Query 029923
Match_columns 185
No_of_seqs 156 out of 510
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 05:47:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029923.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029923hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00021 BBOX B-Box-type zinc f 97.6 4E-05 8.6E-10 47.2 2.6 38 2-45 1-39 (39)
2 smart00336 BBOX B-Box-type zin 97.1 0.00043 9.4E-09 43.0 2.7 39 1-45 3-42 (42)
3 PF00643 zf-B_box: B-box zinc 97.1 0.00041 8.9E-09 43.9 2.5 39 1-45 3-42 (42)
4 PF10446 DUF2457: Protein of u 95.1 0.009 2E-07 56.7 1.1 10 120-129 119-128 (458)
5 PF10446 DUF2457: Protein of u 94.1 0.034 7.4E-07 52.9 2.5 8 120-127 87-94 (458)
6 PF09026 CENP-B_dimeris: Centr 92.0 0.045 9.7E-07 42.9 0.0 10 114-123 34-43 (101)
7 KOG4367 Predicted Zn-finger pr 91.1 0.042 9.2E-07 53.1 -1.1 74 3-76 164-253 (699)
8 PTZ00415 transmission-blocking 88.8 0.22 4.9E-06 54.5 1.8 32 97-128 154-185 (2849)
9 PF03066 Nucleoplasmin: Nucleo 85.8 0.24 5.2E-06 40.3 0.0 6 42-47 63-68 (149)
10 smart00336 BBOX B-Box-type zin 84.1 0.58 1.3E-05 28.7 1.2 34 42-78 2-35 (42)
11 PF14812 PBP1_TM: Transmembran 82.8 0.39 8.4E-06 36.3 0.0 9 120-128 49-57 (81)
12 cd00021 BBOX B-Box-type zinc f 79.8 0.82 1.8E-05 27.7 0.7 31 45-78 2-32 (39)
13 KOG1832 HIV-1 Vpr-binding prot 79.3 1.2 2.6E-05 46.7 2.1 15 40-54 1357-1371(1516)
14 PF00643 zf-B_box: B-box zinc 74.7 0.72 1.6E-05 28.9 -0.6 33 43-78 3-35 (42)
15 KOG4032 Uncharacterized conser 67.0 4.4 9.6E-05 34.8 2.3 16 111-126 143-158 (184)
16 PTZ00415 transmission-blocking 65.0 3.7 8.1E-05 45.7 1.8 8 71-78 113-120 (2849)
17 PF12773 DZR: Double zinc ribb 62.9 8.8 0.00019 24.8 2.7 30 17-52 9-38 (50)
18 KOG3130 Uncharacterized conser 57.7 5.9 0.00013 38.3 1.6 9 117-125 295-303 (514)
19 PF03153 TFIIA: Transcription 57.4 4.5 9.9E-05 36.2 0.8 13 155-167 342-354 (375)
20 PRK14559 putative protein seri 56.8 10 0.00022 37.7 3.1 25 1-30 1-25 (645)
21 KOG3241 Uncharacterized conser 50.6 14 0.0003 32.4 2.5 34 13-46 84-138 (227)
22 PF03115 Astro_capsid: Astrovi 47.9 6.1 0.00013 40.3 0.0 6 121-126 719-724 (787)
23 PTZ00429 beta-adaptin; Provisi 47.1 15 0.00032 37.1 2.5 17 112-128 611-627 (746)
24 PF09073 BUD22: BUD22; InterP 46.9 38 0.00083 31.6 5.1 16 162-177 277-292 (432)
25 KOG2140 Uncharacterized conser 45.7 18 0.00039 36.4 2.8 32 97-128 417-448 (739)
26 PF04889 Cwf_Cwc_15: Cwf15/Cwc 45.3 7.2 0.00016 34.2 0.1 29 145-173 207-238 (244)
27 PF04050 Upf2: Up-frameshift s 44.1 7.5 0.00016 31.8 0.0 8 158-165 118-125 (170)
28 PF04889 Cwf_Cwc_15: Cwf15/Cwc 43.5 11 0.00024 33.1 1.0 7 163-169 198-204 (244)
29 PF08595 RXT2_N: RXT2-like, N- 41.6 14 0.0003 30.5 1.2 6 123-128 94-99 (149)
30 PF09538 FYDLN_acid: Protein o 41.5 57 0.0012 25.5 4.5 26 20-51 9-34 (108)
31 PF02724 CDC45: CDC45-like pro 40.5 24 0.00052 34.7 2.8 8 40-47 75-82 (622)
32 KOG3540 Beta amyloid precursor 40.4 27 0.00058 34.6 3.0 10 46-55 143-152 (615)
33 TIGR00927 2A1904 K+-dependent 40.1 22 0.00048 37.6 2.6 7 121-127 893-899 (1096)
34 PF07975 C1_4: TFIIH C1-like d 39.8 15 0.00032 25.5 0.9 23 11-33 20-42 (51)
35 KOG2652 RNA polymerase II tran 39.7 35 0.00075 32.0 3.6 20 149-168 309-328 (348)
36 TIGR00595 priA primosomal prot 39.4 23 0.00051 33.6 2.5 38 11-53 212-250 (505)
37 PF07649 C1_3: C1-like domain; 38.7 13 0.00028 22.2 0.4 26 2-32 1-27 (30)
38 PLN02400 cellulose synthase 36.9 23 0.00051 37.5 2.2 30 45-74 38-71 (1085)
39 KOG1428 Inhibitor of type V ad 35.6 12 0.00026 41.9 -0.1 43 1-45 3322-3367(3738)
40 PF11942 Spt5_N: Spt5 transcri 34.4 19 0.00041 27.1 0.8 12 160-171 61-74 (97)
41 COG1499 NMD3 NMD protein affec 30.5 35 0.00077 31.7 2.1 44 1-51 6-51 (355)
42 PF02318 FYVE_2: FYVE-type zin 29.4 28 0.00061 26.7 1.1 42 2-51 55-102 (118)
43 KOG0699 Serine/threonine prote 29.2 21 0.00046 34.5 0.5 20 107-126 297-316 (542)
44 PLN02189 cellulose synthase 29.1 41 0.00089 35.6 2.5 30 45-74 36-69 (1040)
45 KOG2140 Uncharacterized conser 28.0 42 0.0009 33.9 2.2 6 51-56 351-356 (739)
46 PRK05580 primosome assembly pr 27.1 45 0.00097 32.9 2.3 38 11-53 380-418 (679)
47 PF14951 DUF4503: Domain of un 27.1 43 0.00094 31.8 2.1 42 2-45 275-317 (389)
48 PF08746 zf-RING-like: RING-li 26.3 10 0.00022 24.8 -1.6 28 20-49 11-43 (43)
49 COG1198 PriA Primosomal protei 25.8 56 0.0012 33.2 2.7 50 11-75 434-484 (730)
50 PF03153 TFIIA: Transcription 25.3 25 0.00053 31.6 0.1 10 115-124 326-335 (375)
51 KOG0127 Nucleolar protein fibr 25.0 47 0.001 33.4 2.0 8 27-34 133-140 (678)
52 PF11827 DUF3347: Protein of u 24.8 40 0.00087 27.8 1.3 13 173-185 150-162 (174)
53 KOG0468 U5 snRNP-specific prot 24.7 55 0.0012 34.0 2.4 17 111-127 44-60 (971)
54 PRK14873 primosome assembly pr 23.8 60 0.0013 32.4 2.5 37 11-52 382-419 (665)
55 PRK14714 DNA polymerase II lar 23.8 54 0.0012 35.6 2.2 7 2-8 668-674 (1337)
56 PF01286 XPA_N: XPA protein N- 23.5 41 0.00088 21.6 0.8 30 20-51 3-32 (34)
57 KOG3576 Ovo and related transc 22.7 16 0.00034 32.8 -1.6 41 3-44 119-168 (267)
58 KOG1999 RNA polymerase II tran 22.6 50 0.0011 34.9 1.7 45 79-123 35-93 (1024)
59 PF09184 PPP4R2: PPP4R2; Inte 22.4 75 0.0016 28.5 2.6 13 2-14 102-114 (288)
60 PF04438 zf-HIT: HIT zinc fing 22.0 32 0.00069 21.1 0.1 23 2-24 3-25 (30)
61 PF01056 Myc_N: Myc amino-term 21.2 32 0.00069 31.8 0.0 19 110-128 233-251 (329)
62 smart00249 PHD PHD zinc finger 20.5 1E+02 0.0022 18.2 2.2 25 4-32 2-26 (47)
63 PF09788 Tmemb_55A: Transmembr 20.4 64 0.0014 29.2 1.7 34 20-56 65-98 (256)
64 PLN02436 cellulose synthase A 20.2 65 0.0014 34.4 2.0 31 45-75 38-72 (1094)
No 1
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=97.65 E-value=4e-05 Score=47.20 Aligned_cols=38 Identities=47% Similarity=0.982 Sum_probs=32.9
Q ss_pred CCCCCCC-CCceEEeccCccccChhhccccccCCcCCCCceeeee
Q 029923 2 KKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (185)
Q Consensus 2 ~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (185)
.+|..++ +++.|||..|++.||..|+...|. .|.|++|
T Consensus 1 ~~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i 39 (39)
T cd00021 1 RLCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL 39 (39)
T ss_pred CCCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence 3688898 699999999999999999988773 7888875
No 2
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.13 E-value=0.00043 Score=43.04 Aligned_cols=39 Identities=44% Similarity=0.821 Sum_probs=33.3
Q ss_pred CCCCCCCC-CCceEEeccCccccChhhccccccCCcCCCCceeeee
Q 029923 1 MKKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (185)
Q Consensus 1 m~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (185)
++.|..+. .++.+||..+++.||..|....| +.|.+++|
T Consensus 3 ~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 3 PPKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred CCcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 35799999 89999999999999999998766 57877764
No 3
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=97.10 E-value=0.00041 Score=43.91 Aligned_cols=39 Identities=28% Similarity=0.589 Sum_probs=33.0
Q ss_pred CCCCCCCC-CCceEEeccCccccChhhccccccCCcCCCCceeeee
Q 029923 1 MKKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (185)
Q Consensus 1 m~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (185)
+++|..+. .++.+||..+...||..|....|.. |..++|
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------HKIVPI 42 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------SEEEEC
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCCC------CEEeEC
Confidence 46899999 6699999999999999999999843 887765
No 4
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=95.06 E-value=0.009 Score=56.72 Aligned_cols=10 Identities=10% Similarity=0.308 Sum_probs=5.6
Q ss_pred CcceeeCCCC
Q 029923 120 ENQVVPWSST 129 (185)
Q Consensus 120 enqvVP~s~~ 129 (185)
+.-.+=|+..
T Consensus 119 ~sd~~~WtP~ 128 (458)
T PF10446_consen 119 GSDYEFWTPG 128 (458)
T ss_pred cccceeeccc
Confidence 3456667643
No 5
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=94.07 E-value=0.034 Score=52.90 Aligned_cols=8 Identities=13% Similarity=-0.022 Sum_probs=3.2
Q ss_pred CcceeeCC
Q 029923 120 ENQVVPWS 127 (185)
Q Consensus 120 enqvVP~s 127 (185)
+...|=|.
T Consensus 87 ~d~~~~~~ 94 (458)
T PF10446_consen 87 DDSTVHDF 94 (458)
T ss_pred cccccccc
Confidence 33344443
No 6
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=92.00 E-value=0.045 Score=42.85 Aligned_cols=10 Identities=40% Similarity=0.790 Sum_probs=0.0
Q ss_pred CCCcCCCcce
Q 029923 114 DEDEDEENQV 123 (185)
Q Consensus 114 ~e~ed~enqv 123 (185)
++++++++-|
T Consensus 34 ddee~de~p~ 43 (101)
T PF09026_consen 34 DDEEEDEVPV 43 (101)
T ss_dssp ----------
T ss_pred cccccccccc
Confidence 3333335544
No 7
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=91.13 E-value=0.042 Score=53.09 Aligned_cols=74 Identities=26% Similarity=0.454 Sum_probs=60.2
Q ss_pred CCCCCC-C--CceEEeccCccccChhhccccccCCcCCCCceeeeecc-------------cccCCCCCcccCCCCCCcc
Q 029923 3 KCELCG-S--PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCH-------------VCQSLTPWNGSGPKLGPTI 66 (185)
Q Consensus 3 ~Cd~C~-a--pA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~-------------~C~~~~A~~~sg~C~~daa 66 (185)
.|.+|+ + .|.|+|..+..+.|.-|..+.|-+--.+++|.-+|-.+ .|..++..-.+..|+.+.+
T Consensus 164 kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~ck~ 243 (699)
T KOG4367|consen 164 KCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQCKM 243 (699)
T ss_pred hhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEecCC
Confidence 689998 4 69999999999999999999998777778887665432 4666666666778999999
Q ss_pred ccccccccCC
Q 029923 67 SVCNVCVGNG 76 (185)
Q Consensus 67 sLC~sCd~~~ 76 (185)
.+|-.|....
T Consensus 244 pvc~~clee~ 253 (699)
T KOG4367|consen 244 PVCYQCLEEG 253 (699)
T ss_pred hHHHHHHHhh
Confidence 9999996554
No 8
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=88.77 E-value=0.22 Score=54.50 Aligned_cols=32 Identities=41% Similarity=0.859 Sum_probs=20.1
Q ss_pred CCcCCCCCCCCCCCCCCCCCcCCCcceeeCCC
Q 029923 97 DDANEEEDDDDDDDDGGDEDEDEENQVVPWSS 128 (185)
Q Consensus 97 ~d~d~~d~~~~~~~~~~~e~ed~enqvVP~s~ 128 (185)
||+||++++|||+++|++|+|+++.||-|+--
T Consensus 154 d~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~d 185 (2849)
T PTZ00415 154 DDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDD 185 (2849)
T ss_pred CCccccccccccccccccccccccccccCCCc
Confidence 34444444455555556667777788999874
No 9
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=85.78 E-value=0.24 Score=40.32 Aligned_cols=6 Identities=17% Similarity=0.257 Sum_probs=2.9
Q ss_pred eeeecc
Q 029923 42 RTLLCH 47 (185)
Q Consensus 42 RvpLC~ 47 (185)
+++|+-
T Consensus 63 kv~lAt 68 (149)
T PF03066_consen 63 KVPLAT 68 (149)
T ss_dssp EEEEEE
T ss_pred EEEEEE
Confidence 455543
No 10
>smart00336 BBOX B-Box-type zinc finger.
Probab=84.11 E-value=0.58 Score=28.75 Aligned_cols=34 Identities=12% Similarity=0.004 Sum_probs=25.7
Q ss_pred eeeecccccCCCCCcccCCCCCCccccccccccCCCC
Q 029923 42 RTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGSG 78 (185)
Q Consensus 42 RvpLC~~C~~~~A~~~sg~C~~daasLC~sCd~~~h~ 78 (185)
|.++|..+...+..++ |..+...||..|....|.
T Consensus 2 ~~~~C~~h~~~~~~~~---C~~c~~~iC~~C~~~~H~ 35 (42)
T smart00336 2 RPPKCDSHGDEPAEFF---CEECGALLCRTCDEAEHR 35 (42)
T ss_pred cCCcCCCCCCCceEEE---CCCCCcccccccChhhcC
Confidence 5677888775444443 999999999999877664
No 11
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=82.80 E-value=0.39 Score=36.27 Aligned_cols=9 Identities=22% Similarity=0.464 Sum_probs=0.0
Q ss_pred CcceeeCCC
Q 029923 120 ENQVVPWSS 128 (185)
Q Consensus 120 enqvVP~s~ 128 (185)
|++.+|+-.
T Consensus 49 eee~m~rK~ 57 (81)
T PF14812_consen 49 EEEPMPRKG 57 (81)
T ss_dssp ---------
T ss_pred hcccccccc
Confidence 445667653
No 12
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=79.85 E-value=0.82 Score=27.70 Aligned_cols=31 Identities=13% Similarity=-0.035 Sum_probs=22.7
Q ss_pred ecccccCCCCCcccCCCCCCccccccccccCCCC
Q 029923 45 LCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGSG 78 (185)
Q Consensus 45 LC~~C~~~~A~~~sg~C~~daasLC~sCd~~~h~ 78 (185)
+|..+...+..+ .|..+.+.||..|....|.
T Consensus 2 ~C~~H~~~~~~~---fC~~~~~~iC~~C~~~~H~ 32 (39)
T cd00021 2 LCDEHGEEPLSL---FCETDRALLCVDCDLSVHS 32 (39)
T ss_pred CCCccCCcceEE---EeCccChhhhhhcChhhcC
Confidence 455555534444 3999999999999988775
No 13
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=79.27 E-value=1.2 Score=46.73 Aligned_cols=15 Identities=20% Similarity=0.264 Sum_probs=7.4
Q ss_pred ceeeeecccccCCCC
Q 029923 40 HSRTLLCHVCQSLTP 54 (185)
Q Consensus 40 H~RvpLC~~C~~~~A 54 (185)
-.|.+|-+.|-.++-
T Consensus 1357 ~v~R~~~Dlct~~~D 1371 (1516)
T KOG1832|consen 1357 PVDRCLLDLCTEPTD 1371 (1516)
T ss_pred ecccchhhhhcCCcc
Confidence 334445555655543
No 14
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=74.72 E-value=0.72 Score=28.89 Aligned_cols=33 Identities=12% Similarity=0.042 Sum_probs=24.6
Q ss_pred eeecccccCCCCCcccCCCCCCccccccccccCCCC
Q 029923 43 TLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGSG 78 (185)
Q Consensus 43 vpLC~~C~~~~A~~~sg~C~~daasLC~sCd~~~h~ 78 (185)
.++|..+....+.+ .|..+...||..|....|.
T Consensus 3 ~~~C~~H~~~~~~~---~C~~C~~~~C~~C~~~~H~ 35 (42)
T PF00643_consen 3 EPKCPEHPEEPLSL---FCEDCNEPLCSECTVSGHK 35 (42)
T ss_dssp SSB-SSTTTSBEEE---EETTTTEEEEHHHHHTSTT
T ss_pred CccCccCCccceEE---EecCCCCccCccCCCCCCC
Confidence 35676666654444 4999999999999999886
No 15
>KOG4032 consensus Uncharacterized conserved protein [Function unknown]
Probab=66.95 E-value=4.4 Score=34.82 Aligned_cols=16 Identities=31% Similarity=0.522 Sum_probs=8.0
Q ss_pred CCCCCCcCCCcceeeC
Q 029923 111 DGGDEDEDEENQVVPW 126 (185)
Q Consensus 111 ~~~~e~ed~enqvVP~ 126 (185)
..+|++.+.+|+-+|-
T Consensus 143 ~~dd~evdae~~~~~~ 158 (184)
T KOG4032|consen 143 EEDDEEVDAEDDEAPS 158 (184)
T ss_pred cchhhhhcccCCCCCC
Confidence 3344455555555553
No 16
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=65.01 E-value=3.7 Score=45.74 Aligned_cols=8 Identities=25% Similarity=0.360 Sum_probs=4.7
Q ss_pred ccccCCCC
Q 029923 71 VCVGNGSG 78 (185)
Q Consensus 71 sCd~~~h~ 78 (185)
.|.-.+||
T Consensus 113 ~~~y~~~g 120 (2849)
T PTZ00415 113 TCFYPIHG 120 (2849)
T ss_pred ceeeeccc
Confidence 45556665
No 17
>PF12773 DZR: Double zinc ribbon
Probab=62.87 E-value=8.8 Score=24.82 Aligned_cols=30 Identities=20% Similarity=0.526 Sum_probs=19.6
Q ss_pred cCccccChhhccccccCCcCCCCceeeeecccccCC
Q 029923 17 SDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSL 52 (185)
Q Consensus 17 aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~~~ 52 (185)
.+.+.+|..|...+- .......+|..|...
T Consensus 9 ~~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP------PPDQSKKICPNCGAE 38 (50)
T ss_pred CccccCChhhcCChh------hccCCCCCCcCCcCC
Confidence 445788888877666 234455677777753
No 18
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.74 E-value=5.9 Score=38.25 Aligned_cols=9 Identities=33% Similarity=0.232 Sum_probs=3.5
Q ss_pred cCCCcceee
Q 029923 117 EDEENQVVP 125 (185)
Q Consensus 117 ed~enqvVP 125 (185)
.|.|.-+|-
T Consensus 295 ~d~e~~~v~ 303 (514)
T KOG3130|consen 295 NDHEALGVG 303 (514)
T ss_pred cchhhhccC
Confidence 333333443
No 19
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=57.40 E-value=4.5 Score=36.20 Aligned_cols=13 Identities=23% Similarity=0.276 Sum_probs=8.2
Q ss_pred Cccccceeeeecc
Q 029923 155 TYSESQMSFSLKH 167 (185)
Q Consensus 155 ~~~~~~~~~~~~~ 167 (185)
.-+++|--|.||-
T Consensus 342 ~r~k~~wk~~lk~ 354 (375)
T PF03153_consen 342 TRVKNKWKCTLKD 354 (375)
T ss_dssp EEETTEEEEEEEE
T ss_pred ccccceeEEEeee
Confidence 3346777777774
No 20
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=56.80 E-value=10 Score=37.68 Aligned_cols=25 Identities=20% Similarity=0.611 Sum_probs=16.5
Q ss_pred CCCCCCCCCCceEEeccCccccChhhcccc
Q 029923 1 MKKCELCGSPAKMFCESDQASLCWDCDAKV 30 (185)
Q Consensus 1 m~~Cd~C~apA~vyC~aD~A~LC~~CDa~V 30 (185)
|.+|-.|+.. -.+.+++|..|.+++
T Consensus 1 M~~Cp~Cg~~-----n~~~akFC~~CG~~l 25 (645)
T PRK14559 1 MLICPQCQFE-----NPNNNRFCQKCGTSL 25 (645)
T ss_pred CCcCCCCCCc-----CCCCCccccccCCCC
Confidence 8899999922 123466777776554
No 21
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.58 E-value=14 Score=32.44 Aligned_cols=34 Identities=24% Similarity=0.379 Sum_probs=20.4
Q ss_pred EEeccCc--cccChhhcccc-------------------ccCCcCCCCceeeeec
Q 029923 13 MFCESDQ--ASLCWDCDAKV-------------------HGANFLVANHSRTLLC 46 (185)
Q Consensus 13 vyC~aD~--A~LC~~CDa~V-------------------HsAN~La~rH~RvpLC 46 (185)
+.|+.++ +..|+.|-..+ |.-+.+..||.|.+|-
T Consensus 84 ~~Cr~CA~e~~vCAKC~ks~~~i~i~d~~p~~~E~~~l~~t~~n~ser~RRt~lR 138 (227)
T KOG3241|consen 84 KLCRGCAKEQKVCAKCCKSVDQILIRDIYPVEAEQKLLDETIKNASERDRRTLLR 138 (227)
T ss_pred HhcccHHHHHHHHHHHhccHHHhhhcCCCCCcHHHHHHHHHHhhhhHHHHHHHHH
Confidence 5566653 67788887532 2233345678787765
No 22
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=47.87 E-value=6.1 Score=40.28 Aligned_cols=6 Identities=50% Similarity=0.535 Sum_probs=0.0
Q ss_pred cceeeC
Q 029923 121 NQVVPW 126 (185)
Q Consensus 121 nqvVP~ 126 (185)
||=+|-
T Consensus 719 NqGi~e 724 (787)
T PF03115_consen 719 NQGIPE 724 (787)
T ss_dssp ------
T ss_pred HcCCCH
Confidence 455554
No 23
>PTZ00429 beta-adaptin; Provisional
Probab=47.09 E-value=15 Score=37.15 Aligned_cols=17 Identities=24% Similarity=0.110 Sum_probs=9.4
Q ss_pred CCCCCcCCCcceeeCCC
Q 029923 112 GGDEDEDEENQVVPWSS 128 (185)
Q Consensus 112 ~~~e~ed~enqvVP~s~ 128 (185)
|++|+||+++++-|-+.
T Consensus 611 ~~~~~~~~~~~~~~~~~ 627 (746)
T PTZ00429 611 EDTEDDDAVELPSTPSM 627 (746)
T ss_pred ccccchhhccCCCCCCC
Confidence 34455566666665543
No 24
>PF09073 BUD22: BUD22; InterPro: IPR015158 BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal [].
Probab=46.92 E-value=38 Score=31.60 Aligned_cols=16 Identities=31% Similarity=0.320 Sum_probs=9.9
Q ss_pred eeeeccccccccCccc
Q 029923 162 SFSLKHDYHQGYSSSS 177 (185)
Q Consensus 162 ~~~~~~~~~~~~~~~~ 177 (185)
..+..|..+.||-|.+
T Consensus 277 ~stfLPsL~~Gy~sg~ 292 (432)
T PF09073_consen 277 SSTFLPSLMGGYISGS 292 (432)
T ss_pred ccccCchhccCcccCc
Confidence 3455666677876543
No 25
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=45.69 E-value=18 Score=36.38 Aligned_cols=32 Identities=28% Similarity=0.625 Sum_probs=15.2
Q ss_pred CCcCCCCCCCCCCCCCCCCCcCCCcceeeCCC
Q 029923 97 DDANEEEDDDDDDDDGGDEDEDEENQVVPWSS 128 (185)
Q Consensus 97 ~d~d~~d~~~~~~~~~~~e~ed~enqvVP~s~ 128 (185)
||+|..+++++|++++.+|++++--|+.-.+.
T Consensus 417 d~~~~s~E~~~eee~e~~ee~~e~~qI~D~T~ 448 (739)
T KOG2140|consen 417 DDEDGSSEDDDEEEDESVEEDEEKLQIIDMTE 448 (739)
T ss_pred ccccccccccccccccccccccccceeecccc
Confidence 33344444444444444444444566665543
No 26
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=45.29 E-value=7.2 Score=34.24 Aligned_cols=29 Identities=21% Similarity=0.411 Sum_probs=16.9
Q ss_pred hhhccCCCCCCcccc---ceeeeecccccccc
Q 029923 145 ASKFCNGGEGTYSES---QMSFSLKHDYHQGY 173 (185)
Q Consensus 145 ~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~ 173 (185)
.+-|.|.-.|-.... -+-=+|+-+|||-|
T Consensus 207 dvvFkN~~~~~~~~~k~~fiND~~rSdfH~kF 238 (244)
T PF04889_consen 207 DVVFKNQARGEPDKKKKEFINDTLRSDFHKKF 238 (244)
T ss_pred ccccccccCCCCCCCCCCcccCCcccHHHHHH
Confidence 445666655443222 34447888999865
No 27
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=44.10 E-value=7.5 Score=31.79 Aligned_cols=8 Identities=25% Similarity=0.679 Sum_probs=4.6
Q ss_pred ccceeeee
Q 029923 158 ESQMSFSL 165 (185)
Q Consensus 158 ~~~~~~~~ 165 (185)
..+++|+|
T Consensus 118 ~~~v~F~l 125 (170)
T PF04050_consen 118 GGKVAFTL 125 (170)
T ss_dssp --EEEEEE
T ss_pred CCeEEEEE
Confidence 46788875
No 28
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=43.53 E-value=11 Score=33.09 Aligned_cols=7 Identities=29% Similarity=0.785 Sum_probs=3.0
Q ss_pred eeecccc
Q 029923 163 FSLKHDY 169 (185)
Q Consensus 163 ~~~~~~~ 169 (185)
|++|+.|
T Consensus 198 ~~~kr~W 204 (244)
T PF04889_consen 198 FKVKRRW 204 (244)
T ss_pred CccccCC
Confidence 3444443
No 29
>PF08595 RXT2_N: RXT2-like, N-terminal; InterPro: IPR013904 The entry represents the N-terminal region of RXT2-like proteins. In Saccharomyces cerevisiae (Baker's yeast), RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth []. A high throughput localisation study has localised RXT2 to the nucleus [].
Probab=41.63 E-value=14 Score=30.48 Aligned_cols=6 Identities=17% Similarity=0.562 Sum_probs=3.1
Q ss_pred eeeCCC
Q 029923 123 VVPWSS 128 (185)
Q Consensus 123 vVP~s~ 128 (185)
+-|.++
T Consensus 94 LaPlt~ 99 (149)
T PF08595_consen 94 LAPLTH 99 (149)
T ss_pred hcccCC
Confidence 445554
No 30
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=41.48 E-value=57 Score=25.47 Aligned_cols=26 Identities=27% Similarity=0.574 Sum_probs=18.4
Q ss_pred cccChhhccccccCCcCCCCceeeeecccccC
Q 029923 20 ASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51 (185)
Q Consensus 20 A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~~ 51 (185)
..+|..|.+|..--|+ +..+|..|..
T Consensus 9 KR~Cp~CG~kFYDLnk------~PivCP~CG~ 34 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNK------DPIVCPKCGT 34 (108)
T ss_pred cccCCCCcchhccCCC------CCccCCCCCC
Confidence 4678999888886652 4445888874
No 31
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=40.45 E-value=24 Score=34.65 Aligned_cols=8 Identities=0% Similarity=-0.010 Sum_probs=3.5
Q ss_pred ceeeeecc
Q 029923 40 HSRTLLCH 47 (185)
Q Consensus 40 H~RvpLC~ 47 (185)
..++.+++
T Consensus 75 ~~~iyViD 82 (622)
T PF02724_consen 75 DVTIYVID 82 (622)
T ss_pred ceEEEEEe
Confidence 44444443
No 32
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=40.40 E-value=27 Score=34.64 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=5.4
Q ss_pred cccccCCCCC
Q 029923 46 CHVCQSLTPW 55 (185)
Q Consensus 46 C~~C~~~~A~ 55 (185)
|+.|+....|
T Consensus 143 mD~cEn~~hw 152 (615)
T KOG3540|consen 143 MDQCENNQHW 152 (615)
T ss_pred cccccchHHH
Confidence 5566655443
No 33
>TIGR00927 2A1904 K+-dependent Na+/Ca+ exchanger.
Probab=40.08 E-value=22 Score=37.62 Aligned_cols=7 Identities=14% Similarity=0.591 Sum_probs=3.3
Q ss_pred cceeeCC
Q 029923 121 NQVVPWS 127 (185)
Q Consensus 121 nqvVP~s 127 (185)
--..||.
T Consensus 893 ~~~~~~P 899 (1096)
T TIGR00927 893 PLSLEWP 899 (1096)
T ss_pred cccccCC
Confidence 3345664
No 34
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=39.75 E-value=15 Score=25.47 Aligned_cols=23 Identities=26% Similarity=0.690 Sum_probs=15.8
Q ss_pred ceEEeccCccccChhhccccccC
Q 029923 11 AKMFCESDQASLCWDCDAKVHGA 33 (185)
Q Consensus 11 A~vyC~aD~A~LC~~CDa~VHsA 33 (185)
.++-|......+|..||.-||..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 46899999999999999999954
No 35
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=39.72 E-value=35 Score=32.04 Aligned_cols=20 Identities=20% Similarity=0.248 Sum_probs=14.2
Q ss_pred cCCCCCCccccceeeeeccc
Q 029923 149 CNGGEGTYSESQMSFSLKHD 168 (185)
Q Consensus 149 ~~~~~~~~~~~~~~~~~~~~ 168 (185)
|--+-..-++.|--|.||--
T Consensus 309 CqyDKV~RsKnKWKc~LKDG 328 (348)
T KOG2652|consen 309 CQYDKVNRSKNKWKCYLKDG 328 (348)
T ss_pred EeeeeeccccceeeEEeecc
Confidence 44456666788889999853
No 36
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.44 E-value=23 Score=33.61 Aligned_cols=38 Identities=24% Similarity=0.512 Sum_probs=26.9
Q ss_pred ceEEeccCc-cccChhhccccccCCcCCCCceeeeecccccCCC
Q 029923 11 AKMFCESDQ-ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLT 53 (185)
Q Consensus 11 A~vyC~aD~-A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~~~~ 53 (185)
..|+|+.+. ..-|..||...-. .++.+.+.|..|....
T Consensus 212 ~~~~C~~Cg~~~~C~~C~~~l~~-----h~~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 212 KNLLCRSCGYILCCPNCDVSLTY-----HKKEGKLRCHYCGYQE 250 (505)
T ss_pred CeeEhhhCcCccCCCCCCCceEE-----ecCCCeEEcCCCcCcC
Confidence 457788884 7789999865532 2456678899998644
No 37
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=38.74 E-value=13 Score=22.21 Aligned_cols=26 Identities=27% Similarity=0.644 Sum_probs=8.5
Q ss_pred CCCCCCC-CCceEEeccCccccChhhcccccc
Q 029923 2 KKCELCG-SPAKMFCESDQASLCWDCDAKVHG 32 (185)
Q Consensus 2 ~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHs 32 (185)
++|++|+ ..-. ...+-|..||..+|.
T Consensus 1 ~~C~~C~~~~~~-----~~~Y~C~~Cdf~lH~ 27 (30)
T PF07649_consen 1 FRCDACGKPIDG-----GWFYRCSECDFDLHE 27 (30)
T ss_dssp ---TTTS----S-------EEE-TTT-----H
T ss_pred CcCCcCCCcCCC-----CceEECccCCCccCh
Confidence 4688998 3221 124668888888873
No 38
>PLN02400 cellulose synthase
Probab=36.85 E-value=23 Score=37.52 Aligned_cols=30 Identities=17% Similarity=0.389 Sum_probs=20.4
Q ss_pred ecccccCCCCCccc----CCCCCCcccccccccc
Q 029923 45 LCHVCQSLTPWNGS----GPKLGPTISVCNVCVG 74 (185)
Q Consensus 45 LC~~C~~~~A~~~s----g~C~~daasLC~sCd~ 74 (185)
+|++|...-..... -.|..++-.+|..|..
T Consensus 38 iCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE 71 (1085)
T PLN02400 38 ICQICGDDVGVTETGDVFVACNECAFPVCRPCYE 71 (1085)
T ss_pred eeeecccccCcCCCCCEEEEEccCCCccccchhh
Confidence 79999853222111 2688999999999963
No 39
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=35.58 E-value=12 Score=41.92 Aligned_cols=43 Identities=28% Similarity=0.547 Sum_probs=31.5
Q ss_pred CCCCCCCC---CCceEEeccCccccChhhccccccCCcCCCCceeeee
Q 029923 1 MKKCELCG---SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (185)
Q Consensus 1 m~~Cd~C~---apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (185)
||.|+.-. ..|.|+|.-+. +||..||.-+|-.-+ .+.|+|-.+
T Consensus 3322 ~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHrr-tktH~~q~f 3367 (3738)
T KOG1428|consen 3322 MPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHRR-TKTHQRQVF 3367 (3738)
T ss_pred CCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHhh-ccchhhhhh
Confidence 78899886 46789997776 999999987763221 356777543
No 40
>PF11942 Spt5_N: Spt5 transcription elongation factor, acidic N-terminal; InterPro: IPR022581 This is the very acidic N-terminal domain of the early transcription elongation factor Spt5 []. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4 [], nor is it essential for RNA polymerase II binding [].
Probab=34.39 E-value=19 Score=27.07 Aligned_cols=12 Identities=25% Similarity=0.434 Sum_probs=6.2
Q ss_pred ceeeeec--ccccc
Q 029923 160 QMSFSLK--HDYHQ 171 (185)
Q Consensus 160 ~~~~~~~--~~~~~ 171 (185)
+++-.|| ..|.+
T Consensus 61 ~lae~~k~~~RY~~ 74 (97)
T PF11942_consen 61 ELAEYLKLSERYAR 74 (97)
T ss_pred HHHHHHHHHHHhcc
Confidence 3444455 66644
No 41
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=30.48 E-value=35 Score=31.70 Aligned_cols=44 Identities=23% Similarity=0.525 Sum_probs=30.2
Q ss_pred CCCCCCCC-CC-ceEEeccCccccChhhccccccCCcCCCCceeeeecccccC
Q 029923 1 MKKCELCG-SP-AKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51 (185)
Q Consensus 1 m~~Cd~C~-ap-A~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~~ 51 (185)
|.+|-.|+ .. +.+ +.||..|....|.- --..+-..+.+|..|.+
T Consensus 6 ~~~C~~CGr~~~~~~------~~lC~dC~~~~~~~-~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 6 TILCVRCGRSVDPLI------DGLCGDCYVETTPL-IEIPDEVNVEVCRHCGA 51 (355)
T ss_pred ccEeccCCCcCchhh------ccccHHHHhccCcc-ccCCCceEEEECCcCCC
Confidence 45788888 33 333 89999999997632 22345667778888884
No 42
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=29.41 E-value=28 Score=26.72 Aligned_cols=42 Identities=26% Similarity=0.700 Sum_probs=28.8
Q ss_pred CCCCCCCC------CceEEeccCccccChhhccccccCCcCCCCceeeeecccccC
Q 029923 2 KKCELCGS------PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51 (185)
Q Consensus 2 ~~Cd~C~a------pA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~~ 51 (185)
+.|-.|+. .....|.......|..|... .+....|||-+|..
T Consensus 55 ~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~--------~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 55 RHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY--------SKKEPIWLCKVCQK 102 (118)
T ss_dssp SB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE--------TSSSCCEEEHHHHH
T ss_pred cchhhhCCcccccCCCCCcCCcCCccccCccCCc--------CCCCCCEEChhhHH
Confidence 35777762 34577888888888888766 34567889988874
No 43
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=29.16 E-value=21 Score=34.48 Aligned_cols=20 Identities=30% Similarity=0.572 Sum_probs=14.1
Q ss_pred CCCCCCCCCCcCCCcceeeC
Q 029923 107 DDDDDGGDEDEDEENQVVPW 126 (185)
Q Consensus 107 ~~~~~~~~e~ed~enqvVP~ 126 (185)
++.+++.++||..|.|.+|.
T Consensus 297 ed~e~e~ddEE~~e~~map~ 316 (542)
T KOG0699|consen 297 EDAEDEQDDEEMVEGSMAPL 316 (542)
T ss_pred cccccccchhhhhhhccccc
Confidence 33445566777788899997
No 44
>PLN02189 cellulose synthase
Probab=29.11 E-value=41 Score=35.62 Aligned_cols=30 Identities=17% Similarity=0.303 Sum_probs=19.6
Q ss_pred ecccccCCCCCcc----cCCCCCCcccccccccc
Q 029923 45 LCHVCQSLTPWNG----SGPKLGPTISVCNVCVG 74 (185)
Q Consensus 45 LC~~C~~~~A~~~----sg~C~~daasLC~sCd~ 74 (185)
+|.+|...-.... --.|..++-.+|..|..
T Consensus 36 ~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye 69 (1040)
T PLN02189 36 VCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE 69 (1040)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhh
Confidence 7888885322111 13688888889988864
No 45
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=27.95 E-value=42 Score=33.91 Aligned_cols=6 Identities=17% Similarity=-0.269 Sum_probs=2.4
Q ss_pred CCCCCc
Q 029923 51 SLTPWN 56 (185)
Q Consensus 51 ~~~A~~ 56 (185)
++|++.
T Consensus 351 ~~p~v~ 356 (739)
T KOG2140|consen 351 SHPAVL 356 (739)
T ss_pred cCCccc
Confidence 344433
No 46
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.09 E-value=45 Score=32.88 Aligned_cols=38 Identities=26% Similarity=0.522 Sum_probs=26.6
Q ss_pred ceEEeccCc-cccChhhccccccCCcCCCCceeeeecccccCCC
Q 029923 11 AKMFCESDQ-ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLT 53 (185)
Q Consensus 11 A~vyC~aD~-A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~~~~ 53 (185)
..++|+.+. ..-|..|+..+.. .+..+.++|..|....
T Consensus 380 ~~~~C~~Cg~~~~C~~C~~~l~~-----h~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 380 PFLLCRDCGWVAECPHCDASLTL-----HRFQRRLRCHHCGYQE 418 (679)
T ss_pred CceEhhhCcCccCCCCCCCceeE-----ECCCCeEECCCCcCCC
Confidence 457788875 5669999875532 2456788999999643
No 47
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=27.09 E-value=43 Score=31.83 Aligned_cols=42 Identities=26% Similarity=0.430 Sum_probs=32.4
Q ss_pred CCCCCCCCCceEEeccC-ccccChhhccccccCCcCCCCceeeee
Q 029923 2 KKCELCGSPAKMFCESD-QASLCWDCDAKVHGANFLVANHSRTLL 45 (185)
Q Consensus 2 ~~Cd~C~apA~vyC~aD-~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (185)
|.|+.|++--.-....| .++.|..|..-|- ++++++|.-|-|
T Consensus 275 PvCd~CGn~rLe~~pe~rg~~~C~~Cs~~V~--sP~~r~~LeVfl 317 (389)
T PF14951_consen 275 PVCDRCGNGRLEQSPEDRGAFSCGDCSRVVT--SPVLRMHLEVFL 317 (389)
T ss_pred ccccccCCccceeCccCCCceeccchhhhcc--CcceeeeEEEEE
Confidence 58999994444444445 5899999999887 789999998876
No 48
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=26.33 E-value=10 Score=24.83 Aligned_cols=28 Identities=25% Similarity=0.774 Sum_probs=11.9
Q ss_pred cccCh--hhcccccc---CCcCCCCceeeeecccc
Q 029923 20 ASLCW--DCDAKVHG---ANFLVANHSRTLLCHVC 49 (185)
Q Consensus 20 A~LC~--~CDa~VHs---AN~La~rH~RvpLC~~C 49 (185)
..+|. .|..++|. ++++ +|.+.+.|..|
T Consensus 11 G~~C~~~~C~~r~H~~C~~~y~--r~~~~~~CP~C 43 (43)
T PF08746_consen 11 GQRCSNRDCNVRLHDDCFKKYF--RHRSNPKCPNC 43 (43)
T ss_dssp SEE-SS--S--EE-HHHHHHHT--TT-SS-B-TTT
T ss_pred eccCCCCccCchHHHHHHHHHH--hcCCCCCCcCC
Confidence 55677 69999994 3433 55665566655
No 49
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=25.76 E-value=56 Score=33.23 Aligned_cols=50 Identities=22% Similarity=0.553 Sum_probs=35.0
Q ss_pred ceEEeccCc-cccChhhccccccCCcCCCCceeeeecccccCCCCCcccCCCCCCccccccccccC
Q 029923 11 AKMFCESDQ-ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGN 75 (185)
Q Consensus 11 A~vyC~aD~-A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~~~~A~~~sg~C~~daasLC~sCd~~ 75 (185)
..|.|+.+. ..=|..||...- ..++.+.+.|..|...... ..-|+.|-..
T Consensus 434 ~~l~C~~Cg~v~~Cp~Cd~~lt-----~H~~~~~L~CH~Cg~~~~~----------p~~Cp~Cgs~ 484 (730)
T COG1198 434 PLLLCRDCGYIAECPNCDSPLT-----LHKATGQLRCHYCGYQEPI----------PQSCPECGSE 484 (730)
T ss_pred ceeecccCCCcccCCCCCcceE-----EecCCCeeEeCCCCCCCCC----------CCCCCCCCCC
Confidence 467788885 677999997654 3366789999999975322 2357778555
No 50
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=25.34 E-value=25 Score=31.56 Aligned_cols=10 Identities=40% Similarity=0.611 Sum_probs=3.4
Q ss_pred CCcCCCccee
Q 029923 115 EDEDEENQVV 124 (185)
Q Consensus 115 e~ed~enqvV 124 (185)
++++.+|-||
T Consensus 326 ~~~~~~~~~~ 335 (375)
T PF03153_consen 326 DDFDTDNVVL 335 (375)
T ss_dssp --STTS-EEE
T ss_pred cccCcCCEEE
Confidence 3334555544
No 51
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=24.99 E-value=47 Score=33.43 Aligned_cols=8 Identities=38% Similarity=0.094 Sum_probs=3.0
Q ss_pred ccccccCC
Q 029923 27 DAKVHGAN 34 (185)
Q Consensus 27 Da~VHsAN 34 (185)
|.+.|-+|
T Consensus 133 dLk~vFs~ 140 (678)
T KOG0127|consen 133 DLKNVFSN 140 (678)
T ss_pred HHHHHHhh
Confidence 33333333
No 52
>PF11827 DUF3347: Protein of unknown function (DUF3347); InterPro: IPR021782 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 169 to 570 amino acids in length.
Probab=24.77 E-value=40 Score=27.80 Aligned_cols=13 Identities=54% Similarity=0.966 Sum_probs=11.0
Q ss_pred cCccccccCCCCC
Q 029923 173 YSSSSQQSKNPYF 185 (185)
Q Consensus 173 ~~~~~~~~~~~~~ 185 (185)
+-|.+...+||||
T Consensus 150 WLs~~~~I~NPYf 162 (174)
T PF11827_consen 150 WLSDSKEIKNPYF 162 (174)
T ss_pred eCCCCCcCcCCCC
Confidence 6778888999998
No 53
>KOG0468 consensus U5 snRNP-specific protein [Translation, ribosomal structure and biogenesis]
Probab=24.70 E-value=55 Score=34.03 Aligned_cols=17 Identities=24% Similarity=0.540 Sum_probs=10.3
Q ss_pred CCCCCCcCCCcceeeCC
Q 029923 111 DGGDEDEDEENQVVPWS 127 (185)
Q Consensus 111 ~~~~e~ed~enqvVP~s 127 (185)
+....|++..||||=-.
T Consensus 44 ~~~~~e~~~~~~vvLhe 60 (971)
T KOG0468|consen 44 EGDHNEDEPQNAVVLHE 60 (971)
T ss_pred ccccccccccceeeecc
Confidence 33445556778888543
No 54
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.84 E-value=60 Score=32.35 Aligned_cols=37 Identities=16% Similarity=0.396 Sum_probs=26.6
Q ss_pred ceEEeccCc-cccChhhccccccCCcCCCCceeeeecccccCC
Q 029923 11 AKMFCESDQ-ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSL 52 (185)
Q Consensus 11 A~vyC~aD~-A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~~~ 52 (185)
..|+|+.+. ..-|..||..+-.. +..+.+.|..|...
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~L~~h-----~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGPLGLP-----SAGGTPRCRWCGRA 419 (665)
T ss_pred CeeEhhhCcCeeECCCCCCceeEe-----cCCCeeECCCCcCC
Confidence 467888885 78899998665421 34567889999863
No 55
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.80 E-value=54 Score=35.64 Aligned_cols=7 Identities=43% Similarity=1.540 Sum_probs=4.9
Q ss_pred CCCCCCC
Q 029923 2 KKCELCG 8 (185)
Q Consensus 2 ~~Cd~C~ 8 (185)
++|..|+
T Consensus 668 rkCPkCG 674 (1337)
T PRK14714 668 RRCPSCG 674 (1337)
T ss_pred EECCCCC
Confidence 4677777
No 56
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=23.47 E-value=41 Score=21.63 Aligned_cols=30 Identities=17% Similarity=0.447 Sum_probs=16.0
Q ss_pred cccChhhccccccCCcCCCCceeeeecccccC
Q 029923 20 ASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51 (185)
Q Consensus 20 A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~~ 51 (185)
+..|..|+....-+ .+.+|-..++|+.|+.
T Consensus 3 ~~~C~eC~~~f~dS--yL~~~F~~~VCD~CRD 32 (34)
T PF01286_consen 3 YPKCDECGKPFMDS--YLLNNFDLPVCDKCRD 32 (34)
T ss_dssp -EE-TTT--EES-S--SCCCCTS-S--TTT-S
T ss_pred CchHhHhCCHHHHH--HHHHhCCccccccccC
Confidence 45788888888744 4678888899998864
No 57
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=22.67 E-value=16 Score=32.75 Aligned_cols=41 Identities=32% Similarity=0.709 Sum_probs=31.4
Q ss_pred CCCCCC-C-------CceEEeccC-ccccChhhccccccCCcCCCCceeee
Q 029923 3 KCELCG-S-------PAKMFCESD-QASLCWDCDAKVHGANFLVANHSRTL 44 (185)
Q Consensus 3 ~Cd~C~-a-------pA~vyC~aD-~A~LC~~CDa~VHsAN~La~rH~Rvp 44 (185)
.|.+|+ . .--|-|++| ..+||..|.+..|-+ +=++||+|.-
T Consensus 119 tCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndt-fdlkrh~rth 168 (267)
T KOG3576|consen 119 TCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDT-FDLKRHTRTH 168 (267)
T ss_pred eeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccch-hhhhhhhccc
Confidence 477776 2 224779999 689999999999954 5578999864
No 58
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=22.64 E-value=50 Score=34.91 Aligned_cols=45 Identities=27% Similarity=0.506 Sum_probs=0.0
Q ss_pred CCccccccCCCcCCCCCCCCcC--------------CCCCCCCCCCCCCCCCcCCCcce
Q 029923 79 STSREETNRGETYTDDDYDDAN--------------EEEDDDDDDDDGGDEDEDEENQV 123 (185)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~d~d--------------~~d~~~~~~~~~~~e~ed~enqv 123 (185)
...++.+.+.|.+++++.++.+ +-|.|+|.+++++++|.+++.+.
T Consensus 35 ~~~~de~D~~e~~e~~~dd~~~~~~k~~s~~gf~~~e~dvDdeveddd~~~edEed~~~ 93 (1024)
T KOG1999|consen 35 EDTEDEGDEEEYDEDRKDDEPDEKDKKESGGGFIDREADVDDEVEDDDDDEEDEEDIEL 93 (1024)
T ss_pred ccccccccchhhcccccCcchhhhccccccccccccccccccccccccchhccCcchhh
No 59
>PF09184 PPP4R2: PPP4R2; InterPro: IPR015267 PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast [], and may confer resistance in higher eukaryotes.
Probab=22.41 E-value=75 Score=28.51 Aligned_cols=13 Identities=38% Similarity=0.725 Sum_probs=6.3
Q ss_pred CCCCCCCCCceEE
Q 029923 2 KKCELCGSPAKMF 14 (185)
Q Consensus 2 ~~Cd~C~apA~vy 14 (185)
|+|++|-.|-..|
T Consensus 102 RlcEl~~~P~~~y 114 (288)
T PF09184_consen 102 RLCELLLDPRKHY 114 (288)
T ss_pred HHHHHHhChhhcc
Confidence 4555555443333
No 60
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=22.01 E-value=32 Score=21.15 Aligned_cols=23 Identities=43% Similarity=0.875 Sum_probs=15.6
Q ss_pred CCCCCCCCCceEEeccCccccCh
Q 029923 2 KKCELCGSPAKMFCESDQASLCW 24 (185)
Q Consensus 2 ~~Cd~C~apA~vyC~aD~A~LC~ 24 (185)
.+|.+|+.++..-|....+..|.
T Consensus 3 ~~C~vC~~~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGNPAKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSSEESEE-TTT--EESS
T ss_pred CCCccCcCCCEEECCCcCCceeC
Confidence 36888888888888888877775
No 61
>PF01056 Myc_N: Myc amino-terminal region; InterPro: IPR012682 The class III basic helix-turn-helix (bHLH) transcription factors have proliferative and apoptotic roles and are characterised by the presence of a leucine zipper adjacent to the bHLH domain. The myc oncogene gene was first discovered in small-cell lung cancer cell lines where it is found to be deregulated []. Although the biochemical function of the gene product is unknown, as a nuclear protein with a short half-life it may play a direct or indirect role in controlling gene expression []. Myc forms a heterodimer with Max, and this complex regulates cell growth through direct activation of genes involved in cell replication []. This entry represents the N-terminal domain found adjacent to the basic helix-loop-helix (bHLH) region (IPR001092 from INTERPRO).; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1EE4_C.
Probab=21.16 E-value=32 Score=31.76 Aligned_cols=19 Identities=32% Similarity=0.510 Sum_probs=0.0
Q ss_pred CCCCCCCcCCCcceeeCCC
Q 029923 110 DDGGDEDEDEENQVVPWSS 128 (185)
Q Consensus 110 ~~~~~e~ed~enqvVP~s~ 128 (185)
+++++++|++|.-||-.--
T Consensus 233 ~~~eeeeeeEEIDVVTVEk 251 (329)
T PF01056_consen 233 EEEEEEEEEEEIDVVTVEK 251 (329)
T ss_dssp -------------------
T ss_pred ccccccCCCcceEEEEeee
Confidence 3444555666677887654
No 62
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=20.37 E-value=64 Score=29.15 Aligned_cols=34 Identities=24% Similarity=0.494 Sum_probs=26.4
Q ss_pred cccChhhccccccCCcCCCCceeeeecccccCCCCCc
Q 029923 20 ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWN 56 (185)
Q Consensus 20 A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~~~~A~~ 56 (185)
...|..|...|+-. -++|+.|..|..|...|+++
T Consensus 65 ~v~CrVCq~~I~i~---gk~~QhVVkC~~CnEATPIr 98 (256)
T PF09788_consen 65 VVTCRVCQSLIDIE---GKMHQHVVKCSVCNEATPIR 98 (256)
T ss_pred eEEeecCCceeccc---CccceeeEECCCCCcccccc
Confidence 45688888888755 46899999999999766543
No 64
>PLN02436 cellulose synthase A
Probab=20.16 E-value=65 Score=34.39 Aligned_cols=31 Identities=16% Similarity=0.319 Sum_probs=20.7
Q ss_pred ecccccCCCCCccc----CCCCCCccccccccccC
Q 029923 45 LCHVCQSLTPWNGS----GPKLGPTISVCNVCVGN 75 (185)
Q Consensus 45 LC~~C~~~~A~~~s----g~C~~daasLC~sCd~~ 75 (185)
+|++|...-..... -.|..++-.+|..|..-
T Consensus 38 iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyey 72 (1094)
T PLN02436 38 TCQICGDEIELTVDGEPFVACNECAFPVCRPCYEY 72 (1094)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhhh
Confidence 89999853221111 26888999999999643
Done!