Query 029117
Match_columns 198
No_of_seqs 163 out of 510
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 07:45:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029117.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029117hhsearch_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 4.6E-05 1E-09 47.3 2.6 38 2-45 1-39 (39)
2 smart00336 BBOX B-Box-type zin 97.1 0.00047 1E-08 43.3 2.8 39 1-45 3-42 (42)
3 PF00643 zf-B_box: B-box zinc 97.0 0.00055 1.2E-08 43.8 2.3 39 1-45 3-42 (42)
4 PF10446 DUF2457: Protein of u 93.7 0.026 5.7E-07 54.2 1.0 7 122-128 121-127 (458)
5 PF10446 DUF2457: Protein of u 93.0 0.068 1.5E-06 51.4 2.5 9 119-127 86-94 (458)
6 PF04931 DNA_pol_phi: DNA poly 91.0 0.17 3.6E-06 50.5 2.8 7 175-181 772-778 (784)
7 PF09026 CENP-B_dimeris: Centr 90.9 0.069 1.5E-06 42.3 0.0 8 117-124 37-44 (101)
8 KOG4367 Predicted Zn-finger pr 88.7 0.088 1.9E-06 51.5 -1.1 74 3-76 164-253 (699)
9 KOG1832 HIV-1 Vpr-binding prot 84.0 0.59 1.3E-05 49.3 1.9 13 41-53 1358-1370(1516)
10 smart00336 BBOX B-Box-type zin 83.7 0.66 1.4E-05 28.8 1.4 34 42-78 2-35 (42)
11 cd00021 BBOX B-Box-type zinc f 79.1 0.87 1.9E-05 27.9 0.7 31 45-78 2-32 (39)
12 PTZ00415 transmission-blocking 76.4 1.5 3.2E-05 49.1 1.8 22 107-128 164-185 (2849)
13 PF00643 zf-B_box: B-box zinc 75.3 0.66 1.4E-05 29.4 -0.7 34 43-79 3-36 (42)
14 PF14812 PBP1_TM: Transmembran 72.9 1.1 2.5E-05 34.1 0.0 9 120-128 49-57 (81)
15 PF12773 DZR: Double zinc ribb 69.7 5.3 0.00012 26.1 2.7 30 17-52 9-38 (50)
16 KOG3130 Uncharacterized conser 63.4 5.9 0.00013 38.6 2.7 14 163-176 338-351 (514)
17 PTZ00415 transmission-blocking 61.9 5.3 0.00011 45.1 2.2 9 70-78 112-120 (2849)
18 PRK14559 putative protein seri 60.0 8.3 0.00018 38.7 3.1 36 1-52 1-36 (645)
19 PF04147 Nop14: Nop14-like fam 55.4 9 0.00019 39.2 2.5 13 159-171 441-453 (840)
20 KOG4032 Uncharacterized conser 53.7 10 0.00022 33.0 2.3 14 112-125 144-157 (184)
21 PF09538 FYDLN_acid: Protein o 51.2 33 0.00071 27.1 4.6 26 20-51 9-34 (108)
22 PF03153 TFIIA: Transcription 49.5 7.7 0.00017 35.1 0.9 10 115-124 326-335 (375)
23 PF03115 Astro_capsid: Astrovi 43.9 7.6 0.00017 40.0 0.0 7 121-127 719-725 (787)
24 PLN02400 cellulose synthase 42.7 18 0.0004 38.6 2.5 30 45-74 38-71 (1085)
25 PTZ00429 beta-adaptin; Provisi 40.6 16 0.00034 37.3 1.6 17 112-128 611-627 (746)
26 PF02724 CDC45: CDC45-like pro 39.4 25 0.00055 34.9 2.8 8 40-47 75-82 (622)
27 KOG3540 Beta amyloid precursor 37.8 32 0.00069 34.5 3.1 10 46-55 143-152 (615)
28 PF07649 C1_3: C1-like domain; 34.9 16 0.00035 22.0 0.4 26 2-32 1-27 (30)
29 TIGR00595 priA primosomal prot 33.2 38 0.00082 32.5 2.9 50 11-75 212-262 (505)
30 KOG0468 U5 snRNP-specific prot 33.2 34 0.00074 35.8 2.6 27 101-127 34-60 (971)
31 COG1499 NMD3 NMD protein affec 33.0 28 0.00062 32.7 1.9 44 1-51 6-51 (355)
32 PF04889 Cwf_Cwc_15: Cwf15/Cwc 31.9 23 0.0005 31.5 1.1 14 169-185 224-237 (244)
33 PF07975 C1_4: TFIIH C1-like d 29.8 25 0.00054 24.6 0.8 23 11-33 20-42 (51)
34 PLN02189 cellulose synthase 28.6 38 0.00082 36.2 2.2 30 45-75 36-70 (1040)
35 KOG3576 Ovo and related transc 28.6 11 0.00023 34.2 -1.6 41 3-44 119-168 (267)
36 KOG4032 Uncharacterized conser 28.3 46 0.00099 29.0 2.3 9 115-123 153-161 (184)
37 PLN02436 cellulose synthase A 27.1 42 0.00091 36.1 2.2 32 44-75 37-72 (1094)
38 PF02318 FYVE_2: FYVE-type zin 27.0 35 0.00077 26.5 1.3 42 2-51 55-102 (118)
39 KOG1999 RNA polymerase II tran 26.8 46 0.001 35.5 2.4 43 79-121 26-89 (1024)
40 PF14951 DUF4503: Domain of un 26.5 43 0.00093 32.2 1.9 42 2-45 275-317 (389)
41 KOG2462 C2H2-type Zn-finger pr 26.4 31 0.00068 31.8 1.0 70 3-73 132-222 (279)
42 KOG1428 Inhibitor of type V ad 26.2 21 0.00045 40.6 -0.2 43 1-45 3322-3367(3738)
43 KOG2140 Uncharacterized conser 25.5 55 0.0012 33.4 2.5 13 115-127 435-447 (739)
44 PRK14714 DNA polymerase II lar 25.0 50 0.0011 36.2 2.3 7 2-8 668-674 (1337)
45 PRK14873 primosome assembly pr 24.3 60 0.0013 32.7 2.6 49 11-75 382-431 (665)
46 PF08746 zf-RING-like: RING-li 23.5 13 0.00028 24.6 -1.5 28 20-49 11-43 (43)
47 KOG2023 Nuclear transport rece 22.6 55 0.0012 34.2 2.0 6 116-121 362-367 (885)
48 PRK05580 primosome assembly pr 22.1 66 0.0014 32.1 2.4 38 11-53 380-418 (679)
49 KOG2652 RNA polymerase II tran 21.9 62 0.0013 30.7 2.0 7 160-166 320-326 (348)
50 PF01286 XPA_N: XPA protein N- 21.6 55 0.0012 21.3 1.2 30 20-51 3-32 (34)
51 COG1198 PriA Primosomal protei 20.6 77 0.0017 32.6 2.6 50 11-75 434-484 (730)
52 PF04438 zf-HIT: HIT zinc fing 20.5 37 0.00079 21.1 0.2 23 2-24 3-25 (30)
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=97.62 E-value=4.6e-05 Score=47.34 Aligned_cols=38 Identities=47% Similarity=0.982 Sum_probs=33.0
Q ss_pred CCCCCCC-CCceEEeccCccccCchhccccccCCccCCCcceeee
Q 029117 2 KKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (198)
Q Consensus 2 ~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (198)
..|..++ +++.|||..|++.+|..|+...|. .|.+++|
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 699999999999999999988873 6988875
No 2
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.10 E-value=0.00047 Score=43.27 Aligned_cols=39 Identities=44% Similarity=0.821 Sum_probs=33.4
Q ss_pred CCCCCCCC-CCceEEeccCccccCchhccccccCCccCCCcceeee
Q 029117 1 MKKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (198)
Q Consensus 1 m~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (198)
++.|..+. .++.+||..+.+.||..|....| +.|.+++|
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 46887764
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=96.98 E-value=0.00055 Score=43.76 Aligned_cols=39 Identities=28% Similarity=0.589 Sum_probs=33.1
Q ss_pred CCCCCCCC-CCceEEeccCccccCchhccccccCCccCCCcceeee
Q 029117 1 MKKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (198)
Q Consensus 1 m~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (198)
++.|..|. .++.+||..+...||..|....|.. |..++|
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 6699999999999999999999844 887765
No 4
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=93.71 E-value=0.026 Score=54.16 Aligned_cols=7 Identities=14% Similarity=0.487 Sum_probs=4.0
Q ss_pred ceeeCCC
Q 029117 122 QVVPWSS 128 (198)
Q Consensus 122 qvvpws~ 128 (198)
-.+=|+.
T Consensus 121 d~~~WtP 127 (458)
T PF10446_consen 121 DYEFWTP 127 (458)
T ss_pred cceeecc
Confidence 4566763
No 5
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=92.98 E-value=0.068 Score=51.44 Aligned_cols=9 Identities=11% Similarity=0.080 Sum_probs=4.3
Q ss_pred CCCceeeCC
Q 029117 119 EENQVVPWS 127 (198)
Q Consensus 119 ~~nqvvpws 127 (198)
.+.-.|=|.
T Consensus 86 D~d~~~~~~ 94 (458)
T PF10446_consen 86 DDDSTVHDF 94 (458)
T ss_pred ccccccccc
Confidence 344455554
No 6
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=90.98 E-value=0.17 Score=50.49 Aligned_cols=7 Identities=43% Similarity=0.705 Sum_probs=2.9
Q ss_pred ccccccc
Q 029117 175 FHSRQQD 181 (198)
Q Consensus 175 ~~~~~~~ 181 (198)
|+-++-|
T Consensus 772 Fk~RvlD 778 (784)
T PF04931_consen 772 FKNRVLD 778 (784)
T ss_pred HHHHHHH
Confidence 4444433
No 7
>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=90.88 E-value=0.069 Score=42.27 Aligned_cols=8 Identities=38% Similarity=0.493 Sum_probs=0.0
Q ss_pred CCCCCcee
Q 029117 117 EDEENQVV 124 (198)
Q Consensus 117 ~~~~nqvv 124 (198)
++.++-|-
T Consensus 37 e~de~p~p 44 (101)
T PF09026_consen 37 EEDEVPVP 44 (101)
T ss_dssp --------
T ss_pred ccccccch
Confidence 33355543
No 8
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=88.66 E-value=0.088 Score=51.46 Aligned_cols=74 Identities=26% Similarity=0.454 Sum_probs=58.0
Q ss_pred CCCCCC-C--CceEEeccCccccCchhccccccCCccCCCcceeeecc-------------cccCCCCCcCCCCCCCCcc
Q 029117 3 KCELCG-S--PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCH-------------VCQSLTPWNGSGPKLGPTI 66 (198)
Q Consensus 3 ~Cd~C~-a--pA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~-------------~C~s~~A~~~sG~C~~d~a 66 (198)
.|.+|+ + .|.|+|.....+.|.-|..+.|-+--.+++|.-+|-.+ .|..++....+..|+.+.+
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 689999 4 78999999999999999999998777788887766443 3555554334556888999
Q ss_pred ccCcccccCC
Q 029117 67 SVCNVCVGNG 76 (198)
Q Consensus 67 sLC~sCd~~~ 76 (198)
.+|-.|....
T Consensus 244 pvc~~clee~ 253 (699)
T KOG4367|consen 244 PVCYQCLEEG 253 (699)
T ss_pred hHHHHHHHhh
Confidence 9999996553
No 9
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=84.03 E-value=0.59 Score=49.32 Aligned_cols=13 Identities=23% Similarity=0.350 Sum_probs=5.9
Q ss_pred ceeeecccccCCC
Q 029117 41 SRTLLCHVCQSLT 53 (198)
Q Consensus 41 ~RvpLC~~C~s~~ 53 (198)
.|.+|-+.|-.++
T Consensus 1358 v~R~~~Dlct~~~ 1370 (1516)
T KOG1832|consen 1358 VDRCLLDLCTEPT 1370 (1516)
T ss_pred cccchhhhhcCCc
Confidence 3334444555444
No 10
>smart00336 BBOX B-Box-type zinc finger.
Probab=83.75 E-value=0.66 Score=28.78 Aligned_cols=34 Identities=12% Similarity=0.004 Sum_probs=25.7
Q ss_pred eeeecccccCCCCCcCCCCCCCCccccCcccccCCCC
Q 029117 42 RTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGSG 78 (198)
Q Consensus 42 RvpLC~~C~s~~A~~~sG~C~~d~asLC~sCd~~~h~ 78 (198)
|.++|..+...+..++ |..+...||..|....|.
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 5677888875444443 899999999999877664
No 11
>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=79.12 E-value=0.87 Score=27.86 Aligned_cols=31 Identities=13% Similarity=-0.050 Sum_probs=22.9
Q ss_pred ecccccCCCCCcCCCCCCCCccccCcccccCCCC
Q 029117 45 LCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGSG 78 (198)
Q Consensus 45 LC~~C~s~~A~~~sG~C~~d~asLC~sCd~~~h~ 78 (198)
+|..+...+..++ |..+.+.||..|....|.
T Consensus 2 ~C~~H~~~~~~~f---C~~~~~~iC~~C~~~~H~ 32 (39)
T cd00021 2 LCDEHGEEPLSLF---CETDRALLCVDCDLSVHS 32 (39)
T ss_pred CCCccCCcceEEE---eCccChhhhhhcChhhcC
Confidence 4666655343443 899999999999988775
No 12
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=76.35 E-value=1.5 Score=49.12 Aligned_cols=22 Identities=32% Similarity=0.746 Sum_probs=13.4
Q ss_pred CCCCCCCCCCCCCCCceeeCCC
Q 029117 107 DDDDDGGDEDEDEENQVVPWSS 128 (198)
Q Consensus 107 ~~~~~~~~~~~~~~nqvvpws~ 128 (198)
||+++|++|+++++-||-|+--
T Consensus 164 ~~~~~~~~e~~~~~~~~~~~~d 185 (2849)
T PTZ00415 164 DDDEEDDEEEEEEEEEIKGFDD 185 (2849)
T ss_pred ccccccccccccccccccCCCc
Confidence 3344445555666668888874
No 13
>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=75.30 E-value=0.66 Score=29.37 Aligned_cols=34 Identities=12% Similarity=0.031 Sum_probs=25.2
Q ss_pred eeecccccCCCCCcCCCCCCCCccccCcccccCCCCC
Q 029117 43 TLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGSGS 79 (198)
Q Consensus 43 vpLC~~C~s~~A~~~sG~C~~d~asLC~sCd~~~h~~ 79 (198)
.++|..+....+.++ |..+...||..|...+|.+
T Consensus 3 ~~~C~~H~~~~~~~~---C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLF---CEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSB-SSTTTSBEEEE---ETTTTEEEEHHHHHTSTTT
T ss_pred CccCccCCccceEEE---ecCCCCccCccCCCCCCCC
Confidence 456777776544443 9999999999999998863
No 14
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=72.91 E-value=1.1 Score=34.12 Aligned_cols=9 Identities=22% Similarity=0.464 Sum_probs=0.0
Q ss_pred CCceeeCCC
Q 029117 120 ENQVVPWSS 128 (198)
Q Consensus 120 ~nqvvpws~ 128 (198)
|.+.||+-.
T Consensus 49 eee~m~rK~ 57 (81)
T PF14812_consen 49 EEEPMPRKG 57 (81)
T ss_dssp ---------
T ss_pred hcccccccc
Confidence 444667754
No 15
>PF12773 DZR: Double zinc ribbon
Probab=69.73 E-value=5.3 Score=26.13 Aligned_cols=30 Identities=20% Similarity=0.526 Sum_probs=20.6
Q ss_pred cCccccCchhccccccCCccCCCcceeeecccccCC
Q 029117 17 SDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSL 52 (198)
Q Consensus 17 aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s~ 52 (198)
.+.+.+|..|...+- .......+|..|...
T Consensus 9 ~~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP------PPDQSKKICPNCGAE 38 (50)
T ss_pred CccccCChhhcCChh------hccCCCCCCcCCcCC
Confidence 445788888877766 334556678888764
No 16
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.43 E-value=5.9 Score=38.62 Aligned_cols=14 Identities=21% Similarity=-0.021 Sum_probs=9.2
Q ss_pred cchhhhhccccccc
Q 029117 163 FSLKHVRNEITKFH 176 (198)
Q Consensus 163 ~~lkr~r~~~~~~~ 176 (198)
.+.||.|++.+-+.
T Consensus 338 ~~~~r~~~~stG~~ 351 (514)
T KOG3130|consen 338 EEAKRKRKNSTGSG 351 (514)
T ss_pred hHHHHHHhcccccc
Confidence 34568888777554
No 17
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=61.87 E-value=5.3 Score=45.06 Aligned_cols=9 Identities=22% Similarity=0.217 Sum_probs=5.6
Q ss_pred cccccCCCC
Q 029117 70 NVCVGNGSG 78 (198)
Q Consensus 70 ~sCd~~~h~ 78 (198)
..|--++|+
T Consensus 112 ~~~~y~~~g 120 (2849)
T PTZ00415 112 ITCFYPIHG 120 (2849)
T ss_pred cceeeeccc
Confidence 456666665
No 18
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=60.05 E-value=8.3 Score=38.66 Aligned_cols=36 Identities=22% Similarity=0.604 Sum_probs=23.1
Q ss_pred CCCCCCCCCCceEEeccCccccCchhccccccCCccCCCcceeeecccccCC
Q 029117 1 MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSL 52 (198)
Q Consensus 1 m~~Cd~C~apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s~ 52 (198)
|.+|-.|++. -.+.+++|..|.+++- | ..|..|...
T Consensus 1 M~~Cp~Cg~~-----n~~~akFC~~CG~~l~--------~---~~Cp~CG~~ 36 (645)
T PRK14559 1 MLICPQCQFE-----NPNNNRFCQKCGTSLT--------H---KPCPQCGTE 36 (645)
T ss_pred CCcCCCCCCc-----CCCCCccccccCCCCC--------C---CcCCCCCCC
Confidence 8899999922 1345677777766652 1 247777764
No 19
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=55.45 E-value=9 Score=39.23 Aligned_cols=13 Identities=8% Similarity=0.181 Sum_probs=8.2
Q ss_pred cccccchhhhhcc
Q 029117 159 SQMSFSLKHVRNE 171 (198)
Q Consensus 159 ~~~~~~lkr~r~~ 171 (198)
....+-++|+|..
T Consensus 441 ~~~~~iI~RIrk~ 453 (840)
T PF04147_consen 441 EDQPTIIQRIRKC 453 (840)
T ss_pred HHHhHHHHHHHHh
Confidence 3456667777764
No 20
>KOG4032 consensus Uncharacterized conserved protein [Function unknown]
Probab=53.73 E-value=10 Score=32.96 Aligned_cols=14 Identities=36% Similarity=0.610 Sum_probs=6.8
Q ss_pred CCCCCCCCCCceee
Q 029117 112 GGDEDEDEENQVVP 125 (198)
Q Consensus 112 ~~~~~~~~~nqvvp 125 (198)
.+|++.+.+|+=+|
T Consensus 144 ~dd~evdae~~~~~ 157 (184)
T KOG4032|consen 144 EDDEEVDAEDDEAP 157 (184)
T ss_pred chhhhhcccCCCCC
Confidence 34445555555444
No 21
>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=51.22 E-value=33 Score=27.09 Aligned_cols=26 Identities=27% Similarity=0.574 Sum_probs=19.4
Q ss_pred cccCchhccccccCCccCCCcceeeecccccC
Q 029117 20 ASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51 (198)
Q Consensus 20 A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s 51 (198)
..+|..|.++..--|+ +..+|..|+.
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 4689999999887662 4456888885
No 22
>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=49.47 E-value=7.7 Score=35.11 Aligned_cols=10 Identities=40% Similarity=0.611 Sum_probs=3.5
Q ss_pred CCCCCCCcee
Q 029117 115 EDEDEENQVV 124 (198)
Q Consensus 115 ~~~~~~nqvv 124 (198)
++++.+|-||
T Consensus 326 ~~~~~~~~~~ 335 (375)
T PF03153_consen 326 DDFDTDNVVL 335 (375)
T ss_dssp --STTS-EEE
T ss_pred cccCcCCEEE
Confidence 3345555554
No 23
>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=43.87 E-value=7.6 Score=39.99 Aligned_cols=7 Identities=43% Similarity=0.468 Sum_probs=0.0
Q ss_pred CceeeCC
Q 029117 121 NQVVPWS 127 (198)
Q Consensus 121 nqvvpws 127 (198)
||=+|=.
T Consensus 719 NqGi~ee 725 (787)
T PF03115_consen 719 NQGIPEE 725 (787)
T ss_dssp -------
T ss_pred HcCCCHH
Confidence 5555544
No 24
>PLN02400 cellulose synthase
Probab=42.73 E-value=18 Score=38.63 Aligned_cols=30 Identities=17% Similarity=0.389 Sum_probs=19.6
Q ss_pred ecccccCCCCCcCC----CCCCCCccccCccccc
Q 029117 45 LCHVCQSLTPWNGS----GPKLGPTISVCNVCVG 74 (198)
Q Consensus 45 LC~~C~s~~A~~~s----G~C~~d~asLC~sCd~ 74 (198)
+|++|...-..... -+|..++..+|..|..
T Consensus 38 iCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE 71 (1085)
T PLN02400 38 ICQICGDDVGVTETGDVFVACNECAFPVCRPCYE 71 (1085)
T ss_pred eeeecccccCcCCCCCEEEEEccCCCccccchhh
Confidence 79999853211111 2588899899988864
No 25
>PTZ00429 beta-adaptin; Provisional
Probab=40.58 E-value=16 Score=37.27 Aligned_cols=17 Identities=24% Similarity=0.110 Sum_probs=10.5
Q ss_pred CCCCCCCCCCceeeCCC
Q 029117 112 GGDEDEDEENQVVPWSS 128 (198)
Q Consensus 112 ~~~~~~~~~nqvvpws~ 128 (198)
|++||++++||+-|-+.
T Consensus 611 ~~~~~~~~~~~~~~~~~ 627 (746)
T PTZ00429 611 EDTEDDDAVELPSTPSM 627 (746)
T ss_pred ccccchhhccCCCCCCC
Confidence 33456667777766654
No 26
>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=39.42 E-value=25 Score=34.86 Aligned_cols=8 Identities=0% Similarity=-0.010 Sum_probs=3.4
Q ss_pred cceeeecc
Q 029117 40 HSRTLLCH 47 (198)
Q Consensus 40 H~RvpLC~ 47 (198)
+.++.+++
T Consensus 75 ~~~iyViD 82 (622)
T PF02724_consen 75 DVTIYVID 82 (622)
T ss_pred ceEEEEEe
Confidence 44444443
No 27
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=37.81 E-value=32 Score=34.48 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=5.2
Q ss_pred cccccCCCCC
Q 029117 46 CHVCQSLTPW 55 (198)
Q Consensus 46 C~~C~s~~A~ 55 (198)
|+.|+.+..|
T Consensus 143 mD~cEn~~hw 152 (615)
T KOG3540|consen 143 MDQCENNQHW 152 (615)
T ss_pred cccccchHHH
Confidence 5556554443
No 28
>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=34.85 E-value=16 Score=22.02 Aligned_cols=26 Identities=27% Similarity=0.644 Sum_probs=8.6
Q ss_pred CCCCCCC-CCceEEeccCccccCchhcccccc
Q 029117 2 KKCELCG-SPAKMFCESDQASLCWDCDAKVHG 32 (198)
Q Consensus 2 ~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHs 32 (198)
+.|++|+ ..-. ...+-|..||..+|.
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 3688999 3221 124668888888873
No 29
>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=33.22 E-value=38 Score=32.55 Aligned_cols=50 Identities=24% Similarity=0.535 Sum_probs=32.5
Q ss_pred ceEEeccCc-cccCchhccccccCCccCCCcceeeecccccCCCCCcCCCCCCCCccccCcccccC
Q 029117 11 AKMFCESDQ-ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGN 75 (198)
Q Consensus 11 A~vyC~aD~-A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s~~A~~~sG~C~~d~asLC~sCd~~ 75 (198)
..|+|+.+. ..-|..||...-. .++.+.+.|..|....+. -..|..|...
T Consensus 212 ~~~~C~~Cg~~~~C~~C~~~l~~-----h~~~~~l~Ch~Cg~~~~~----------~~~Cp~C~s~ 262 (505)
T TIGR00595 212 KNLLCRSCGYILCCPNCDVSLTY-----HKKEGKLRCHYCGYQEPI----------PKTCPQCGSE 262 (505)
T ss_pred CeeEhhhCcCccCCCCCCCceEE-----ecCCCeEEcCCCcCcCCC----------CCCCCCCCCC
Confidence 456788774 6779999865432 245668899999865432 1257777553
No 30
>KOG0468 consensus U5 snRNP-specific protein [Translation, ribosomal structure and biogenesis]
Probab=33.18 E-value=34 Score=35.80 Aligned_cols=27 Identities=30% Similarity=0.609 Sum_probs=15.0
Q ss_pred ccCCCCCCCCCCCCCCCCCCCceeeCC
Q 029117 101 EEEDDDDDDDDGGDEDEDEENQVVPWS 127 (198)
Q Consensus 101 e~~~~~~~~~~~~~~~~~~~nqvvpws 127 (198)
|.+.+++++......|++..||||=-.
T Consensus 34 e~~~~d~~e~~~~~~e~~~~~~vvLhe 60 (971)
T KOG0468|consen 34 EVDQDDEDEMEGDHNEDEPQNAVVLHE 60 (971)
T ss_pred hccCCcccccccccccccccceeeecc
Confidence 333333333333455666789998665
No 31
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=32.97 E-value=28 Score=32.66 Aligned_cols=44 Identities=23% Similarity=0.478 Sum_probs=30.9
Q ss_pred CCCCCCCC-CC-ceEEeccCccccCchhccccccCCccCCCcceeeecccccC
Q 029117 1 MKKCELCG-SP-AKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51 (198)
Q Consensus 1 m~~Cd~C~-ap-A~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s 51 (198)
|.+|-.|+ .. +. .+.||..|....|. +.-..+-..+.+|..|.+
T Consensus 6 ~~~C~~CGr~~~~~------~~~lC~dC~~~~~~-~~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 6 TILCVRCGRSVDPL------IDGLCGDCYVETTP-LIEIPDEVNVEVCRHCGA 51 (355)
T ss_pred ccEeccCCCcCchh------hccccHHHHhccCc-cccCCCceEEEECCcCCC
Confidence 45788888 33 33 38999999999773 223345667788999985
No 32
>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=31.88 E-value=23 Score=31.47 Aligned_cols=14 Identities=21% Similarity=0.309 Sum_probs=8.5
Q ss_pred hcccccccccccccccc
Q 029117 169 RNEITKFHSRQQDYHQG 185 (198)
Q Consensus 169 r~~~~~~~~~~~~~~~~ 185 (198)
+=-++.|+| |||+-
T Consensus 224 ~fiND~~rS---dfH~k 237 (244)
T PF04889_consen 224 EFINDTLRS---DFHKK 237 (244)
T ss_pred CcccCCccc---HHHHH
Confidence 344566777 67753
No 33
>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=29.76 E-value=25 Score=24.62 Aligned_cols=23 Identities=26% Similarity=0.690 Sum_probs=15.6
Q ss_pred ceEEeccCccccCchhccccccC
Q 029117 11 AKMFCESDQASLCWDCDAKVHGA 33 (198)
Q Consensus 11 A~vyC~aD~A~LC~~CDa~VHsA 33 (198)
.++-|......+|..||.-||..
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 46889999999999999999954
No 34
>PLN02189 cellulose synthase
Probab=28.64 E-value=38 Score=36.23 Aligned_cols=30 Identities=17% Similarity=0.208 Sum_probs=19.3
Q ss_pred ecccccCCCC-----CcCCCCCCCCccccCcccccC
Q 029117 45 LCHVCQSLTP-----WNGSGPKLGPTISVCNVCVGN 75 (198)
Q Consensus 45 LC~~C~s~~A-----~~~sG~C~~d~asLC~sCd~~ 75 (198)
+|.+|...-. ..+ -+|..++-.+|..|..-
T Consensus 36 ~C~iCgd~vg~~~~g~~f-vaC~~C~fpvCr~Cyey 70 (1040)
T PLN02189 36 VCEICGDEIGLTVDGDLF-VACNECGFPVCRPCYEY 70 (1040)
T ss_pred cccccccccCcCCCCCEE-EeeccCCCccccchhhh
Confidence 7888875311 111 25888888888888643
No 35
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=28.62 E-value=11 Score=34.19 Aligned_cols=41 Identities=32% Similarity=0.709 Sum_probs=31.8
Q ss_pred CCCCCC-C-------CceEEeccC-ccccCchhccccccCCccCCCcceee
Q 029117 3 KCELCG-S-------PAKMFCESD-QASLCWDCDAKVHGANFLVANHSRTL 44 (198)
Q Consensus 3 ~Cd~C~-a-------pA~vyC~aD-~A~LC~~CDa~VHsAN~La~rH~Rvp 44 (198)
.|.+|+ . .--|-|++| ..+||..|.+..|-+ +-++||+|.-
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 577887 2 224679999 689999999999954 6679999874
No 36
>KOG4032 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.29 E-value=46 Score=29.05 Aligned_cols=9 Identities=33% Similarity=0.520 Sum_probs=3.8
Q ss_pred CCCCCCCce
Q 029117 115 EDEDEENQV 123 (198)
Q Consensus 115 ~~~~~~nqv 123 (198)
.++..-++|
T Consensus 153 ~~~~~~~~~ 161 (184)
T KOG4032|consen 153 DDEAPSGPV 161 (184)
T ss_pred CCCCCCCCC
Confidence 333444444
No 37
>PLN02436 cellulose synthase A
Probab=27.12 E-value=42 Score=36.10 Aligned_cols=32 Identities=16% Similarity=0.292 Sum_probs=20.4
Q ss_pred eecccccCCCCCcCC----CCCCCCccccCcccccC
Q 029117 44 LLCHVCQSLTPWNGS----GPKLGPTISVCNVCVGN 75 (198)
Q Consensus 44 pLC~~C~s~~A~~~s----G~C~~d~asLC~sCd~~ 75 (198)
.+|++|...-..... -+|..++-.+|..|..-
T Consensus 37 ~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyey 72 (1094)
T PLN02436 37 QTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEY 72 (1094)
T ss_pred ccccccccccCcCCCCCEEEeeccCCCccccchhhh
Confidence 389999853211111 25888888999988643
No 38
>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=27.00 E-value=35 Score=26.46 Aligned_cols=42 Identities=26% Similarity=0.700 Sum_probs=29.1
Q ss_pred CCCCCCCC------CceEEeccCccccCchhccccccCCccCCCcceeeecccccC
Q 029117 2 KKCELCGS------PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51 (198)
Q Consensus 2 ~~Cd~C~a------pA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s 51 (198)
..|-.|+. .....|.......|..|... .+....|||-+|..
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 39
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=26.78 E-value=46 Score=35.52 Aligned_cols=43 Identities=28% Similarity=0.553 Sum_probs=0.0
Q ss_pred CCccccccCCCCCCCCCCCccCccCCCC---------------------CCCCCCCCCCCCCCC
Q 029117 79 STSREETNRGETYTDDDYDDANEEEDDD---------------------DDDDDGGDEDEDEEN 121 (198)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~~d~de~~~~~---------------------~~~~~~~~~~~~~~n 121 (198)
+..+.....++.++|.+.++.++.++++ |||.+++++++|+|+
T Consensus 26 ~~s~~~~~~~~~~de~D~~e~~e~~~dd~~~~~~k~~s~~gf~~~e~dvDdeveddd~~~edEe 89 (1024)
T KOG1999|consen 26 GESNSPADDEDTEDEGDEEEYDEDRKDDEPDEKDKKESGGGFIDREADVDDEVEDDDDDEEDEE 89 (1024)
T ss_pred ccccCCCccccccccccchhhcccccCcchhhhccccccccccccccccccccccccchhccCc
No 40
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=26.48 E-value=43 Score=32.19 Aligned_cols=42 Identities=26% Similarity=0.430 Sum_probs=32.6
Q ss_pred CCCCCCCCCceEEeccC-ccccCchhccccccCCccCCCcceeee
Q 029117 2 KKCELCGSPAKMFCESD-QASLCWDCDAKVHGANFLVANHSRTLL 45 (198)
Q Consensus 2 ~~Cd~C~apA~vyC~aD-~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (198)
|.|+.|++.-.-....| .++.|..|..-|- ++++++|.-|-|
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 58999994444444444 5799999999887 789999998876
No 41
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=26.41 E-value=31 Score=31.76 Aligned_cols=70 Identities=29% Similarity=0.452 Sum_probs=46.5
Q ss_pred CCCCCC-CCce---------EEeccC--ccccCchhccccccCCccCCCcceee----ecccccC--CCCCcCCCCCC--
Q 029117 3 KCELCG-SPAK---------MFCESD--QASLCWDCDAKVHGANFLVANHSRTL----LCHVCQS--LTPWNGSGPKL-- 62 (198)
Q Consensus 3 ~Cd~C~-apA~---------vyC~aD--~A~LC~~CDa~VHsAN~La~rH~Rvp----LC~~C~s--~~A~~~sG~C~-- 62 (198)
.|.-|+ .-|+ ++|..| .|+-|..|++.-=+- +.+++|.|+- .|.+|.. -.+|+.-|--.
T Consensus 132 ~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSm-pALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTH 210 (279)
T KOG2462|consen 132 KCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSM-PALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTH 210 (279)
T ss_pred eccccccccccccccchhhcccccccccccccCCCCCceeeeh-HHHhhHhhccCCCcccccccccccchHHhhcccccc
Confidence 466677 3332 567777 588999999766544 4468899975 4888874 23677544322
Q ss_pred -CCccccCcccc
Q 029117 63 -GPTISVCNVCV 73 (198)
Q Consensus 63 -~d~asLC~sCd 73 (198)
+..-+.|+.|-
T Consensus 211 TGEKPF~C~hC~ 222 (279)
T KOG2462|consen 211 TGEKPFSCPHCG 222 (279)
T ss_pred cCCCCccCCccc
Confidence 56778888883
No 42
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=26.16 E-value=21 Score=40.59 Aligned_cols=43 Identities=28% Similarity=0.555 Sum_probs=31.1
Q ss_pred CCCCCCCC---CCceEEeccCccccCchhccccccCCccCCCcceeee
Q 029117 1 MKKCELCG---SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (198)
Q Consensus 1 m~~Cd~C~---apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (198)
||.|+.-. ..|.|+|.-+. .||..||.-.|-.- -.+.|+|-.+
T Consensus 3322 ~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHr-rtktH~~q~f 3367 (3738)
T KOG1428|consen 3322 MPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHR-RTKTHQRQVF 3367 (3738)
T ss_pred CCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHh-hccchhhhhh
Confidence 78898887 46788887776 99999998776321 1356887544
No 43
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=25.47 E-value=55 Score=33.41 Aligned_cols=13 Identities=23% Similarity=0.570 Sum_probs=5.9
Q ss_pred CCCCCCCceeeCC
Q 029117 115 EDEDEENQVVPWS 127 (198)
Q Consensus 115 ~~~~~~nqvvpws 127 (198)
|++++--||.--+
T Consensus 435 ee~~e~~qI~D~T 447 (739)
T KOG2140|consen 435 EEDEEKLQIIDMT 447 (739)
T ss_pred ccccccceeeccc
Confidence 3333355555443
No 44
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.96 E-value=50 Score=36.25 Aligned_cols=7 Identities=43% Similarity=1.540 Sum_probs=4.9
Q ss_pred CCCCCCC
Q 029117 2 KKCELCG 8 (198)
Q Consensus 2 ~~Cd~C~ 8 (198)
++|..|+
T Consensus 668 rkCPkCG 674 (1337)
T PRK14714 668 RRCPSCG 674 (1337)
T ss_pred EECCCCC
Confidence 4677777
No 45
>PRK14873 primosome assembly protein PriA; Provisional
Probab=24.27 E-value=60 Score=32.69 Aligned_cols=49 Identities=18% Similarity=0.415 Sum_probs=32.5
Q ss_pred ceEEeccC-ccccCchhccccccCCccCCCcceeeecccccCCCCCcCCCCCCCCccccCcccccC
Q 029117 11 AKMFCESD-QASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGN 75 (198)
Q Consensus 11 A~vyC~aD-~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s~~A~~~sG~C~~d~asLC~sCd~~ 75 (198)
..|+|+.+ ...-|..|+...-. .+..+.+.|..|..... -..|..|-..
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~L~~-----h~~~~~l~Ch~CG~~~~-----------p~~Cp~Cgs~ 431 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGPLGL-----PSAGGTPRCRWCGRAAP-----------DWRCPRCGSD 431 (665)
T ss_pred CeeEhhhCcCeeECCCCCCceeE-----ecCCCeeECCCCcCCCc-----------CccCCCCcCC
Confidence 46788888 47889999865532 13456788999986421 2357777554
No 46
>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=23.51 E-value=13 Score=24.62 Aligned_cols=28 Identities=25% Similarity=0.723 Sum_probs=12.1
Q ss_pred cccCc--hhcccccc---CCccCCCcceeeecccc
Q 029117 20 ASLCW--DCDAKVHG---ANFLVANHSRTLLCHVC 49 (198)
Q Consensus 20 A~LC~--~CDa~VHs---AN~La~rH~RvpLC~~C 49 (198)
..+|. .|..++|. +++ .+|++.+.|..|
T Consensus 11 G~~C~~~~C~~r~H~~C~~~y--~r~~~~~~CP~C 43 (43)
T PF08746_consen 11 GQRCSNRDCNVRLHDDCFKKY--FRHRSNPKCPNC 43 (43)
T ss_dssp SEE-SS--S--EE-HHHHHHH--TTT-SS-B-TTT
T ss_pred eccCCCCccCchHHHHHHHHH--HhcCCCCCCcCC
Confidence 56677 69999995 333 356666667665
No 47
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=22.64 E-value=55 Score=34.17 Aligned_cols=6 Identities=33% Similarity=0.506 Sum_probs=2.4
Q ss_pred CCCCCC
Q 029117 116 DEDEEN 121 (198)
Q Consensus 116 ~~~~~n 121 (198)
|+|..+
T Consensus 362 DdD~~~ 367 (885)
T KOG2023|consen 362 DDDAFS 367 (885)
T ss_pred cccccc
Confidence 444433
No 48
>PRK05580 primosome assembly protein PriA; Validated
Probab=22.10 E-value=66 Score=32.05 Aligned_cols=38 Identities=26% Similarity=0.522 Sum_probs=26.3
Q ss_pred ceEEeccCc-cccCchhccccccCCccCCCcceeeecccccCCC
Q 029117 11 AKMFCESDQ-ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLT 53 (198)
Q Consensus 11 A~vyC~aD~-A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s~~ 53 (198)
..++|+.+. ..-|..|+..... .+..+.++|..|....
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 457777775 5568889865432 2456788999999754
No 49
>KOG2652 consensus RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription]
Probab=21.87 E-value=62 Score=30.75 Aligned_cols=7 Identities=29% Similarity=0.244 Sum_probs=2.7
Q ss_pred ccccchh
Q 029117 160 QMSFSLK 166 (198)
Q Consensus 160 ~~~~~lk 166 (198)
+--+.||
T Consensus 320 KWKc~LK 326 (348)
T KOG2652|consen 320 KWKCYLK 326 (348)
T ss_pred eeeEEee
Confidence 3333443
No 50
>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=21.60 E-value=55 Score=21.27 Aligned_cols=30 Identities=17% Similarity=0.447 Sum_probs=15.5
Q ss_pred cccCchhccccccCCccCCCcceeeecccccC
Q 029117 20 ASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51 (198)
Q Consensus 20 A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s 51 (198)
+..|..|+....-+ .+.+|-..++|+.|..
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 45688888877744 4678888888888864
No 51
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.64 E-value=77 Score=32.59 Aligned_cols=50 Identities=22% Similarity=0.553 Sum_probs=34.8
Q ss_pred ceEEeccCc-cccCchhccccccCCccCCCcceeeecccccCCCCCcCCCCCCCCccccCcccccC
Q 029117 11 AKMFCESDQ-ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGN 75 (198)
Q Consensus 11 A~vyC~aD~-A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s~~A~~~sG~C~~d~asLC~sCd~~ 75 (198)
..|.|+.+. ..=|..||...- ..++.+.+.|..|...... ..-|..|-..
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 467788774 667999987653 3367789999999975321 3457788655
No 52
>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=20.49 E-value=37 Score=21.13 Aligned_cols=23 Identities=43% Similarity=0.875 Sum_probs=15.6
Q ss_pred CCCCCCCCCceEEeccCccccCc
Q 029117 2 KKCELCGSPAKMFCESDQASLCW 24 (198)
Q Consensus 2 ~~Cd~C~apA~vyC~aD~A~LC~ 24 (198)
.+|.+|+.++..-|....+..|.
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 36888888888888888777775
Done!