Query 019989
Match_columns 332
No_of_seqs 124 out of 135
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 06:08:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019989.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019989hhsearch_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-60 1.4E-64 435.3 20.6 260 3-332 3-262 (264)
2 smart00451 ZnF_U1 U1-like zinc 97.9 6.9E-06 1.5E-10 54.4 2.3 33 34-66 2-34 (35)
3 PF12171 zf-C2H2_jaz: Zinc-fin 97.5 4.1E-05 8.9E-10 48.8 1.3 27 35-61 1-27 (27)
4 COG5246 PRP11 Splicing factor 96.7 0.0018 4E-08 59.7 4.5 50 23-72 41-90 (222)
5 KOG0717 Molecular chaperone (D 96.7 0.00087 1.9E-08 68.8 2.5 35 36-70 293-327 (508)
6 PF12874 zf-met: Zinc-finger o 96.7 0.00083 1.8E-08 41.5 1.4 25 36-60 1-25 (25)
7 KOG0227 Splicing factor 3a, su 96.1 0.0061 1.3E-07 56.7 4.1 64 4-69 24-87 (222)
8 PLN02748 tRNA dimethylallyltra 94.3 0.028 6.1E-07 58.1 2.5 36 34-69 417-453 (468)
9 KOG3408 U1-like Zn-finger-cont 88.8 0.21 4.5E-06 43.6 1.3 38 32-69 54-91 (129)
10 KOG4727 U1-like Zn-finger prot 88.6 0.53 1.2E-05 43.4 3.9 42 26-67 66-107 (193)
11 PF06220 zf-U1: U1 zinc finger 86.5 0.54 1.2E-05 32.8 2.1 31 36-66 4-36 (38)
12 KOG4722 Zn-finger protein [Gen 77.3 1.3 2.9E-05 46.0 1.7 33 35-67 493-525 (672)
13 COG5112 UFD2 U1-like Zn-finger 69.8 2.5 5.3E-05 36.5 1.3 40 31-70 51-90 (126)
14 PF12756 zf-C2H2_2: C2H2 type 65.1 2 4.4E-05 33.1 -0.1 31 35-65 50-80 (100)
15 PF12476 DUF3696: Protein of u 62.9 2.8 6E-05 30.6 0.3 17 203-219 33-49 (52)
16 PF12013 DUF3505: Protein of u 58.7 5.1 0.00011 33.0 1.2 32 30-62 6-37 (109)
17 PTZ00448 hypothetical protein; 56.7 9.7 0.00021 38.8 3.0 36 33-68 312-347 (373)
18 PF03037 KMP11: Kinetoplastid 55.2 46 0.00099 27.1 6.0 43 208-256 28-70 (90)
19 KOG3032 Uncharacterized conser 55.0 1.6E+02 0.0035 28.8 10.6 16 163-178 134-149 (264)
20 PF13912 zf-C2H2_6: C2H2-type 48.7 9.5 0.00021 23.5 1.0 21 36-56 2-22 (27)
21 PF13894 zf-C2H2_4: C2H2-type 47.6 9.5 0.00021 22.0 0.8 20 37-56 2-21 (24)
22 PF03879 Cgr1: Cgr1 family; I 46.7 1.6E+02 0.0035 25.2 8.4 56 231-286 43-101 (108)
23 PF05477 SURF2: Surfeit locus 46.0 26 0.00056 33.9 3.9 50 5-62 3-53 (244)
24 KOG2785 C2H2-type Zn-finger pr 42.4 22 0.00048 36.5 3.0 37 34-70 2-38 (390)
25 KOG2785 C2H2-type Zn-finger pr 38.2 12 0.00025 38.5 0.3 34 36-69 69-102 (390)
26 PF00096 zf-C2H2: Zinc finger, 34.8 13 0.00029 21.9 0.0 21 37-57 2-22 (23)
27 PF14968 CCDC84: Coiled coil p 34.7 21 0.00045 36.0 1.4 28 37-67 1-28 (336)
28 PF04959 ARS2: Arsenite-resist 34.3 29 0.00062 32.9 2.2 43 27-70 69-111 (214)
29 smart00238 BIR Baculoviral inh 33.3 27 0.00059 26.2 1.6 26 30-55 30-60 (71)
30 KOG2384 Major histocompatibili 30.6 14 0.0003 35.1 -0.5 45 22-67 71-115 (223)
31 smart00734 ZnF_Rad18 Rad18-lik 29.0 27 0.00059 22.3 0.8 20 36-56 2-21 (26)
32 PF04988 AKAP95: A-kinase anch 28.2 40 0.00088 30.9 2.0 31 37-67 2-32 (165)
33 KOG3454 U1 snRNP-specific prot 28.1 35 0.00077 31.3 1.6 31 36-66 4-36 (165)
34 KOG1029 Endocytic adaptor prot 26.5 4.1E+02 0.0089 30.5 9.4 22 202-223 304-326 (1118)
35 PF07535 zf-DBF: DBF zinc fing 25.8 44 0.00095 24.8 1.5 27 36-65 6-32 (49)
36 COG2433 Uncharacterized conser 25.1 4.4E+02 0.0096 29.1 9.2 18 273-290 492-509 (652)
37 cd07628 BAR_Atg24p The Bin/Amp 24.8 2.2E+02 0.0048 25.8 6.2 39 230-283 142-180 (185)
38 PF08271 TF_Zn_Ribbon: TFIIB z 22.9 34 0.00074 23.8 0.4 15 32-46 16-30 (43)
39 COG5188 PRP9 Splicing factor 3 22.7 38 0.00082 34.9 0.9 37 32-68 235-271 (470)
40 smart00355 ZnF_C2H2 zinc finge 22.5 39 0.00085 19.3 0.6 20 37-56 2-21 (26)
41 PF10475 DUF2450: Protein of u 22.3 7E+02 0.015 23.9 9.5 10 204-213 2-11 (291)
42 cd00022 BIR Baculoviral inhibi 22.1 56 0.0012 24.3 1.5 23 34-56 33-59 (69)
43 PF14942 Muted: Organelle biog 21.9 2.4E+02 0.0053 25.1 5.7 22 228-249 103-124 (145)
44 cd07666 BAR_SNX7 The Bin/Amphi 21.3 3E+02 0.0065 26.5 6.6 14 268-281 223-236 (243)
45 PRK12495 hypothetical protein; 21.3 36 0.00079 32.6 0.4 40 19-59 26-65 (226)
46 cd07629 BAR_Atg20p The Bin/Amp 21.2 2.7E+02 0.0058 25.4 6.0 21 228-248 142-162 (187)
47 PF00645 zf-PARP: Poly(ADP-rib 20.9 44 0.00095 25.9 0.7 21 30-50 2-22 (82)
48 cd07622 BAR_SNX4 The Bin/Amphi 20.8 3.3E+02 0.0072 25.2 6.6 19 268-286 179-197 (201)
49 cd07624 BAR_SNX7_30 The Bin/Am 20.1 3.1E+02 0.0067 25.0 6.2 14 268-281 180-193 (200)
No 1
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=6.6e-60 Score=435.27 Aligned_cols=260 Identities=42% Similarity=0.640 Sum_probs=196.7
Q ss_pred HHHHhHHHHHHHHHHHhhhcccCcccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHHhhccCCCCCccccCC
Q 019989 3 AARKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGATGNNTRVVSDA 82 (332)
Q Consensus 3 ~~~~ka~~R~~lr~~r~~~rI~~P~A~Y~~~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k~~~~~~~~~~~~~~ 82 (332)
-+++|+|||++|+..+...||++|||+||.+|+|+|+|||++|| ++||++|++||+||++|..||..+. ..
T Consensus 3 q~~~krl~k~k~~~kk~~~ri~splakyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~~~--------Kv 73 (264)
T KOG3032|consen 3 QAKKKRLFKSKLNAKKKDTRIDSPLAKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSRGS--------KV 73 (264)
T ss_pred hHHHHHHHHHHhhccCcccccccHhhccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhhhc--------cc
Confidence 48999999999999999999999999999999999999999999 9999999999999999999993111 01
Q ss_pred CCCCCCCCCCCCCCCccchhhhhhhccccCCCCCCCCCCCCccCcccCCCCCcCcccccCCCCCCCCCCccccccccchh
Q 019989 83 AKPEAGVDSSRSESGSASQNAELENSAKLGKARPPSVLPSNFFDNQEVKRPKTDSVKLVDPDSTKPSGVSAKTQALKSVV 162 (332)
Q Consensus 83 a~~~~~~~k~K~~~~~~~~~k~~k~~~~~~~~~~~s~LP~dFFd~~~~~~~~~~~~~~l~~d~~~~~~~~~~~~v~~~~~ 162 (332)
+.+.+ .+.+..+.++..+ .+ -.+.+.+|.||.+||+....+.+. +++.++.
T Consensus 74 ~k~~~---T~~p~~p~spn~k-ts----~~pnk~pstlPdk~~~~eqekh~~---------------gd~e~ka------ 124 (264)
T KOG3032|consen 74 AKTRP---TKIPALPKSPNSK-TS----FFPNKEPSTLPDKSKNLEQEKHTI---------------GDEENKA------ 124 (264)
T ss_pred ccCcC---ccCccCCCCCCcc-cc----ccCCCCCCcCCCCCcchhcccCCC---------------Cccchhc------
Confidence 11111 1111111111111 11 012234589999998876433221 1111111
Q ss_pred hcccccCCCCCCcccccCCCCCCCCCcchhccccchhhhhcCCCCCCCCCChhhhhhhhcCCCCCCChHHHHHHHHHHHH
Q 019989 163 LENEMDELPNGNAVHAEKGQPFKEHPEKSKQNAGSEAKQIKGALPEGFFDNKDADLLARGIKPVKPDVKDEYKEYEKLIQ 242 (332)
Q Consensus 163 ~e~~~~~LP~~~~~~~~~~~~~~~~s~s~~k~~~~E~~~~~~~LPeGFFDD~~~DakaR~v~~~k~~~e~Ew~eFqkeI~ 242 (332)
.| +|+. + .+..++.++||+|||||++.|+.||+|..++++|++||++||++|+
T Consensus 125 ----qG-----nfs~----~--------------penent~e~lPegFFDdke~d~~vr~~~e~k~~~d~Ey~rfqkeI~ 177 (264)
T KOG3032|consen 125 ----QG-----NFSN----Q--------------PENENTNENLPEGFFDDKEADLLVRGIKEVKPDIDDEYKRFQKEIQ 177 (264)
T ss_pred ----cc-----cccC----C--------------ccccchhhcCcccccCchhhhhhhhhccccchhHHHHHHHHHHHHH
Confidence 11 2332 1 1335689999999999999999999999999999999999999999
Q ss_pred HHHHHhHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCccccccCCCCCCCCCCCchhhh
Q 019989 243 EDLKQVDDRLEEEEIDAAEMIEEYESVDQKTYREKVEALRKKKKEWEASSRSAKSRGSSEVARKEPPKEELSSDDDSEEI 322 (332)
Q Consensus 243 ee~~es~~~~EeEe~~~~~ere~~eidEQi~~~~RV~~Lk~kk~~~~~~~~~k~~~~~~~~~~~~~~~~~sssdde~~~d 322 (332)
+++++++.|++|++++++..|++.||+|||.||+||+.|+.++.+++.+.+.+..+ +.... +.++|++|.|++++
T Consensus 178 ~~~tesd~iveEeeed~~l~reieeidEQi~~~kkvekl~~qK~ellnkkRe~~~k----~ev~k-e~eesddDgeddDl 252 (264)
T KOG3032|consen 178 DDLTESDSIVEEEEEDAALTREIEEIDEQISYKKKVEKLKRQKMELLNKKREKTSK----GEVKK-EEEESDDDGEDDDL 252 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc----cccCc-ccccCccccchhhh
Confidence 99999999999999999999999999999999999999999999999875444333 11111 24666777788888
Q ss_pred hhhcccccCC
Q 019989 323 FAVDWRAQHL 332 (332)
Q Consensus 323 ~~~DWRaK~~ 332 (332)
+++|||+|||
T Consensus 253 ~a~DWRaKnl 262 (264)
T KOG3032|consen 253 SAVDWRAKNL 262 (264)
T ss_pred hhhhhhhhhc
Confidence 8899999996
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=97.91 E-value=6.9e-06 Score=54.41 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=30.9
Q ss_pred CCceeecccccccCcchhHHhhCChHHHHHHHH
Q 019989 34 DQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKN 66 (332)
Q Consensus 34 G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~ 66 (332)
|...|.+|+..+.++..|..|+.|+.|+.++.+
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=97.51 E-value=4.1e-05 Score=48.82 Aligned_cols=27 Identities=37% Similarity=0.642 Sum_probs=25.1
Q ss_pred CceeecccccccCcchhHHhhCChHHH
Q 019989 35 QPVCRVCDVVLKSDSQWDAHQASRKHH 61 (332)
Q Consensus 35 ~L~C~lC~~~vk~EslW~aH~~sk~Hr 61 (332)
|..|.+|+..+.++..|..|+.|+.||
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 568999999999999999999999997
No 4
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=96.74 E-value=0.0018 Score=59.73 Aligned_cols=50 Identities=18% Similarity=0.386 Sum_probs=45.0
Q ss_pred ccCcccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHHhhccC
Q 019989 23 INSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGAT 72 (332)
Q Consensus 23 I~~P~A~Y~~~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k~~~~ 72 (332)
.+.||..-|.+|++.|.||+..-.+|+-.-.|..+|+|.+|+.+....+.
T Consensus 41 ~dDPyl~knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~eks 90 (222)
T COG5246 41 MDDPYLSKNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSEEKS 90 (222)
T ss_pred ccCcchhhcCCCcEEeeeeccccccHHHHHHhhccchhhhhHHHHHHHhh
Confidence 45699999999999999999999999999999999999999999765444
No 5
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=96.71 E-value=0.00087 Score=68.85 Aligned_cols=35 Identities=31% Similarity=0.633 Sum_probs=33.7
Q ss_pred ceeecccccccCcchhHHhhCChHHHHHHHHHhhc
Q 019989 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (332)
Q Consensus 36 L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k~~ 70 (332)
|.|.+||...|+|..|.-|..||+|+++|+.|++.
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqe 327 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQE 327 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999864
No 6
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.69 E-value=0.00083 Score=41.48 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=23.8
Q ss_pred ceeecccccccCcchhHHhhCChHH
Q 019989 36 PVCRVCDVVLKSDSQWDAHQASRKH 60 (332)
Q Consensus 36 L~C~lC~~~vk~EslW~aH~~sk~H 60 (332)
+.|.+|++...++..|..|+.|+.|
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 7
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=96.12 E-value=0.0061 Score=56.68 Aligned_cols=64 Identities=16% Similarity=0.292 Sum_probs=50.3
Q ss_pred HHHhHHHHHHHHHHHhhhcccCcccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHHhh
Q 019989 4 ARKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (332)
Q Consensus 4 ~~~ka~~R~~lr~~r~~~rI~~P~A~Y~~~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k~ 69 (332)
..|+--+|.|+-..-. --..||.--|-.|.+.|.||+..-.+|.-.-+|..||+|.+||++.-+
T Consensus 24 ~~RrerlrqLaletid--l~kDPy~mkNh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa 87 (222)
T KOG0227|consen 24 RDRRERLRQLALETID--LNKDPYFMKNHLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAA 87 (222)
T ss_pred HHHHHHHHHHHHhhcc--cccCchhhhccCcceeehhhhhhhcchhhhhhhhccchhhHHHHHHHH
Confidence 3455556666554321 123599999999999999999999999999999999999999998543
No 8
>PLN02748 tRNA dimethylallyltransferase
Probab=94.27 E-value=0.028 Score=58.13 Aligned_cols=36 Identities=31% Similarity=0.759 Sum_probs=31.9
Q ss_pred CCceeecccc-cccCcchhHHhhCChHHHHHHHHHhh
Q 019989 34 DQPVCRVCDV-VLKSDSQWDAHQASRKHHEAIKNIKA 69 (332)
Q Consensus 34 G~L~C~lC~~-~vk~EslW~aH~~sk~Hr~~~~~~k~ 69 (332)
-+.+|-+|+. ++..|--|..|+.|+.||.++.+++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k 453 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ 453 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence 3457999997 78899999999999999999998874
No 9
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=88.79 E-value=0.21 Score=43.60 Aligned_cols=38 Identities=16% Similarity=0.284 Sum_probs=35.5
Q ss_pred CCCCceeecccccccCcchhHHhhCChHHHHHHHHHhh
Q 019989 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (332)
Q Consensus 32 ~~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k~ 69 (332)
..||-.|+.|.-..-++..-..|..+|.|+.+|..|+.
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 67999999999998899999999999999999999873
No 10
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=88.65 E-value=0.53 Score=43.39 Aligned_cols=42 Identities=21% Similarity=0.337 Sum_probs=35.4
Q ss_pred cccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHH
Q 019989 26 PLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (332)
Q Consensus 26 P~A~Y~~~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~ 67 (332)
+-+.-+..|..-|-||+.+||.=.-+=-||++|.|.-|+..+
T Consensus 66 k~tp~sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 66 KSTPRSQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred cCCcccccCceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 344456778899999999999877788999999999999764
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=86.52 E-value=0.54 Score=32.79 Aligned_cols=31 Identities=32% Similarity=0.520 Sum_probs=19.2
Q ss_pred ceeecccccccCcc--hhHHhhCChHHHHHHHH
Q 019989 36 PVCRVCDVVLKSDS--QWDAHQASRKHHEAIKN 66 (332)
Q Consensus 36 L~C~lC~~~vk~Es--lW~aH~~sk~Hr~~~~~ 66 (332)
--|-.|+.-|.+.+ .|..|..|.+|+.|+..
T Consensus 4 yyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 4 YYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp -B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred eecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 35999999995444 79999999999999975
No 12
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=77.33 E-value=1.3 Score=46.00 Aligned_cols=33 Identities=27% Similarity=0.641 Sum_probs=30.0
Q ss_pred CceeecccccccCcchhHHhhCChHHHHHHHHH
Q 019989 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (332)
Q Consensus 35 ~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~ 67 (332)
+-.|.|||+.|-+|-..-.||.|++|.+.|..+
T Consensus 493 kkqcslcnvlissevylfshvkgrkhqqal~e~ 525 (672)
T KOG4722|consen 493 KKQCSLCNVLISSEVYLFSHVKGRKHQQALNEL 525 (672)
T ss_pred hhccchhhhhhhhhhhhhhhhcchhHHHHHHHH
Confidence 446999999999999999999999999998765
No 13
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=69.79 E-value=2.5 Score=36.50 Aligned_cols=40 Identities=15% Similarity=0.309 Sum_probs=36.6
Q ss_pred CCCCCceeecccccccCcchhHHhhCChHHHHHHHHHhhc
Q 019989 31 NEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (332)
Q Consensus 31 ~~~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k~~ 70 (332)
...||--|+-|...+-+|-.--.|..|+-|+.++..|++.
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRev 90 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELREV 90 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcC
Confidence 4689999999999988999999999999999999999863
No 14
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=65.13 E-value=2 Score=33.12 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=26.0
Q ss_pred CceeecccccccCcchhHHhhCChHHHHHHH
Q 019989 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (332)
Q Consensus 35 ~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~ 65 (332)
.+.|.+|+...++-..+..|+.++.|.....
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 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=62.85 E-value=2.8 Score=30.62 Aligned_cols=17 Identities=53% Similarity=0.820 Sum_probs=13.1
Q ss_pred cCCCCCCCCCChhhhhh
Q 019989 203 KGALPEGFFDNKDADLL 219 (332)
Q Consensus 203 ~~~LPeGFFDD~~~Dak 219 (332)
...-|+||||.-..|+.
T Consensus 33 l~~WP~GFFDq~~~~l~ 49 (52)
T PF12476_consen 33 LSNWPEGFFDQWDKDLR 49 (52)
T ss_pred CccCCCchhhHHHHHHH
Confidence 47799999997766643
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=58.70 E-value=5.1 Score=32.97 Aligned_cols=32 Identities=25% Similarity=0.527 Sum_probs=26.0
Q ss_pred cCCCCCceeecccccccCcchhHHhhCChHHHH
Q 019989 30 YNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHE 62 (332)
Q Consensus 30 Y~~~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~ 62 (332)
.....-|+|+.|...|.. +-|.+|+.++-|..
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 336778999999998887 45999999877655
No 17
>PTZ00448 hypothetical protein; Provisional
Probab=56.69 E-value=9.7 Score=38.84 Aligned_cols=36 Identities=22% Similarity=0.352 Sum_probs=31.7
Q ss_pred CCCceeecccccccCcchhHHhhCChHHHHHHHHHh
Q 019989 33 FDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (332)
Q Consensus 33 ~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k 68 (332)
++..+|+.|++.+.+...-..|..|-=||-|+.+.-
T Consensus 312 ~~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl 347 (373)
T PTZ00448 312 SNMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNA 347 (373)
T ss_pred cCCccccccccccCCHHHHHHHhhhhHHHHHHHHHh
Confidence 356789999999988889999999999999998753
No 18
>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=55.25 E-value=46 Score=27.09 Aligned_cols=43 Identities=26% Similarity=0.646 Sum_probs=32.7
Q ss_pred CCCCCChhhhhhhhcCCCCCCChHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 019989 208 EGFFDNKDADLLARGIKPVKPDVKDEYKEYEKLIQEDLKQVDDRLEEEE 256 (332)
Q Consensus 208 eGFFDD~~~DakaR~v~~~k~~~e~Ew~eFqkeI~ee~~es~~~~EeEe 256 (332)
..||-|+--++.. -+.|.+-|++|.+-|+|-+..-+..+-|..
T Consensus 28 ~kffadkpdestl------spemkehyekfe~miqehtdkfnkkm~ehs 70 (90)
T PF03037_consen 28 KKFFADKPDESTL------SPEMKEHYEKFERMIQEHTDKFNKKMHEHS 70 (90)
T ss_pred HhhhcCCCccccc------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3688877666543 478999999999999988887776665533
No 19
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=55.00 E-value=1.6e+02 Score=28.76 Aligned_cols=16 Identities=31% Similarity=0.345 Sum_probs=12.7
Q ss_pred hcccccCCCCCCcccc
Q 019989 163 LENEMDELPNGNAVHA 178 (332)
Q Consensus 163 ~e~~~~~LP~~~~~~~ 178 (332)
.++..++||++||+-.
T Consensus 134 nent~e~lPegFFDdk 149 (264)
T KOG3032|consen 134 NENTNENLPEGFFDDK 149 (264)
T ss_pred ccchhhcCcccccCch
Confidence 3556789999999983
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=48.67 E-value=9.5 Score=23.47 Aligned_cols=21 Identities=24% Similarity=0.346 Sum_probs=19.2
Q ss_pred ceeecccccccCcchhHHhhC
Q 019989 36 PVCRVCDVVLKSDSQWDAHQA 56 (332)
Q Consensus 36 L~C~lC~~~vk~EslW~aH~~ 56 (332)
..|..|+....+...|..|..
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=47.62 E-value=9.5 Score=21.97 Aligned_cols=20 Identities=25% Similarity=0.594 Sum_probs=16.0
Q ss_pred eeecccccccCcchhHHhhC
Q 019989 37 VCRVCDVVLKSDSQWDAHQA 56 (332)
Q Consensus 37 ~C~lC~~~vk~EslW~aH~~ 56 (332)
.|.+|+...++-..|..|+.
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
>PF03879 Cgr1: Cgr1 family; InterPro: IPR005579 Cgr1 is involved in nucleolar integrity and is required for processing pre-rRNA for the 60S ribosome subunit. In Saccharomyces cerevisiae, this protein is conserved and contributes to compartmentalisation of nucleolar constituents []. Cgr1 is a small hydrophilic protein and members of this family are coiled-coil proteins []. Its primary role appears to be in ribosome biogenesis [, ]. Expression of CGR1 is also associated with a cessation of yeast cell growth, which is a prerequisite for germination in this organism [].
Probab=46.74 E-value=1.6e+02 Score=25.24 Aligned_cols=56 Identities=30% Similarity=0.405 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHHHHhHH-HHHH--HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Q 019989 231 KDEYKEYEKLIQEDLKQVDD-RLEE--EEIDAAEMIEEYESVDQKTYREKVEALRKKKK 286 (332)
Q Consensus 231 e~Ew~eFqkeI~ee~~es~~-~~Ee--Ee~~~~~ere~~eidEQi~~~~RV~~Lk~kk~ 286 (332)
...+..+++||.++...--. +++. +=-.+.++.+-+|..-++.+-.||..|+.+.-
T Consensus 43 ~~~~K~~ekElKeEKe~er~~r~~~~kerr~~keEkeR~E~~a~km~~kKv~Rmkrkek 101 (108)
T PF03879_consen 43 LKAIKEKEKELKEEKEAERQRRIQRIKERRKRKEEKERYEKMAAKMHAKKVERMKRKEK 101 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 56789999999977654432 2211 11223344455677777888899999966543
No 23
>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=46.03 E-value=26 Score=33.87 Aligned_cols=50 Identities=12% Similarity=0.147 Sum_probs=39.2
Q ss_pred HHhHHHHHHHHHHHhhhcccCcccccCCCCCceeecccccccC-cchhHHhhCChHHHH
Q 019989 5 RKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKS-DSQWDAHQASRKHHE 62 (332)
Q Consensus 5 ~~ka~~R~~lr~~r~~~rI~~P~A~Y~~~G~L~C~lC~~~vk~-EslW~aH~~sk~Hr~ 62 (332)
.+-..|+++|+ .||+..|...|.+.|+|=+--|.. -..-..|+.||.-+.
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 55678888887 499999999999999998733332 235789999999883
No 24
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=42.40 E-value=22 Score=36.51 Aligned_cols=37 Identities=24% Similarity=0.341 Sum_probs=33.1
Q ss_pred CCceeecccccccCcchhHHhhCChHHHHHHHHHhhc
Q 019989 34 DQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (332)
Q Consensus 34 G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k~~ 70 (332)
+.+.|..|++.+++.-+-.+|.-|-=||=||.+..+.
T Consensus 2 t~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~ 38 (390)
T KOG2785|consen 2 TGFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVAS 38 (390)
T ss_pred CcceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhc
Confidence 4589999999999999999999999999999886543
No 25
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=38.22 E-value=12 Score=38.48 Aligned_cols=34 Identities=26% Similarity=0.486 Sum_probs=31.3
Q ss_pred ceeecccccccCcchhHHhhCChHHHHHHHHHhh
Q 019989 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (332)
Q Consensus 36 L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k~ 69 (332)
..|.+|+....++..-.-|+.|+.|+.++.+...
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 5799999999999999999999999999998653
No 26
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=34.78 E-value=13 Score=21.93 Aligned_cols=21 Identities=24% Similarity=0.509 Sum_probs=18.5
Q ss_pred eeecccccccCcchhHHhhCC
Q 019989 37 VCRVCDVVLKSDSQWDAHQAS 57 (332)
Q Consensus 37 ~C~lC~~~vk~EslW~aH~~s 57 (332)
.|..|+....+-+.+..|+..
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 27
>PF14968 CCDC84: Coiled coil protein 84
Probab=34.72 E-value=21 Score=36.01 Aligned_cols=28 Identities=29% Similarity=0.447 Sum_probs=22.9
Q ss_pred eeecccccccCcchhHHhhCChHHHHHHHHH
Q 019989 37 VCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (332)
Q Consensus 37 ~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~ 67 (332)
.|.||+..-= .|..|+.|+.|+.+|..+
T Consensus 1 yC~vCr~~h~---~gr~H~Y~~~Hq~~L~~~ 28 (336)
T PF14968_consen 1 YCEVCRRNHD---QGRRHVYSPKHQKSLSAF 28 (336)
T ss_pred CcchhhCccc---ccCCCccCHHHHHHHHHH
Confidence 3999986543 399999999999999864
No 28
>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=34.27 E-value=29 Score=32.87 Aligned_cols=43 Identities=21% Similarity=0.334 Sum_probs=32.5
Q ss_pred ccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHHhhc
Q 019989 27 LVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (332)
Q Consensus 27 ~A~Y~~~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k~~ 70 (332)
+..--+-++-.|.+|....|..-.|.-||. ++|-+.|+.++..
T Consensus 69 ~~~e~~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~e 111 (214)
T PF04959_consen 69 NTKEEDEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKE 111 (214)
T ss_dssp EE-SSSSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHH
T ss_pred HHHHHcCCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHH
Confidence 333346678999999999999999999998 5699999988754
No 29
>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=33.26 E-value=27 Score=26.17 Aligned_cols=26 Identities=27% Similarity=0.705 Sum_probs=19.2
Q ss_pred cCCCC-Cceeeccccccc----CcchhHHhh
Q 019989 30 YNEFD-QPVCRVCDVVLK----SDSQWDAHQ 55 (332)
Q Consensus 30 Y~~~G-~L~C~lC~~~vk----~EslW~aH~ 55 (332)
|+..| .+.|..|+..+. .+..|.-|.
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 66634 899999998874 466677774
No 30
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=30.64 E-value=14 Score=35.07 Aligned_cols=45 Identities=22% Similarity=0.410 Sum_probs=34.3
Q ss_pred cccCcccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHH
Q 019989 22 RINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (332)
Q Consensus 22 rI~~P~A~Y~~~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~ 67 (332)
--.||--+-..-----|-+|.+.|+ ++-|..|..|-.|--++..+
T Consensus 71 ets~p~nss~~e~lfyCE~Cd~~ip-~~~~snH~tSttHllsl~~~ 115 (223)
T KOG2384|consen 71 ETSHPMNSSRDEALFYCEVCDIYIP-NSKKSNHFTSTTHLLSLQHI 115 (223)
T ss_pred cCCCcccCCCCCccchhhhhhhhcc-CCCCccchhhHHHHhhhccC
Confidence 3455655444444467999999999 57899999999999888764
No 31
>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=28.96 E-value=27 Score=22.35 Aligned_cols=20 Identities=20% Similarity=0.395 Sum_probs=16.4
Q ss_pred ceeecccccccCcchhHHhhC
Q 019989 36 PVCRVCDVVLKSDSQWDAHQA 56 (332)
Q Consensus 36 L~C~lC~~~vk~EslW~aH~~ 56 (332)
..|.+|+..| ++..-..|+-
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 5799999999 5678888875
No 32
>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=28.22 E-value=40 Score=30.92 Aligned_cols=31 Identities=26% Similarity=0.512 Sum_probs=27.9
Q ss_pred eeecccccccCcchhHHhhCChHHHHHHHHH
Q 019989 37 VCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (332)
Q Consensus 37 ~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~ 67 (332)
.|.+|...-=.|-=...|+.|+-|++-+.-+
T Consensus 2 ~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i 32 (165)
T PF04988_consen 2 TCSFCKFRTFEEKEIEKHLESKFHKETLKYI 32 (165)
T ss_pred ccceeeeecccHHHHHHHHccchHHHHHHHH
Confidence 6999998877777789999999999999888
No 33
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=28.10 E-value=35 Score=31.28 Aligned_cols=31 Identities=35% Similarity=0.642 Sum_probs=25.4
Q ss_pred ceeecccccccCcc--hhHHhhCChHHHHHHHH
Q 019989 36 PVCRVCDVVLKSDS--QWDAHQASRKHHEAIKN 66 (332)
Q Consensus 36 L~C~lC~~~vk~Es--lW~aH~~sk~Hr~~~~~ 66 (332)
-.|--|++-+-+.| +-..|++|++|+.|+..
T Consensus 4 YyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 4 YYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred chhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence 35899997766664 57899999999999875
No 34
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=26.45 E-value=4.1e+02 Score=30.47 Aligned_cols=22 Identities=23% Similarity=0.341 Sum_probs=14.8
Q ss_pred hcCCCC-CCCCCChhhhhhhhcC
Q 019989 202 IKGALP-EGFFDNKDADLLARGI 223 (332)
Q Consensus 202 ~~~~LP-eGFFDD~~~DakaR~v 223 (332)
....|| .-=|.|+.++.=.||-
T Consensus 304 p~kklP~~~TFEDKrkeNy~kGq 326 (1118)
T KOG1029|consen 304 PPKKLPAPVTFEDKRKENYEKGQ 326 (1118)
T ss_pred ccccCCCCcchhhhhHHhHhhhh
Confidence 556688 2457778888777654
No 35
>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=25.78 E-value=44 Score=24.76 Aligned_cols=27 Identities=26% Similarity=0.476 Sum_probs=21.1
Q ss_pred ceeecccccccCcchhHHhhCChHHHHHHH
Q 019989 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (332)
Q Consensus 36 L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~ 65 (332)
--|-.|.+.-.+ -..||.|.+||.=+.
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 458888876653 789999999997653
No 36
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=25.05 E-value=4.4e+02 Score=29.09 Aligned_cols=18 Identities=28% Similarity=0.410 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 019989 273 TYREKVEALRKKKKEWEA 290 (332)
Q Consensus 273 ~~~~RV~~Lk~kk~~~~~ 290 (332)
+..++|++|+.++..+++
T Consensus 492 e~~~~ve~L~~~l~~l~k 509 (652)
T COG2433 492 EKKKRVEELERKLAELRK 509 (652)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 455777788777777764
No 37
>cd07628 BAR_Atg24p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Atg24p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Atg24p is involved in membrane fusion events at the vacuolar surface during pexophagy. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=24.77 E-value=2.2e+02 Score=25.76 Aligned_cols=39 Identities=13% Similarity=0.210 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 019989 230 VKDEYKEYEKLIQEDLKQVDDRLEEEEIDAAEMIEEYESVDQKTYREKVEALRK 283 (332)
Q Consensus 230 ~e~Ew~eFqkeI~ee~~es~~~~EeEe~~~~~ere~~eidEQi~~~~RV~~Lk~ 283 (332)
+.+||..|++..+.+...+= ....+-||.+|+++..+..
T Consensus 142 ~~~E~~rF~~~k~~elk~~l---------------~~~a~~qi~~y~~~~~~W~ 180 (185)
T cd07628 142 VLKEYPNFERIKKQEIKDSL---------------GALADGHIDFYQGLVEDWE 180 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHH
Confidence 45556666655555544442 1224566666666655543
No 38
>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=22.88 E-value=34 Score=23.84 Aligned_cols=15 Identities=40% Similarity=0.749 Sum_probs=11.7
Q ss_pred CCCCceeeccccccc
Q 019989 32 EFDQPVCRVCDVVLK 46 (332)
Q Consensus 32 ~~G~L~C~lC~~~vk 46 (332)
..|.++|+.|+.+|-
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 39
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=22.68 E-value=38 Score=34.89 Aligned_cols=37 Identities=14% Similarity=0.306 Sum_probs=31.3
Q ss_pred CCCCceeecccccccCcchhHHhhCChHHHHHHHHHh
Q 019989 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (332)
Q Consensus 32 ~~G~L~C~lC~~~vk~EslW~aH~~sk~Hr~~~~~~k 68 (332)
.+...-|.+|..-++.=++..+|+.||.|..+.....
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 4557899999988887789999999999998877543
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=22.49 E-value=39 Score=19.28 Aligned_cols=20 Identities=35% Similarity=0.569 Sum_probs=17.2
Q ss_pred eeecccccccCcchhHHhhC
Q 019989 37 VCRVCDVVLKSDSQWDAHQA 56 (332)
Q Consensus 37 ~C~lC~~~vk~EslW~aH~~ 56 (332)
.|..|.....+.+.+..|+.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 69999999888888888876
No 41
>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=22.33 E-value=7e+02 Score=23.94 Aligned_cols=10 Identities=30% Similarity=0.796 Sum_probs=8.6
Q ss_pred CCCCCCCCCC
Q 019989 204 GALPEGFFDN 213 (332)
Q Consensus 204 ~~LPeGFFDD 213 (332)
++||++||+.
T Consensus 2 ~si~~~yF~~ 11 (291)
T PF10475_consen 2 ESIPAIYFDE 11 (291)
T ss_pred CCCcHhhcCC
Confidence 5799999996
No 42
>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=22.13 E-value=56 Score=24.34 Aligned_cols=23 Identities=35% Similarity=0.865 Sum_probs=17.2
Q ss_pred CCceeecccccccC----cchhHHhhC
Q 019989 34 DQPVCRVCDVVLKS----DSQWDAHQA 56 (332)
Q Consensus 34 G~L~C~lC~~~vk~----EslW~aH~~ 56 (332)
..+.|..|+..+.. ...|..|.+
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 43
>PF14942 Muted: Organelle biogenesis, Muted-like protein
Probab=21.93 E-value=2.4e+02 Score=25.09 Aligned_cols=22 Identities=32% Similarity=0.463 Sum_probs=17.0
Q ss_pred CChHHHHHHHHHHHHHHHHHhH
Q 019989 228 PDVKDEYKEYEKLIQEDLKQVD 249 (332)
Q Consensus 228 ~~~e~Ew~eFqkeI~ee~~es~ 249 (332)
.....+|+.|+++|....+.++
T Consensus 103 ~~~~~~we~f~~e~~~~~~~vd 124 (145)
T PF14942_consen 103 EQRKQEWEEFMKEQQQKKQRVD 124 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3457899999999996666664
No 44
>cd07666 BAR_SNX7 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX7 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=21.29 E-value=3e+02 Score=26.54 Aligned_cols=14 Identities=21% Similarity=0.254 Sum_probs=7.3
Q ss_pred hHHHHHHHHHHHHH
Q 019989 268 SVDQKTYREKVEAL 281 (332)
Q Consensus 268 idEQi~~~~RV~~L 281 (332)
.+-||.+++.+..+
T Consensus 223 ae~~i~~~~~~~~~ 236 (243)
T cd07666 223 AENNISYYEECLAT 236 (243)
T ss_pred HHHHHHHHHHHHHH
Confidence 34555555555444
No 45
>PRK12495 hypothetical protein; Provisional
Probab=21.27 E-value=36 Score=32.64 Aligned_cols=40 Identities=10% Similarity=0.184 Sum_probs=24.9
Q ss_pred hhhcccCcccccCCCCCceeecccccccCcchhHHhhCChH
Q 019989 19 KEKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRK 59 (332)
Q Consensus 19 ~~~rI~~P~A~Y~~~G~L~C~lC~~~vk~EslW~aH~~sk~ 59 (332)
..+||.--|.++..-.-.+|..|+.+|- ..-+...|.+=+
T Consensus 26 ~~~~ma~lL~~gatmsa~hC~~CG~PIp-a~pG~~~Cp~CQ 65 (226)
T PRK12495 26 ATERMSELLLQGATMTNAHCDECGDPIF-RHDGQEFCPTCQ 65 (226)
T ss_pred HHHHHHHHHHhhcccchhhcccccCccc-CCCCeeECCCCC
Confidence 3446666666777777788888888877 223444444433
No 46
>cd07629 BAR_Atg20p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Atg20p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The function of Atg20p is unknown but it has been shown to interact with Atg11p, which plays a role in linking cargo molecules with vesicle-forming components. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=21.25 E-value=2.7e+02 Score=25.37 Aligned_cols=21 Identities=10% Similarity=0.340 Sum_probs=14.6
Q ss_pred CChHHHHHHHHHHHHHHHHHh
Q 019989 228 PDVKDEYKEYEKLIQEDLKQV 248 (332)
Q Consensus 228 ~~~e~Ew~eFqkeI~ee~~es 248 (332)
..|++||.+|+++...+....
T Consensus 142 ~~~~~el~rF~~ek~~dl~~~ 162 (187)
T cd07629 142 TIKQKDLPRFQREREADLREI 162 (187)
T ss_pred HHHHHHHHHHHHHhHHHHHHH
Confidence 446778888888877665554
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=20.88 E-value=44 Score=25.94 Aligned_cols=21 Identities=14% Similarity=0.427 Sum_probs=15.0
Q ss_pred cCCCCCceeecccccccCcch
Q 019989 30 YNEFDQPVCRVCDVVLKSDSQ 50 (332)
Q Consensus 30 Y~~~G~L~C~lC~~~vk~Esl 50 (332)
|..+|.-.|..|+..|.--.|
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 788899999999987754443
No 48
>cd07622 BAR_SNX4 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 4. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX4 is involved in recycling traffic from the sorting endosome (post-Golgi endosome) back to the late Golgi. It is also implicated in the regulation of plasma membrane receptor trafficking and interacts with receptors for EGF, insulin, platelet-derived growth factor and leptin. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and
Probab=20.84 E-value=3.3e+02 Score=25.19 Aligned_cols=19 Identities=16% Similarity=-0.125 Sum_probs=12.5
Q ss_pred hHHHHHHHHHHHHHHHHHH
Q 019989 268 SVDQKTYREKVEALRKKKK 286 (332)
Q Consensus 268 idEQi~~~~RV~~Lk~kk~ 286 (332)
.+-||.+|+++.....+..
T Consensus 179 A~~qi~~~~~~~~~W~~~~ 197 (201)
T cd07622 179 AKLQIKLAKKGLQTWTNIK 197 (201)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4667777777776655443
No 49
>cd07624 BAR_SNX7_30 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 7 and 30. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX7, SNX30, and similar proteins. The specific functions of SNX7 and SNX30 have not been elucidated. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=20.10 E-value=3.1e+02 Score=25.00 Aligned_cols=14 Identities=29% Similarity=0.235 Sum_probs=7.2
Q ss_pred hHHHHHHHHHHHHH
Q 019989 268 SVDQKTYREKVEAL 281 (332)
Q Consensus 268 idEQi~~~~RV~~L 281 (332)
.+-||.++.++...
T Consensus 180 a~~qi~~~~~~~~~ 193 (200)
T cd07624 180 AEKQIQYYEQCLAA 193 (200)
T ss_pred HHHHHHHHHHHHHH
Confidence 34555555555444
Done!