Query 019927
Match_columns 334
No_of_seqs 118 out of 130
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 05:38:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019927.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019927hhsearch_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 1.8E-59 4E-64 432.8 19.7 261 2-334 2-262 (264)
2 smart00451 ZnF_U1 U1-like zinc 97.9 8.2E-06 1.8E-10 54.1 2.3 33 34-66 2-34 (35)
3 PF12171 zf-C2H2_jaz: Zinc-fin 97.5 3.9E-05 8.5E-10 49.0 1.3 27 35-61 1-27 (27)
4 KOG0717 Molecular chaperone (D 96.7 0.00097 2.1E-08 68.6 2.6 35 36-70 293-327 (508)
5 COG5246 PRP11 Splicing factor 96.6 0.0027 5.8E-08 58.8 4.7 51 23-73 41-91 (222)
6 PF12874 zf-met: Zinc-finger o 96.6 0.001 2.2E-08 41.1 1.4 25 36-60 1-25 (25)
7 KOG0227 Splicing factor 3a, su 95.7 0.013 2.8E-07 54.7 4.3 62 6-69 26-87 (222)
8 PLN02748 tRNA dimethylallyltra 94.6 0.023 4.9E-07 58.8 2.7 36 34-69 417-453 (468)
9 KOG3408 U1-like Zn-finger-cont 88.6 0.22 4.7E-06 43.6 1.3 37 32-68 54-90 (129)
10 KOG4727 U1-like Zn-finger prot 88.1 0.6 1.3E-05 43.1 3.8 42 26-67 66-107 (193)
11 PF06220 zf-U1: U1 zinc finger 86.6 0.54 1.2E-05 32.9 2.1 31 36-66 4-36 (38)
12 KOG4722 Zn-finger protein [Gen 77.7 1.3 2.8E-05 46.2 1.7 34 35-68 493-526 (672)
13 KOG3032 Uncharacterized conser 71.0 38 0.00082 33.0 9.6 16 166-181 135-150 (264)
14 COG5112 UFD2 U1-like Zn-finger 69.2 2.6 5.6E-05 36.4 1.4 39 31-69 51-89 (126)
15 PF12756 zf-C2H2_2: C2H2 type 65.1 2.1 4.5E-05 33.1 0.0 32 35-66 50-81 (100)
16 PF12476 DUF3696: Protein of u 64.4 2.5 5.5E-05 30.9 0.3 17 205-221 33-49 (52)
17 PF12013 DUF3505: Protein of u 60.3 4.7 0.0001 33.2 1.3 31 31-62 7-37 (109)
18 PTZ00448 hypothetical protein; 58.6 8.4 0.00018 39.3 2.9 36 33-68 312-347 (373)
19 PF13894 zf-C2H2_4: C2H2-type 47.2 9.8 0.00021 21.9 0.9 20 37-56 2-21 (24)
20 PF13912 zf-C2H2_6: C2H2-type 47.0 11 0.00023 23.3 1.0 21 36-56 2-22 (27)
21 PF03879 Cgr1: Cgr1 family; I 43.4 1.8E+02 0.0038 25.0 8.1 56 233-288 43-101 (108)
22 KOG2785 C2H2-type Zn-finger pr 43.0 21 0.00045 36.8 2.9 37 34-70 2-38 (390)
23 PF05477 SURF2: Surfeit locus 40.3 35 0.00076 33.0 3.9 50 5-62 3-53 (244)
24 KOG2785 C2H2-type Zn-finger pr 37.0 12 0.00027 38.3 0.3 34 36-69 69-102 (390)
25 PF04959 ARS2: Arsenite-resist 35.4 28 0.00061 33.0 2.4 40 31-71 73-112 (214)
26 PF00096 zf-C2H2: Zinc finger, 35.1 13 0.00028 22.0 0.1 21 37-57 2-22 (23)
27 smart00238 BIR Baculoviral inh 34.7 25 0.00054 26.4 1.6 26 30-55 30-60 (71)
28 KOG1029 Endocytic adaptor prot 34.2 2.3E+02 0.0051 32.3 9.2 23 203-225 303-326 (1118)
29 PF14968 CCDC84: Coiled coil p 33.6 22 0.00048 35.8 1.4 27 38-67 2-28 (336)
30 PF04988 AKAP95: A-kinase anch 30.7 35 0.00076 31.4 2.0 31 37-67 2-32 (165)
31 PF03037 KMP11: Kinetoplastid 30.1 1.8E+02 0.0038 23.9 5.7 41 210-256 28-68 (90)
32 KOG2384 Major histocompatibili 29.9 14 0.00031 35.1 -0.5 46 21-67 70-115 (223)
33 smart00734 ZnF_Rad18 Rad18-lik 27.8 30 0.00064 22.2 0.8 20 36-56 2-21 (26)
34 KOG3564 GTPase-activating prot 27.0 3.5E+02 0.0077 29.2 8.8 13 213-225 12-24 (604)
35 COG5188 PRP9 Splicing factor 3 25.8 30 0.00065 35.6 0.9 37 32-68 235-271 (470)
36 KOG3454 U1 snRNP-specific prot 25.3 43 0.00093 30.8 1.6 30 37-66 5-36 (165)
37 cd00022 BIR Baculoviral inhibi 24.4 47 0.001 24.8 1.5 23 34-56 33-59 (69)
38 PF07535 zf-DBF: DBF zinc fing 24.2 49 0.0011 24.6 1.5 27 36-65 6-32 (49)
39 PF14942 Muted: Organelle biog 23.0 2.4E+02 0.0052 25.2 5.9 22 229-250 102-123 (145)
40 smart00355 ZnF_C2H2 zinc finge 22.1 41 0.00088 19.2 0.6 20 37-56 2-21 (26)
41 cd07666 BAR_SNX7 The Bin/Amphi 20.9 2.8E+02 0.006 26.8 6.3 7 50-56 18-24 (243)
42 PRK12495 hypothetical protein; 20.7 50 0.0011 31.8 1.2 26 21-46 28-53 (226)
43 TIGR03047 PS_II_psb28 photosys 20.4 72 0.0016 27.5 2.0 13 233-245 86-98 (109)
44 cd07628 BAR_Atg24p The Bin/Amp 20.4 3E+02 0.0066 24.9 6.2 20 231-250 141-160 (185)
45 PRK13610 photosystem II reacti 20.3 72 0.0016 27.7 2.0 13 233-245 93-105 (113)
46 PLN00039 photosystem II reacti 20.3 72 0.0016 27.6 2.0 13 233-245 87-99 (111)
No 1
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.8e-59 Score=432.81 Aligned_cols=261 Identities=42% Similarity=0.657 Sum_probs=195.3
Q ss_pred cHHHHHHHHHHHHHHHHhhhccCCCccccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHHhhhhcCCCCCCCCC
Q 019927 2 DAARKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGATGNNSRMVSD 81 (334)
Q Consensus 2 ~~~~~ka~~R~llr~~r~~~rI~~P~A~Yn~~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk~~~~~~~~~~~~~ 81 (334)
..|++|+|||.+|+..+...||++|||+||.+|+|+|+|||++|| ++||++|++||+||++|..||-... .
T Consensus 2 nq~~~krl~k~k~~~kk~~~ri~splakyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~~~--------K 72 (264)
T KOG3032|consen 2 NQAKKKRLFKSKLNAKKKDTRIDSPLAKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSRGS--------K 72 (264)
T ss_pred chHHHHHHHHHHhhccCcccccccHhhccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhhhc--------c
Confidence 348999999999999999999999999999999999999999999 9999999999999999999982111 1
Q ss_pred CCCCCCCCCCCCCCCcccchhhhhhhhhhccCCCCCCCCCCCccCccccCCCCccCCCccccCCCCCcccCcccccccch
Q 019927 82 AAKPEAGRESSRSESRSASQNAEIESSAKLGKARTSSVLPSNFFDSQEAKRPKTATDSVKLVDPDSNKTSGVSAKTQAMK 161 (334)
Q Consensus 82 ~a~p~~~~~~~k~~~~~~~~~k~~k~~~~~~~~~~~S~LP~dFFd~~~~~~~~~~~~~~~ll~~d~~~~~~~~~~~~~~~ 161 (334)
.+++.+ .+-+..+.++..+.. .-+.+.+|.||.+||+....+-+ .|+. .++.
T Consensus 73 v~k~~~---T~~p~~p~spn~kts-----~~pnk~pstlPdk~~~~eqekh~----------~gd~-------e~ka--- 124 (264)
T KOG3032|consen 73 VAKTRP---TKIPALPKSPNSKTS-----FFPNKEPSTLPDKSKNLEQEKHT----------IGDE-------ENKA--- 124 (264)
T ss_pred cccCcC---ccCccCCCCCCcccc-----ccCCCCCCcCCCCCcchhcccCC----------CCcc-------chhc---
Confidence 111111 111111100111110 01122358899999887533220 0011 1110
Q ss_pred hhhhhhcccCCCCCCccccCCCCCCCCCCccccccchhhhhhhcCCCCCCCCCChhhhhhhhcCCCCCCChHHHHHHHHH
Q 019927 162 SVVLENEMDELPNGNAVDAKKGQPLKEHPEKSKQSVDSEAKQIKGALPEGFFDNKEADLLARGIKPVKPDVKDEYKEYEK 241 (334)
Q Consensus 162 ~~~~~~~~~~LP~d~~~~~~~~~~~~~~s~s~~k~~~~E~~~~~~~LPeGFFDD~~~DaKvR~v~~~k~~~eeEw~~FqK 241 (334)
.| +|++.+ +..++.++||+|||||+..|+.||+|..++++|++||++||+
T Consensus 125 -------qG-----nfs~~p------------------enent~e~lPegFFDdke~d~~vr~~~e~k~~~d~Ey~rfqk 174 (264)
T KOG3032|consen 125 -------QG-----NFSNQP------------------ENENTNENLPEGFFDDKEADLLVRGIKEVKPDIDDEYKRFQK 174 (264)
T ss_pred -------cc-----cccCCc------------------cccchhhcCcccccCchhhhhhhhhccccchhHHHHHHHHHH
Confidence 11 233322 335689999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhhhHhhhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCccccccCCCcccCCCCCch
Q 019927 242 LIQEDLKQVDDRFEEEEIDAAEMIEEYESVDQKTFREKVEALRKKKMEWEAASRSAKSRGSSEVARKEPTKEELSSDDDS 321 (334)
Q Consensus 242 eI~ee~~es~~~~Eeee~~a~~ere~~eidEQi~~~~RV~~L~~kk~~~~~~~~~k~~~~~~~~~~~~~~~~~sssdde~ 321 (334)
+|++++++++.|+||++++++..|++.||||||.||+||+.|+.++++++.+.+.++... + ..++ .++|++|.|+
T Consensus 175 eI~~~~tesd~iveEeeed~~l~reieeidEQi~~~kkvekl~~qK~ellnkkRe~~~k~--e-v~ke--~eesddDged 249 (264)
T KOG3032|consen 175 EIQDDLTESDSIVEEEEEDAALTREIEEIDEQISYKKKVEKLKRQKMELLNKKREKTSKG--E-VKKE--EEESDDDGED 249 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc--c-cCcc--cccCccccch
Confidence 999999999999999999999999999999999999999999999999998754443331 1 1111 3666666777
Q ss_pred hhhhhhcccccCC
Q 019927 322 EEIFAVDWRAQHL 334 (334)
Q Consensus 322 d~d~~~DWRaK~~ 334 (334)
++++++|||+|||
T Consensus 250 dDl~a~DWRaKnl 262 (264)
T KOG3032|consen 250 DDLSAVDWRAKNL 262 (264)
T ss_pred hhhhhhhhhhhhc
Confidence 7788889999996
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=97.88 E-value=8.2e-06 Score=54.07 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=30.9
Q ss_pred CCceeecccccccCcchhHHhhCChhHHHHHHH
Q 019927 34 DQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKN 66 (334)
Q Consensus 34 GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~ 66 (334)
|...|.+|+..+.+...|..|+.|++|+.++.+
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=97.52 E-value=3.9e-05 Score=48.98 Aligned_cols=27 Identities=37% Similarity=0.642 Sum_probs=25.1
Q ss_pred CceeecccccccCcchhHHhhCChhHH
Q 019927 35 QPVCRVCDVVLKSDSQWDAHQASRKHH 61 (334)
Q Consensus 35 qL~C~lC~~~vksEslW~aH~~Sk~Hr 61 (334)
|..|.+|+..+.++..|..|+.|+.||
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
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=96.69 E-value=0.00097 Score=68.58 Aligned_cols=35 Identities=31% Similarity=0.633 Sum_probs=33.8
Q ss_pred ceeecccccccCcchhHHhhCChhHHHHHHHHhhh
Q 019927 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (334)
Q Consensus 36 L~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk~~ 70 (334)
|.|.+||...|+|..|.-|..||+|+++|+.|+++
T Consensus 293 lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqe 327 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQE 327 (508)
T ss_pred eEEeeccccccchHHHHhhHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999864
No 5
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=96.62 E-value=0.0027 Score=58.76 Aligned_cols=51 Identities=18% Similarity=0.381 Sum_probs=45.5
Q ss_pred cCCCccccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHHhhhhcC
Q 019927 23 INSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGATG 73 (334)
Q Consensus 23 I~~P~A~Yn~~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk~~~~~ 73 (334)
-+.||..-|.+|++.|.||+..-.+|+-.-.|..+|+|++|+.+...++..
T Consensus 41 ~dDPyl~knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs~ekss 91 (222)
T COG5246 41 MDDPYLSKNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRSEEKSS 91 (222)
T ss_pred ccCcchhhcCCCcEEeeeeccccccHHHHHHhhccchhhhhHHHHHHHhhc
Confidence 457999999999999999999999999999999999999999998655443
No 6
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.61 E-value=0.001 Score=41.13 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=23.7
Q ss_pred ceeecccccccCcchhHHhhCChhH
Q 019927 36 PVCRVCDVVLKSDSQWDAHQASRKH 60 (334)
Q Consensus 36 L~C~lC~~~vksEslW~aH~~Sk~H 60 (334)
+.|.+|++...++..|..|+.|+.|
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=95.69 E-value=0.013 Score=54.66 Aligned_cols=62 Identities=16% Similarity=0.306 Sum_probs=48.0
Q ss_pred HHHHHHHHHHHHHhhhccCCCccccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHHhh
Q 019927 6 KKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (334)
Q Consensus 6 ~ka~~R~llr~~r~~~rI~~P~A~Yn~~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk~ 69 (334)
|+--+|.|+-..- ---..||.--|-+|.+.|.||+..-.+|.-.-+|..||+|.+||++..+
T Consensus 26 RrerlrqLaleti--dl~kDPy~mkNh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarraa 87 (222)
T KOG0227|consen 26 RRERLRQLALETI--DLNKDPYFMKNHLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAA 87 (222)
T ss_pred HHHHHHHHHHhhc--ccccCchhhhccCcceeehhhhhhhcchhhhhhhhccchhhHHHHHHHH
Confidence 4444455444321 1223599988999999999999999999999999999999999998543
No 8
>PLN02748 tRNA dimethylallyltransferase
Probab=94.57 E-value=0.023 Score=58.81 Aligned_cols=36 Identities=31% Similarity=0.759 Sum_probs=32.0
Q ss_pred CCceeecccc-cccCcchhHHhhCChhHHHHHHHHhh
Q 019927 34 DQPVCRVCDV-VLKSDSQWDAHQASRKHHEAIKNIKA 69 (334)
Q Consensus 34 GqL~C~lC~~-~vksEslW~aH~~Sk~Hr~~~~~lk~ 69 (334)
-+.+|-+|+. .+..|--|..|+.|+.||.++.++++
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k 453 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ 453 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence 3457999997 79999999999999999999998875
No 9
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=88.58 E-value=0.22 Score=43.58 Aligned_cols=37 Identities=16% Similarity=0.292 Sum_probs=34.9
Q ss_pred CCCCceeecccccccCcchhHHhhCChhHHHHHHHHh
Q 019927 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (334)
Q Consensus 32 ~~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk 68 (334)
..||--|+.|....=++..-..|..+|.|+.+|..|+
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~ 90 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELR 90 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcc
Confidence 5799999999999889999999999999999999987
No 10
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=88.06 E-value=0.6 Score=43.10 Aligned_cols=42 Identities=21% Similarity=0.337 Sum_probs=35.2
Q ss_pred CccccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHH
Q 019927 26 PLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (334)
Q Consensus 26 P~A~Yn~~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~l 67 (334)
+-+.-+..|..-|-||+.+||.=.-+--||++|.|.-|+..+
T Consensus 66 k~tp~sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms 107 (193)
T KOG4727|consen 66 KSTPRSQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS 107 (193)
T ss_pred cCCcccccCceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence 333446778899999999999877788999999999998864
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=86.60 E-value=0.54 Score=32.89 Aligned_cols=31 Identities=32% Similarity=0.520 Sum_probs=19.2
Q ss_pred ceeecccccccCcc--hhHHhhCChhHHHHHHH
Q 019927 36 PVCRVCDVVLKSDS--QWDAHQASRKHHEAIKN 66 (334)
Q Consensus 36 L~C~lC~~~vksEs--lW~aH~~Sk~Hr~~~~~ 66 (334)
--|-.|+.-|.+.+ .|..|..|.+|+.|+++
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 35899999995444 79999999999999975
No 12
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=77.66 E-value=1.3 Score=46.17 Aligned_cols=34 Identities=26% Similarity=0.601 Sum_probs=30.4
Q ss_pred CceeecccccccCcchhHHhhCChhHHHHHHHHh
Q 019927 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (334)
Q Consensus 35 qL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk 68 (334)
+-.|.|||+.|-+|-..-.|+.|.+|.+.|..+-
T Consensus 493 kkqcslcnvlissevylfshvkgrkhqqal~e~~ 526 (672)
T KOG4722|consen 493 KKQCSLCNVLISSEVYLFSHVKGRKHQQALNELL 526 (672)
T ss_pred hhccchhhhhhhhhhhhhhhhcchhHHHHHHHHh
Confidence 4469999999999999999999999999988753
No 13
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=70.96 E-value=38 Score=32.98 Aligned_cols=16 Identities=38% Similarity=0.522 Sum_probs=11.8
Q ss_pred hhcccCCCCCCccccC
Q 019927 166 ENEMDELPNGNAVDAK 181 (334)
Q Consensus 166 ~~~~~~LP~d~~~~~~ 181 (334)
+++.++||++|||...
T Consensus 135 ent~e~lPegFFDdke 150 (264)
T KOG3032|consen 135 ENTNENLPEGFFDDKE 150 (264)
T ss_pred cchhhcCcccccCchh
Confidence 4457789999998844
No 14
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=69.20 E-value=2.6 Score=36.43 Aligned_cols=39 Identities=15% Similarity=0.345 Sum_probs=35.9
Q ss_pred CCCCCceeecccccccCcchhHHhhCChhHHHHHHHHhh
Q 019927 31 NEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (334)
Q Consensus 31 n~~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk~ 69 (334)
...||--|+-|....-++-.--.|..|+-|+.++..|++
T Consensus 51 PGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRe 89 (126)
T COG5112 51 PGLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELRE 89 (126)
T ss_pred CCCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhc
Confidence 368999999999998899999999999999999999885
No 15
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=65.06 E-value=2.1 Score=33.05 Aligned_cols=32 Identities=19% Similarity=0.397 Sum_probs=26.0
Q ss_pred CceeecccccccCcchhHHhhCChhHHHHHHH
Q 019927 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIKN 66 (334)
Q Consensus 35 qL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~ 66 (334)
.+.|.+|+...++-..+..|+.++.|......
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~~ 81 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNSE 81 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S--
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCcccc
Confidence 69999999999999999999999999876543
No 16
>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=64.38 E-value=2.5 Score=30.89 Aligned_cols=17 Identities=47% Similarity=0.780 Sum_probs=12.9
Q ss_pred cCCCCCCCCCChhhhhh
Q 019927 205 KGALPEGFFDNKEADLL 221 (334)
Q Consensus 205 ~~~LPeGFFDD~~~DaK 221 (334)
...-|+||||.-..|+.
T Consensus 33 l~~WP~GFFDq~~~~l~ 49 (52)
T PF12476_consen 33 LSNWPEGFFDQWDKDLR 49 (52)
T ss_pred CccCCCchhhHHHHHHH
Confidence 36689999997766643
No 17
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=60.31 E-value=4.7 Score=33.19 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=25.6
Q ss_pred CCCCCceeecccccccCcchhHHhhCChhHHH
Q 019927 31 NEFDQPVCRVCDVVLKSDSQWDAHQASRKHHE 62 (334)
Q Consensus 31 n~~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~ 62 (334)
....-|+|+.|...|.. +-|..|+.++-|..
T Consensus 7 ~~~~vlIC~~C~~av~~-~~v~~HL~~~H~~~ 37 (109)
T PF12013_consen 7 PEYRVLICRQCQYAVQP-SEVESHLRKRHHIL 37 (109)
T ss_pred CcCCEEEeCCCCcccCc-hHHHHHHHHhcccc
Confidence 36778999999998887 45999999877655
No 18
>PTZ00448 hypothetical protein; Provisional
Probab=58.58 E-value=8.4 Score=39.32 Aligned_cols=36 Identities=22% Similarity=0.352 Sum_probs=31.8
Q ss_pred CCCceeecccccccCcchhHHhhCChhHHHHHHHHh
Q 019927 33 FDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (334)
Q Consensus 33 ~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk 68 (334)
++..+|..|++.+.+...-..|..|-=||-|+.+.-
T Consensus 312 ~~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRkl 347 (373)
T PTZ00448 312 SNMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRNA 347 (373)
T ss_pred cCCccccccccccCCHHHHHHHhhhhHHHHHHHHHh
Confidence 356789999999988889999999999999998854
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=47.15 E-value=9.8 Score=21.94 Aligned_cols=20 Identities=25% Similarity=0.594 Sum_probs=16.0
Q ss_pred eeecccccccCcchhHHhhC
Q 019927 37 VCRVCDVVLKSDSQWDAHQA 56 (334)
Q Consensus 37 ~C~lC~~~vksEslW~aH~~ 56 (334)
.|.+|+...++-..|..|+.
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 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=46.97 E-value=11 Score=23.29 Aligned_cols=21 Identities=24% Similarity=0.346 Sum_probs=19.2
Q ss_pred ceeecccccccCcchhHHhhC
Q 019927 36 PVCRVCDVVLKSDSQWDAHQA 56 (334)
Q Consensus 36 L~C~lC~~~vksEslW~aH~~ 56 (334)
..|..|+....+...|..|..
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
>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=43.38 E-value=1.8e+02 Score=25.04 Aligned_cols=56 Identities=29% Similarity=0.379 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHhhhhh-hHhh--hHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Q 019927 233 KDEYKEYEKLIQEDLKQVDD-RFEE--EEIDAAEMIEEYESVDQKTFREKVEALRKKKM 288 (334)
Q Consensus 233 eeEw~~FqKeI~ee~~es~~-~~Ee--ee~~a~~ere~~eidEQi~~~~RV~~L~~kk~ 288 (334)
...+..+++||+++....-. ++.. +=-.+.++.+.+|..-++.+-.||+.|+.+..
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 46788999999977654332 1111 11223344556677777788899998877654
No 22
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=43.04 E-value=21 Score=36.75 Aligned_cols=37 Identities=24% Similarity=0.341 Sum_probs=33.1
Q ss_pred CCceeecccccccCcchhHHhhCChhHHHHHHHHhhh
Q 019927 34 DQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (334)
Q Consensus 34 GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk~~ 70 (334)
+.+.|..|++.+++.-+-.+|..|-=||-||.+.-+.
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 4589999999999999999999999999999986543
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=40.25 E-value=35 Score=33.01 Aligned_cols=50 Identities=12% Similarity=0.147 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHhhhccCCCccccCCCCCceeecccccccC-cchhHHhhCChhHHH
Q 019927 5 RKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKS-DSQWDAHQASRKHHE 62 (334)
Q Consensus 5 ~~ka~~R~llr~~r~~~rI~~P~A~Yn~~GqL~C~lC~~~vks-EslW~aH~~Sk~Hr~ 62 (334)
..-..|+++|+ .||+..|...|.+.|+|=+--|.. -..-..|+.||.-+.
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 45567888887 599999999999999998733322 234789999999884
No 24
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=37.04 E-value=12 Score=38.29 Aligned_cols=34 Identities=26% Similarity=0.486 Sum_probs=31.6
Q ss_pred ceeecccccccCcchhHHhhCChhHHHHHHHHhh
Q 019927 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (334)
Q Consensus 36 L~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk~ 69 (334)
+.|.+|+....++..-.-|+.|+.|+.++.+...
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 5799999999999999999999999999999764
No 25
>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=35.44 E-value=28 Score=32.97 Aligned_cols=40 Identities=23% Similarity=0.385 Sum_probs=31.9
Q ss_pred CCCCCceeecccccccCcchhHHhhCChhHHHHHHHHhhhh
Q 019927 31 NEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGA 71 (334)
Q Consensus 31 n~~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk~~~ 71 (334)
-+-++-.|.+|....|..-.|.-||. .+|-+.|+.++++.
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ev 112 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKEV 112 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHHH
Confidence 46678999999999999999999998 56999999887654
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=35.13 E-value=13 Score=21.99 Aligned_cols=21 Identities=24% Similarity=0.509 Sum_probs=18.5
Q ss_pred eeecccccccCcchhHHhhCC
Q 019927 37 VCRVCDVVLKSDSQWDAHQAS 57 (334)
Q Consensus 37 ~C~lC~~~vksEslW~aH~~S 57 (334)
.|..|+....+-+.+..|+..
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 599999999999999999864
No 27
>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=34.71 E-value=25 Score=26.43 Aligned_cols=26 Identities=31% Similarity=0.696 Sum_probs=19.1
Q ss_pred cCC-CCCceeeccccccc----CcchhHHhh
Q 019927 30 YNE-FDQPVCRVCDVVLK----SDSQWDAHQ 55 (334)
Q Consensus 30 Yn~-~GqL~C~lC~~~vk----sEslW~aH~ 55 (334)
|+. .+.+.|..|+..+. .+..|.-|.
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 665 34899999998874 466677774
No 28
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=34.24 E-value=2.3e+02 Score=32.32 Aligned_cols=23 Identities=22% Similarity=0.361 Sum_probs=15.4
Q ss_pred hhcCCCC-CCCCCChhhhhhhhcC
Q 019927 203 QIKGALP-EGFFDNKEADLLARGI 225 (334)
Q Consensus 203 ~~~~~LP-eGFFDD~~~DaKvR~v 225 (334)
.....|| .-=|.|+.++.=+||-
T Consensus 303 ep~kklP~~~TFEDKrkeNy~kGq 326 (1118)
T KOG1029|consen 303 EPPKKLPAPVTFEDKRKENYEKGQ 326 (1118)
T ss_pred CccccCCCCcchhhhhHHhHhhhh
Confidence 3566677 2457778888777664
No 29
>PF14968 CCDC84: Coiled coil protein 84
Probab=33.60 E-value=22 Score=35.84 Aligned_cols=27 Identities=30% Similarity=0.477 Sum_probs=22.5
Q ss_pred eecccccccCcchhHHhhCChhHHHHHHHH
Q 019927 38 CRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (334)
Q Consensus 38 C~lC~~~vksEslW~aH~~Sk~Hr~~~~~l 67 (334)
|.||+..-= .|..|+.|+.|+.+|..+
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 899986543 399999999999999874
No 30
>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=30.67 E-value=35 Score=31.38 Aligned_cols=31 Identities=26% Similarity=0.512 Sum_probs=28.0
Q ss_pred eeecccccccCcchhHHhhCChhHHHHHHHH
Q 019927 37 VCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (334)
Q Consensus 37 ~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~l 67 (334)
.|.+|..+-=.|-=...|+.|+-|++-+.-|
T Consensus 2 ~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i 32 (165)
T PF04988_consen 2 TCSFCKFRTFEEKEIEKHLESKFHKETLKYI 32 (165)
T ss_pred ccceeeeecccHHHHHHHHccchHHHHHHHH
Confidence 6999999877777788999999999999988
No 31
>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=30.12 E-value=1.8e+02 Score=23.86 Aligned_cols=41 Identities=27% Similarity=0.689 Sum_probs=30.1
Q ss_pred CCCCCChhhhhhhhcCCCCCCChHHHHHHHHHHHHHHHhhhhhhHhh
Q 019927 210 EGFFDNKEADLLARGIKPVKPDVKDEYKEYEKLIQEDLKQVDDRFEE 256 (334)
Q Consensus 210 eGFFDD~~~DaKvR~v~~~k~~~eeEw~~FqKeI~ee~~es~~~~Ee 256 (334)
..||-|+--++. --+.|.+-|++|.+-|+|-+..-+..+-|
T Consensus 28 ~kffadkpdest------lspemkehyekfe~miqehtdkfnkkm~e 68 (90)
T PF03037_consen 28 KKFFADKPDEST------LSPEMKEHYEKFERMIQEHTDKFNKKMHE 68 (90)
T ss_pred HhhhcCCCcccc------cCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 368877655532 26778999999999999887776665544
No 32
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=29.94 E-value=14 Score=35.06 Aligned_cols=46 Identities=22% Similarity=0.421 Sum_probs=35.0
Q ss_pred hccCCCccccCCCCCceeecccccccCcchhHHhhCChhHHHHHHHH
Q 019927 21 KRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (334)
Q Consensus 21 ~rI~~P~A~Yn~~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~l 67 (334)
.--.||--+-..-----|-+|.+-|+ ++-|..|..|-.|.-++..+
T Consensus 70 ~ets~p~nss~~e~lfyCE~Cd~~ip-~~~~snH~tSttHllsl~~~ 115 (223)
T KOG2384|consen 70 RETSHPMNSSRDEALFYCEVCDIYIP-NSKKSNHFTSTTHLLSLQHI 115 (223)
T ss_pred ccCCCcccCCCCCccchhhhhhhhcc-CCCCccchhhHHHHhhhccC
Confidence 34556665544444467999999999 57899999999999888764
No 33
>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=27.79 E-value=30 Score=22.24 Aligned_cols=20 Identities=20% Similarity=0.395 Sum_probs=16.3
Q ss_pred ceeecccccccCcchhHHhhC
Q 019927 36 PVCRVCDVVLKSDSQWDAHQA 56 (334)
Q Consensus 36 L~C~lC~~~vksEslW~aH~~ 56 (334)
+.|.+|+..| ++..-..|+-
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 5799999999 5677888875
No 34
>KOG3564 consensus GTPase-activating protein [General function prediction only]
Probab=27.00 E-value=3.5e+02 Score=29.25 Aligned_cols=13 Identities=23% Similarity=0.294 Sum_probs=9.9
Q ss_pred CCChhhhhhhhcC
Q 019927 213 FDNKEADLLARGI 225 (334)
Q Consensus 213 FDD~~~DaKvR~v 225 (334)
|+++..|+++-+-
T Consensus 12 f~~l~r~~~~l~~ 24 (604)
T KOG3564|consen 12 FEQLVRDIEILGE 24 (604)
T ss_pred HHHHHHHHHHhcC
Confidence 7788888887655
No 35
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=25.85 E-value=30 Score=35.62 Aligned_cols=37 Identities=14% Similarity=0.306 Sum_probs=31.7
Q ss_pred CCCCceeecccccccCcchhHHhhCChhHHHHHHHHh
Q 019927 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (334)
Q Consensus 32 ~~GqL~C~lC~~~vksEslW~aH~~Sk~Hr~~~~~lk 68 (334)
.+...-|.+|..-++.=++..+|+.||.|..+.+..+
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 4557899999998888789999999999998887644
No 36
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=25.29 E-value=43 Score=30.82 Aligned_cols=30 Identities=37% Similarity=0.698 Sum_probs=25.0
Q ss_pred eeecccccccCcc--hhHHhhCChhHHHHHHH
Q 019927 37 VCRVCDVVLKSDS--QWDAHQASRKHHEAIKN 66 (334)
Q Consensus 37 ~C~lC~~~vksEs--lW~aH~~Sk~Hr~~~~~ 66 (334)
.|--|++-+-+.| +-..|++|++|+.|+..
T Consensus 5 yCDYCdt~LthDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 5 YCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred hhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence 5899997766654 57899999999999975
No 37
>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=24.42 E-value=47 Score=24.78 Aligned_cols=23 Identities=35% Similarity=0.865 Sum_probs=17.1
Q ss_pred CCceeecccccccC----cchhHHhhC
Q 019927 34 DQPVCRVCDVVLKS----DSQWDAHQA 56 (334)
Q Consensus 34 GqL~C~lC~~~vks----EslW~aH~~ 56 (334)
+.+.|..|+..+.. ...|..|.+
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 556776653
No 38
>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=24.15 E-value=49 Score=24.56 Aligned_cols=27 Identities=26% Similarity=0.476 Sum_probs=20.9
Q ss_pred ceeecccccccCcchhHHhhCChhHHHHHH
Q 019927 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (334)
Q Consensus 36 L~C~lC~~~vksEslW~aH~~Sk~Hr~~~~ 65 (334)
--|-.|.+.-.+ -..|+.|.+||.-+.
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 358888776653 789999999997654
No 39
>PF14942 Muted: Organelle biogenesis, Muted-like protein
Probab=22.97 E-value=2.4e+02 Score=25.19 Aligned_cols=22 Identities=27% Similarity=0.433 Sum_probs=16.6
Q ss_pred CCChHHHHHHHHHHHHHHHhhh
Q 019927 229 KPDVKDEYKEYEKLIQEDLKQV 250 (334)
Q Consensus 229 k~~~eeEw~~FqKeI~ee~~es 250 (334)
......+|+.|+++|....+.+
T Consensus 102 ~~~~~~~we~f~~e~~~~~~~v 123 (145)
T PF14942_consen 102 REQRKQEWEEFMKEQQQKKQRV 123 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3445789999999999655555
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=22.10 E-value=41 Score=19.24 Aligned_cols=20 Identities=35% Similarity=0.569 Sum_probs=17.2
Q ss_pred eeecccccccCcchhHHhhC
Q 019927 37 VCRVCDVVLKSDSQWDAHQA 56 (334)
Q Consensus 37 ~C~lC~~~vksEslW~aH~~ 56 (334)
.|..|.....+.+.+..|+.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 69999999888888888876
No 41
>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=20.92 E-value=2.8e+02 Score=26.79 Aligned_cols=7 Identities=14% Similarity=0.700 Sum_probs=4.7
Q ss_pred hhHHhhC
Q 019927 50 QWDAHQA 56 (334)
Q Consensus 50 lW~aH~~ 56 (334)
-|.+|..
T Consensus 18 ~W~~~~~ 24 (243)
T cd07666 18 AWELSSH 24 (243)
T ss_pred hHHHHHH
Confidence 4888653
No 42
>PRK12495 hypothetical protein; Provisional
Probab=20.70 E-value=50 Score=31.77 Aligned_cols=26 Identities=15% Similarity=0.340 Sum_probs=15.6
Q ss_pred hccCCCccccCCCCCceeeccccccc
Q 019927 21 KRINSPLVRYNEFDQPVCRVCDVVLK 46 (334)
Q Consensus 21 ~rI~~P~A~Yn~~GqL~C~lC~~~vk 46 (334)
++|.--|.++..-...+|..|+.+|-
T Consensus 28 ~~ma~lL~~gatmsa~hC~~CG~PIp 53 (226)
T PRK12495 28 ERMSELLLQGATMTNAHCDECGDPIF 53 (226)
T ss_pred HHHHHHHHhhcccchhhcccccCccc
Confidence 35544455555666666777776665
No 43
>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=20.38 E-value=72 Score=27.54 Aligned_cols=13 Identities=15% Similarity=0.690 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHH
Q 019927 233 KDEYKEYEKLIQE 245 (334)
Q Consensus 233 eeEw~~FqKeI~e 245 (334)
+++|++|++.|.-
T Consensus 86 ~~~WdRFMRFmeR 98 (109)
T TIGR03047 86 EDEWDRFMRFMER 98 (109)
T ss_pred HHHHHHHHHHHHH
Confidence 7899999999973
No 44
>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=20.37 E-value=3e+02 Score=24.92 Aligned_cols=20 Identities=25% Similarity=0.669 Sum_probs=11.3
Q ss_pred ChHHHHHHHHHHHHHHHhhh
Q 019927 231 DVKDEYKEYEKLIQEDLKQV 250 (334)
Q Consensus 231 ~~eeEw~~FqKeI~ee~~es 250 (334)
.|..||.+|++..+.+...+
T Consensus 141 ~~~~E~~rF~~~k~~elk~~ 160 (185)
T cd07628 141 EVLKEYPNFERIKKQEIKDS 160 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34556666666666555444
No 45
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=20.29 E-value=72 Score=27.71 Aligned_cols=13 Identities=0% Similarity=0.468 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHH
Q 019927 233 KDEYKEYEKLIQE 245 (334)
Q Consensus 233 eeEw~~FqKeI~e 245 (334)
+++|++|++.|.-
T Consensus 93 ~~~WdRFMRFMeR 105 (113)
T PRK13610 93 EEAFERFMRFASR 105 (113)
T ss_pred HHHHHHHHHHHHH
Confidence 7899999999973
No 46
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=20.29 E-value=72 Score=27.62 Aligned_cols=13 Identities=8% Similarity=0.516 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHH
Q 019927 233 KDEYKEYEKLIQE 245 (334)
Q Consensus 233 eeEw~~FqKeI~e 245 (334)
+++|++|++.|.-
T Consensus 87 ~~~WdRFMRFMeR 99 (111)
T PLN00039 87 PREWDRFMRFMER 99 (111)
T ss_pred HHHHHHHHHHHHH
Confidence 7899999999973
Done!