-65 6-19 (57)
No 1
>KOG0227|consensus
Probab=100.00 E-value=7.1e-105 Score=705.40 Aligned_cols=210 Identities=74% Similarity=1.154 Sum_probs=202.3
Q ss_pred CCCCCCCCCCCCCCcccChhhhhHHHHHHHHHHHhhhhCCCCCCceeccCCcceeeeeeeeeecCCCcceeecccchhhh
Q psy9880 1 MDYQNRPGGKTGGGGVASWSESNRDRRERLRQLALETIDLNKDPYFMKNHLGSYECKLCLTLHNNEGSYLAHTQGKKHQA 80 (280)
Q Consensus 1 MDyqnR~GsK~G~GGvAS~s~~n~~RReRlr~LaletiDl~kDPY~~KNHlG~~eCKLClT~H~ne~SYlaHtqGKKHq~ 80 (280)
||||||+|||+|||||||+||+|+|||||||+||+|||||.+||||||||+|+||||||||||+|||||++||||||||+
T Consensus 1 md~~~r~GsK~G~ggvAS~se~n~~RrerlrqLaletidl~kDPy~mkNh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~ 80 (222)
T KOG0227|consen 1 MDYQNRAGSKTGSGGVASESEFNRDRRERLRQLALETIDLNKDPYFMKNHLGKYECKLCLTLHNNEGSYLAHTQGKKHQT 80 (222)
T ss_pred CCcccccCccCCCCcccchhhhhHHHHHHHHHHHHhhcccccCchhhhccCcceeehhhhhhhcchhhhhhhhccchhhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHhccCCccchhhhhhcccccccccccchhcccCCCCCCCCCCCcCCccceeccCCceeEEEeeCCCCCceeE
Q psy9880 81 NLARRAAKEAKDAPQQSCDELLLTSDAVYTHKDSILISTLDWGPPAPEKPRVEPKKFVKIGRPGYRVTKQRDPSNGQQSL 160 (280)
Q Consensus 81 NL~RR~a~e~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~k~~~KiGrPgYkVtKvrDpet~q~gl 160 (280)
|||||+++|+++++.. +++++..+++|++||||||||||||+|||++||+||
T Consensus 81 Nlarraa~e~k~s~~~----------------------------~~~~k~~v~vk~~vkigrpgykvtk~r~~~~gq~~L 132 (222)
T KOG0227|consen 81 NLARRAAKEAKESPDL----------------------------PQPQKIIVEVKKFVKIGRPGYKVTKQRDPENGQQGL 132 (222)
T ss_pred HHHHHHHHHhhcCccc----------------------------cccccchhhhhhhhhcCCCcceeeeeecCccCceee
Confidence 9999999999997732 556677888999999999999999999999999999
Q ss_pred EEEEeCCCccccccccccchhhhhhhcccCCcCccCCCCCceeeeeccccccCCCCCCceEEEEEeCCCcccceeecCCc
Q psy9880 161 LFQVDYPEIADDVFPRHRFMSAYSLLFQVDYPEIADDVFPRHRFMSAYEQRIEPPDRKWQYLLFAAEPYETIAFKVSDRT 240 (280)
Q Consensus 161 lfqV~Ypei~~~~~p~~r~ms~y~l~~~~~~~e~~~~~~P~~RfmSa~Eq~vE~~d~~~QYLviAaEPYEtIafkIPn~e 240 (280)
+|||+||+|++ +.+|+|||||+|||.+|+||++|||||||||||||||||||++|
T Consensus 133 ~fQv~Yp~i~~-------------------------~~~Pr~rfmssyeq~ve~~dk~~qyLvfaaePyE~Iafk~p~~E 187 (222)
T KOG0227|consen 133 LFQVNYPEIEE-------------------------GIMPRHRFMSSYEQKVEPPDKSWQYLVFAAEPYENIAFKVPSRE 187 (222)
T ss_pred EEEecchhhhh-------------------------ccCCcchhhhhhHhhcCCccccceEEEEEeccccceeeecCchh
Confidence 99999999987 68999999999999999999999999999999999999999999
Q ss_pred c---------ceecCCCeEEEEEEEeecCCCc
Q psy9880 241 G---------LYERITSGLVLVDHVKLTCQNQ 263 (280)
Q Consensus 241 I---------~WD~dtK~f~lQ~~Fk~~~~~~ 263 (280)
| |||.+||+|+|||+|+.+.+.+
T Consensus 188 id~se~Kf~t~wd~~tk~y~lqF~fk~~~~~~ 219 (222)
T KOG0227|consen 188 IDKSEGKFWTHWDAETKQYTLQFFFKQAEPEQ 219 (222)
T ss_pred hhhccCceeeeecCCCceEEEEEEecccCccC
Confidence 9 9999999999999999888765
No 2
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=100.00 E-value=9.1e-81 Score=549.69 Aligned_cols=213 Identities=35% Similarity=0.561 Sum_probs=189.2
Q ss_pred CCCCCCCCCCCCCCcccChhhhhHHHHHHHHHHHhhhhCCCCCCceeccCCcceeeeeeeeeecCCCcceeecccchhhh
Q psy9880 1 MDYQNRPGGKTGGGGVASWSESNRDRRERLRQLALETIDLNKDPYFMKNHLGSYECKLCLTLHNNEGSYLAHTQGKKHQA 80 (280)
Q Consensus 1 MDyqnR~GsK~G~GGvAS~s~~n~~RReRlr~LaletiDl~kDPY~~KNHlG~~eCKLClT~H~ne~SYlaHtqGKKHq~ 80 (280)
|||++|+|||+|+||+||.++.|.+||+|++.|+++++||.+|||+||||+|+|||+||+|+|+||+||++|++||||++
T Consensus 1 Mny~~r~Gsk~Gggg~Ase~~~n~~rR~r~~~L~~~gqDl~dDPyl~knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~ 80 (222)
T COG5246 1 MNYGGRGGSKTGGGGTASEIKKNKKRRSRQLLLEAYGQDLMDDPYLSKNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKE 80 (222)
T ss_pred CCcccccccccCCCcchhHHHhhHHHHHHHHHHHhcCcccccCcchhhcCCCcEEeeeeccccccHHHHHHhhccchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHhccCCccchhhhhhcccccccccccchhcccCCCCCCCCCCCcC-CccceeccCCceeEEEeeCCCCCcee
Q psy9880 81 NLARRAAKEAKDAPQQSCDELLLTSDAVYTHKDSILISTLDWGPPAPEKPRVE-PKKFVKIGRPGYRVTKQRDPSNGQQS 159 (280)
Q Consensus 81 NL~RR~a~e~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~-~k~~~KiGrPgYkVtKvrDpet~q~g 159 (280)
|++||.+.+.+-+....+.-++.++| .-++ ++..+++|+|+|||.+++.|+.|..|
T Consensus 81 n~~rrs~eksslgrEnqtthdfrqqQ-----------------------kiieaKqSlk~~GiP~ykv~~~~epk~G~~G 137 (222)
T COG5246 81 NSSRRSEEKSSLGRENQTTHDFRQQQ-----------------------KIIEAKQSLKRSGIPSYKVRSLVEPKGGRRG 137 (222)
T ss_pred hHHHHHHHhhcccccCCchhhhhhHH-----------------------HHHHHHHHHHhcCCCceeEEEeecCCCCcee
Confidence 99999665544433221221222221 1223 44556999999999999999999999
Q ss_pred EEEEEeCCCccccccccccchhhhhhhcccCCcCccCCCCCceeeeeccccccCCCCCCceEEEEEeCCCcccceeecCC
Q psy9880 160 LLFQVDYPEIADDVFPRHRFMSAYSLLFQVDYPEIADDVFPRHRFMSAYEQRIEPPDRKWQYLLFAAEPYETIAFKVSDR 239 (280)
Q Consensus 160 llfqV~Ypei~~~~~p~~r~ms~y~l~~~~~~~e~~~~~~P~~RfmSa~Eq~vE~~d~~~QYLviAaEPYEtIafkIPn~ 239 (280)
|.|||+||++.. .++|++||||+|||++|.+|+++||||||||||||||||||+.
T Consensus 138 l~iqvnY~Dd~a-------------------------~~~P~yRivs~lEq~ve~~d~~f~yLV~a~ePyEnIafk~~~~ 192 (222)
T COG5246 138 LGIQVNYEDDLA-------------------------EEMPQYRIVSSLEQNVEEYDESFRYLVFACEPYENIAFKFENK 192 (222)
T ss_pred eEEEEeccchhh-------------------------ccCcceehhhhhhhcchhhcccceEEEEEeccccceeeecCCC
Confidence 999999998765 5799999999999999999999999999999999999999999
Q ss_pred cc-------ceecCCCeEEEEEEEeecCC
Q psy9880 240 TG-------LYERITSGLVLVDHVKLTCQ 261 (280)
Q Consensus 240 eI-------~WD~dtK~f~lQ~~Fk~~~~ 261 (280)
|| +||..|+.|+|||||+...+
T Consensus 193 ei~f~s~~~~wDa~~~tYt~qFff~~a~~ 221 (222)
T COG5246 193 EIDFLSIYEDWDAETGTYTLQFFFLEAGP 221 (222)
T ss_pred ccchhhhcccccccCceEEEEEeeecccC
Confidence 99 99999999999999997654
No 3
>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=99.59 E-value=4.4e-15 Score=124.82 Aligned_cols=76 Identities=32% Similarity=0.449 Sum_probs=64.1
Q ss_pred CCCCCceeEEEEEeCCCccccccccccchhhhhhhcccCCcCccCCCCCceeeeeccccccCCCCCCceEEEE-EeCCCc
Q psy9880 152 DPSNGQQSLLFQVDYPEIADDVFPRHRFMSAYSLLFQVDYPEIADDVFPRHRFMSAYEQRIEPPDRKWQYLLF-AAEPYE 230 (280)
Q Consensus 152 Dpet~q~gllfqV~Ypei~~~~~p~~r~ms~y~l~~~~~~~e~~~~~~P~~RfmSa~Eq~vE~~d~~~QYLvi-AaEPYE 230 (280)
.|-.-.+|+.|+|.||++.+. +..|.+|||+ + +.++.+|+|+| |++|||
T Consensus 35 pPPK~vqGYkFnIfYPdL~d~------------------------~~~P~y~i~~-----~-~~~~~~~~L~F~AgpPYe 84 (125)
T PF09732_consen 35 PPPKIVQGYKFNIFYPDLIDK------------------------SKTPRYRIEP-----D-EDNPDFCILRFHAGPPYE 84 (125)
T ss_pred CCCceeeeeEEEEECCcccCC------------------------CCCCcEEEEE-----C-CCCCCEEEEEEeCCCCCc
Confidence 455667999999999999763 5689999999 2 33799999999 569999
Q ss_pred ccceeecCCcc----------ceecCCCeEEEEEEEeec
Q psy9880 231 TIAFKVSDRTG----------LYERITSGLVLVDHVKLT 259 (280)
Q Consensus 231 tIafkIPn~eI----------~WD~dtK~f~lQ~~Fk~~ 259 (280)
.|||+|+|+|+ .||. ..|.|+|.||..
T Consensus 85 DIAFkIvnrEWd~s~k~Gfr~~Fd~--gilqL~F~FKr~ 121 (125)
T PF09732_consen 85 DIAFKIVNREWDYSHKRGFRCSFDR--GILQLYFNFKRY 121 (125)
T ss_pred CEEEEEecCeeecCCCCCceEEeeC--CEEEEEEEEEhh
Confidence 99999999998 6665 689999999854
No 4
>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=97.96 E-value=1.3e-06 Score=56.28 Aligned_cols=34 Identities=41% Similarity=0.692 Sum_probs=31.8
Q ss_pred CcceeeeeeeeeecCCCcceeecccchhhhhHHH
Q psy9880 51 LGSYECKLCLTLHNNEGSYLAHTQGKKHQANLAR 84 (280)
Q Consensus 51 lG~~eCKLClT~H~ne~SYlaHtqGKKHq~NL~R 84 (280)
.|.|-|.+|++...+..++..|+.||+|..|+++
T Consensus 1 ~~~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 1 TGGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CcCeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 3789999999999999999999999999999976
No 5
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.36 E-value=1.9e-05 Score=47.78 Aligned_cols=25 Identities=32% Similarity=0.643 Sum_probs=24.3
Q ss_pred eeeeeeeeeecCCCcceeecccchh
Q psy9880 54 YECKLCLTLHNNEGSYLAHTQGKKH 78 (280)
Q Consensus 54 ~eCKLClT~H~ne~SYlaHtqGKKH 78 (280)
|.|.+|+..-.++.+|..|++||||
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 6899999999999999999999999
No 6
>KOG2370|consensus
Probab=96.63 E-value=0.0017 Score=65.99 Aligned_cols=72 Identities=26% Similarity=0.303 Sum_probs=48.7
Q ss_pred ceeEEEEEeCCCccccccccccchhhhhhhcccCCcCccCCCCCceeeeeccccccCCCCCCceEEEEEeCCCcccceee
Q psy9880 157 QQSLLFQVDYPEIADDVFPRHRFMSAYSLLFQVDYPEIADDVFPRHRFMSAYEQRIEPPDRKWQYLLFAAEPYETIAFKV 236 (280)
Q Consensus 157 q~gllfqV~Ypei~~~~~p~~r~ms~y~l~~~~~~~e~~~~~~P~~RfmSa~Eq~vE~~d~~~QYLviAaEPYEtIafkI 236 (280)
-+|.-|.|-||++-+. +..|.++|-+.-. +.|-+ --=..|.+|||.|||+|
T Consensus 538 VQGYkFNIFYPDLidk------------------------~~aP~y~ie~~~d----~~d~c-iIRF~aGpPYeDIAFkI 588 (623)
T KOG2370|consen 538 VQGYKFNIFYPDLIDK------------------------GRAPTYRIERCRD----KNDFC-IIRFHAGPPYEDIAFKI 588 (623)
T ss_pred hcceeecccchhhhcc------------------------ccCCeeeeeecCC----CCceE-EEEeccCCcchhhhhhh
Confidence 4799999999988653 6789999876621 11222 12246899999999999
Q ss_pred cCCcc--------ceecCCCeEEEEEEEe
Q psy9880 237 SDRTG--------LYERITSGLVLVDHVK 257 (280)
Q Consensus 237 Pn~eI--------~WD~dtK~f~lQ~~Fk 257 (280)
=|+|. -=-.++..|.|=|+||
T Consensus 589 VnkeWeyshKrGfKcqF~ngvlqL~F~FK 617 (623)
T KOG2370|consen 589 VNKEWEYSHKRGFKCQFDNGVLQLWFRFK 617 (623)
T ss_pred hcchhhhhhhcCccceeeCCeeeeeehhh
Confidence 99986 1122344555555555
No 7
>KOG0227|consensus
Probab=94.45 E-value=0.012 Score=53.98 Aligned_cols=26 Identities=46% Similarity=0.718 Sum_probs=23.2
Q ss_pred ccccchhhhh------------hhcccCCcCccCCCCC
Q psy9880 175 PRHRFMSAYS------------LLFQVDYPEIADDVFP 200 (280)
Q Consensus 175 p~~r~ms~y~------------l~~~~~~~e~~~~~~P 200 (280)
|+|||||+|+ |+|+++|+|+|+...|
T Consensus 147 Pr~rfmssyeq~ve~~dk~~qyLvfaaePyE~Iafk~p 184 (222)
T KOG0227|consen 147 PRHRFMSSYEQKVEPPDKSWQYLVFAAEPYENIAFKVP 184 (222)
T ss_pred CcchhhhhhHhhcCCccccceEEEEEeccccceeeecC
Confidence 8999999998 9999999999966555
No 8
>KOG4727|consensus
Probab=93.62 E-value=0.025 Score=51.14 Aligned_cols=40 Identities=33% Similarity=0.602 Sum_probs=34.6
Q ss_pred CceeccCCcceeeeeeeeeecCCCcceeecccchhhhhHH
Q psy9880 44 PYFMKNHLGSYECKLCLTLHNNEGSYLAHTQGKKHQANLA 83 (280)
Q Consensus 44 PY~~KNHlG~~eCKLClT~H~ne~SYlaHtqGKKHq~NL~ 83 (280)
|-+-+--.|.|=|..|+-+--.--+||-|+.||+||-||.
T Consensus 66 k~tp~sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlg 105 (193)
T KOG4727|consen 66 KSTPRSQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLG 105 (193)
T ss_pred cCCcccccCceeeeecceeehhhHHHHHHhccHHHHHHHh
Confidence 3444556799999999999888899999999999999985
No 9
>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=93.53 E-value=0.011 Score=36.81 Aligned_cols=27 Identities=26% Similarity=0.566 Sum_probs=24.9
Q ss_pred ceeeeeeeeeecCCCcceeecccchhh
Q psy9880 53 SYECKLCLTLHNNEGSYLAHTQGKKHQ 79 (280)
Q Consensus 53 ~~eCKLClT~H~ne~SYlaHtqGKKHq 79 (280)
.|.|.+|.-.=.++..+..|..||+|+
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 478999999999999999999999996
No 10
>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=90.13 E-value=0.083 Score=36.27 Aligned_cols=33 Identities=30% Similarity=0.584 Sum_probs=19.8
Q ss_pred ceeeeeeeeeecCCC-cc-eeecccchhhhhHHHH
Q psy9880 53 SYECKLCLTLHNNEG-SY-LAHTQGKKHQANLARR 85 (280)
Q Consensus 53 ~~eCKLClT~H~ne~-SY-laHtqGKKHq~NL~RR 85 (280)
+|=|.-|.+.=++.+ |. ..|..|+||+.|+++.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~ 37 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY 37 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence 577999999876665 44 8999999999999864
No 11
>KOG3032|consensus
Probab=88.99 E-value=0.15 Score=47.99 Aligned_cols=49 Identities=20% Similarity=0.298 Sum_probs=38.7
Q ss_pred hhhCCCCCCc-eeccCCcceeeeeeeeeecCCCcceeecccchhhhhHHHH
Q psy9880 36 ETIDLNKDPY-FMKNHLGSYECKLCLTLHNNEGSYLAHTQGKKHQANLARR 85 (280)
Q Consensus 36 etiDl~kDPY-~~KNHlG~~eCKLClT~H~ne~SYlaHtqGKKHq~NL~RR 85 (280)
.+-|+.-||= .--|-+|.+.|.+|++-=- ++=.-.|..||||..+++.-
T Consensus 17 kk~~~ri~splakyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~l 66 (264)
T KOG3032|consen 17 KKKDTRIDSPLAKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSL 66 (264)
T ss_pred cCcccccccHhhccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHH
Confidence 3455555544 4458999999999999766 88888999999999998764
No 12
>PLN02748 tRNA dimethylallyltransferase
Probab=85.89 E-value=0.26 Score=49.74 Aligned_cols=36 Identities=22% Similarity=0.487 Sum_probs=31.8
Q ss_pred cceeeeeeee-eecCCCcceeecccchhhhhHHHHHH
Q psy9880 52 GSYECKLCLT-LHNNEGSYLAHTQGKKHQANLARRAA 87 (280)
Q Consensus 52 G~~eCKLClT-~H~ne~SYlaHtqGKKHq~NL~RR~a 87 (280)
=.|+|.+|.. +.+.|-....|++||+|.-++.+...
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k 453 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ 453 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence 5689999998 78899999999999999999887653
No 13
>KOG0150|consensus
Probab=77.92 E-value=0.62 Score=45.47 Aligned_cols=36 Identities=31% Similarity=0.521 Sum_probs=31.6
Q ss_pred Ccceeeeeeeee-ecCCCcceeecccchhhhhHHHHH
Q psy9880 51 LGSYECKLCLTL-HNNEGSYLAHTQGKKHQANLARRA 86 (280)
Q Consensus 51 lG~~eCKLClT~-H~ne~SYlaHtqGKKHq~NL~RR~ 86 (280)
.|++=|..|-.. -+|-.|..-|-+||+|+.||++|-
T Consensus 8 ~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~Kri 44 (336)
T KOG0150|consen 8 QPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAKRI 44 (336)
T ss_pred ccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHHHH
Confidence 378889999874 578899999999999999999985
No 14
>KOG3454|consensus
Probab=69.79 E-value=1.1 Score=40.09 Aligned_cols=32 Identities=31% Similarity=0.609 Sum_probs=26.9
Q ss_pred ceeeeeeeee--ecCCCcceeecccchhhhhHHH
Q psy9880 53 SYECKLCLTL--HNNEGSYLAHTQGKKHQANLAR 84 (280)
Q Consensus 53 ~~eCKLClT~--H~ne~SYlaHtqGKKHq~NL~R 84 (280)
+|=|-.|.|+ |-|-++=-.|..|+||..|+.-
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence 5789999974 6666778899999999999864
No 15
>KOG4722|consensus
Probab=66.79 E-value=1.7 Score=44.58 Aligned_cols=32 Identities=34% Similarity=0.614 Sum_probs=28.1
Q ss_pred eeeeeeeeeecCCCcceeecccchhhhhHHHH
Q psy9880 54 YECKLCLTLHNNEGSYLAHTQGKKHQANLARR 85 (280)
Q Consensus 54 ~eCKLClT~H~ne~SYlaHtqGKKHq~NL~RR 85 (280)
-.|.||+.+-.+|--+-+|..|+|||.-|---
T Consensus 494 kqcslcnvlissevylfshvkgrkhqqal~e~ 525 (672)
T KOG4722|consen 494 KQCSLCNVLISSEVYLFSHVKGRKHQQALNEL 525 (672)
T ss_pred hccchhhhhhhhhhhhhhhhcchhHHHHHHHH
Confidence 47999999999999999999999999876443
No 16
>smart00500 SFM Splicing Factor Motif, present in Prp18 and Pr04.
Probab=61.08 E-value=6.8 Score=28.04 Aligned_cols=25 Identities=36% Similarity=0.654 Sum_probs=19.0
Q ss_pred cChhhhhHHHHHHHHHHHhhhhCCC
Q psy9880 17 ASWSESNRDRRERLRQLALETIDLN 41 (280)
Q Consensus 17 AS~s~~n~~RReRlr~LaletiDl~ 41 (280)
.-..|.+.+||+||++|..+.-+++
T Consensus 18 ~lFGE~~~~Rr~RL~~ll~~~~e~~ 42 (44)
T smart00500 18 TLFGEDDQERRQRLRQLLIVQDELD 42 (44)
T ss_pred eecCCChHHHHHHHHHHHHcccccc
Confidence 3456888999999999987654444
No 17
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=61.01 E-value=4.1 Score=37.62 Aligned_cols=36 Identities=31% Similarity=0.447 Sum_probs=27.6
Q ss_pred ccccchhhhh------------hhcccCCcCccCCCCC--ceeeeecccc
Q psy9880 175 PRHRFMSAYS------------LLFQVDYPEIADDVFP--RHRFMSAYEQ 210 (280)
Q Consensus 175 p~~r~ms~y~------------l~~~~~~~e~~~~~~P--~~RfmSa~Eq 210 (280)
|+.||||.|| |.++|+|+|.|....| -.-|.|-||-
T Consensus 153 P~yRivs~lEq~ve~~d~~f~yLV~a~ePyEnIafk~~~~ei~f~s~~~~ 202 (222)
T COG5246 153 PQYRIVSSLEQNVEEYDESFRYLVFACEPYENIAFKFENKEIDFLSIYED 202 (222)
T ss_pred cceehhhhhhhcchhhcccceEEEEEeccccceeeecCCCccchhhhccc
Confidence 8899999998 8899999998855444 3556676664
No 18
>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=58.71 E-value=8.4 Score=25.66 Aligned_cols=16 Identities=56% Similarity=0.960 Sum_probs=11.9
Q ss_pred hhhhhHHHHHHHHHHH
Q psy9880 19 WSESNRDRRERLRQLA 34 (280)
Q Consensus 19 ~s~~n~~RReRlr~La 34 (280)
..|++.+||+||++|.
T Consensus 15 FGE~~~~R~~RLr~l~ 30 (30)
T PF08799_consen 15 FGETDADRRERLRRLL 30 (30)
T ss_dssp TT--HHHHHHHHHHHH
T ss_pred hCCChHHHHHHHHHhC
Confidence 4588999999999984
No 19
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=38.93 E-value=10 Score=28.10 Aligned_cols=31 Identities=23% Similarity=0.481 Sum_probs=0.0
Q ss_pred eeeeeeeeecCCCcceeecccchhhhhHHHHH
Q psy9880 55 ECKLCLTLHNNEGSYLAHTQGKKHQANLARRA 86 (280)
Q Consensus 55 eCKLClT~H~ne~SYlaHtqGKKHq~NL~RR~ 86 (280)
+|.+|.+.-.+..+++.|+. ++|+.++....
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~-~~H~~~~~~~~ 31 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMK-KKHGFDIPDQK 31 (100)
T ss_dssp --------------------------------
T ss_pred Cccccccccccccccccccc-ccccccccccc
Confidence 69999999999999999994 99999987443
No 20
>smart00355 ZnF_C2H2 zinc finger.
Probab=37.45 E-value=3.5 Score=23.32 Aligned_cols=21 Identities=19% Similarity=0.547 Sum_probs=18.2
Q ss_pred eeeeeeeeeecCCCcceeecc
Q psy9880 54 YECKLCLTLHNNEGSYLAHTQ 74 (280)
Q Consensus 54 ~eCKLClT~H~ne~SYlaHtq 74 (280)
|+|..|...-.+.+++..|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 689999999999988888875
No 21
>PF15470 DUF4637: Domain of unknown function (DUF4637)
Probab=36.50 E-value=10 Score=33.93 Aligned_cols=19 Identities=47% Similarity=0.847 Sum_probs=15.9
Q ss_pred ceeeeeeeeeecCCCcceee
Q psy9880 53 SYECKLCLTLHNNEGSYLAH 72 (280)
Q Consensus 53 ~~eCKLClT~H~ne~SYlaH 72 (280)
.|-||-|-|+|.. .+|.+|
T Consensus 139 ILfCkKC~tLHs~-payVaH 157 (173)
T PF15470_consen 139 ILFCKKCRTLHSH-PAYVAH 157 (173)
T ss_pred eeeehhhccccCc-hHHHHH
Confidence 4889999999965 678887
No 22
>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=36.46 E-value=4.9 Score=24.28 Aligned_cols=20 Identities=20% Similarity=0.469 Sum_probs=18.9
Q ss_pred eeeeeeeeeecCCCcceeec
Q psy9880 54 YECKLCLTLHNNEGSYLAHT 73 (280)
Q Consensus 54 ~eCKLClT~H~ne~SYlaHt 73 (280)
|+|..|...=.+..++.+|.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHK 21 (27)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCccCCccCChhHHHHHh
Confidence 79999999999999999998
No 23
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=34.62 E-value=5.9 Score=29.39 Aligned_cols=35 Identities=17% Similarity=0.443 Sum_probs=25.9
Q ss_pred ccCCc-ceeeeeeeeeecCCCcceeecccchhhhhH
Q psy9880 48 KNHLG-SYECKLCLTLHNNEGSYLAHTQGKKHQANL 82 (280)
Q Consensus 48 KNHlG-~~eCKLClT~H~ne~SYlaHtqGKKHq~NL 82 (280)
+.-++ .+.|..|...=.+..++..|...+.|....
T Consensus 44 ~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~ 79 (100)
T PF12756_consen 44 RKKVKESFRCPYCNKTFRSREALQEHMRSKHHKKRN 79 (100)
T ss_dssp -----SSEEBSSSS-EESSHHHHHHHHHHTTTTC-S
T ss_pred ccccCCCCCCCccCCCCcCHHHHHHHHcCccCCCcc
Confidence 33344 599999999999999999999999998753
No 24
>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=33.73 E-value=19 Score=33.98 Aligned_cols=65 Identities=18% Similarity=0.284 Sum_probs=45.6
Q ss_pred HHHHHHHHHh--hhhCC-CCCCceec--cCCcceeeeeeeee-ecCCCcceeecccchhhhhHHHHHHHHh
Q psy9880 26 RRERLRQLAL--ETIDL-NKDPYFMK--NHLGSYECKLCLTL-HNNEGSYLAHTQGKKHQANLARRAAKEA 90 (280)
Q Consensus 26 RReRlr~Lal--etiDl-~kDPY~~K--NHlG~~eCKLClT~-H~ne~SYlaHtqGKKHq~NL~RR~a~e~ 90 (280)
+-++.+.|+. ..+|+ .=.|||+- ++-..|-|+|=++. --++..+++|++|||-+--|++-....+
T Consensus 47 ~gKKy~~l~~~~~~~d~~~yeP~ivps~~~~~~LfCkLT~~~iNk~pe~V~rHv~GKRf~kaLek~ee~~~ 117 (244)
T PF05477_consen 47 RGKKYQRLIRAKPEFDFSKYEPHIVPSTKNPHKLFCKLTGRHINKSPEHVERHVNGKRFQKALEKYEECQK 117 (244)
T ss_pred ccHHHHHHHhcccCCChHhcCCccccccCCCceeEEechHhHhccCHHHHHHHhhhHHHHHHHHHHHHHHh
Confidence 3355566632 23553 34788774 57889999987653 3467889999999999999988754333
No 25
>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=33.45 E-value=5.5 Score=23.16 Aligned_cols=21 Identities=19% Similarity=0.575 Sum_probs=18.3
Q ss_pred eeeeeeeeeecCCCcceeecc
Q psy9880 54 YECKLCLTLHNNEGSYLAHTQ 74 (280)
Q Consensus 54 ~eCKLClT~H~ne~SYlaHtq 74 (280)
|+|..|...=.+++++.+|..
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 789999999999999888864
No 26
>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=30.99 E-value=19 Score=28.75 Aligned_cols=40 Identities=18% Similarity=0.255 Sum_probs=29.7
Q ss_pred CCcceeeeeeeeeecCCCcceeecccchhhh-hHHHHHHHHh
Q psy9880 50 HLGSYECKLCLTLHNNEGSYLAHTQGKKHQA-NLARRAAKEA 90 (280)
Q Consensus 50 HlG~~eCKLClT~H~ne~SYlaHtqGKKHq~-NL~RR~a~e~ 90 (280)
..--+.|+.|.+.=.- +++.+|+..+-|.+ ..++++..++
T Consensus 8 ~~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~ 48 (109)
T PF12013_consen 8 EYRVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEA 48 (109)
T ss_pred cCCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHH
Confidence 4467899999875444 89999999999888 5556655444
No 27
>PRK01175 phosphoribosylformylglycinamidine synthase I; Provisional
Probab=29.46 E-value=59 Score=30.41 Aligned_cols=34 Identities=21% Similarity=0.389 Sum_probs=26.9
Q ss_pred ceeccCCcceeeeeeeeeecC-C--------Ccce----eecccchh
Q psy9880 45 YFMKNHLGSYECKLCLTLHNN-E--------GSYL----AHTQGKKH 78 (280)
Q Consensus 45 Y~~KNHlG~~eCKLClT~H~n-e--------~SYl----aHtqGKKH 78 (280)
=+.+|-+|+|||+-+.+-..+ . ++.+ +|-+||=.
T Consensus 121 ~L~~N~s~~f~~~~~~~~v~~~~s~~~~~~~~~~~~~piah~eG~~~ 167 (261)
T PRK01175 121 ALTVNESNRFECRPTYLKKENRKCIFTKLLKKDVFQVPVAHAEGRVV 167 (261)
T ss_pred eEeecCCCCeEEeeeEEEECCCCChhHhccCCCEEEEeeEcCCcceE
Confidence 499999999999998766655 2 4555 88888866
No 28
>PF13507 GATase_5: CobB/CobQ-like glutamine amidotransferase domain; PDB: 3D54_L 3UMM_A 3UJN_A 3UGJ_A 1T3T_A.
Probab=28.02 E-value=43 Score=31.41 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=15.7
Q ss_pred CCCCCceeccCCcceeeeeeeeeecC
Q psy9880 40 LNKDPYFMKNHLGSYECKLCLTLHNN 65 (280)
Q Consensus 40 l~kDPY~~KNHlG~~eCKLClT~H~n 65 (280)
-..+|-+.+|-+|+|||+-+.+ +.+
T Consensus 117 ~~~~~~L~~N~s~~fe~rwv~~-~v~ 141 (259)
T PF13507_consen 117 SEQSPALTPNASGRFESRWVNL-VVN 141 (259)
T ss_dssp -TT--EEE--TTSS-EEEEEEE-EE-
T ss_pred cCCCcEEcCCCCCCeEEEEEEE-EEe
Confidence 3556779999999999999998 653
No 29
>PHA00626 hypothetical protein
Probab=25.54 E-value=31 Score=26.45 Aligned_cols=21 Identities=19% Similarity=0.327 Sum_probs=16.4
Q ss_pred eeccCCcceeeeeeeeeecCC
Q psy9880 46 FMKNHLGSYECKLCLTLHNNE 66 (280)
Q Consensus 46 ~~KNHlG~~eCKLClT~H~ne 66 (280)
+.|.|+..|+|+-|+-.-+-+
T Consensus 16 ~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 16 TMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred eecccCcceEcCCCCCeechh
Confidence 356899999999998765543
No 30
>PF11520 Cren7: Chromatin protein Cren7; InterPro: IPR020906 Cren7 is a chromatin protein found in Crenarchaeota and has a higher affinity for double-stranded DNA than for single-stranded DNA. The protein contains negative DNA supercoils and is associated with genomic DNA in vivo. Cren7 interacts with duplex DNA through a beta-sheet and a long flexible loop. Its binding to double-stranded DNA is without sequence specificity. There is approximately 1 Cren7 molecule for 12 bp of DNA. The function of Cren7 has not been completely determined but it is thought that the protein may have a role similar to that of archaeal proteins in Euryarchaea [].; GO: 0003690 double-stranded DNA binding, 0005737 cytoplasm; PDB: 3KXT_A 3LWH_A 3LWI_A 2JTM_A.
Probab=25.52 E-value=55 Score=25.19 Aligned_cols=24 Identities=33% Similarity=0.601 Sum_probs=14.7
Q ss_pred Cccce--eccCCceeEEEeeCCCCCc
Q psy9880 134 PKKFV--KIGRPGYRVTKQRDPSNGQ 157 (280)
Q Consensus 134 ~k~~~--KiGrPgYkVtKvrDpet~q 157 (280)
.|-|+ .-||||.+|---+||+||.
T Consensus 24 ~KvW~L~PkGrkGV~igLFk~P~tGk 49 (60)
T PF11520_consen 24 IKVWVLQPKGRKGVKIGLFKDPETGK 49 (60)
T ss_dssp SEEEEE--TTS--EEEEEEE-TTT--
T ss_pred eEEEEEcCCCCCceEEEEEeCCCCCc
Confidence 34444 6799999999999999985
No 31
>PF09034 TRADD_N: TRADD, N-terminal domain; InterPro: IPR009095 TRADD is a signalling adaptor protein involved in tumour necrosis factor-receptor I (TNFR1)-associated apoptosis and cell survival. The decision between apoptosis and cell survival involves the interplay between two sequential signalling complexes. The plasma membrane-bound complex I is comprised of TNFR1, TRADD, the kinase RIP1, and TRAF2, which together mediate the activation of NF-kappaB. Subsequently, complex II is formed in the cytoplasm, where TRADD and RIP1 associate with FADD and caspase-8. If NF-kappaB is activated by complex I, then complex II will associate with the caspase-8 inhibitor FLIP(L) and the cell survives, while the failure to activate NF-kappaB leads to apoptosis []. The TRADD C-terminal death domain is responsible for its association with TNFR1, and with the death-domain proteins FADD and RIP1, which promote apoptosis. The TRADD N-terminal domain binds TRAF2 and promotes TRAF2 recruitment to TNFR1, thereby mediating the activation of NK-kappaB and JNK/AP1, which promote cell survival []. The N-terminal TRADD domain is composed of an alpha-beta sandwich, where the beta strands form an antiparallel beta-sheet.; GO: 0004871 signal transducer activity, 0006917 induction of apoptosis, 0043123 positive regulation of I-kappaB kinase/NF-kappaB cascade, 0005737 cytoplasm; PDB: 1F3V_A 1F2H_A.
Probab=24.04 E-value=20 Score=30.40 Aligned_cols=38 Identities=26% Similarity=0.473 Sum_probs=24.3
Q ss_pred ccCCceeEEEeeCCCCCceeEEEEEeCCCccccccccccchhhhh
Q psy9880 140 IGRPGYRVTKQRDPSNGQQSLLFQVDYPEIADDVFPRHRFMSAYS 184 (280)
Q Consensus 140 iGrPgYkVtKvrDpet~q~gllfqV~Ypei~~~~~p~~r~ms~y~ 184 (280)
+|..||.|-||.|..-. |.+||.|-. ++|=-||...|.
T Consensus 4 G~~~g~~iLKiH~sdpq---LiVqlkF~~----~~~C~rFL~sYr 41 (111)
T PF09034_consen 4 GSPDGYQILKIHDSDPQ---LIVQLKFCG----REPCRRFLRSYR 41 (111)
T ss_dssp --TTTEEEEEEEEETTC---EEEEEEEES----HHHHHHHHHHHH
T ss_pred CCcchhheeeeecCCCe---eEEEEEEcC----chhHHHHHHHHh
Confidence 67889999999986543 678888853 234445554443
No 32
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=23.10 E-value=8.3 Score=35.00 Aligned_cols=32 Identities=25% Similarity=0.427 Sum_probs=25.2
Q ss_pred ceeeeeeeee--ecCCCcceeecccchhhhhHHH
Q psy9880 53 SYECKLCLTL--HNNEGSYLAHTQGKKHQANLAR 84 (280)
Q Consensus 53 ~~eCKLClT~--H~ne~SYlaHtqGKKHq~NL~R 84 (280)
.|-|..|..+ |-.-++=-+|.+|++|.+|.+-
T Consensus 3 RY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~d 36 (188)
T COG5136 3 RYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKD 36 (188)
T ss_pred chHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHH
Confidence 5779999876 5555677789999999988653
No 33
>PRK07080 hypothetical protein; Validated
Probab=22.46 E-value=80 Score=31.08 Aligned_cols=31 Identities=23% Similarity=0.324 Sum_probs=19.0
Q ss_pred ChhhhhHHHHHHHHHHHhh---------hhCCCCCCceecc
Q psy9880 18 SWSESNRDRRERLRQLALE---------TIDLNKDPYFMKN 49 (280)
Q Consensus 18 S~s~~n~~RReRlr~Lale---------tiDl~kDPY~~KN 49 (280)
|.++. .+.|++..+.+.+ .+|+.+||+|.|+
T Consensus 186 t~e~v-~~~r~~w~e~~~~l~~~LgL~~~ve~AnDPFF~~~ 225 (317)
T PRK07080 186 TPEQI-VAFRQSWIERGTAMADALGLPVEIDLANDPFFGRG 225 (317)
T ss_pred CHHHH-HHHHHHHHHHHHHHHHHhCCceeEeecCCcccccc
Confidence 44444 4555554444333 2789999999965
No 34
>KOG3608|consensus
Probab=21.97 E-value=16 Score=36.95 Aligned_cols=34 Identities=26% Similarity=0.577 Sum_probs=29.1
Q ss_pred CCCCCce-----------------eccCCcceeeeeeeeeecCCCcceeec
Q psy9880 40 LNKDPYF-----------------MKNHLGSYECKLCLTLHNNEGSYLAHT 73 (280)
Q Consensus 40 l~kDPY~-----------------~KNHlG~~eCKLClT~H~ne~SYlaHt 73 (280)
|+++||. ++||+..|.|.||.-+...-+|+-.|+
T Consensus 233 l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~ 283 (467)
T KOG3608|consen 233 LNTNSFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHI 283 (467)
T ss_pred hcCCchHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHH
Confidence 7888885 689999999999999888888877764
No 35
>KOG1280|consensus
Probab=20.26 E-value=25 Score=35.21 Aligned_cols=22 Identities=23% Similarity=0.484 Sum_probs=20.5
Q ss_pred ceeeeeeeeeecCCCcceeecc
Q psy9880 53 SYECKLCLTLHNNEGSYLAHTQ 74 (280)
Q Consensus 53 ~~eCKLClT~H~ne~SYlaHtq 74 (280)
+|+|.-|++||.+|..+.-|..
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~ 100 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVL 100 (381)
T ss_pred cccCCcccccccchhHHHHHhh
Confidence 8999999999999999998864
No 36
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=20.17 E-value=21 Score=26.95 Aligned_cols=14 Identities=36% Similarity=0.819 Sum_probs=11.6
Q ss_pred cceeeeeeeeeecC
Q psy9880 52 GSYECKLCLTLHNN 65 (280)
Q Consensus 52 G~~eCKLClT~H~n 65 (280)
-.|.|.||+|.|.-
T Consensus 6 sry~CDLCn~~~p~ 19 (57)
T PF14445_consen 6 SRYSCDLCNSSHPI 19 (57)
T ss_pred hhHhHHhhcccCcH
Confidence 46899999998864
Done!