Query 022517
Match_columns 296
No_of_seqs 121 out of 131
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 04:08:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022517.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022517hhsearch_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-45 3.9E-50 336.0 12.3 198 2-264 2-199 (264)
2 smart00451 ZnF_U1 U1-like zinc 98.0 4.1E-06 9E-11 54.5 2.2 33 34-66 2-34 (35)
3 PF12171 zf-C2H2_jaz: Zinc-fin 97.6 3E-05 6.4E-10 48.8 1.1 27 35-61 1-27 (27)
4 KOG0717 Molecular chaperone (D 97.0 0.00036 7.9E-09 70.6 2.6 36 35-70 292-327 (508)
5 PF12874 zf-met: Zinc-finger o 96.7 0.00088 1.9E-08 40.8 1.4 25 36-60 1-25 (25)
6 COG5246 PRP11 Splicing factor 95.9 0.011 2.4E-07 54.2 4.5 50 23-72 41-90 (222)
7 KOG0227 Splicing factor 3a, su 95.0 0.027 5.8E-07 52.0 3.9 45 24-68 42-86 (222)
8 PLN02748 tRNA dimethylallyltra 94.8 0.017 3.7E-07 58.6 2.5 39 34-72 417-456 (468)
9 PF06220 zf-U1: U1 zinc finger 89.6 0.27 5.9E-06 34.0 2.1 30 37-66 5-36 (38)
10 KOG4727 U1-like Zn-finger prot 88.5 0.55 1.2E-05 42.9 3.8 42 27-68 67-108 (193)
11 KOG3408 U1-like Zn-finger-cont 87.2 0.3 6.5E-06 42.3 1.3 38 32-69 54-91 (129)
12 KOG4722 Zn-finger protein [Gen 71.9 2.2 4.8E-05 44.1 1.7 33 35-67 493-525 (672)
13 COG5112 UFD2 U1-like Zn-finger 67.3 2.8 6E-05 36.0 1.1 39 32-70 52-90 (126)
14 PF12476 DUF3696: Protein of u 67.0 2.4 5.3E-05 30.5 0.7 17 203-219 33-49 (52)
15 PF12756 zf-C2H2_2: C2H2 type 64.2 2 4.4E-05 32.3 -0.2 31 35-65 50-80 (100)
16 PF03037 KMP11: Kinetoplastid 56.6 11 0.00023 30.5 2.7 40 209-254 29-68 (90)
17 PF12013 DUF3505: Protein of u 54.6 6.9 0.00015 31.6 1.3 32 30-62 6-37 (109)
18 PTZ00448 hypothetical protein; 49.3 12 0.00025 37.8 2.2 35 33-67 312-346 (373)
19 PF13894 zf-C2H2_4: C2H2-type 44.9 11 0.00024 21.4 0.8 20 37-56 2-21 (24)
20 PF13912 zf-C2H2_6: C2H2-type 44.7 12 0.00026 22.7 1.0 21 36-56 2-22 (27)
21 KOG2785 C2H2-type Zn-finger pr 42.7 8.8 0.00019 38.8 0.2 34 36-69 69-102 (390)
22 PF04959 ARS2: Arsenite-resist 36.9 34 0.00073 31.9 3.1 43 28-71 70-112 (214)
23 PF07535 zf-DBF: DBF zinc fing 35.6 24 0.00052 25.9 1.5 27 36-65 6-32 (49)
24 PF14968 CCDC84: Coiled coil p 35.3 20 0.00044 35.5 1.4 27 38-67 2-28 (336)
25 KOG2785 C2H2-type Zn-finger pr 35.1 34 0.00074 34.7 3.0 36 34-69 2-37 (390)
26 PF01491 Frataxin_Cyay: Fratax 33.9 1.1E+02 0.0024 25.3 5.3 52 235-286 4-55 (109)
27 smart00238 BIR Baculoviral inh 33.6 30 0.00065 25.5 1.8 26 30-55 30-60 (71)
28 PF14942 Muted: Organelle biog 33.1 50 0.0011 29.0 3.4 28 228-255 103-130 (145)
29 PF00096 zf-C2H2: Zinc finger, 32.5 14 0.00031 21.5 -0.1 21 37-57 2-22 (23)
30 smart00586 ZnF_DBF Zinc finger 31.6 23 0.0005 26.1 0.8 27 36-65 6-32 (49)
31 KOG2384 Major histocompatibili 31.1 14 0.0003 34.8 -0.4 45 22-67 71-115 (223)
32 KOG0100 Molecular chaperones G 30.5 33 0.00072 35.9 2.1 22 265-286 43-64 (663)
33 PRK01379 cyaY frataxin-like pr 29.4 1.3E+02 0.0028 25.1 5.0 49 235-286 4-52 (103)
34 KOG3454 U1 snRNP-specific prot 28.3 32 0.00069 31.2 1.4 30 37-66 5-36 (165)
35 PF05477 SURF2: Surfeit locus 25.4 89 0.0019 29.8 3.8 51 5-63 3-54 (244)
36 PF09276 Pertus-S5-tox: Pertus 25.0 40 0.00087 27.5 1.3 15 269-283 23-37 (97)
37 PRK13729 conjugal transfer pil 24.8 19 0.00041 37.3 -0.8 61 205-265 56-119 (475)
38 PF04988 AKAP95: A-kinase anch 23.9 53 0.0011 29.9 1.9 31 37-67 2-32 (165)
39 cd00022 BIR Baculoviral inhibi 23.3 54 0.0012 24.0 1.6 22 34-55 33-58 (69)
40 COG5188 PRP9 Splicing factor 3 23.3 36 0.00078 34.7 0.8 37 32-68 235-271 (470)
41 COG1965 CyaY Protein implicate 23.2 1.8E+02 0.004 24.7 4.9 49 235-285 4-52 (106)
42 TIGR03421 FeS_CyaY iron donor 21.5 2E+02 0.0043 23.7 4.7 48 235-286 3-50 (102)
43 PRK00446 cyaY frataxin-like pr 21.2 2E+02 0.0044 23.8 4.8 48 235-286 4-52 (105)
44 smart00734 ZnF_Rad18 Rad18-lik 21.0 46 0.00099 21.2 0.7 20 36-56 2-21 (26)
No 1
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.8e-45 Score=336.04 Aligned_cols=198 Identities=41% Similarity=0.651 Sum_probs=150.3
Q ss_pred cHHHHHHHHHHHHHHHHhhhccCCCccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHHhhccCCCCCCCCcc
Q 022517 2 DAARKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGATGNNSRMVSD 81 (296)
Q Consensus 2 daa~~ka~~Rallrqqr~~krI~~P~A~Y~~~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK~~~~~~~~~~~~~ 81 (296)
..+++|++||++|+..+...||++|||+||++|||+|+|||++|| ++||++|++||+||++|+.||.......
T Consensus 2 nq~~~krl~k~k~~~kk~~~ri~splakyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~~~Kv~------ 74 (264)
T KOG3032|consen 2 NQAKKKRLFKSKLNAKKKDTRIDSPLAKYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSRGSKVA------ 74 (264)
T ss_pred chHHHHHHHHHHhhccCcccccccHhhccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhhhcccc------
Confidence 348999999999999999999999999999999999999999999 8999999999999999999994322211
Q ss_pred CCCCCCCCCCCCCCCCccchhhhhhhhhhcccCCCCCCCCCcccCcccccCCCCCCccccCCCCCcccCCcccccccccc
Q 022517 82 AAKPEAGRESSRSESRSASQNAEIESSAKLGKARTSSVLPSNFFDSQEAKRPKTDSVKLVDPDSNKTSGVSAKTQAMKSV 161 (296)
Q Consensus 82 ~a~~~~~s~krk~~~~~~~~~K~~k~s~~~~~~q~sS~LP~dFFD~~~~~~~~~~~l~lld~d~~~~s~~~~~t~~~~~~ 161 (296)
.+ ++.+.+..+.+...|..-. +.+.+|.||++||+....+- ... |++.
T Consensus 75 --k~---~~T~~p~~p~spn~kts~~-----pnk~pstlPdk~~~~eqekh-~~g-------d~e~-------------- 122 (264)
T KOG3032|consen 75 --KT---RPTKIPALPKSPNSKTSFF-----PNKEPSTLPDKSKNLEQEKH-TIG-------DEEN-------------- 122 (264)
T ss_pred --cC---cCccCccCCCCCCcccccc-----CCCCCCcCCCCCcchhcccC-CCC-------ccch--------------
Confidence 11 1234444443333332211 23356999999987543221 000 0000
Q ss_pred cccccccCCCCCCccccCCCCCCCCCCccccccchhhHhhhhcCCCCCCCCCHHhhhhhhcCCCCCcchHHHHHHHHHHH
Q 022517 162 VLENEMDELPNGNAVDAKKGQPLKEHPEKSKQSVDSEAKQIKGALPEGFFDNKEADLLARGIKPVKPDVKDEYKEYEKLI 241 (296)
Q Consensus 162 p~e~~k~~LP~d~f~~~~~~~~~~e~s~s~~ka~~~E~k~~~~~LPeGFFDD~~~DakaR~v~~~k~~~~~E~~eFqkeI 241 (296)
.+. ++|++++ ++..+.++||+|||||++.|++||||..++++|++||++||++|
T Consensus 123 ----kaq----Gnfs~~p------------------enent~e~lPegFFDdke~d~~vr~~~e~k~~~d~Ey~rfqkeI 176 (264)
T KOG3032|consen 123 ----KAQ----GNFSNQP------------------ENENTNENLPEGFFDDKEADLLVRGIKEVKPDIDDEYKRFQKEI 176 (264)
T ss_pred ----hcc----ccccCCc------------------cccchhhcCcccccCchhhhhhhhhccccchhHHHHHHHHHHHH
Confidence 011 1233222 34568999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhhhhhhccccCccc
Q 022517 242 QEDLKQVDDRFEEEEVSCFSPFS 264 (296)
Q Consensus 242 ~E~~~e~d~r~EEeE~~a~~~~~ 264 (296)
+++++++|.+.||||+|++.-++
T Consensus 177 ~~~~tesd~iveEeeed~~l~re 199 (264)
T KOG3032|consen 177 QDDLTESDSIVEEEEEDAALTRE 199 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999986653
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=97.98 E-value=4.1e-06 Score=54.47 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=30.9
Q ss_pred CCceeecccccccCcchhHHhhCChHHHHHHHH
Q 022517 34 DQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKN 66 (296)
Q Consensus 34 GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~ 66 (296)
|...|.+|+..+.++..|..|+.|++|+.++++
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 678999999999999999999999999999975
No 3
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.56 E-value=3e-05 Score=48.82 Aligned_cols=27 Identities=37% Similarity=0.642 Sum_probs=25.0
Q ss_pred CceeecccccccCcchhHHhhCChHHH
Q 022517 35 QPVCRVCDVVLKSDSQWDAHQASRKHH 61 (296)
Q Consensus 35 qL~C~lCn~~VKsEslW~aHv~Sk~Hr 61 (296)
|..|.+|+...++|..|..|+.|++||
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence 468999999999999999999999997
No 4
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=97.02 E-value=0.00036 Score=70.63 Aligned_cols=36 Identities=31% Similarity=0.601 Sum_probs=34.1
Q ss_pred CceeecccccccCcchhHHhhCChHHHHHHHHHhhc
Q 022517 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (296)
Q Consensus 35 qL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK~~ 70 (296)
+|.|.+||...|+|..|.-|.+||+|+++|+.|++.
T Consensus 292 ~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqe 327 (508)
T KOG0717|consen 292 VLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQE 327 (508)
T ss_pred ceEEeeccccccchHHHHhhHHHHHHHHHHHHHHHH
Confidence 399999999999999999999999999999999864
No 5
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.68 E-value=0.00088 Score=40.76 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=23.7
Q ss_pred ceeecccccccCcchhHHhhCChHH
Q 022517 36 PVCRVCDVVLKSDSQWDAHQASRKH 60 (296)
Q Consensus 36 L~C~lCn~~VKsEslW~aHv~Sk~H 60 (296)
..|.+|++...++..|..|++|++|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 3699999999999999999999998
No 6
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=95.87 E-value=0.011 Score=54.24 Aligned_cols=50 Identities=18% Similarity=0.386 Sum_probs=43.9
Q ss_pred cCCCccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHHhhccC
Q 022517 23 INSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGAT 72 (296)
Q Consensus 23 I~~P~A~Y~~~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK~~~~ 72 (296)
-+.||..-|.+|++.|.||+..--+|+-.-.|..+|+|++|+.+-...+.
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 45699999999999999999988889999999999999999998644433
No 7
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=94.96 E-value=0.027 Score=52.03 Aligned_cols=45 Identities=18% Similarity=0.428 Sum_probs=40.9
Q ss_pred CCCccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHHh
Q 022517 24 NSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (296)
Q Consensus 24 ~~P~A~Y~~~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK 68 (296)
+.||---|-.|.+.|.||+.--.+|.-.-+|.-||+|.+||++--
T Consensus 42 kDPy~mkNh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarra 86 (222)
T KOG0227|consen 42 KDPYFMKNHLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRA 86 (222)
T ss_pred cCchhhhccCcceeehhhhhhhcchhhhhhhhccchhhHHHHHHH
Confidence 358888899999999999999889999999999999999999843
No 8
>PLN02748 tRNA dimethylallyltransferase
Probab=94.84 E-value=0.017 Score=58.55 Aligned_cols=39 Identities=31% Similarity=0.711 Sum_probs=33.5
Q ss_pred CCceeecccc-cccCcchhHHhhCChHHHHHHHHHhhccC
Q 022517 34 DQPVCRVCDV-VLKSDSQWDAHQASRKHHEAIKNIKAGAT 72 (296)
Q Consensus 34 GqL~C~lCn~-~VKsEslW~aHv~Sk~Hre~v~~lK~~~~ 72 (296)
-+-+|-+|+. .+..|--|..|+.|+.||.++.++++.+.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~~~ 456 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQKQT 456 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhhhh
Confidence 3447999997 78889999999999999999999876444
No 9
>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=89.56 E-value=0.27 Score=33.96 Aligned_cols=30 Identities=33% Similarity=0.572 Sum_probs=19.2
Q ss_pred eeecccccccCcc--hhHHhhCChHHHHHHHH
Q 022517 37 VCRVCDVVLKSDS--QWDAHQASRKHHEAIKN 66 (296)
Q Consensus 37 ~C~lCn~~VKsEs--lW~aHv~Sk~Hre~v~~ 66 (296)
-|-.|++-|.+.+ .|..|..|.+|++|+.+
T Consensus 5 yCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 5 YCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred ecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 5889999995444 89999999999999976
No 10
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=88.51 E-value=0.55 Score=42.90 Aligned_cols=42 Identities=21% Similarity=0.331 Sum_probs=34.7
Q ss_pred ccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHHh
Q 022517 27 LVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (296)
Q Consensus 27 ~A~Y~~~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK 68 (296)
-+.-+..|..-|-||+.+||.-.-+--|+|+|.|.-|+..+-
T Consensus 67 ~tp~sq~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgmsm 108 (193)
T KOG4727|consen 67 STPRSQKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMSM 108 (193)
T ss_pred CCcccccCceeeeecceeehhhHHHHHHhccHHHHHHHhhhh
Confidence 334467788999999999997666888999999999998743
No 11
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=87.18 E-value=0.3 Score=42.30 Aligned_cols=38 Identities=16% Similarity=0.284 Sum_probs=35.2
Q ss_pred CCCCceeecccccccCcchhHHhhCChHHHHHHHHHhh
Q 022517 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (296)
Q Consensus 32 ~~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK~ 69 (296)
-.||--|+.|....=+++.-..|..+|.||-+|..|+.
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 67999999999988889999999999999999999874
No 12
>KOG4722 consensus Zn-finger protein [General function prediction only]
Probab=71.89 E-value=2.2 Score=44.06 Aligned_cols=33 Identities=27% Similarity=0.641 Sum_probs=30.1
Q ss_pred CceeecccccccCcchhHHhhCChHHHHHHHHH
Q 022517 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (296)
Q Consensus 35 qL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~l 67 (296)
+-.|.+||+.|-+|-..-.||.|++|.+.|..+
T Consensus 493 kkqcslcnvlissevylfshvkgrkhqqal~e~ 525 (672)
T KOG4722|consen 493 KKQCSLCNVLISSEVYLFSHVKGRKHQQALNEL 525 (672)
T ss_pred hhccchhhhhhhhhhhhhhhhcchhHHHHHHHH
Confidence 457999999999999999999999999998775
No 13
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=67.27 E-value=2.8 Score=35.98 Aligned_cols=39 Identities=15% Similarity=0.325 Sum_probs=36.0
Q ss_pred CCCCceeecccccccCcchhHHhhCChHHHHHHHHHhhc
Q 022517 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAG 70 (296)
Q Consensus 32 ~~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK~~ 70 (296)
..||--|+-|....-+|...-.|..|+-||.++..|+..
T Consensus 52 GlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRev 90 (126)
T COG5112 52 GLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELREV 90 (126)
T ss_pred CCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcC
Confidence 679999999999988899999999999999999998864
No 14
>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=66.99 E-value=2.4 Score=30.47 Aligned_cols=17 Identities=47% Similarity=0.780 Sum_probs=14.0
Q ss_pred hcCCCCCCCCCHHhhhh
Q 022517 203 KGALPEGFFDNKEADLL 219 (296)
Q Consensus 203 ~~~LPeGFFDD~~~Dak 219 (296)
...-|+||||.-..|+.
T Consensus 33 l~~WP~GFFDq~~~~l~ 49 (52)
T PF12476_consen 33 LSNWPEGFFDQWDKDLR 49 (52)
T ss_pred CccCCCchhhHHHHHHH
Confidence 37889999999887764
No 15
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=64.16 E-value=2 Score=32.29 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=25.8
Q ss_pred CceeecccccccCcchhHHhhCChHHHHHHH
Q 022517 35 QPVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (296)
Q Consensus 35 qL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~ 65 (296)
.+.|.+|+...++-..+..|+.++.|.....
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 6999999999999999999999999987644
No 16
>PF03037 KMP11: Kinetoplastid membrane protein 11; InterPro: IPR004132 Kinetoplastid membrane protein 11 is a major cell surface glycoprotein of the parasite Leishmania donovani. It stimulates T-cell proliferation and may play a role in the immunlogy of the dieases Leishmaniasis.; GO: 0006952 defense response, 0008284 positive regulation of cell proliferation
Probab=56.58 E-value=11 Score=30.53 Aligned_cols=40 Identities=28% Similarity=0.696 Sum_probs=31.0
Q ss_pred CCCCCHHhhhhhhcCCCCCcchHHHHHHHHHHHHHHHHhhhhhhhh
Q 022517 209 GFFDNKEADLLARGIKPVKPDVKDEYKEYEKLIQEDLKQVDDRFEE 254 (296)
Q Consensus 209 GFFDD~~~DakaR~v~~~k~~~~~E~~eFqkeI~E~~~e~d~r~EE 254 (296)
.||-|+--++- --++|++-|+.|++-|+|-+..-..+.-|
T Consensus 29 kffadkpdest------lspemkehyekfe~miqehtdkfnkkm~e 68 (90)
T PF03037_consen 29 KFFADKPDEST------LSPEMKEHYEKFERMIQEHTDKFNKKMHE 68 (90)
T ss_pred hhhcCCCcccc------cCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58887766533 35789999999999999988877666544
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=54.65 E-value=6.9 Score=31.57 Aligned_cols=32 Identities=25% Similarity=0.527 Sum_probs=26.3
Q ss_pred cCCCCCceeecccccccCcchhHHhhCChHHHH
Q 022517 30 YNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHE 62 (296)
Q Consensus 30 Y~~~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre 62 (296)
..+..-|+|+.|...|.. +-|..|+..+-|..
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 346777999999999987 66999999877655
No 18
>PTZ00448 hypothetical protein; Provisional
Probab=49.32 E-value=12 Score=37.81 Aligned_cols=35 Identities=23% Similarity=0.366 Sum_probs=31.1
Q ss_pred CCCceeecccccccCcchhHHhhCChHHHHHHHHH
Q 022517 33 FDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (296)
Q Consensus 33 ~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~l 67 (296)
++..+|..|++...+...-..|..|-=||-|+.+-
T Consensus 312 ~~~~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRk 346 (373)
T PTZ00448 312 SNMLLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRN 346 (373)
T ss_pred cCCccccccccccCCHHHHHHHhhhhHHHHHHHHH
Confidence 35678999999998888999999999999999873
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=44.90 E-value=11 Score=21.36 Aligned_cols=20 Identities=25% Similarity=0.594 Sum_probs=15.7
Q ss_pred eeecccccccCcchhHHhhC
Q 022517 37 VCRVCDVVLKSDSQWDAHQA 56 (296)
Q Consensus 37 ~C~lCn~~VKsEslW~aHv~ 56 (296)
.|.+|+...++-.-|..|+.
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 59999999999888998874
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=44.69 E-value=12 Score=22.67 Aligned_cols=21 Identities=24% Similarity=0.346 Sum_probs=19.1
Q ss_pred ceeecccccccCcchhHHhhC
Q 022517 36 PVCRVCDVVLKSDSQWDAHQA 56 (296)
Q Consensus 36 L~C~lCn~~VKsEslW~aHv~ 56 (296)
..|..|+....+...|..|..
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
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=42.68 E-value=8.8 Score=38.80 Aligned_cols=34 Identities=26% Similarity=0.486 Sum_probs=31.9
Q ss_pred ceeecccccccCcchhHHhhCChHHHHHHHHHhh
Q 022517 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (296)
Q Consensus 36 L~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK~ 69 (296)
..|.+||....++..-.-|+.|+.|++++.+...
T Consensus 69 ~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 69 VYCEACNKSFASPKAHENHLKSKKHVENLSNHQR 102 (390)
T ss_pred eehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence 6799999999999999999999999999999765
No 22
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=36.93 E-value=34 Score=31.92 Aligned_cols=43 Identities=21% Similarity=0.358 Sum_probs=33.0
Q ss_pred cccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHHhhcc
Q 022517 28 VRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKAGA 71 (296)
Q Consensus 28 A~Y~~~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK~~~ 71 (296)
..--+-++-.|.+|..-.|.+-.|.=||. ++|-+.|+.+++..
T Consensus 70 ~~e~~~~K~~C~lc~KlFkg~eFV~KHI~-nKH~e~ve~~~~ev 112 (214)
T PF04959_consen 70 TKEEDEDKWRCPLCGKLFKGPEFVRKHIF-NKHPEKVEEVKKEV 112 (214)
T ss_dssp E-SSSSEEEEE-SSS-EESSHHHHHHHHH-HH-HHHHHHHHHHH
T ss_pred HHHHcCCEECCCCCCcccCChHHHHHHHh-hcCHHHHHHHHHHH
Confidence 33346788999999999999999999998 56999999987654
No 23
>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=35.63 E-value=24 Score=25.90 Aligned_cols=27 Identities=26% Similarity=0.476 Sum_probs=21.6
Q ss_pred ceeecccccccCcchhHHhhCChHHHHHHH
Q 022517 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (296)
Q Consensus 36 L~C~lCn~~VKsEslW~aHv~Sk~Hre~v~ 65 (296)
--|-.|++.-.+ -..|+.|.+||.=+.
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 358888877664 799999999997653
No 24
>PF14968 CCDC84: Coiled coil protein 84
Probab=35.27 E-value=20 Score=35.53 Aligned_cols=27 Identities=30% Similarity=0.477 Sum_probs=22.6
Q ss_pred eecccccccCcchhHHhhCChHHHHHHHHH
Q 022517 38 CRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (296)
Q Consensus 38 C~lCn~~VKsEslW~aHv~Sk~Hre~v~~l 67 (296)
|.||+..-= .|.-|+.|++|+.+|..+
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 399999999999998874
No 25
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=35.06 E-value=34 Score=34.74 Aligned_cols=36 Identities=25% Similarity=0.347 Sum_probs=32.0
Q ss_pred CCceeecccccccCcchhHHhhCChHHHHHHHHHhh
Q 022517 34 DQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIKA 69 (296)
Q Consensus 34 GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK~ 69 (296)
+.++|.-|++.+++.-+-.+|-.|-=||=||.+--+
T Consensus 2 t~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA 37 (390)
T KOG2785|consen 2 TGFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVA 37 (390)
T ss_pred CcceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhh
Confidence 458999999999999999999999999999988433
No 26
>PF01491 Frataxin_Cyay: Frataxin-like domain; InterPro: IPR002908 The eukaryotic proteins in this entry include frataxin, the protein that is mutated in Friedreich's ataxia [], and related sequences. Friedreich's ataxia is a progressive neurodegenerative disorder caused by loss of function mutations in the gene encoding frataxin (FRDA). Frataxin mRNA is predominantly expressed in tissues with a high metabolic rate (including liver, kidney, brown fat and heart). Mouse and yeast frataxin homologues contain a potential N-terminal mitochondrial targeting sequence, and human frataxin has been observed to co-localise with a mitochondrial protein. Furthermore, disruption of the yeast gene has been shown to result in mitochondrial dysfunction. Friedreich's ataxia is thus believed to be a mitochondrial disease caused by a mutation in the nuclear genome (specifically, expansion of an intronic GAA triplet repeat) [, , ]. The bacterial proteins in this entry are iron-sulphur cluster (FeS) metabolism CyaY proteins hmologous to eukaryotic frataxin. Partial Phylogenetic Profiling [] suggests that CyaY most likely functions as part of the ISC system for FeS cluster biosynthesis, and is supported by expermimental data in some species [, ]. ; PDB: 1EW4_A 2P1X_A 1SOY_A 2EFF_A 3T3T_B 3S4M_A 3T3K_A 3S5D_A 1LY7_A 3T3X_B ....
Probab=33.92 E-value=1.1e+02 Score=25.26 Aligned_cols=52 Identities=19% Similarity=0.252 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHhhhhhhhhhhccccCccccccccceeeeeecceeeeeEcc
Q 022517 235 KEYEKLIQEDLKQVDDRFEEEEVSCFSPFSQSLNHSCLGIYMSGRVLIILNG 286 (296)
Q Consensus 235 ~eFqkeI~E~~~e~d~r~EEeE~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~ 286 (296)
.+|.+.+.+.+..+.+.+|+-..+...-++-.++..-|-|-+.++--||+|-
T Consensus 4 ~~f~~lad~~l~~i~~~le~~~d~~~~d~d~e~~~gVLti~~~~~~~~VINk 55 (109)
T PF01491_consen 4 SEFHQLADETLDSIEDALEELDDEQDADIDVERSGGVLTIEFPDGGQYVINK 55 (109)
T ss_dssp HHHHHHHHHHHHHHHHHHHTCTTSSSSTEEEEEETTEEEEEETTSEEEEEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCceEEEccCCEEEEEECCCCEEEEeC
Confidence 4799999999999999999776666666777777778888886666666663
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=33.62 E-value=30 Score=25.47 Aligned_cols=26 Identities=31% Similarity=0.696 Sum_probs=18.7
Q ss_pred cCC-CCCceeeccccccc----CcchhHHhh
Q 022517 30 YNE-FDQPVCRVCDVVLK----SDSQWDAHQ 55 (296)
Q Consensus 30 Y~~-~GqL~C~lCn~~VK----sEslW~aHv 55 (296)
|+. .+.+.|..|...+. .+..|.-|.
T Consensus 30 y~~~~d~v~C~~C~~~l~~w~~~d~p~~~H~ 60 (71)
T smart00238 30 YTGVGDEVKCFFCGGELDNWEPGDDPWEEHK 60 (71)
T ss_pred ECCCCCEEEeCCCCCCcCCCCCCCCHHHHHh
Confidence 555 44899999999884 356677664
No 28
>PF14942 Muted: Organelle biogenesis, Muted-like protein
Probab=33.14 E-value=50 Score=28.97 Aligned_cols=28 Identities=32% Similarity=0.546 Sum_probs=22.6
Q ss_pred cchHHHHHHHHHHHHHHHHhhhhhhhhh
Q 022517 228 PDVKDEYKEYEKLIQEDLKQVDDRFEEE 255 (296)
Q Consensus 228 ~~~~~E~~eFqkeI~E~~~e~d~r~EEe 255 (296)
...+.+|++|+++|....+++|.--++-
T Consensus 103 ~~~~~~we~f~~e~~~~~~~vdee~~~~ 130 (145)
T PF14942_consen 103 EQRKQEWEEFMKEQQQKKQRVDEEFREK 130 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999887655543
No 29
>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=32.49 E-value=14 Score=21.53 Aligned_cols=21 Identities=24% Similarity=0.509 Sum_probs=18.2
Q ss_pred eeecccccccCcchhHHhhCC
Q 022517 37 VCRVCDVVLKSDSQWDAHQAS 57 (296)
Q Consensus 37 ~C~lCn~~VKsEslW~aHv~S 57 (296)
.|..|+...++.+.+..|+..
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 699999999998999999754
No 30
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=31.57 E-value=23 Score=26.14 Aligned_cols=27 Identities=22% Similarity=0.400 Sum_probs=21.0
Q ss_pred ceeecccccccCcchhHHhhCChHHHHHHH
Q 022517 36 PVCRVCDVVLKSDSQWDAHQASRKHHEAIK 65 (296)
Q Consensus 36 L~C~lCn~~VKsEslW~aHv~Sk~Hre~v~ 65 (296)
--|-.|...-.. ...|+.|++||.=+.
T Consensus 6 GYCE~Cr~kfd~---l~~Hi~s~~Hr~FA~ 32 (49)
T smart00586 6 GYCENCREKYDD---LETHLLSEKHRRFAE 32 (49)
T ss_pred cccccHhHHHhh---HHHHhccHHHHHHHc
Confidence 458888876654 789999999997554
No 31
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=31.13 E-value=14 Score=34.79 Aligned_cols=45 Identities=22% Similarity=0.400 Sum_probs=34.3
Q ss_pred ccCCCccccCCCCCceeecccccccCcchhHHhhCChHHHHHHHHH
Q 022517 22 RINSPLVRYNEFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (296)
Q Consensus 22 rI~~P~A~Y~~~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~l 67 (296)
--.||--+-.+.----|-+|.+-|+. +-|..|..|-.|..++..+
T Consensus 71 ets~p~nss~~e~lfyCE~Cd~~ip~-~~~snH~tSttHllsl~~~ 115 (223)
T KOG2384|consen 71 ETSHPMNSSRDEALFYCEVCDIYIPN-SKKSNHFTSTTHLLSLQHI 115 (223)
T ss_pred cCCCcccCCCCCccchhhhhhhhccC-CCCccchhhHHHHhhhccC
Confidence 34555544334444679999999995 8999999999999988764
No 32
>KOG0100 consensus Molecular chaperones GRP78/BiP/KAR2, HSP70 superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=30.46 E-value=33 Score=35.89 Aligned_cols=22 Identities=45% Similarity=0.771 Sum_probs=18.8
Q ss_pred cccccceeeeeecceeeeeEcc
Q 022517 265 QSLNHSCLGIYMSGRVLIILNG 286 (296)
Q Consensus 265 ~~~~~~~~~~~~~~~~~~~~~~ 286 (296)
---..||.|+|-.|||-||.|-
T Consensus 43 LGTTYsCVgV~kNgrvEIiANd 64 (663)
T KOG0100|consen 43 LGTTYSCVGVYKNGRVEIIAND 64 (663)
T ss_pred cCCceeeEEEEeCCeEEEEecC
Confidence 3446899999999999999984
No 33
>PRK01379 cyaY frataxin-like protein; Provisional
Probab=29.38 E-value=1.3e+02 Score=25.15 Aligned_cols=49 Identities=16% Similarity=0.376 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHhhhhhhhhhhccccCccccccccceeeeeecceeeeeEcc
Q 022517 235 KEYEKLIQEDLKQVDDRFEEEEVSCFSPFSQSLNHSCLGIYMSGRVLIILNG 286 (296)
Q Consensus 235 ~eFqkeI~E~~~e~d~r~EEeE~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~ 286 (296)
.+|.+...+.+....+.+|+.+.|+ .+.-.++..-|-|-..+.. ||+|-
T Consensus 4 ~ef~~lad~~L~~ie~~ie~~~~d~--d~D~e~~~gVLtl~~~~gt-~VINk 52 (103)
T PRK01379 4 SEFSKIAETTIAYIADKIEEQDKEA--SIDVDLQGDILNLDTDKGI-YVINK 52 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCc--ceeeeccCCEEEEEeCCcE-EEEeC
Confidence 4799999999999999998655432 3444455666666665555 66663
No 34
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=28.26 E-value=32 Score=31.23 Aligned_cols=30 Identities=37% Similarity=0.698 Sum_probs=24.3
Q ss_pred eeecccccccCc--chhHHhhCChHHHHHHHH
Q 022517 37 VCRVCDVVLKSD--SQWDAHQASRKHHEAIKN 66 (296)
Q Consensus 37 ~C~lCn~~VKsE--slW~aHv~Sk~Hre~v~~ 66 (296)
.|--|++-+-+. |+-..|++|++|+.|+.-
T Consensus 5 yCDYCdt~LthDslsvRK~H~~GrkH~~nvk~ 36 (165)
T KOG3454|consen 5 YCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD 36 (165)
T ss_pred hhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence 588898665544 568999999999999976
No 35
>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=25.39 E-value=89 Score=29.82 Aligned_cols=51 Identities=12% Similarity=0.136 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHhhhccCCCccccCCCCCceeecccccccC-cchhHHhhCChHHHHH
Q 022517 5 RKKAIFRAKLNAQKKEKRINSPLVRYNEFDQPVCRVCDVVLKS-DSQWDAHQASRKHHEA 63 (296)
Q Consensus 5 ~~ka~~Rallrqqr~~krI~~P~A~Y~~~GqL~C~lCn~~VKs-EslW~aHv~Sk~Hre~ 63 (296)
..-..|+++|+ .||+..|..+|.+.|++=+=.+-. -..-..|++||+-+..
T Consensus 3 ~~~~~v~~~L~--------~~p~l~~~~~~rvrC~lTGHEmp~~~~~l~~y~~gKKy~~l 54 (244)
T PF05477_consen 3 ELPKEVQAFLK--------SHPFLELTENGRVRCTLTGHEMPCRLDELQQYIRGKKYQRL 54 (244)
T ss_pred cchHHHHHHHh--------cCCceEecCCCeEEEeecCcccCCCHHHHHHHhccHHHHHH
Confidence 45677888887 499999999999999998743332 1357899999999843
No 36
>PF09276 Pertus-S5-tox: Pertussis toxin S5 subunit ; InterPro: IPR015356 Members of this family of Bordetella pertussis toxins adopt a structure consisting of an OB fold, with a closed or partly opened beta-barrel in a Greek-key topology []. ; PDB: 1BCP_F 1PTO_L 1PRT_L.
Probab=25.02 E-value=40 Score=27.46 Aligned_cols=15 Identities=47% Similarity=0.840 Sum_probs=10.8
Q ss_pred cceeeeeecceeeee
Q 022517 269 HSCLGIYMSGRVLII 283 (296)
Q Consensus 269 ~~~~~~~~~~~~~~~ 283 (296)
..||..|||||-|+-
T Consensus 23 efcltafmsgrslvr 37 (97)
T PF09276_consen 23 EFCLTAFMSGRSLVR 37 (97)
T ss_dssp EEEEEEE-TTS-EEE
T ss_pred hhhhhhhcccHHHHH
Confidence 469999999998763
No 37
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=24.82 E-value=19 Score=37.34 Aligned_cols=61 Identities=13% Similarity=0.192 Sum_probs=46.6
Q ss_pred CCCCCCCCCHHhhhhhhcCCCCCcchHHHHHHHHHHHH---HHHHhhhhhhhhhhccccCcccc
Q 022517 205 ALPEGFFDNKEADLLARGIKPVKPDVKDEYKEYEKLIQ---EDLKQVDDRFEEEEVSCFSPFSQ 265 (296)
Q Consensus 205 ~LPeGFFDD~~~DakaR~v~~~k~~~~~E~~eFqkeI~---E~~~e~d~r~EEeE~~a~~~~~~ 265 (296)
+|=.=.||++..+.++-....+..+++++++.+.++++ ...++.+.++++-|.+-..+-.|
T Consensus 56 ~vV~~~FddkVnqSALteqQ~kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Q 119 (475)
T PRK13729 56 GVVDTTFDDKVRQHATTEMQVTAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQ 119 (475)
T ss_pred ceecchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 34455789988888887777777788999999998887 66677777788777776666555
No 38
>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=23.87 E-value=53 Score=29.86 Aligned_cols=31 Identities=26% Similarity=0.512 Sum_probs=27.8
Q ss_pred eeecccccccCcchhHHhhCChHHHHHHHHH
Q 022517 37 VCRVCDVVLKSDSQWDAHQASRKHHEAIKNI 67 (296)
Q Consensus 37 ~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~l 67 (296)
.|.+|...-=.|.=...|+.|+-|++-+.-+
T Consensus 2 ~Cs~CKfrtf~~~ei~~HleS~~H~E~~~~i 32 (165)
T PF04988_consen 2 TCSFCKFRTFEEKEIEKHLESKFHKETLKYI 32 (165)
T ss_pred ccceeeeecccHHHHHHHHccchHHHHHHHH
Confidence 6999998877777788999999999999988
No 39
>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=23.32 E-value=54 Score=23.96 Aligned_cols=22 Identities=36% Similarity=0.913 Sum_probs=16.6
Q ss_pred CCceeecccccccC----cchhHHhh
Q 022517 34 DQPVCRVCDVVLKS----DSQWDAHQ 55 (296)
Q Consensus 34 GqL~C~lCn~~VKs----EslW~aHv 55 (296)
+.+.|..|+..+.. +..|..|.
T Consensus 33 d~v~C~~C~~~~~~w~~~d~p~~~H~ 58 (69)
T cd00022 33 DEVKCFFCGLELKNWEPGDDPWEEHK 58 (69)
T ss_pred CEEEeCCCCCCccCCCCCCCHHHHHh
Confidence 56999999998764 45666664
No 40
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=23.27 E-value=36 Score=34.71 Aligned_cols=37 Identities=14% Similarity=0.306 Sum_probs=31.5
Q ss_pred CCCCceeecccccccCcchhHHhhCChHHHHHHHHHh
Q 022517 32 EFDQPVCRVCDVVLKSDSQWDAHQASRKHHEAIKNIK 68 (296)
Q Consensus 32 ~~GqL~C~lCn~~VKsEslW~aHv~Sk~Hre~v~~lK 68 (296)
.+-..-|..|..-++.-+++.+|+.||.|..+.+..+
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 4567899999998887799999999999998877643
No 41
>COG1965 CyaY Protein implicated in iron transport, frataxin homolog [Inorganic ion transport and metabolism]
Probab=23.22 E-value=1.8e+02 Score=24.68 Aligned_cols=49 Identities=18% Similarity=0.342 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHhhhhhhhhhhccccCccccccccceeeeeecceeeeeEc
Q 022517 235 KEYEKLIQEDLKQVDDRFEEEEVSCFSPFSQSLNHSCLGIYMSGRVLIILN 285 (296)
Q Consensus 235 ~eFqkeI~E~~~e~d~r~EEeE~~a~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 (296)
.+|.+.+..-+....+++|+.+.++- |---+++..|-|-..-+-.||+|
T Consensus 4 ~efh~lad~~~~~Ied~le~~~~~~d--~D~d~qg~VlTl~f~ngs~iiIN 52 (106)
T COG1965 4 SEFHRLADALLLKIEDQLDEQDDEGD--IDCEIQGGVLTLTFDNGSQIIIN 52 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccCCC--cceecCCCEEEEEECCCcEEEEe
Confidence 48999999999999999999844443 33344577777777666666666
No 42
>TIGR03421 FeS_CyaY iron donor protein CyaY. Members of this protein family are the iron-sulfur cluster (FeS) metabolism protein CyaY, a homolog of eukaryotic frataxin. ISC is one of several bacterial systems for FeS assembly; we find by Partial Phylogenetic Profiling vs. the ISC system that CyaY most like work with the ISC system for FeS cluster biosynthesis. A study of of cyaY mutants in Salmonella enterica bears this out. Although the trusted cutoff is set low enough to include eukaryotic frataxin sequences, a narrower, exception-type model (TIGR03421) identifies identifies members of that specific set.
Probab=21.52 E-value=2e+02 Score=23.73 Aligned_cols=48 Identities=15% Similarity=0.307 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhhhhhhhhhhccccCccccccccceeeeeecceeeeeEcc
Q 022517 235 KEYEKLIQEDLKQVDDRFEEEEVSCFSPFSQSLNHSCLGIYMSGRVLIILNG 286 (296)
Q Consensus 235 ~eFqkeI~E~~~e~d~r~EEeE~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~ 286 (296)
.+|.+...+.+....+.+|+.+. -++-.++..-|-|-+.++--||+|-
T Consensus 3 ~ef~~~ad~~l~~ie~~ld~~~~----d~D~e~~~gVLti~f~~~~~~VINk 50 (102)
T TIGR03421 3 SEFHQLAEALLDAIEEAIDDADA----DIDCERAGGVLTLTFENGSQIIINK 50 (102)
T ss_pred HHHHHHHHHHHHHHHHHHhccCC----CeeeecCCCEEEEEECCCCEEEEeC
Confidence 47888899989888899985333 3566667778888776666666663
No 43
>PRK00446 cyaY frataxin-like protein; Provisional
Probab=21.23 E-value=2e+02 Score=23.81 Aligned_cols=48 Identities=15% Similarity=0.326 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHhhhhhhhh-hhccccCccccccccceeeeeecceeeeeEcc
Q 022517 235 KEYEKLIQEDLKQVDDRFEE-EEVSCFSPFSQSLNHSCLGIYMSGRVLIILNG 286 (296)
Q Consensus 235 ~eFqkeI~E~~~e~d~r~EE-eE~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~ 286 (296)
.+|.+...+.+...++.+|+ .+.| ++-.++..-|-|-+.++--||+|-
T Consensus 4 ~ef~~~ad~~l~~ie~~ld~~~~~d----~D~e~~~gVLti~f~~~~~~VINk 52 (105)
T PRK00446 4 SEFHQLADALWQAIEEQLDDDGDAD----IDCERNGGVLTLTFENGSKIIINR 52 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCC----eeeeccCCEEEEEECCCCEEEEeC
Confidence 47888888888888888886 3333 455556667777777666677763
No 44
>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=20.98 E-value=46 Score=21.16 Aligned_cols=20 Identities=20% Similarity=0.378 Sum_probs=16.0
Q ss_pred ceeecccccccCcchhHHhhC
Q 022517 36 PVCRVCDVVLKSDSQWDAHQA 56 (296)
Q Consensus 36 L~C~lCn~~VKsEslW~aHv~ 56 (296)
+.|.+|+..|. +..-..|+-
T Consensus 2 v~CPiC~~~v~-~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREVP-ENLINSHLD 21 (26)
T ss_pred CcCCCCcCccc-HHHHHHHHH
Confidence 57999999994 577888874
Done!