Query 024130
Match_columns 272
No_of_seqs 123 out of 131
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 09:13:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024130.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024130hhsearch_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 6.6E-46 1.4E-50 335.2 15.9 205 2-271 2-206 (264)
2 smart00451 ZnF_U1 U1-like zinc 98.1 2E-06 4.3E-11 55.4 2.3 33 34-66 2-34 (35)
3 PF12171 zf-C2H2_jaz: Zinc-fin 97.7 1.6E-05 3.4E-10 49.5 1.3 27 35-61 1-27 (27)
4 KOG0717 Molecular chaperone (D 97.2 0.00018 3.9E-09 72.0 2.6 35 36-70 293-327 (508)
5 PF12874 zf-met: Zinc-finger o 96.9 0.00046 1E-08 41.5 1.4 25 36-60 1-25 (25)
6 COG5246 PRP11 Splicing factor 96.4 0.0043 9.4E-08 56.1 4.8 52 23-74 41-92 (222)
7 KOG0227 Splicing factor 3a, su 95.8 0.012 2.5E-07 53.7 4.2 63 5-69 25-87 (222)
8 PLN02748 tRNA dimethylallyltra 95.2 0.012 2.6E-07 59.1 2.6 38 34-71 417-455 (468)
9 KOG4727 U1-like Zn-finger prot 91.9 0.19 4.1E-06 45.2 3.9 42 26-67 66-107 (193)
10 PF06220 zf-U1: U1 zinc finger 91.2 0.16 3.6E-06 34.5 2.1 30 37-66 5-36 (38)
11 KOG3408 U1-like Zn-finger-cont 89.7 0.17 3.7E-06 43.2 1.4 38 32-69 54-91 (129)
12 KOG4722 Zn-finger protein [Gen 78.3 1.2 2.6E-05 45.3 1.7 33 35-67 493-525 (672)
13 COG5112 UFD2 U1-like Zn-finger 74.7 1.6 3.5E-05 36.8 1.3 40 31-70 51-90 (126)
14 PF12756 zf-C2H2_2: C2H2 type 72.8 1.2 2.6E-05 33.3 0.1 31 35-65 50-80 (100)
15 PF12476 DUF3696: Protein of u 64.7 2.8 6.1E-05 29.8 0.6 17 203-219 33-49 (52)
16 PF12013 DUF3505: Protein of u 61.7 4.5 9.8E-05 32.3 1.4 32 30-62 6-37 (109)
17 PTZ00448 hypothetical protein; 61.0 5.9 0.00013 39.3 2.3 34 33-66 312-345 (373)
18 PF13912 zf-C2H2_6: C2H2-type 53.5 7.5 0.00016 23.3 1.1 21 36-56 2-22 (27)
19 PF13894 zf-C2H2_4: C2H2-type 53.1 7 0.00015 21.9 0.8 20 37-56 2-21 (24)
20 KOG2785 C2H2-type Zn-finger pr 52.9 5.5 0.00012 39.7 0.6 34 36-69 69-102 (390)
21 PF03037 KMP11: Kinetoplastid 51.2 24 0.00052 28.1 3.8 43 208-256 28-70 (90)
22 PF14942 Muted: Organelle biog 50.1 46 0.001 28.8 5.7 28 228-255 103-130 (145)
23 PF14968 CCDC84: Coiled coil p 45.4 11 0.00024 36.8 1.4 27 38-67 2-28 (336)
24 PF05477 SURF2: Surfeit locus 44.6 31 0.00066 32.5 4.1 51 5-63 3-54 (244)
25 smart00238 BIR Baculoviral inh 43.9 16 0.00034 26.7 1.7 26 30-55 30-60 (71)
26 PF04959 ARS2: Arsenite-resist 43.6 26 0.00056 32.2 3.4 43 28-71 70-112 (214)
27 KOG2785 C2H2-type Zn-finger pr 43.2 17 0.00037 36.4 2.3 33 34-66 2-34 (390)
28 PF07535 zf-DBF: DBF zinc fing 42.3 16 0.00035 26.4 1.5 27 36-65 6-32 (49)
29 KOG2384 Major histocompatibili 41.8 7.3 0.00016 36.1 -0.4 46 21-67 70-115 (223)
30 PF00096 zf-C2H2: Zinc finger, 41.6 9 0.0002 22.1 0.1 21 37-57 2-22 (23)
31 smart00586 ZnF_DBF Zinc finger 38.0 15 0.00033 26.6 0.8 27 36-65 6-32 (49)
32 KOG3454 U1 snRNP-specific prot 36.6 19 0.00042 32.2 1.4 30 37-66 5-36 (165)
33 cd00022 BIR Baculoviral inhibi 32.9 29 0.00063 25.1 1.6 23 34-56 33-59 (69)
34 COG5188 PRP9 Splicing factor 3 32.8 19 0.00042 36.1 0.9 38 32-69 235-272 (470)
35 PF04988 AKAP95: A-kinase anch 31.8 34 0.00074 30.6 2.1 31 37-67 2-32 (165)
36 PRK12495 hypothetical protein; 29.6 21 0.00046 33.3 0.5 36 21-57 28-63 (226)
37 smart00734 ZnF_Rad18 Rad18-lik 28.5 28 0.00061 21.8 0.8 20 36-56 2-21 (26)
38 PLN00039 photosystem II reacti 27.6 44 0.00094 28.2 2.0 13 231-243 87-99 (111)
39 PRK13610 photosystem II reacti 27.5 44 0.00095 28.3 2.0 14 230-243 92-105 (113)
40 TIGR03047 PS_II_psb28 photosys 27.5 44 0.00096 28.1 2.0 14 230-243 85-98 (109)
41 PRK13612 photosystem II reacti 26.7 47 0.001 28.1 2.0 14 230-243 88-101 (113)
42 CHL00128 psbW photosystem II p 25.6 50 0.0011 27.9 2.0 13 231-243 89-101 (113)
43 PRK13729 conjugal transfer pil 25.6 61 0.0013 33.4 3.0 62 205-266 56-120 (475)
44 smart00355 ZnF_C2H2 zinc finge 24.0 35 0.00076 18.9 0.6 20 37-56 2-21 (26)
45 PRK13611 photosystem II reacti 23.8 57 0.0012 27.2 2.0 14 230-243 81-94 (104)
46 PRK12495 hypothetical protein; 23.2 41 0.0009 31.5 1.2 22 23-46 48-69 (226)
47 PF00645 zf-PARP: Poly(ADP-rib 22.3 40 0.00086 25.4 0.7 21 30-50 2-22 (82)
48 PLN02847 triacylglycerol lipas 22.0 94 0.002 33.1 3.6 38 231-268 497-534 (633)
49 TIGR00357 methionine-R-sulfoxi 21.6 71 0.0015 27.6 2.2 34 14-47 19-52 (134)
50 PF08271 TF_Zn_Ribbon: TFIIB z 20.6 43 0.00093 22.7 0.6 15 32-46 16-30 (43)
No 1
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=6.6e-46 Score=335.24 Aligned_cols=205 Identities=43% Similarity=0.649 Sum_probs=155.1
Q ss_pred cHHHHHHHHHHHHHHHHhhhcccCCccccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHhhhhccCCCCcccCC
Q 024130 2 DAARKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGATGNNTRVVSD 81 (272)
Q Consensus 2 d~~~~ka~~Rallr~~r~~krI~~P~A~Yn~~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~lk~~~~~~~~~~~~~ 81 (272)
--+++|+|||++|+..+...||++|||+||++|+|+|+|||++|| ++||++|++||+||++|..||........
T Consensus 2 nq~~~krl~k~k~~~kk~~~ri~splakyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~~~Kv~k----- 75 (264)
T KOG3032|consen 2 NQAKKKRLFKSKLNAKKKDTRIDSPLAKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSRGSKVAK----- 75 (264)
T ss_pred chHHHHHHHHHHhhccCcccccccHhhccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhhhccccc-----
Confidence 348999999999999999999999999999999999999999999 89999999999999999999942222211
Q ss_pred CCCCCCCCCCCCCCCCcchhhhhhhhhcccCCCCCCCCCCCCccccccccCCCCCCccccCCCCCCCCCCcccchhccch
Q 024130 82 AAKPEAGVDSSRSESGSASQNAELENSAKLGKARPPSVLPSNFFDNQEVKRPKTDSVKLVDPDSTKPSGVSAKTQALKSV 161 (272)
Q Consensus 82 ~a~p~~~~~krk~~~~~~~~~k~~K~~~~~~~~~~~S~LP~dFFd~~~~~~~~~~~~~ll~~d~~~~~~~~~~~~~~~~~ 161 (272)
+. +.+.+..+.+...+. .. -+.+.+|.||++||+....+.+. |+...+.
T Consensus 76 ---~~---~T~~p~~p~spn~kt-s~----~pnk~pstlPdk~~~~eqekh~~---------------gd~e~ka----- 124 (264)
T KOG3032|consen 76 ---TR---PTKIPALPKSPNSKT-SF----FPNKEPSTLPDKSKNLEQEKHTI---------------GDEENKA----- 124 (264)
T ss_pred ---Cc---CccCccCCCCCCccc-cc----cCCCCCCcCCCCCcchhcccCCC---------------Cccchhc-----
Confidence 11 112222221111111 11 12235699999998754222211 1111111
Q ss_pred hhhccccCCCCCCccccCCCCCCCCCCcchhccchhhhhhhhcCCCCCCCCChhhhhhhhCCCCCCccHHHHHHHHHHHH
Q 024130 162 VLENEMDELPNGNAVHAEKGQPFKEHPEKSKQNAGSEAKQIKGALPEGFFDNKDADLLARGIKPVKPDVKDEYKEYEKLI 241 (272)
Q Consensus 162 p~e~~~~~LP~d~~~~~~~~~p~~~hs~s~~k~~~~E~k~~~~~LPeGFFDD~~~DakaR~v~~~k~~~~~E~~eF~k~i 241 (272)
. ++|+. +| ++..+.++||+|||||++.|++||||..++++|++||++|+++|
T Consensus 125 -----q-----Gnfs~----~p--------------enent~e~lPegFFDdke~d~~vr~~~e~k~~~d~Ey~rfqkeI 176 (264)
T KOG3032|consen 125 -----Q-----GNFSN----QP--------------ENENTNENLPEGFFDDKEADLLVRGIKEVKPDIDDEYKRFQKEI 176 (264)
T ss_pred -----c-----ccccC----Cc--------------cccchhhcCcccccCchhhhhhhhhccccchhHHHHHHHHHHHH
Confidence 1 13432 22 24558999999999999999999999999999999999999999
Q ss_pred HHHHHHhhHHHhhHHHHHHHHHHHhhhhhc
Q 024130 242 QEDLKQVDDRLEEEEIDAAEMIEEYESVDQ 271 (272)
Q Consensus 242 ~e~~~e~d~~~EEee~~aa~~~~e~~~~eq 271 (272)
++++++++.++||+++|++..|+.-|--||
T Consensus 177 ~~~~tesd~iveEeeed~~l~reieeidEQ 206 (264)
T KOG3032|consen 177 QDDLTESDSIVEEEEEDAALTREIEEIDEQ 206 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999998887777
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=98.09 E-value=2e-06 Score=55.41 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=30.9
Q ss_pred CCceeecccccccCcchhHHhhCChhHHHHHHH
Q 024130 34 DQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKN 66 (272)
Q Consensus 34 GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~ 66 (272)
|...|.+|++.+.+...|..|+.|++|+.++.+
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 678999999999999999999999999999975
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=97.69 E-value=1.6e-05 Score=49.47 Aligned_cols=27 Identities=37% Similarity=0.642 Sum_probs=25.1
Q ss_pred CceeecccccccCcchhHHhhCChhHH
Q 024130 35 QPVCRVCDVVLKSDSQWDAHQASRKHH 61 (272)
Q Consensus 35 qL~C~lC~~~VKsEslW~aH~~Sk~Hr 61 (272)
|..|.+|+..++++..|..|+.|+.||
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=97.22 E-value=0.00018 Score=72.00 Aligned_cols=35 Identities=31% Similarity=0.633 Sum_probs=33.7
Q ss_pred ceeecccccccCcchhHHhhCChhHHHHHHHhhhh
Q 024130 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (272)
Q Consensus 36 L~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~lk~~ 70 (272)
|.|+|||...|+|..|.-|.+||+|+++|..|++.
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqe 327 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQE 327 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999873
No 5
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.91 E-value=0.00046 Score=41.52 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=23.7
Q ss_pred ceeecccccccCcchhHHhhCChhH
Q 024130 36 PVCRVCDVVLKSDSQWDAHQASRKH 60 (272)
Q Consensus 36 L~C~lC~~~VKsEslW~aH~~Sk~H 60 (272)
+.|.+|++...++..|..|++|++|
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 4699999999999999999999998
No 6
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=96.44 E-value=0.0043 Score=56.14 Aligned_cols=52 Identities=17% Similarity=0.355 Sum_probs=45.6
Q ss_pred ccCCccccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHhhhhccCC
Q 024130 23 INSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGATGN 74 (272)
Q Consensus 23 I~~P~A~Yn~~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~lk~~~~~~ 74 (272)
.+.||..-|.+|.+.|.||+..--+|+-.-.|..||+|++|+.+-...+...
T Consensus 41 ~dDPyl~knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~ekssl 92 (222)
T COG5246 41 MDDPYLSKNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSEEKSSL 92 (222)
T ss_pred ccCcchhhcCCCcEEeeeeccccccHHHHHHhhccchhhhhHHHHHHHhhcc
Confidence 5679999999999999999998888999999999999999999875544444
No 7
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=95.76 E-value=0.012 Score=53.67 Aligned_cols=63 Identities=16% Similarity=0.300 Sum_probs=48.4
Q ss_pred HHHHHHHHHHHHHHhhhcccCCccccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHhhh
Q 024130 5 RKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (272)
Q Consensus 5 ~~ka~~Rallr~~r~~krI~~P~A~Yn~~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~lk~ 69 (272)
.|+--+|.|+-..- ---+.||---|-.|.+.|.||+.--.+|.-.-+|..||+|.+||++--.
T Consensus 25 ~RrerlrqLaleti--dl~kDPy~mkNh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa 87 (222)
T KOG0227|consen 25 DRRERLRQLALETI--DLNKDPYFMKNHLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAA 87 (222)
T ss_pred HHHHHHHHHHHhhc--ccccCchhhhccCcceeehhhhhhhcchhhhhhhhccchhhHHHHHHHH
Confidence 34444555544331 1124599988999999999999999999999999999999999998433
No 8
>PLN02748 tRNA dimethylallyltransferase
Probab=95.23 E-value=0.012 Score=59.07 Aligned_cols=38 Identities=29% Similarity=0.708 Sum_probs=32.8
Q ss_pred CCceeecccc-cccCcchhHHhhCChhHHHHHHHhhhhc
Q 024130 34 DQPVCRVCDV-VLKSDSQWDAHQASRKHHEAIKNIKAGA 71 (272)
Q Consensus 34 GqL~C~lC~~-~VKsEslW~aH~~Sk~Hr~~v~~lk~~~ 71 (272)
-+-+|-+|+. .+..|--|..|+.|+.||.++.++++.+
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~~ 455 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQKQ 455 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhhh
Confidence 3447999997 7889999999999999999999887643
No 9
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=91.94 E-value=0.19 Score=45.20 Aligned_cols=42 Identities=21% Similarity=0.337 Sum_probs=34.7
Q ss_pred CccccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHh
Q 024130 26 PLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (272)
Q Consensus 26 P~A~Yn~~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~l 67 (272)
+-..-+..|..-|-||+.+||.-.-+--|||+|.|.-|+..+
T Consensus 66 k~tp~sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 66 KSTPRSQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred cCCcccccCceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 333446778899999999999866688899999999999764
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=91.17 E-value=0.16 Score=34.54 Aligned_cols=30 Identities=33% Similarity=0.572 Sum_probs=19.2
Q ss_pred eeecccccccCcc--hhHHhhCChhHHHHHHH
Q 024130 37 VCRVCDVVLKSDS--QWDAHQASRKHHEAIKN 66 (272)
Q Consensus 37 ~C~lC~~~VKsEs--lW~aH~~Sk~Hr~~v~~ 66 (272)
-|-.|++-|.+.+ .|..|..|.+|++|+.+
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 5899999995444 89999999999999975
No 11
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=89.69 E-value=0.17 Score=43.20 Aligned_cols=38 Identities=16% Similarity=0.284 Sum_probs=35.4
Q ss_pred CCCCceeecccccccCcchhHHhhCChhHHHHHHHhhh
Q 024130 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (272)
Q Consensus 32 ~~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~lk~ 69 (272)
..||--|+.|....=+++.-..|..+|.||-+|..|+.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~ 91 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELRE 91 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhccc
Confidence 67999999999998889999999999999999999874
No 12
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=78.31 E-value=1.2 Score=45.32 Aligned_cols=33 Identities=27% Similarity=0.641 Sum_probs=30.0
Q ss_pred CceeecccccccCcchhHHhhCChhHHHHHHHh
Q 024130 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (272)
Q Consensus 35 qL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~l 67 (272)
+-.|.|||+-|-+|-..-.||.|++|.+.|..+
T Consensus 493 kkqcslcnvlissevylfshvkgrkhqqal~e~ 525 (672)
T KOG4722|consen 493 KKQCSLCNVLISSEVYLFSHVKGRKHQQALNEL 525 (672)
T ss_pred hhccchhhhhhhhhhhhhhhhcchhHHHHHHHH
Confidence 457999999999999999999999999998765
No 13
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=74.69 E-value=1.6 Score=36.83 Aligned_cols=40 Identities=15% Similarity=0.309 Sum_probs=36.4
Q ss_pred CCCCCceeecccccccCcchhHHhhCChhHHHHHHHhhhh
Q 024130 31 NEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (272)
Q Consensus 31 n~~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~lk~~ 70 (272)
...||--|+-|....-++...-.|..|+-||.++..|++.
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRev 90 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELREV 90 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcC
Confidence 3689999999999999999999999999999999998763
No 14
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=72.76 E-value=1.2 Score=33.27 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=25.9
Q ss_pred CceeecccccccCcchhHHhhCChhHHHHHH
Q 024130 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (272)
Q Consensus 35 qL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~ 65 (272)
.+.|.+|+...++-..+..|+.++.|.....
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 6999999999999999999999999987644
No 15
>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=64.73 E-value=2.8 Score=29.76 Aligned_cols=17 Identities=53% Similarity=0.820 Sum_probs=14.1
Q ss_pred hcCCCCCCCCChhhhhh
Q 024130 203 KGALPEGFFDNKDADLL 219 (272)
Q Consensus 203 ~~~LPeGFFDD~~~Dak 219 (272)
...-|+||||.-..|+.
T Consensus 33 l~~WP~GFFDq~~~~l~ 49 (52)
T PF12476_consen 33 LSNWPEGFFDQWDKDLR 49 (52)
T ss_pred CccCCCchhhHHHHHHH
Confidence 38899999999887764
No 16
>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=61.66 E-value=4.5 Score=32.27 Aligned_cols=32 Identities=25% Similarity=0.527 Sum_probs=26.5
Q ss_pred cCCCCCceeecccccccCcchhHHhhCChhHHH
Q 024130 30 YNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHE 62 (272)
Q Consensus 30 Yn~~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~ 62 (272)
.....-|+|+.|...|.. +-|..|+.++-|..
T Consensus 6 ~~~~~vlIC~~C~~av~~-~~v~~HL~~~H~~~ 37 (109)
T PF12013_consen 6 NPEYRVLICRQCQYAVQP-SEVESHLRKRHHIL 37 (109)
T ss_pred cCcCCEEEeCCCCcccCc-hHHHHHHHHhcccc
Confidence 346778999999999987 66999999877655
No 17
>PTZ00448 hypothetical protein; Provisional
Probab=60.98 E-value=5.9 Score=39.33 Aligned_cols=34 Identities=24% Similarity=0.404 Sum_probs=30.7
Q ss_pred CCCceeecccccccCcchhHHhhCChhHHHHHHH
Q 024130 33 FDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKN 66 (272)
Q Consensus 33 ~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~ 66 (272)
++..+|..|++.+.+...-..|..|-=||-|+.+
T Consensus 312 ~~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKR 345 (373)
T PTZ00448 312 SNMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKR 345 (373)
T ss_pred cCCccccccccccCCHHHHHHHhhhhHHHHHHHH
Confidence 3567899999999888899999999999999987
No 18
>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=53.46 E-value=7.5 Score=23.29 Aligned_cols=21 Identities=24% Similarity=0.346 Sum_probs=19.2
Q ss_pred ceeecccccccCcchhHHhhC
Q 024130 36 PVCRVCDVVLKSDSQWDAHQA 56 (272)
Q Consensus 36 L~C~lC~~~VKsEslW~aH~~ 56 (272)
..|.+|+....+...|..|..
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 19
>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=53.15 E-value=7 Score=21.89 Aligned_cols=20 Identities=25% Similarity=0.594 Sum_probs=15.8
Q ss_pred eeecccccccCcchhHHhhC
Q 024130 37 VCRVCDVVLKSDSQWDAHQA 56 (272)
Q Consensus 37 ~C~lC~~~VKsEslW~aH~~ 56 (272)
.|.+|+...++-.-|..|+.
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 59999999999888999875
No 20
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=52.92 E-value=5.5 Score=39.73 Aligned_cols=34 Identities=26% Similarity=0.486 Sum_probs=31.8
Q ss_pred ceeecccccccCcchhHHhhCChhHHHHHHHhhh
Q 024130 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (272)
Q Consensus 36 L~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~lk~ 69 (272)
..|.+||....++..-.-|+.|+.|+.++.+...
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 6799999999999999999999999999999765
No 21
>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=51.16 E-value=24 Score=28.12 Aligned_cols=43 Identities=26% Similarity=0.669 Sum_probs=32.6
Q ss_pred CCCCCChhhhhhhhCCCCCCccHHHHHHHHHHHHHHHHHHhhHHHhhHH
Q 024130 208 EGFFDNKDADLLARGIKPVKPDVKDEYKEYEKLIQEDLKQVDDRLEEEE 256 (272)
Q Consensus 208 eGFFDD~~~DakaR~v~~~k~~~~~E~~eF~k~i~e~~~e~d~~~EEee 256 (272)
..||-|+--++- --++|++-|+.|.+.|+|-+..-...+-|.-
T Consensus 28 ~kffadkpdest------lspemkehyekfe~miqehtdkfnkkm~ehs 70 (90)
T PF03037_consen 28 KKFFADKPDEST------LSPEMKEHYEKFERMIQEHTDKFNKKMHEHS 70 (90)
T ss_pred HhhhcCCCcccc------cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 358888765532 2578999999999999998888876665543
No 22
>PF14942 Muted: Organelle biogenesis, Muted-like protein
Probab=50.10 E-value=46 Score=28.82 Aligned_cols=28 Identities=29% Similarity=0.487 Sum_probs=22.4
Q ss_pred ccHHHHHHHHHHHHHHHHHHhhHHHhhH
Q 024130 228 PDVKDEYKEYEKLIQEDLKQVDDRLEEE 255 (272)
Q Consensus 228 ~~~~~E~~eF~k~i~e~~~e~d~~~EEe 255 (272)
.....+|++|+++|..-.+++|.-.++-
T Consensus 103 ~~~~~~we~f~~e~~~~~~~vdee~~~~ 130 (145)
T PF14942_consen 103 EQRKQEWEEFMKEQQQKKQRVDEEFREK 130 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999998888654443
No 23
>PF14968 CCDC84: Coiled coil protein 84
Probab=45.39 E-value=11 Score=36.84 Aligned_cols=27 Identities=30% Similarity=0.477 Sum_probs=22.9
Q ss_pred eecccccccCcchhHHhhCChhHHHHHHHh
Q 024130 38 CRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (272)
Q Consensus 38 C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~l 67 (272)
|.||+..-= .|..|+.|+.|+.+|..+
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 999987643 399999999999998874
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=44.63 E-value=31 Score=32.48 Aligned_cols=51 Identities=12% Similarity=0.136 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHhhhcccCCccccCCCCCceeecccccccC-cchhHHhhCChhHHHH
Q 024130 5 RKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKS-DSQWDAHQASRKHHEA 63 (272)
Q Consensus 5 ~~ka~~Rallr~~r~~krI~~P~A~Yn~~GqL~C~lC~~~VKs-EslW~aH~~Sk~Hr~~ 63 (272)
.+-..|+++|+ .||+..|..+|.+.|++=+=.|-. -..-..|++||+-+..
T Consensus 3 ~~~~~v~~~L~--------~~p~l~~~~~~rvrC~lTGHEmp~~~~~l~~y~~gKKy~~l 54 (244)
T PF05477_consen 3 ELPKEVQAFLK--------SHPFLELTENGRVRCTLTGHEMPCRLDELQQYIRGKKYQRL 54 (244)
T ss_pred cchHHHHHHHh--------cCCceEecCCCeEEEeecCcccCCCHHHHHHHhccHHHHHH
Confidence 45677888886 589999999999999998833332 1457899999999843
No 25
>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=43.95 E-value=16 Score=26.66 Aligned_cols=26 Identities=31% Similarity=0.703 Sum_probs=18.9
Q ss_pred cCC-CCCceeecccccccC----cchhHHhh
Q 024130 30 YNE-FDQPVCRVCDVVLKS----DSQWDAHQ 55 (272)
Q Consensus 30 Yn~-~GqL~C~lC~~~VKs----EslW~aH~ 55 (272)
|+. .+.+.|..|+..|.. +..|.-|.
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 555 448999999998843 56677764
No 26
>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=43.62 E-value=26 Score=32.24 Aligned_cols=43 Identities=21% Similarity=0.358 Sum_probs=32.8
Q ss_pred cccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHhhhhc
Q 024130 28 VRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGA 71 (272)
Q Consensus 28 A~Yn~~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~lk~~~ 71 (272)
..--+-++-.|.+|..-.|.+-.|.=||. ++|-+.|+.++...
T Consensus 70 ~~e~~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ev 112 (214)
T PF04959_consen 70 TKEEDEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKEV 112 (214)
T ss_dssp E-SSSSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHHH
T ss_pred HHHHcCCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHHH
Confidence 33346788999999999999999999998 56999999887643
No 27
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=43.22 E-value=17 Score=36.36 Aligned_cols=33 Identities=24% Similarity=0.392 Sum_probs=30.7
Q ss_pred CCceeecccccccCcchhHHhhCChhHHHHHHH
Q 024130 34 DQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKN 66 (272)
Q Consensus 34 GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~ 66 (272)
+.++|+-|++.+++.-+-.+|..|-=||=||.+
T Consensus 2 t~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKR 34 (390)
T KOG2785|consen 2 TGFTCNTCNVEFDDADEQRAHYKSDWHRYNLKR 34 (390)
T ss_pred CcceeeceeeeeccHHHHHHHhhhhHHHhhHHh
Confidence 458999999999999999999999999999987
No 28
>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=42.25 E-value=16 Score=26.36 Aligned_cols=27 Identities=26% Similarity=0.476 Sum_probs=22.0
Q ss_pred ceeecccccccCcchhHHhhCChhHHHHHH
Q 024130 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (272)
Q Consensus 36 L~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~ 65 (272)
--|-.|++.-.+ -..||.|.+||.=+.
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 468899887765 799999999997653
No 29
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=41.82 E-value=7.3 Score=36.07 Aligned_cols=46 Identities=22% Similarity=0.411 Sum_probs=35.8
Q ss_pred hcccCCccccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHh
Q 024130 21 KRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (272)
Q Consensus 21 krI~~P~A~Yn~~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~l 67 (272)
+-..||--+-...----|-+|.+-|+. +-|..|..|-.|..++..+
T Consensus 70 ~ets~p~nss~~e~lfyCE~Cd~~ip~-~~~snH~tSttHllsl~~~ 115 (223)
T KOG2384|consen 70 RETSHPMNSSRDEALFYCEVCDIYIPN-SKKSNHFTSTTHLLSLQHI 115 (223)
T ss_pred ccCCCcccCCCCCccchhhhhhhhccC-CCCccchhhHHHHhhhccC
Confidence 345666555444444679999999995 8999999999999998764
No 30
>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=41.63 E-value=9 Score=22.06 Aligned_cols=21 Identities=24% Similarity=0.509 Sum_probs=18.4
Q ss_pred eeecccccccCcchhHHhhCC
Q 024130 37 VCRVCDVVLKSDSQWDAHQAS 57 (272)
Q Consensus 37 ~C~lC~~~VKsEslW~aH~~S 57 (272)
.|..|+...++-+.|..|+..
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 31
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=37.98 E-value=15 Score=26.61 Aligned_cols=27 Identities=22% Similarity=0.400 Sum_probs=21.5
Q ss_pred ceeecccccccCcchhHHhhCChhHHHHHH
Q 024130 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (272)
Q Consensus 36 L~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~ 65 (272)
--|-.|.+.-.. ...||.|++||.=+.
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 468889877664 789999999997554
No 32
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=36.63 E-value=19 Score=32.17 Aligned_cols=30 Identities=37% Similarity=0.698 Sum_probs=24.5
Q ss_pred eeecccccccCc--chhHHhhCChhHHHHHHH
Q 024130 37 VCRVCDVVLKSD--SQWDAHQASRKHHEAIKN 66 (272)
Q Consensus 37 ~C~lC~~~VKsE--slW~aH~~Sk~Hr~~v~~ 66 (272)
.|--|++-+-+. |+-..|++|++|+.|+.-
T Consensus 5 yCDYCdt~LthDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 5 YCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred hhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence 588899665544 568999999999999876
No 33
>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=32.85 E-value=29 Score=25.10 Aligned_cols=23 Identities=35% Similarity=0.865 Sum_probs=17.2
Q ss_pred CCceeecccccccC----cchhHHhhC
Q 024130 34 DQPVCRVCDVVLKS----DSQWDAHQA 56 (272)
Q Consensus 34 GqL~C~lC~~~VKs----EslW~aH~~ 56 (272)
+.+.|..|+..+.. +..|..|..
T Consensus 33 d~v~C~~C~~~~~~w~~~d~p~~~H~~ 59 (69)
T cd00022 33 DEVKCFFCGLELKNWEPGDDPWEEHKR 59 (69)
T ss_pred CEEEeCCCCCCccCCCCCCCHHHHHhH
Confidence 56999999998864 556666643
No 34
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=32.82 E-value=19 Score=36.09 Aligned_cols=38 Identities=13% Similarity=0.298 Sum_probs=32.1
Q ss_pred CCCCceeecccccccCcchhHHhhCChhHHHHHHHhhh
Q 024130 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (272)
Q Consensus 32 ~~GqL~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~lk~ 69 (272)
.+-..-|.+|..-++.-+++.+|+.||.|..+++..+.
T Consensus 235 ~~~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~~ 272 (470)
T COG5188 235 WFPKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEE 272 (470)
T ss_pred hccceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhhH
Confidence 45578999999888877999999999999988776443
No 35
>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=31.75 E-value=34 Score=30.62 Aligned_cols=31 Identities=26% Similarity=0.512 Sum_probs=28.0
Q ss_pred eeecccccccCcchhHHhhCChhHHHHHHHh
Q 024130 37 VCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (272)
Q Consensus 37 ~C~lC~~~VKsEslW~aH~~Sk~Hr~~v~~l 67 (272)
.|.+|...-=.|.=...|+.|+-|++-+.-|
T Consensus 2 ~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i 32 (165)
T PF04988_consen 2 TCSFCKFRTFEEKEIEKHLESKFHKETLKYI 32 (165)
T ss_pred ccceeeeecccHHHHHHHHccchHHHHHHHH
Confidence 6999998887777788999999999999888
No 36
>PRK12495 hypothetical protein; Provisional
Probab=29.58 E-value=21 Score=33.31 Aligned_cols=36 Identities=11% Similarity=0.215 Sum_probs=20.0
Q ss_pred hcccCCccccCCCCCceeecccccccCcchhHHhhCC
Q 024130 21 KRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQAS 57 (272)
Q Consensus 21 krI~~P~A~Yn~~GqL~C~lC~~~VKsEslW~aH~~S 57 (272)
+||.--|.++..-....|..|+.+|- ..-|...|..
T Consensus 28 ~~ma~lL~~gatmsa~hC~~CG~PIp-a~pG~~~Cp~ 63 (226)
T PRK12495 28 ERMSELLLQGATMTNAHCDECGDPIF-RHDGQEFCPT 63 (226)
T ss_pred HHHHHHHHhhcccchhhcccccCccc-CCCCeeECCC
Confidence 45555555666666667777776665 2234444443
No 37
>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=28.54 E-value=28 Score=21.75 Aligned_cols=20 Identities=20% Similarity=0.378 Sum_probs=16.1
Q ss_pred ceeecccccccCcchhHHhhC
Q 024130 36 PVCRVCDVVLKSDSQWDAHQA 56 (272)
Q Consensus 36 L~C~lC~~~VKsEslW~aH~~ 56 (272)
+.|-+|+..|. +..-..|+-
T Consensus 2 v~CPiC~~~v~-~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREVP-ENLINSHLD 21 (26)
T ss_pred CcCCCCcCccc-HHHHHHHHH
Confidence 57999999994 577888875
No 38
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=27.64 E-value=44 Score=28.20 Aligned_cols=13 Identities=8% Similarity=0.516 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHH
Q 024130 231 KDEYKEYEKLIQE 243 (272)
Q Consensus 231 ~~E~~eF~k~i~e 243 (272)
+++|++||++|..
T Consensus 87 ~~~WdRFMRFMeR 99 (111)
T PLN00039 87 PREWDRFMRFMER 99 (111)
T ss_pred HHHHHHHHHHHHH
Confidence 6799999999975
No 39
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=27.48 E-value=44 Score=28.27 Aligned_cols=14 Identities=0% Similarity=0.411 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHH
Q 024130 230 VKDEYKEYEKLIQE 243 (272)
Q Consensus 230 ~~~E~~eF~k~i~e 243 (272)
-+++|++||++|..
T Consensus 92 s~~~WdRFMRFMeR 105 (113)
T PRK13610 92 SEEAFERFMRFASR 105 (113)
T ss_pred CHHHHHHHHHHHHH
Confidence 36799999999974
No 40
>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=27.47 E-value=44 Score=28.07 Aligned_cols=14 Identities=14% Similarity=0.617 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHH
Q 024130 230 VKDEYKEYEKLIQE 243 (272)
Q Consensus 230 ~~~E~~eF~k~i~e 243 (272)
-+++|++||++|..
T Consensus 85 s~~~WdRFMRFmeR 98 (109)
T TIGR03047 85 SEDEWDRFMRFMER 98 (109)
T ss_pred CHHHHHHHHHHHHH
Confidence 37799999999975
No 41
>PRK13612 photosystem II reaction center protein Psb28; Provisional
Probab=26.67 E-value=47 Score=28.10 Aligned_cols=14 Identities=7% Similarity=0.527 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHH
Q 024130 230 VKDEYKEYEKLIQE 243 (272)
Q Consensus 230 ~~~E~~eF~k~i~e 243 (272)
-+++|++||++|..
T Consensus 88 s~~~WdRFMRFMeR 101 (113)
T PRK13612 88 SEQEWDRFMRFMER 101 (113)
T ss_pred CHHHHHHHHHHHHH
Confidence 37899999999975
No 42
>CHL00128 psbW photosystem II protein W; Reviewed
Probab=25.62 E-value=50 Score=27.94 Aligned_cols=13 Identities=0% Similarity=0.501 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHH
Q 024130 231 KDEYKEYEKLIQE 243 (272)
Q Consensus 231 ~~E~~eF~k~i~e 243 (272)
+++|++||++|..
T Consensus 89 ~~~WdRFMRFMeR 101 (113)
T CHL00128 89 PEAWDRFMRFMER 101 (113)
T ss_pred HHHHHHHHHHHHH
Confidence 6799999999975
No 43
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=25.59 E-value=61 Score=33.36 Aligned_cols=62 Identities=16% Similarity=0.283 Sum_probs=43.8
Q ss_pred CCCCCCCCChhhhhhhhCCCCCCccHHHHHHHHHHHHH---HHHHHhhHHHhhHHHHHHHHHHHh
Q 024130 205 ALPEGFFDNKDADLLARGIKPVKPDVKDEYKEYEKLIQ---EDLKQVDDRLEEEEIDAAEMIEEY 266 (272)
Q Consensus 205 ~LPeGFFDD~~~DakaR~v~~~k~~~~~E~~eF~k~i~---e~~~e~d~~~EEee~~aa~~~~e~ 266 (272)
+|=.=.||++..+.+.-....+..+++++++.+..+++ ...+..+.++++-|.+-++.+...
T Consensus 56 ~vV~~~FddkVnqSALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 56 GVVDTTFDDKVRQHATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred ceecchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 34445788888888776666556688888888887777 666667777777776666655554
No 44
>smart00355 ZnF_C2H2 zinc finger.
Probab=24.05 E-value=35 Score=18.90 Aligned_cols=20 Identities=35% Similarity=0.569 Sum_probs=17.0
Q ss_pred eeecccccccCcchhHHhhC
Q 024130 37 VCRVCDVVLKSDSQWDAHQA 56 (272)
Q Consensus 37 ~C~lC~~~VKsEslW~aH~~ 56 (272)
.|..|.....+.+-+..|+.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 69999999888888888876
No 45
>PRK13611 photosystem II reaction center protein Psb28; Provisional
Probab=23.84 E-value=57 Score=27.22 Aligned_cols=14 Identities=7% Similarity=0.503 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHH
Q 024130 230 VKDEYKEYEKLIQE 243 (272)
Q Consensus 230 ~~~E~~eF~k~i~e 243 (272)
-+++|++||++|..
T Consensus 81 s~~~wdRFMRFmeR 94 (104)
T PRK13611 81 TEAEWDRFLRFMER 94 (104)
T ss_pred CHHHHHHHHHHHHH
Confidence 36799999999975
No 46
>PRK12495 hypothetical protein; Provisional
Probab=23.23 E-value=41 Score=31.47 Aligned_cols=22 Identities=23% Similarity=0.490 Sum_probs=18.4
Q ss_pred ccCCccccCCCCCceeeccccccc
Q 024130 23 INSPLVRYNEFDQPVCRVCDVVLK 46 (272)
Q Consensus 23 I~~P~A~Yn~~GqL~C~lC~~~VK 46 (272)
-..||-+| .|...|++|...|-
T Consensus 48 CG~PIpa~--pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 48 CGDPIFRH--DGQEFCPTCQQPVT 69 (226)
T ss_pred ccCcccCC--CCeeECCCCCCccc
Confidence 46788888 79999999997765
No 47
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=22.32 E-value=40 Score=25.39 Aligned_cols=21 Identities=14% Similarity=0.427 Sum_probs=15.2
Q ss_pred cCCCCCceeecccccccCcch
Q 024130 30 YNEFDQPVCRVCDVVLKSDSQ 50 (272)
Q Consensus 30 Yn~~GqL~C~lC~~~VKsEsl 50 (272)
|..+|.-.|..|+..|--..|
T Consensus 2 yAks~Ra~Ck~C~~~I~kg~l 22 (82)
T PF00645_consen 2 YAKSGRAKCKGCKKKIAKGEL 22 (82)
T ss_dssp E-SSSTEBETTTSCBE-TTSE
T ss_pred cCCCCCccCcccCCcCCCCCE
Confidence 778899999999987765444
No 48
>PLN02847 triacylglycerol lipase
Probab=22.02 E-value=94 Score=33.12 Aligned_cols=38 Identities=37% Similarity=0.414 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHhhHHHhhHHHHHHHHHHHhhh
Q 024130 231 KDEYKEYEKLIQEDLKQVDDRLEEEEIDAAEMIEEYES 268 (272)
Q Consensus 231 ~~E~~eF~k~i~e~~~e~d~~~EEee~~aa~~~~e~~~ 268 (272)
.+-|.++.+++.....+++.+.-|||.++|.+|-|.|.
T Consensus 497 ~~lw~~~~~~l~~~~~~~~~~~~~e~~~~~~ei~~ee~ 534 (633)
T PLN02847 497 GELWYELEKELQRQETEVDAQAQEEEAAAAKEITEEEN 534 (633)
T ss_pred hHHHHHHHHHHHHhhhhhccccchhhHHHHHHHHHHHH
Confidence 55899999999998888887666777777766655443
No 49
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=21.63 E-value=71 Score=27.60 Aligned_cols=34 Identities=18% Similarity=0.020 Sum_probs=24.4
Q ss_pred HHHHHhhhcccCCccccCCCCCceeecccccccC
Q 024130 14 LNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKS 47 (272)
Q Consensus 14 lr~~r~~krI~~P~A~Yn~~GqL~C~lC~~~VKs 47 (272)
||+...++--..+|......|.-.|++|+.++=+
T Consensus 19 ~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~ 52 (134)
T TIGR00357 19 TQNAGTEPPFTNEYWDNKEEGIYVDITCGEPLFS 52 (134)
T ss_pred HHHhCCCCCCCCCCCCCCCCeEEEccCCCCcccc
Confidence 3344445556666677778999999999988754
No 50
>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=20.64 E-value=43 Score=22.68 Aligned_cols=15 Identities=40% Similarity=0.749 Sum_probs=11.8
Q ss_pred CCCCceeeccccccc
Q 024130 32 EFDQPVCRVCDVVLK 46 (272)
Q Consensus 32 ~~GqL~C~lC~~~VK 46 (272)
..|.++|..|..+|-
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 579999999997764
Done!