Query 020249
Match_columns 329
No_of_seqs 121 out of 136
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:13:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020249.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020249hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3032 Uncharacterized conser 100.0 7.9E-57 1.7E-61 414.7 20.1 258 2-329 2-262 (264)
2 smart00451 ZnF_U1 U1-like zinc 97.9 7.9E-06 1.7E-10 54.0 2.5 33 34-66 2-34 (35)
3 PF12171 zf-C2H2_jaz: Zinc-fin 97.5 3.8E-05 8.2E-10 49.0 1.5 27 35-61 1-27 (27)
4 KOG0717 Molecular chaperone (D 96.9 0.00057 1.2E-08 70.1 2.7 35 36-70 293-327 (508)
5 PF12874 zf-met: Zinc-finger o 96.6 0.001 2.2E-08 41.1 1.5 25 36-60 1-25 (25)
6 COG5246 PRP11 Splicing factor 96.5 0.0035 7.5E-08 58.0 4.9 54 23-76 41-94 (222)
7 KOG0227 Splicing factor 3a, su 95.9 0.0098 2.1E-07 55.3 4.3 62 6-69 26-87 (222)
8 PLN02748 tRNA dimethylallyltra 94.7 0.02 4.4E-07 59.0 2.7 36 34-69 417-453 (468)
9 KOG3408 U1-like Zn-finger-cont 89.0 0.21 4.5E-06 43.7 1.4 37 32-68 54-90 (129)
10 KOG4727 U1-like Zn-finger prot 88.8 0.53 1.1E-05 43.4 4.0 43 25-67 65-107 (193)
11 PF06220 zf-U1: U1 zinc finger 86.9 0.51 1.1E-05 32.9 2.1 30 37-66 5-36 (38)
12 KOG4722 Zn-finger protein [Gen 77.8 1.3 2.8E-05 46.1 1.8 33 35-67 493-525 (672)
13 KOG3032 Uncharacterized conser 77.5 12 0.00027 36.2 8.1 29 256-284 200-230 (264)
14 COG5112 UFD2 U1-like Zn-finger 71.0 2.3 5E-05 36.7 1.4 39 31-69 51-89 (126)
15 PF12756 zf-C2H2_2: C2H2 type 65.2 2.2 4.7E-05 32.9 0.1 31 35-65 50-80 (100)
16 PF03037 KMP11: Kinetoplastid 64.7 21 0.00046 29.0 5.6 41 208-254 28-68 (90)
17 PF12013 DUF3505: Protein of u 59.7 5 0.00011 33.0 1.3 31 31-62 7-37 (109)
18 PTZ00448 hypothetical protein; 58.7 8.5 0.00019 39.2 3.0 36 33-68 312-347 (373)
19 PF12476 DUF3696: Protein of u 56.7 4 8.7E-05 29.7 0.3 16 204-219 34-49 (52)
20 PF13912 zf-C2H2_6: C2H2-type 49.3 10 0.00022 23.4 1.2 21 36-56 2-22 (27)
21 PF13894 zf-C2H2_4: C2H2-type 47.6 10 0.00022 21.8 1.0 20 37-56 2-21 (24)
22 PF05477 SURF2: Surfeit locus 41.3 36 0.00077 32.9 4.0 50 5-62 3-53 (244)
23 KOG2785 C2H2-type Zn-finger pr 40.5 24 0.00053 36.2 3.0 35 34-68 2-36 (390)
24 KOG1029 Endocytic adaptor prot 39.9 1.4E+02 0.003 33.9 8.6 23 201-223 303-326 (1118)
25 KOG2785 C2H2-type Zn-finger pr 39.1 12 0.00026 38.3 0.6 34 36-69 69-102 (390)
26 smart00238 BIR Baculoviral inh 36.6 23 0.00049 26.6 1.6 26 30-55 30-60 (71)
27 PF04959 ARS2: Arsenite-resist 36.4 28 0.0006 33.0 2.4 40 31-71 73-112 (214)
28 PF00096 zf-C2H2: Zinc finger, 36.2 13 0.00028 22.0 0.2 21 37-57 2-22 (23)
29 PF14968 CCDC84: Coiled coil p 34.9 21 0.00045 36.0 1.4 27 38-67 2-28 (336)
30 KOG2384 Major histocompatibili 34.5 11 0.00024 35.7 -0.5 47 20-67 69-115 (223)
31 PF04988 AKAP95: A-kinase anch 33.4 31 0.00067 31.7 2.2 31 37-67 2-32 (165)
32 COG2433 Uncharacterized conser 32.3 2.5E+02 0.0055 30.8 9.0 35 254-288 465-510 (652)
33 COG5188 PRP9 Splicing factor 3 29.2 25 0.00054 36.2 0.9 37 32-68 235-271 (470)
34 PF15303 RNF111_N: E3 ubiquiti 29.1 82 0.0018 30.9 4.4 17 270-286 205-221 (269)
35 smart00734 ZnF_Rad18 Rad18-lik 29.0 28 0.00061 22.3 0.9 20 36-56 2-21 (26)
36 PF07535 zf-DBF: DBF zinc fing 27.9 38 0.00082 25.1 1.5 27 36-65 6-32 (49)
37 PRK13610 photosystem II reacti 27.3 44 0.00095 29.0 2.0 15 229-243 91-105 (113)
38 TIGR03047 PS_II_psb28 photosys 27.2 44 0.00096 28.8 2.0 14 230-243 85-98 (109)
39 PLN00039 photosystem II reacti 27.2 44 0.00095 28.9 2.0 14 230-243 86-99 (111)
40 cd00022 BIR Baculoviral inhibi 26.6 41 0.00089 25.0 1.5 23 34-56 33-59 (69)
41 PRK13612 photosystem II reacti 26.4 47 0.001 28.8 2.0 14 230-243 88-101 (113)
42 PF14942 Muted: Organelle biog 25.7 1.5E+02 0.0032 26.4 5.1 21 229-249 104-124 (145)
43 PF05400 FliT: Flagellar prote 25.3 2.9E+02 0.0063 20.6 7.2 54 232-285 8-74 (84)
44 CHL00128 psbW photosystem II p 25.2 50 0.0011 28.6 2.0 14 230-243 88-101 (113)
45 KOG3454 U1 snRNP-specific prot 24.2 41 0.0009 30.9 1.3 30 37-66 5-36 (165)
46 PF10475 DUF2450: Protein of u 24.1 5.1E+02 0.011 24.9 8.8 10 204-213 2-11 (291)
47 PRK13611 photosystem II reacti 23.5 58 0.0013 27.9 2.0 14 230-243 81-94 (104)
48 PRK12495 hypothetical protein; 23.0 42 0.00091 32.2 1.2 20 24-45 49-68 (226)
49 smart00355 ZnF_C2H2 zinc finge 22.9 40 0.00087 19.2 0.7 20 37-56 2-21 (26)
50 PF03912 Psb28: Psb28 protein; 21.7 52 0.0011 28.3 1.4 13 231-243 86-98 (108)
51 PF08271 TF_Zn_Ribbon: TFIIB z 21.7 38 0.00082 23.6 0.5 15 32-46 16-30 (43)
52 smart00586 ZnF_DBF Zinc finger 20.8 46 0.001 24.8 0.8 27 36-65 6-32 (49)
53 KOG3915 Transcription regulato 20.3 5.3E+02 0.011 27.9 8.5 18 202-220 480-497 (641)
54 PF07911 DUF1677: Protein of u 20.2 16 0.00035 30.5 -1.9 21 28-50 26-46 (91)
55 COG1645 Uncharacterized Zn-fin 20.2 44 0.00096 29.6 0.7 20 22-43 33-52 (131)
No 1
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=7.9e-57 Score=414.74 Aligned_cols=258 Identities=41% Similarity=0.622 Sum_probs=194.3
Q ss_pred cHHHHHHHHHHHHHHHHhhhcccCCccccCCCCCceeecCcccccCchhhHHhhCChHHHHHHHHhhhhccCCCCcccCC
Q 020249 2 DAARKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGATGNNTRVVSD 81 (329)
Q Consensus 2 ~~~~~ka~~Rallr~~r~~krI~~P~A~Yn~~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk~~~~~~~~~~~~~ 81 (329)
--+++|+|||++|+..+...||++|||+||.+|+|+|+|||++|| ++||++|++||+||++|..||-.. +.
T Consensus 2 nq~~~krl~k~k~~~kk~~~ri~splakyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~~--------~K 72 (264)
T KOG3032|consen 2 NQAKKKRLFKSKLNAKKKDTRIDSPLAKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSRG--------SK 72 (264)
T ss_pred chHHHHHHHHHHhhccCcccccccHhhccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhhh--------cc
Confidence 348999999999999999999999999999999999999999999 999999999999999999999210 01
Q ss_pred CCCCCCCCCCCCCCCCCcchhhhhhhhcccCCCCCCCCCCCcccCCccCCCCCcCCccccCCCCCCCCCCcccccccccc
Q 020249 82 AAKPEAGVDSSRSESGSASQNAELENSAKLGKARPPSVLPSNFFDNQEVKRPKTDSVKLVDPDSTKPSGVSAKTQALKSV 161 (329)
Q Consensus 82 ~a~p~~~~~k~k~~~~~~~~~k~~k~~~~~~~~q~~S~LP~dFFd~~~~~~~~~~~~~ll~~d~~~~s~~~~~~~v~~~~ 161 (329)
.+++.+ .+-+..+..+..+..- -+.+.+|.||++||+....+.+.- +...+.
T Consensus 73 v~k~~~---T~~p~~p~spn~kts~-----~pnk~pstlPdk~~~~eqekh~~g---------------d~e~ka----- 124 (264)
T KOG3032|consen 73 VAKTRP---TKIPALPKSPNSKTSF-----FPNKEPSTLPDKSKNLEQEKHTIG---------------DEENKA----- 124 (264)
T ss_pred cccCcC---ccCccCCCCCCccccc-----cCCCCCCcCCCCCcchhcccCCCC---------------ccchhc-----
Confidence 111111 1111111001111110 122345899999987753322211 111111
Q ss_pred ccccccCCCCCCCccccCCCCCCCCCCcchhccchhhhhhhccCCCCCCCCChhhhhhhhcCCCCCCCHHHHHHHHHHHH
Q 020249 162 VLENEMDELPNGNAVHAEKGQPFKEHPEKSKQNAGSEAKQIKGALPEGFFDNKDADLLARGIKPVKPDVKDEYKEYEKLI 241 (329)
Q Consensus 162 ~~e~~~~~LP~~~~~~~~~~~p~~~~s~s~~k~~~~E~~~~~~~LPeGFFDd~~~DakaR~v~~~~~~~~~Ew~~FqkeI 241 (329)
.| +|.+.+ ++.++.++||+|||||+..|+.||||..++++|++||++||++|
T Consensus 125 -----qG-----nfs~~p------------------enent~e~lPegFFDdke~d~~vr~~~e~k~~~d~Ey~rfqkeI 176 (264)
T KOG3032|consen 125 -----QG-----NFSNQP------------------ENENTNENLPEGFFDDKEADLLVRGIKEVKPDIDDEYKRFQKEI 176 (264)
T ss_pred -----cc-----cccCCc------------------cccchhhcCcccccCchhhhhhhhhccccchhHHHHHHHHHHHH
Confidence 12 233322 44668999999999999999999999999999999999999999
Q ss_pred HHHHHHhhHHHhHHHHHHHHHHHhhhhHHHH---HHHHHHHHHHHHHHHhhhhhhccCCcccccCCCCCcCCCCCCchhh
Q 020249 242 QEDLKQVDDRLEEEEIDAAEMIEEYESVDQK---EKVEALRKKKKEWEASSRSAKSRGSSEVARKEPPKEELSSDDDSEE 318 (329)
Q Consensus 242 ~ee~~es~a~~EEeee~a~~eRe~~Ei~EQi---~Rve~Lk~kk~~~~~~r~~k~~~~~~~~~~~~~~~e~sssdde~~~ 318 (329)
++++++++.|+||++++++..|+|.||+||| .||+.|+.++.+++...+.+..++ + ...+.++|.+|.|+++
T Consensus 177 ~~~~tesd~iveEeeed~~l~reieeidEQi~~~kkvekl~~qK~ellnkkRe~~~k~--e---v~ke~eesddDgeddD 251 (264)
T KOG3032|consen 177 QDDLTESDSIVEEEEEDAALTREIEEIDEQISYKKKVEKLKRQKMELLNKKREKTSKG--E---VKKEEEESDDDGEDDD 251 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc--c---cCcccccCccccchhh
Confidence 9999999999999999999999999999999 999999999999988655554431 1 1113466666777788
Q ss_pred hhhhcccccCC
Q 020249 319 IFAVDWRAQHL 329 (329)
Q Consensus 319 d~~~DWRaK~~ 329 (329)
++++|||+||+
T Consensus 252 l~a~DWRaKnl 262 (264)
T KOG3032|consen 252 LSAVDWRAKNL 262 (264)
T ss_pred hhhhhhhhhhc
Confidence 88889999996
No 2
>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=97.90 E-value=7.9e-06 Score=54.05 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=30.9
Q ss_pred CCceeecCcccccCchhhHHhhCChHHHHHHHH
Q 020249 34 DQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKN 66 (329)
Q Consensus 34 G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~ 66 (329)
|...|.+|+..+.+...|..|+.|+.|+.++.+
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 678999999999999999999999999999875
No 3
>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=97.54 E-value=3.8e-05 Score=48.96 Aligned_cols=27 Identities=37% Similarity=0.642 Sum_probs=25.1
Q ss_pred CceeecCcccccCchhhHHhhCChHHH
Q 020249 35 QPVCRVCDVVLKSDSQWDAHQASRKHH 61 (329)
Q Consensus 35 ~L~C~lC~~~vKsEslW~aH~~Sk~Hr 61 (329)
|..|.+|+..++++..|..|+.|+.||
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 468999999999999999999999997
No 4
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=96.89 E-value=0.00057 Score=70.13 Aligned_cols=35 Identities=31% Similarity=0.633 Sum_probs=33.7
Q ss_pred ceeecCcccccCchhhHHhhCChHHHHHHHHhhhh
Q 020249 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (329)
Q Consensus 36 L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk~~ 70 (329)
|.|++||...|+|..|.-|..||+|+++|..|+++
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqe 327 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQE 327 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999864
No 5
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.65 E-value=0.001 Score=41.06 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=23.7
Q ss_pred ceeecCcccccCchhhHHhhCChHH
Q 020249 36 PVCRVCDVVLKSDSQWDAHQASRKH 60 (329)
Q Consensus 36 L~C~lC~~~vKsEslW~aH~~Sk~H 60 (329)
+.|.+|++...++..|..|+.|+.|
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 3699999999999999999999998
No 6
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=96.54 E-value=0.0035 Score=57.97 Aligned_cols=54 Identities=17% Similarity=0.343 Sum_probs=47.6
Q ss_pred ccCCccccCCCCCceeecCcccccCchhhHHhhCChHHHHHHHHhhhhccCCCC
Q 020249 23 INSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGATGNNT 76 (329)
Q Consensus 23 I~~P~A~Yn~~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk~~~~~~~~ 76 (329)
.+.||..-|.+|++.|.||+..-.+|+-.-.|..+|+|++|+.+...++..+.+
T Consensus 41 ~dDPyl~knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~eksslgr 94 (222)
T COG5246 41 MDDPYLSKNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSEEKSSLGR 94 (222)
T ss_pred ccCcchhhcCCCcEEeeeeccccccHHHHHHhhccchhhhhHHHHHHHhhcccc
Confidence 567999999999999999999988999999999999999999998665555543
No 7
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=95.87 E-value=0.0098 Score=55.34 Aligned_cols=62 Identities=16% Similarity=0.306 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHHhhhcccCCccccCCCCCceeecCcccccCchhhHHhhCChHHHHHHHHhhh
Q 020249 6 KKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (329)
Q Consensus 6 ~ka~~Rallr~~r~~krI~~P~A~Yn~~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk~ 69 (329)
|+--+|.|+-..- ---..||.--|-+|.+.|.||+..-.+|.-.-+|..+|+|.+||++...
T Consensus 26 RrerlrqLaleti--dl~kDPy~mkNh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa 87 (222)
T KOG0227|consen 26 RRERLRQLALETI--DLNKDPYFMKNHLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAA 87 (222)
T ss_pred HHHHHHHHHHhhc--ccccCchhhhccCcceeehhhhhhhcchhhhhhhhccchhhHHHHHHHH
Confidence 4444555544331 1134699999999999999999999999999999999999999998543
No 8
>PLN02748 tRNA dimethylallyltransferase
Probab=94.71 E-value=0.02 Score=59.03 Aligned_cols=36 Identities=31% Similarity=0.759 Sum_probs=32.0
Q ss_pred CCceeecCcc-cccCchhhHHhhCChHHHHHHHHhhh
Q 020249 34 DQPVCRVCDV-VLKSDSQWDAHQASRKHHEAIKNIKA 69 (329)
Q Consensus 34 G~L~C~lC~~-~vKsEslW~aH~~Sk~Hr~~v~~lk~ 69 (329)
-+.+|-+|+. ++..|--|..|+.|+.||.++.++++
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k 453 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ 453 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence 3457999997 79999999999999999999998875
No 9
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=88.99 E-value=0.21 Score=43.66 Aligned_cols=37 Identities=16% Similarity=0.292 Sum_probs=34.9
Q ss_pred CCCCceeecCcccccCchhhHHhhCChHHHHHHHHhh
Q 020249 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (329)
Q Consensus 32 ~~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk 68 (329)
..||-.|+.|....=++..-..|..+|.|+-+|..|.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~ 90 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELR 90 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcc
Confidence 5799999999999889999999999999999999987
No 10
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=88.85 E-value=0.53 Score=43.43 Aligned_cols=43 Identities=21% Similarity=0.341 Sum_probs=35.5
Q ss_pred CCccccCCCCCceeecCcccccCchhhHHhhCChHHHHHHHHh
Q 020249 25 SPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (329)
Q Consensus 25 ~P~A~Yn~~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~l 67 (329)
.+-+.-+..|..-|-||+.+||.=.-+--||++|.|.-|+..+
T Consensus 65 tk~tp~sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 65 TKSTPRSQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred ccCCcccccCceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 3444456778899999999999877788999999999999864
No 11
>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=86.86 E-value=0.51 Score=32.94 Aligned_cols=30 Identities=33% Similarity=0.572 Sum_probs=19.2
Q ss_pred eeecCcccccCch--hhHHhhCChHHHHHHHH
Q 020249 37 VCRVCDVVLKSDS--QWDAHQASRKHHEAIKN 66 (329)
Q Consensus 37 ~C~lC~~~vKsEs--lW~aH~~Sk~Hr~~v~~ 66 (329)
-|-.|+.-|.+.+ .|..|..|.+|+.|+.+
T Consensus 5 yCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 5 YCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred ecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 5999999995444 79999999999999975
No 12
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=77.80 E-value=1.3 Score=46.13 Aligned_cols=33 Identities=27% Similarity=0.641 Sum_probs=30.2
Q ss_pred CceeecCcccccCchhhHHhhCChHHHHHHHHh
Q 020249 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (329)
Q Consensus 35 ~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~l 67 (329)
+-.|.|||+.|-+|-..-.|+.|.+|.+.|..+
T Consensus 493 kkqcslcnvlissevylfshvkgrkhqqal~e~ 525 (672)
T KOG4722|consen 493 KKQCSLCNVLISSEVYLFSHVKGRKHQQALNEL 525 (672)
T ss_pred hhccchhhhhhhhhhhhhhhhcchhHHHHHHHH
Confidence 456999999999999999999999999998875
No 13
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.52 E-value=12 Score=36.17 Aligned_cols=29 Identities=28% Similarity=0.343 Sum_probs=17.5
Q ss_pred HHHHHHHHHhhhhHHHH--HHHHHHHHHHHH
Q 020249 256 EIDAAEMIEEYESVDQK--EKVEALRKKKKE 284 (329)
Q Consensus 256 ee~a~~eRe~~Ei~EQi--~Rve~Lk~kk~~ 284 (329)
.++.-++|...+-++-| +++++|.++++.
T Consensus 200 ieeidEQi~~~kkvekl~~qK~ellnkkRe~ 230 (264)
T KOG3032|consen 200 IEEIDEQISYKKKVEKLKRQKMELLNKKREK 230 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 33444667777777777 555555554443
No 14
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=71.02 E-value=2.3 Score=36.71 Aligned_cols=39 Identities=15% Similarity=0.345 Sum_probs=35.8
Q ss_pred CCCCCceeecCcccccCchhhHHhhCChHHHHHHHHhhh
Q 020249 31 NEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (329)
Q Consensus 31 n~~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk~ 69 (329)
...||--|+-|...+-+|-.--.|..|+-|+.++..|.+
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRe 89 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELRE 89 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhc
Confidence 357999999999999999999999999999999999885
No 15
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=65.24 E-value=2.2 Score=32.88 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=25.9
Q ss_pred CceeecCcccccCchhhHHhhCChHHHHHHH
Q 020249 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (329)
Q Consensus 35 ~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~ 65 (329)
.+.|.+|+...++-..+..|+.++.|.....
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 5999999999999999999999999987654
No 16
>PF03037 KMP11: Kinetoplastid membrane protein 11; InterPro: IPR004132 Kinetoplastid membrane protein 11 is a major cell surface glycoprotein of the parasite Leishmania donovani. It stimulates T-cell proliferation and may play a role in the immunlogy of the dieases Leishmaniasis.; GO: 0006952 defense response, 0008284 positive regulation of cell proliferation
Probab=64.74 E-value=21 Score=29.01 Aligned_cols=41 Identities=27% Similarity=0.673 Sum_probs=30.0
Q ss_pred CCCCCChhhhhhhhcCCCCCCCHHHHHHHHHHHHHHHHHHhhHHHhH
Q 020249 208 EGFFDNKDADLLARGIKPVKPDVKDEYKEYEKLIQEDLKQVDDRLEE 254 (329)
Q Consensus 208 eGFFDd~~~DakaR~v~~~~~~~~~Ew~~FqkeI~ee~~es~a~~EE 254 (329)
..||-|+--++.. -+.|.+-|+.|.+-|+|-+..-...+-|
T Consensus 28 ~kffadkpdestl------spemkehyekfe~miqehtdkfnkkm~e 68 (90)
T PF03037_consen 28 KKFFADKPDESTL------SPEMKEHYEKFERMIQEHTDKFNKKMHE 68 (90)
T ss_pred HhhhcCCCccccc------CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4689887554332 4689999999999999887776654433
No 17
>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=59.66 E-value=5 Score=32.96 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=25.6
Q ss_pred CCCCCceeecCcccccCchhhHHhhCChHHHH
Q 020249 31 NEFDQPVCRVCDVVLKSDSQWDAHQASRKHHE 62 (329)
Q Consensus 31 n~~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~ 62 (329)
....-|+|+.|...|.. +-|..|+.++-|..
T Consensus 7 ~~~~vlIC~~C~~av~~-~~v~~HL~~~H~~~ 37 (109)
T PF12013_consen 7 PEYRVLICRQCQYAVQP-SEVESHLRKRHHIL 37 (109)
T ss_pred CcCCEEEeCCCCcccCc-hHHHHHHHHhcccc
Confidence 36678999999998887 55999999877655
No 18
>PTZ00448 hypothetical protein; Provisional
Probab=58.68 E-value=8.5 Score=39.21 Aligned_cols=36 Identities=22% Similarity=0.352 Sum_probs=31.8
Q ss_pred CCCceeecCcccccCchhhHHhhCChHHHHHHHHhh
Q 020249 33 FDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (329)
Q Consensus 33 ~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk 68 (329)
++..+|..|++.+.+...-..|..|-=||-|+.+.-
T Consensus 312 ~~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl 347 (373)
T PTZ00448 312 SNMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNA 347 (373)
T ss_pred cCCccccccccccCCHHHHHHHhhhhHHHHHHHHHh
Confidence 356789999999998889999999999999998853
No 19
>PF12476 DUF3696: Protein of unknown function (DUF3696); InterPro: IPR022532 This domain is found in bacteria and archaea, and is approximately 50 amino acids in length.
Probab=56.72 E-value=4 Score=29.75 Aligned_cols=16 Identities=56% Similarity=0.914 Sum_probs=12.9
Q ss_pred cCCCCCCCCChhhhhh
Q 020249 204 GALPEGFFDNKDADLL 219 (329)
Q Consensus 204 ~~LPeGFFDd~~~Dak 219 (329)
..-|+||||.-..|+.
T Consensus 34 ~~WP~GFFDq~~~~l~ 49 (52)
T PF12476_consen 34 SNWPEGFFDQWDKDLR 49 (52)
T ss_pred ccCCCchhhHHHHHHH
Confidence 6789999998876654
No 20
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=49.30 E-value=10 Score=23.38 Aligned_cols=21 Identities=24% Similarity=0.346 Sum_probs=19.2
Q ss_pred ceeecCcccccCchhhHHhhC
Q 020249 36 PVCRVCDVVLKSDSQWDAHQA 56 (329)
Q Consensus 36 L~C~lC~~~vKsEslW~aH~~ 56 (329)
..|..|+....+...|..|..
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 479999999999999999984
No 21
>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=47.64 E-value=10 Score=21.83 Aligned_cols=20 Identities=25% Similarity=0.594 Sum_probs=15.9
Q ss_pred eeecCcccccCchhhHHhhC
Q 020249 37 VCRVCDVVLKSDSQWDAHQA 56 (329)
Q Consensus 37 ~C~lC~~~vKsEslW~aH~~ 56 (329)
.|.+|+...++-..|..|+.
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHH
Confidence 59999999999999999975
No 22
>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=41.28 E-value=36 Score=32.92 Aligned_cols=50 Identities=12% Similarity=0.147 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHhhhcccCCccccCCCCCceeecCcccccC-chhhHHhhCChHHHH
Q 020249 5 RKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKS-DSQWDAHQASRKHHE 62 (329)
Q Consensus 5 ~~ka~~Rallr~~r~~krI~~P~A~Yn~~G~L~C~lC~~~vKs-EslW~aH~~Sk~Hr~ 62 (329)
..-..|+++|+ .||+..|...|.+.|+|=+--|.. -..-..|+.||.-+.
T Consensus 3 ~~~~~v~~~L~--------~~p~l~~~~~~rvrC~lTGHEmp~~~~~l~~y~~gKKy~~ 53 (244)
T PF05477_consen 3 ELPKEVQAFLK--------SHPFLELTENGRVRCTLTGHEMPCRLDELQQYIRGKKYQR 53 (244)
T ss_pred cchHHHHHHHh--------cCCceEecCCCeEEEeecCcccCCCHHHHHHHhccHHHHH
Confidence 45667888886 589999999999999998733222 234789999999883
No 23
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=40.53 E-value=24 Score=36.17 Aligned_cols=35 Identities=23% Similarity=0.334 Sum_probs=32.0
Q ss_pred CCceeecCcccccCchhhHHhhCChHHHHHHHHhh
Q 020249 34 DQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (329)
Q Consensus 34 G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk 68 (329)
+.+.|+.|++.+++.-+-.+|..|-=||-||.+.-
T Consensus 2 t~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkV 36 (390)
T KOG2785|consen 2 TGFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKV 36 (390)
T ss_pred CcceeeceeeeeccHHHHHHHhhhhHHHhhHHhHh
Confidence 45899999999999999999999999999998854
No 24
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=39.86 E-value=1.4e+02 Score=33.93 Aligned_cols=23 Identities=22% Similarity=0.351 Sum_probs=15.4
Q ss_pred hhccCCC-CCCCCChhhhhhhhcC
Q 020249 201 QIKGALP-EGFFDNKDADLLARGI 223 (329)
Q Consensus 201 ~~~~~LP-eGFFDd~~~DakaR~v 223 (329)
+....|| .-=|.|+.++.-.||-
T Consensus 303 ep~kklP~~~TFEDKrkeNy~kGq 326 (1118)
T KOG1029|consen 303 EPPKKLPAPVTFEDKRKENYEKGQ 326 (1118)
T ss_pred CccccCCCCcchhhhhHHhHhhhh
Confidence 3455677 3468888888777664
No 25
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=39.10 E-value=12 Score=38.29 Aligned_cols=34 Identities=26% Similarity=0.486 Sum_probs=31.5
Q ss_pred ceeecCcccccCchhhHHhhCChHHHHHHHHhhh
Q 020249 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (329)
Q Consensus 36 L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk~ 69 (329)
+.|.+|+....++..-.-|+.|+.|+.++.+...
T Consensus 69 ~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 69 VYCEACNKSFASPKAHENHLKSKKHVENLSNHQR 102 (390)
T ss_pred eehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence 5699999999999999999999999999999764
No 26
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=36.55 E-value=23 Score=26.58 Aligned_cols=26 Identities=31% Similarity=0.696 Sum_probs=19.0
Q ss_pred cCC-CCCceeecCccccc----CchhhHHhh
Q 020249 30 YNE-FDQPVCRVCDVVLK----SDSQWDAHQ 55 (329)
Q Consensus 30 Yn~-~G~L~C~lC~~~vK----sEslW~aH~ 55 (329)
|+. .+.+.|..|+..+. .+..|.-|.
T Consensus 30 y~~~~d~v~C~~C~~~l~~w~~~d~p~~~H~ 60 (71)
T smart00238 30 YTGVGDEVKCFFCGGELDNWEPGDDPWEEHK 60 (71)
T ss_pred ECCCCCEEEeCCCCCCcCCCCCCCCHHHHHh
Confidence 655 34899999998874 466677774
No 27
>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=36.37 E-value=28 Score=32.96 Aligned_cols=40 Identities=23% Similarity=0.385 Sum_probs=31.7
Q ss_pred CCCCCceeecCcccccCchhhHHhhCChHHHHHHHHhhhhc
Q 020249 31 NEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGA 71 (329)
Q Consensus 31 n~~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk~~~ 71 (329)
-+-++-.|.+|....|..-.|.-||. .+|-+.|+.++++.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ev 112 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKEV 112 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHHH
Confidence 46678999999999999999999998 56999999887643
No 28
>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=36.20 E-value=13 Score=21.96 Aligned_cols=21 Identities=24% Similarity=0.509 Sum_probs=18.5
Q ss_pred eeecCcccccCchhhHHhhCC
Q 020249 37 VCRVCDVVLKSDSQWDAHQAS 57 (329)
Q Consensus 37 ~C~lC~~~vKsEslW~aH~~S 57 (329)
.|..|+....+-+.+..|+..
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHhH
Confidence 699999999999999999864
No 29
>PF14968 CCDC84: Coiled coil protein 84
Probab=34.87 E-value=21 Score=36.01 Aligned_cols=27 Identities=30% Similarity=0.477 Sum_probs=22.4
Q ss_pred eecCcccccCchhhHHhhCChHHHHHHHHh
Q 020249 38 CRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (329)
Q Consensus 38 C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~l 67 (329)
|.||+..-= .|..|+.|+.|+.+|..+
T Consensus 2 C~vCr~~h~---~gr~H~Y~~~Hq~~L~~~ 28 (336)
T PF14968_consen 2 CEVCRRNHD---QGRRHVYSPKHQKSLSAF 28 (336)
T ss_pred cchhhCccc---ccCCCccCHHHHHHHHHH
Confidence 999986543 399999999999999864
No 30
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=34.52 E-value=11 Score=35.74 Aligned_cols=47 Identities=21% Similarity=0.422 Sum_probs=36.6
Q ss_pred hhcccCCccccCCCCCceeecCcccccCchhhHHhhCChHHHHHHHHh
Q 020249 20 EKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (329)
Q Consensus 20 ~krI~~P~A~Yn~~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~l 67 (329)
.+-..||--+-..-----|-+|.+-|+. +-|..|..|-.|.-++..+
T Consensus 69 ~~ets~p~nss~~e~lfyCE~Cd~~ip~-~~~snH~tSttHllsl~~~ 115 (223)
T KOG2384|consen 69 DRETSHPMNSSRDEALFYCEVCDIYIPN-SKKSNHFTSTTHLLSLQHI 115 (223)
T ss_pred hccCCCcccCCCCCccchhhhhhhhccC-CCCccchhhHHHHhhhccC
Confidence 3345677666554445679999999994 8899999999999888764
No 31
>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=33.42 E-value=31 Score=31.66 Aligned_cols=31 Identities=26% Similarity=0.512 Sum_probs=28.2
Q ss_pred eeecCcccccCchhhHHhhCChHHHHHHHHh
Q 020249 37 VCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (329)
Q Consensus 37 ~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~l 67 (329)
.|.+|..+-=.|.=...|+.|+-|++-+.-|
T Consensus 2 ~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i 32 (165)
T PF04988_consen 2 TCSFCKFRTFEEKEIEKHLESKFHKETLKYI 32 (165)
T ss_pred ccceeeeecccHHHHHHHHccchHHHHHHHH
Confidence 6999999887787789999999999999988
No 32
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=32.26 E-value=2.5e+02 Score=30.83 Aligned_cols=35 Identities=20% Similarity=0.092 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHhhhhHHHH-----------HHHHHHHHHHHHHHHh
Q 020249 254 EEEIDAAEMIEEYESVDQK-----------EKVEALRKKKKEWEAS 288 (329)
Q Consensus 254 Eeee~a~~eRe~~Ei~EQi-----------~Rve~Lk~kk~~~~~~ 288 (329)
+...+..+.|++...++-| .++++|+.+++.+++-
T Consensus 465 ~~~~~~~~~rei~~~~~~I~~L~~~L~e~~~~ve~L~~~l~~l~k~ 510 (652)
T COG2433 465 EVRDKVRKDREIRARDRRIERLEKELEEKKKRVEELERKLAELRKM 510 (652)
T ss_pred HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555556655444444 7788888888777653
No 33
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=29.22 E-value=25 Score=36.17 Aligned_cols=37 Identities=14% Similarity=0.306 Sum_probs=31.7
Q ss_pred CCCCceeecCcccccCchhhHHhhCChHHHHHHHHhh
Q 020249 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (329)
Q Consensus 32 ~~G~L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~~lk 68 (329)
.+...-|.+|..-++.=++..+|+.||.|..+.+..+
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 4567899999988887789999999999998887644
No 34
>PF15303 RNF111_N: E3 ubiquitin-protein ligase Arkadia N-terminus
Probab=29.07 E-value=82 Score=30.91 Aligned_cols=17 Identities=35% Similarity=0.487 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHH
Q 020249 270 DQKEKVEALRKKKKEWE 286 (329)
Q Consensus 270 EQi~Rve~Lk~kk~~~~ 286 (329)
-|.+|+.+||+|++.+.
T Consensus 205 KqKERi~lqRkKREa~A 221 (269)
T PF15303_consen 205 KQKERIRLQRKKREAAA 221 (269)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45588999998888654
No 35
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=28.98 E-value=28 Score=22.30 Aligned_cols=20 Identities=20% Similarity=0.395 Sum_probs=16.3
Q ss_pred ceeecCcccccCchhhHHhhC
Q 020249 36 PVCRVCDVVLKSDSQWDAHQA 56 (329)
Q Consensus 36 L~C~lC~~~vKsEslW~aH~~ 56 (329)
+.|.+|+..| ++..-..|+-
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 5799999999 5677888875
No 36
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=27.93 E-value=38 Score=25.10 Aligned_cols=27 Identities=26% Similarity=0.476 Sum_probs=21.2
Q ss_pred ceeecCcccccCchhhHHhhCChHHHHHHH
Q 020249 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (329)
Q Consensus 36 L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~ 65 (329)
--|-.|.+.-.+ -..|+.|.+||.-+.
T Consensus 6 GYCE~C~~ky~~---l~~Hi~s~~Hr~FA~ 32 (49)
T PF07535_consen 6 GYCENCRVKYDD---LEEHIQSEKHRKFAE 32 (49)
T ss_pred ccCccccchhhh---HHHHhCCHHHHHHHc
Confidence 358888876654 789999999998654
No 37
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=27.29 E-value=44 Score=28.97 Aligned_cols=15 Identities=0% Similarity=0.432 Sum_probs=12.3
Q ss_pred CHHHHHHHHHHHHHH
Q 020249 229 DVKDEYKEYEKLIQE 243 (329)
Q Consensus 229 ~~~~Ew~~FqkeI~e 243 (329)
.-+++|++||+.|.-
T Consensus 91 ~s~~~WdRFMRFMeR 105 (113)
T PRK13610 91 NSEEAFERFMRFASR 105 (113)
T ss_pred CCHHHHHHHHHHHHH
Confidence 348899999999963
No 38
>TIGR03047 PS_II_psb28 photosystem II reaction center protein Psb28. Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW.
Probab=27.24 E-value=44 Score=28.77 Aligned_cols=14 Identities=14% Similarity=0.617 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHH
Q 020249 230 VKDEYKEYEKLIQE 243 (329)
Q Consensus 230 ~~~Ew~~FqkeI~e 243 (329)
-+++|++||+.|.-
T Consensus 85 s~~~WdRFMRFmeR 98 (109)
T TIGR03047 85 SEDEWDRFMRFMER 98 (109)
T ss_pred CHHHHHHHHHHHHH
Confidence 38899999999974
No 39
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=27.24 E-value=44 Score=28.88 Aligned_cols=14 Identities=7% Similarity=0.456 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHH
Q 020249 230 VKDEYKEYEKLIQE 243 (329)
Q Consensus 230 ~~~Ew~~FqkeI~e 243 (329)
-+++|++||+.|.-
T Consensus 86 s~~~WdRFMRFMeR 99 (111)
T PLN00039 86 SPREWDRFMRFMER 99 (111)
T ss_pred CHHHHHHHHHHHHH
Confidence 38899999999974
No 40
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=26.58 E-value=41 Score=25.04 Aligned_cols=23 Identities=35% Similarity=0.865 Sum_probs=17.1
Q ss_pred CCceeecCcccccC----chhhHHhhC
Q 020249 34 DQPVCRVCDVVLKS----DSQWDAHQA 56 (329)
Q Consensus 34 G~L~C~lC~~~vKs----EslW~aH~~ 56 (329)
+.+.|..|+..+.. ...|..|.+
T Consensus 33 d~v~C~~C~~~~~~w~~~d~p~~~H~~ 59 (69)
T cd00022 33 DEVKCFFCGLELKNWEPGDDPWEEHKR 59 (69)
T ss_pred CEEEeCCCCCCccCCCCCCCHHHHHhH
Confidence 56999999988764 566777653
No 41
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=26.36 E-value=47 Score=28.80 Aligned_cols=14 Identities=7% Similarity=0.527 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHH
Q 020249 230 VKDEYKEYEKLIQE 243 (329)
Q Consensus 230 ~~~Ew~~FqkeI~e 243 (329)
-+++|++||+.|.-
T Consensus 88 s~~~WdRFMRFMeR 101 (113)
T PRK13612 88 SEQEWDRFMRFMER 101 (113)
T ss_pred CHHHHHHHHHHHHH
Confidence 38899999999974
No 42
>PF14942 Muted: Organelle biogenesis, Muted-like protein
Probab=25.65 E-value=1.5e+02 Score=26.42 Aligned_cols=21 Identities=33% Similarity=0.493 Sum_probs=17.2
Q ss_pred CHHHHHHHHHHHHHHHHHHhh
Q 020249 229 DVKDEYKEYEKLIQEDLKQVD 249 (329)
Q Consensus 229 ~~~~Ew~~FqkeI~ee~~es~ 249 (329)
....+|+.|++++....+.++
T Consensus 104 ~~~~~we~f~~e~~~~~~~vd 124 (145)
T PF14942_consen 104 QRKQEWEEFMKEQQQKKQRVD 124 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999987777665
No 43
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=25.34 E-value=2.9e+02 Score=20.59 Aligned_cols=54 Identities=17% Similarity=0.270 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHhhHHHh--------HHHHHHHHHHHhhhhHHHH-----HHHHHHHHHHHHH
Q 020249 232 DEYKEYEKLIQEDLKQVDDRLE--------EEEIDAAEMIEEYESVDQK-----EKVEALRKKKKEW 285 (329)
Q Consensus 232 ~Ew~~FqkeI~ee~~es~a~~E--------Eeee~a~~eRe~~Ei~EQi-----~Rve~Lk~kk~~~ 285 (329)
.+|+.|.....+-....+.+.+ ..+.....-+.+.+++.+| .|...|......+
T Consensus 8 ~dWe~l~~l~~~R~~ll~~l~~~~~~~~~~~~~~~~~~l~~Il~~d~~i~~ll~~~~~~l~~~l~~~ 74 (84)
T PF05400_consen 8 GDWEELEELLDERQELLERLFEEQAALSPPEQEELRELLRRILELDQEIRALLQARRDELKQELRQL 74 (84)
T ss_dssp T-HHHHHHHHHHHHHHHHHHHHCHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred CcHHHHHHHHHHHHHHHHHHhhccccCChhhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788888777766655533322 2233333345566777777 4444444444333
No 44
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=25.23 E-value=50 Score=28.61 Aligned_cols=14 Identities=0% Similarity=0.413 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHH
Q 020249 230 VKDEYKEYEKLIQE 243 (329)
Q Consensus 230 ~~~Ew~~FqkeI~e 243 (329)
-+++|++||+.|.-
T Consensus 88 s~~~WdRFMRFMeR 101 (113)
T CHL00128 88 NPEAWDRFMRFMER 101 (113)
T ss_pred CHHHHHHHHHHHHH
Confidence 38899999999974
No 45
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=24.16 E-value=41 Score=30.86 Aligned_cols=30 Identities=37% Similarity=0.698 Sum_probs=24.9
Q ss_pred eeecCcccccCch--hhHHhhCChHHHHHHHH
Q 020249 37 VCRVCDVVLKSDS--QWDAHQASRKHHEAIKN 66 (329)
Q Consensus 37 ~C~lC~~~vKsEs--lW~aH~~Sk~Hr~~v~~ 66 (329)
.|--|++-+-+.+ +-..|++|++|+.|+..
T Consensus 5 yCDYCdt~LthDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 5 YCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred hhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence 5999997766554 57899999999999975
No 46
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=24.08 E-value=5.1e+02 Score=24.86 Aligned_cols=10 Identities=30% Similarity=0.796 Sum_probs=8.6
Q ss_pred cCCCCCCCCC
Q 020249 204 GALPEGFFDN 213 (329)
Q Consensus 204 ~~LPeGFFDd 213 (329)
+.||++||+.
T Consensus 2 ~si~~~yF~~ 11 (291)
T PF10475_consen 2 ESIPAIYFDE 11 (291)
T ss_pred CCCcHhhcCC
Confidence 5799999997
No 47
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=23.46 E-value=58 Score=27.87 Aligned_cols=14 Identities=7% Similarity=0.503 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHH
Q 020249 230 VKDEYKEYEKLIQE 243 (329)
Q Consensus 230 ~~~Ew~~FqkeI~e 243 (329)
-+++|++||+.|.-
T Consensus 81 s~~~wdRFMRFmeR 94 (104)
T PRK13611 81 TEAEWDRFLRFMER 94 (104)
T ss_pred CHHHHHHHHHHHHH
Confidence 38899999999974
No 48
>PRK12495 hypothetical protein; Provisional
Probab=23.03 E-value=42 Score=32.22 Aligned_cols=20 Identities=25% Similarity=0.556 Sum_probs=0.0
Q ss_pred cCCccccCCCCCceeecCcccc
Q 020249 24 NSPLVRYNEFDQPVCRVCDVVL 45 (329)
Q Consensus 24 ~~P~A~Yn~~G~L~C~lC~~~v 45 (329)
..||-+| .|...|+.|...|
T Consensus 49 G~PIpa~--pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 49 GDPIFRH--DGQEFCPTCQQPV 68 (226)
T ss_pred cCcccCC--CCeeECCCCCCcc
No 49
>smart00355 ZnF_C2H2 zinc finger.
Probab=22.93 E-value=40 Score=19.21 Aligned_cols=20 Identities=35% Similarity=0.569 Sum_probs=17.2
Q ss_pred eeecCcccccCchhhHHhhC
Q 020249 37 VCRVCDVVLKSDSQWDAHQA 56 (329)
Q Consensus 37 ~C~lC~~~vKsEslW~aH~~ 56 (329)
.|..|.....+.+-+..|+.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 69999999888888888876
No 50
>PF03912 Psb28: Psb28 protein; InterPro: IPR005610 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein Psb28 (PsbW) found in PSII, where it is a subunit of the oxygen-evolving complex. Psb28 appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of Psb28, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 1 Psb28.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0016020 membrane; PDB: 2KVO_A.
Probab=21.75 E-value=52 Score=28.33 Aligned_cols=13 Identities=8% Similarity=0.639 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHH
Q 020249 231 KDEYKEYEKLIQE 243 (329)
Q Consensus 231 ~~Ew~~FqkeI~e 243 (329)
+++|++||+.|.-
T Consensus 86 ~~~WdRFMRFMeR 98 (108)
T PF03912_consen 86 EEEWDRFMRFMER 98 (108)
T ss_dssp SHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 6899999999974
No 51
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.65 E-value=38 Score=23.59 Aligned_cols=15 Identities=40% Similarity=0.749 Sum_probs=11.6
Q ss_pred CCCCceeecCccccc
Q 020249 32 EFDQPVCRVCDVVLK 46 (329)
Q Consensus 32 ~~G~L~C~lC~~~vK 46 (329)
..|.++|..|+.+|-
T Consensus 16 ~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 16 ERGELVCPNCGLVLE 30 (43)
T ss_dssp TTTEEEETTT-BBEE
T ss_pred CCCeEECCCCCCEee
Confidence 579999999997754
No 52
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=20.79 E-value=46 Score=24.76 Aligned_cols=27 Identities=22% Similarity=0.400 Sum_probs=20.3
Q ss_pred ceeecCcccccCchhhHHhhCChHHHHHHH
Q 020249 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (329)
Q Consensus 36 L~C~lC~~~vKsEslW~aH~~Sk~Hr~~v~ 65 (329)
--|-.|..--.. ...|+.|.+||.=+.
T Consensus 6 GYCE~Cr~kfd~---l~~Hi~s~~Hr~FA~ 32 (49)
T smart00586 6 GYCENCREKYDD---LETHLLSEKHRRFAE 32 (49)
T ss_pred cccccHhHHHhh---HHHHhccHHHHHHHc
Confidence 357788765553 789999999997554
No 53
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=20.26 E-value=5.3e+02 Score=27.87 Aligned_cols=18 Identities=33% Similarity=0.111 Sum_probs=11.5
Q ss_pred hccCCCCCCCCChhhhhhh
Q 020249 202 IKGALPEGFFDNKDADLLA 220 (329)
Q Consensus 202 ~~~~LPeGFFDd~~~Daka 220 (329)
...+||.||= .+-.++-+
T Consensus 480 ~~~al~gG~~-gp~i~ada 497 (641)
T KOG3915|consen 480 HGQALPGGFP-GPFIFADA 497 (641)
T ss_pred CCCcCCCCCC-Cccccccc
Confidence 4567888886 55555544
No 54
>PF07911 DUF1677: Protein of unknown function (DUF1677); InterPro: IPR012876 The sequences found in this family are all derived from hypothetical plant proteins of unknown function. The region features a number of highly conserved cysteine residues.
Probab=20.24 E-value=16 Score=30.48 Aligned_cols=21 Identities=29% Similarity=0.537 Sum_probs=17.9
Q ss_pred cccCCCCCceeecCcccccCchh
Q 020249 28 VRYNEFDQPVCRVCDVVLKSDSQ 50 (329)
Q Consensus 28 A~Yn~~G~L~C~lC~~~vKsEsl 50 (329)
++| .|..+|-||...||.|..
T Consensus 26 ~ry--~GrWvCGLC~EAVkeE~~ 46 (91)
T PF07911_consen 26 ERY--GGRWVCGLCSEAVKEEVG 46 (91)
T ss_pred HHh--CCeehhhcCHHHHHHHHh
Confidence 357 899999999999998754
No 55
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.21 E-value=44 Score=29.58 Aligned_cols=20 Identities=30% Similarity=0.632 Sum_probs=17.3
Q ss_pred cccCCccccCCCCCceeecCcc
Q 020249 22 RINSPLVRYNEFDQPVCRVCDV 43 (329)
Q Consensus 22 rI~~P~A~Yn~~G~L~C~lC~~ 43 (329)
+=..||.+| +|.+.|.+|..
T Consensus 33 ~Cg~PLF~K--dG~v~CPvC~~ 52 (131)
T COG1645 33 KCGTPLFRK--DGEVFCPVCGY 52 (131)
T ss_pred ccCCcceee--CCeEECCCCCc
Confidence 467899996 89999999994
Done!