Query 029229
Match_columns 197
No_of_seqs 152 out of 511
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 09:34:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029229.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029229hhsearch_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 97.7 3.5E-05 7.7E-10 47.8 2.6 38 2-45 1-39 (39)
2 smart00336 BBOX B-Box-type zin 97.2 0.00039 8.5E-09 43.6 2.8 39 1-45 3-42 (42)
3 PF00643 zf-B_box: B-box zinc 97.1 0.00044 9.6E-09 44.1 2.5 39 1-45 3-42 (42)
4 PF09026 CENP-B_dimeris: Centr 93.8 0.017 3.7E-07 45.6 0.0 15 111-125 31-45 (101)
5 PF10446 DUF2457: Protein of u 90.8 0.12 2.7E-06 49.7 1.7 8 121-128 120-127 (458)
6 KOG4367 Predicted Zn-finger pr 90.5 0.054 1.2E-06 52.9 -1.1 74 3-76 164-253 (699)
7 PF10446 DUF2457: Protein of u 89.3 0.27 5.8E-06 47.4 2.5 16 166-181 140-155 (458)
8 smart00336 BBOX B-Box-type zin 76.6 1.7 3.6E-05 26.9 1.5 33 42-77 2-34 (42)
9 KOG1832 HIV-1 Vpr-binding prot 75.0 1.6 3.6E-05 46.2 1.7 15 40-54 1357-1371(1516)
10 PTZ00415 transmission-blocking 73.6 1.9 4.1E-05 48.3 1.8 20 109-128 166-185 (2849)
11 PF14812 PBP1_TM: Transmembran 66.9 1.8 4E-05 33.0 0.0 9 120-128 49-57 (81)
12 PF12773 DZR: Double zinc ribb 66.0 7 0.00015 25.5 2.7 30 17-52 9-38 (50)
13 PF04147 Nop14: Nop14-like fam 58.4 7.4 0.00016 39.7 2.5 14 159-172 441-454 (840)
14 PRK14559 putative protein seri 58.0 9.3 0.0002 38.3 3.1 25 1-30 1-25 (645)
15 PF03153 TFIIA: Transcription 56.5 4.9 0.00011 36.3 0.8 10 115-124 326-335 (375)
16 KOG3130 Uncharacterized conser 56.3 8 0.00017 37.7 2.2 14 163-176 338-351 (514)
17 PF03115 Astro_capsid: Astrovi 53.3 4.4 9.6E-05 41.6 0.0 7 121-127 719-725 (787)
18 PTZ00415 transmission-blocking 52.5 8.1 0.00018 43.7 1.7 9 70-78 112-120 (2849)
19 PF07649 C1_3: C1-like domain; 38.4 13 0.00028 22.4 0.4 26 2-32 1-27 (30)
20 PTZ00429 beta-adaptin; Provisi 37.2 19 0.00041 36.7 1.6 17 112-128 611-627 (746)
21 PF07975 C1_4: TFIIH C1-like d 37.1 16 0.00036 25.5 0.8 23 11-33 20-42 (51)
22 KOG3241 Uncharacterized conser 36.8 30 0.00065 30.7 2.5 35 13-47 84-139 (227)
23 KOG0699 Serine/threonine prote 33.8 22 0.00048 34.7 1.4 24 103-126 293-316 (542)
24 KOG1428 Inhibitor of type V ad 33.4 13 0.00028 42.1 -0.3 43 1-45 3322-3367(3738)
25 TIGR00595 priA primosomal prot 29.7 43 0.00094 32.1 2.6 50 11-75 212-262 (505)
26 PF02724 CDC45: CDC45-like pro 28.3 47 0.001 33.0 2.7 7 40-46 75-81 (622)
27 KOG3540 Beta amyloid precursor 28.2 41 0.00088 33.7 2.1 10 46-55 143-152 (615)
28 COG1499 NMD3 NMD protein affec 27.0 43 0.00093 31.5 2.0 44 1-51 6-51 (355)
29 PLN02189 cellulose synthase 26.4 43 0.00092 35.8 2.1 30 45-74 36-69 (1040)
30 PF02318 FYVE_2: FYVE-type zin 26.1 31 0.00068 26.7 0.8 42 2-51 55-102 (118)
31 PRK14873 primosome assembly pr 26.1 46 0.00099 33.5 2.1 49 11-75 382-431 (665)
32 PF08746 zf-RING-like: RING-li 25.5 10 0.00023 25.0 -1.7 28 20-49 11-43 (43)
33 KOG2140 Uncharacterized conser 25.1 58 0.0013 33.2 2.6 11 118-128 438-448 (739)
34 PLN02400 cellulose synthase 24.0 59 0.0013 35.0 2.6 30 45-74 38-71 (1085)
35 PF04438 zf-HIT: HIT zinc fing 23.1 30 0.00065 21.5 0.2 23 2-24 3-25 (30)
36 PF14951 DUF4503: Domain of un 22.8 57 0.0012 31.4 2.0 42 2-45 275-317 (389)
37 KOG4032 Uncharacterized conser 21.7 72 0.0016 27.8 2.3 10 115-124 147-156 (184)
38 PRK14714 DNA polymerase II lar 21.6 65 0.0014 35.4 2.3 7 2-8 668-674 (1337)
39 KOG0468 U5 snRNP-specific prot 21.2 68 0.0015 33.7 2.3 15 113-127 46-60 (971)
40 KOG2177 Predicted E3 ubiquitin 21.2 80 0.0017 24.8 2.2 24 10-33 95-119 (386)
41 KOG4032 Uncharacterized conser 21.0 82 0.0018 27.5 2.5 9 115-123 153-161 (184)
42 COG1198 PriA Primosomal protei 20.3 78 0.0017 32.5 2.5 50 11-75 434-484 (730)
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=97.67 E-value=3.5e-05 Score=47.83 Aligned_cols=38 Identities=47% Similarity=0.982 Sum_probs=33.1
Q ss_pred CCCCCCC-CCceEEeccCccccCchhccccccCCCCCCcceeeec
Q 029229 2 KKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (197)
Q Consensus 2 ~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (197)
.+|..++ .++.|||..|++.+|..|+...|. .|.|++|
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 699999999999999999988874 6988875
No 2
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.15 E-value=0.00039 Score=43.60 Aligned_cols=39 Identities=44% Similarity=0.821 Sum_probs=33.4
Q ss_pred CCCCCCCC-CCceEEeccCccccCchhccccccCCCCCCcceeeec
Q 029229 1 MKKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (197)
Q Consensus 1 m~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (197)
++.|..+. .++.+||..+++.||..|....| +.|.+++|
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 35799998 89999999999999999998866 46887765
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=97.07 E-value=0.00044 Score=44.14 Aligned_cols=39 Identities=28% Similarity=0.589 Sum_probs=33.2
Q ss_pred CCCCCCCC-CCceEEeccCccccCchhccccccCCCCCCcceeeec
Q 029229 1 MKKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (197)
Q Consensus 1 m~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (197)
+++|..+. .++.+||..+...||..|....|.. |..++|
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 6699999999999999999999854 888775
No 4
>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=93.81 E-value=0.017 Score=45.59 Aligned_cols=15 Identities=33% Similarity=0.585 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCceee
Q 029229 111 DGGDEDEDEENQVVP 125 (197)
Q Consensus 111 ~~~~~~~~~~nqvvp 125 (197)
|+++++++.++-|--
T Consensus 31 Dddddee~de~p~p~ 45 (101)
T PF09026_consen 31 DDDDDEEEDEVPVPE 45 (101)
T ss_dssp ---------------
T ss_pred ccccccccccccchh
Confidence 334444444665543
No 5
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=90.83 E-value=0.12 Score=49.66 Aligned_cols=8 Identities=13% Similarity=0.464 Sum_probs=4.5
Q ss_pred CceeeCCC
Q 029229 121 NQVVPWSS 128 (197)
Q Consensus 121 nqvvpws~ 128 (197)
--.+=|+.
T Consensus 120 sd~~~WtP 127 (458)
T PF10446_consen 120 SDYEFWTP 127 (458)
T ss_pred ccceeecc
Confidence 34566763
No 6
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=90.45 E-value=0.054 Score=52.87 Aligned_cols=74 Identities=26% Similarity=0.449 Sum_probs=60.0
Q ss_pred CCCCCC---CCceEEeccCccccCchhccccccCCCCCCcceeeeccc-------------cccCCCCCccCCCCCCCcc
Q 029229 3 KCELCG---SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCH-------------VCQSLTPWNGSGPKLGPTI 66 (197)
Q Consensus 3 ~Cd~C~---apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~-------------~C~s~~A~~~sG~C~~daa 66 (197)
.|.+|+ ..|.|+|.....+.|.-|..+.|-+--.+++|.-+|-.. .|..++....+.+|+.+.+
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 478999999999999999999998877788887766433 4666665556678889999
Q ss_pred ccCcccccCC
Q 029229 67 SVCNVCVGNG 76 (197)
Q Consensus 67 sLC~sCd~~~ 76 (197)
.+|-.|.-..
T Consensus 244 pvc~~clee~ 253 (699)
T KOG4367|consen 244 PVCYQCLEEG 253 (699)
T ss_pred hHHHHHHHhh
Confidence 9999997654
No 7
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=89.28 E-value=0.27 Score=47.44 Aligned_cols=16 Identities=13% Similarity=0.019 Sum_probs=6.6
Q ss_pred hhhhccccccCccccc
Q 029229 166 KHVRNEITKFHSRQDY 181 (197)
Q Consensus 166 kr~r~~~~~~~s~~~~ 181 (197)
.-+|.....-.|+-.|
T Consensus 140 ~~~r~~~~~~~S~sS~ 155 (458)
T PF10446_consen 140 DVRRRSSHRRSSDSSI 155 (458)
T ss_pred cccccccccCCCCCcc
Confidence 3344433334444444
No 8
>smart00336 BBOX B-Box-type zinc finger.
Probab=76.64 E-value=1.7 Score=26.89 Aligned_cols=33 Identities=12% Similarity=0.028 Sum_probs=24.5
Q ss_pred eeeccccccCCCCCccCCCCCCCccccCcccccCCC
Q 029229 42 RTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGS 77 (197)
Q Consensus 42 RvpLC~~C~s~~A~~~sG~C~~daasLC~sCd~~~h 77 (197)
|.++|..+...++.+ .|..+...||..|....|
T Consensus 2 ~~~~C~~h~~~~~~~---~C~~c~~~iC~~C~~~~H 34 (42)
T smart00336 2 RPPKCDSHGDEPAEF---FCEECGALLCRTCDEAEH 34 (42)
T ss_pred cCCcCCCCCCCceEE---ECCCCCcccccccChhhc
Confidence 567788877544333 389999999999987655
No 9
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=75.01 E-value=1.6 Score=46.19 Aligned_cols=15 Identities=20% Similarity=0.264 Sum_probs=7.8
Q ss_pred ceeeeccccccCCCC
Q 029229 40 HSRTLLCHVCQSLTP 54 (197)
Q Consensus 40 H~RvpLC~~C~s~~A 54 (197)
-.|.+|-+.|..++-
T Consensus 1357 ~v~R~~~Dlct~~~D 1371 (1516)
T KOG1832|consen 1357 PVDRCLLDLCTEPTD 1371 (1516)
T ss_pred ecccchhhhhcCCcc
Confidence 344455555665553
No 10
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=73.56 E-value=1.9 Score=48.27 Aligned_cols=20 Identities=25% Similarity=0.664 Sum_probs=12.1
Q ss_pred CCCCCCCCCCCCCceeeCCC
Q 029229 109 DDDGGDEDEDEENQVVPWSS 128 (197)
Q Consensus 109 ~~~~~~~~~~~~nqvvpws~ 128 (197)
+++|++|+++++-||-|+--
T Consensus 166 ~~~~~~e~~~~~~~~~~~~d 185 (2849)
T PTZ00415 166 DEEDDEEEEEEEEEIKGFDD 185 (2849)
T ss_pred ccccccccccccccccCCCc
Confidence 33344455555668888874
No 11
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=66.94 E-value=1.8 Score=33.00 Aligned_cols=9 Identities=22% Similarity=0.464 Sum_probs=0.0
Q ss_pred CCceeeCCC
Q 029229 120 ENQVVPWSS 128 (197)
Q Consensus 120 ~nqvvpws~ 128 (197)
|.+.||+-.
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 12
>PF12773 DZR: Double zinc ribbon
Probab=65.97 E-value=7 Score=25.52 Aligned_cols=30 Identities=20% Similarity=0.526 Sum_probs=20.1
Q ss_pred cCccccCchhccccccCCCCCCcceeeeccccccCC
Q 029229 17 SDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSL 52 (197)
Q Consensus 17 aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s~ 52 (197)
.+.+.+|..|...+- .......+|..|...
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 334556678888764
No 13
>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=58.38 E-value=7.4 Score=39.75 Aligned_cols=14 Identities=7% Similarity=0.152 Sum_probs=8.9
Q ss_pred cccccchhhhhccc
Q 029229 159 SQMSFSLKHVRNEI 172 (197)
Q Consensus 159 ~~~~~~lkr~r~~~ 172 (197)
....+-++|+|...
T Consensus 441 ~~~~~iI~RIrk~~ 454 (840)
T PF04147_consen 441 EDQPTIIQRIRKCY 454 (840)
T ss_pred HHHhHHHHHHHHhC
Confidence 34566678888643
No 14
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=57.96 E-value=9.3 Score=38.28 Aligned_cols=25 Identities=20% Similarity=0.611 Sum_probs=16.9
Q ss_pred CCCCCCCCCCceEEeccCccccCchhcccc
Q 029229 1 MKKCELCGSPAKMFCESDQASLCWDCDAKV 30 (197)
Q Consensus 1 m~~Cd~C~apA~vyC~aD~A~LC~~CDa~V 30 (197)
|.+|-.|++. -.+.|++|..|.+++
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 8999999922 134467777776655
No 15
>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=56.48 E-value=4.9 Score=36.31 Aligned_cols=10 Identities=40% Similarity=0.611 Sum_probs=3.5
Q ss_pred CCCCCCCcee
Q 029229 115 EDEDEENQVV 124 (197)
Q Consensus 115 ~~~~~~nqvv 124 (197)
++++.+|-||
T Consensus 326 ~~~~~~~~~~ 335 (375)
T PF03153_consen 326 DDFDTDNVVL 335 (375)
T ss_dssp --STTS-EEE
T ss_pred cccCcCCEEE
Confidence 3344555554
No 16
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=56.35 E-value=8 Score=37.74 Aligned_cols=14 Identities=21% Similarity=-0.021 Sum_probs=8.0
Q ss_pred cchhhhhccccccC
Q 029229 163 FSLKHVRNEITKFH 176 (197)
Q Consensus 163 ~~lkr~r~~~~~~~ 176 (197)
.+.||.|++.+-+.
T Consensus 338 ~~~~r~~~~stG~~ 351 (514)
T KOG3130|consen 338 EEAKRKRKNSTGSG 351 (514)
T ss_pred hHHHHHHhcccccc
Confidence 34567777666443
No 17
>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=53.27 E-value=4.4 Score=41.61 Aligned_cols=7 Identities=43% Similarity=0.468 Sum_probs=0.0
Q ss_pred CceeeCC
Q 029229 121 NQVVPWS 127 (197)
Q Consensus 121 nqvvpws 127 (197)
||=+|=.
T Consensus 719 NqGi~ee 725 (787)
T PF03115_consen 719 NQGIPEE 725 (787)
T ss_dssp -------
T ss_pred HcCCCHH
Confidence 5555544
No 18
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=52.45 E-value=8.1 Score=43.69 Aligned_cols=9 Identities=22% Similarity=0.217 Sum_probs=5.0
Q ss_pred cccccCCCC
Q 029229 70 NVCVGNGSG 78 (197)
Q Consensus 70 ~sCd~~~h~ 78 (197)
.+|--.+|+
T Consensus 112 ~~~~y~~~g 120 (2849)
T PTZ00415 112 ITCFYPIHG 120 (2849)
T ss_pred cceeeeccc
Confidence 455556655
No 19
>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=38.36 E-value=13 Score=22.41 Aligned_cols=26 Identities=27% Similarity=0.644 Sum_probs=8.6
Q ss_pred CCCCCCC-CCceEEeccCccccCchhcccccc
Q 029229 2 KKCELCG-SPAKMFCESDQASLCWDCDAKVHG 32 (197)
Q Consensus 2 ~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHs 32 (197)
+.|++|+ ..-. ...+-|..||..+|.
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 3688998 3221 124668888888883
No 20
>PTZ00429 beta-adaptin; Provisional
Probab=37.24 E-value=19 Score=36.67 Aligned_cols=17 Identities=24% Similarity=0.110 Sum_probs=10.3
Q ss_pred CCCCCCCCCCceeeCCC
Q 029229 112 GGDEDEDEENQVVPWSS 128 (197)
Q Consensus 112 ~~~~~~~~~nqvvpws~ 128 (197)
|++||++++||+-|-+.
T Consensus 611 ~~~~~~~~~~~~~~~~~ 627 (746)
T PTZ00429 611 EDTEDDDAVELPSTPSM 627 (746)
T ss_pred ccccchhhccCCCCCCC
Confidence 34456667777766553
No 21
>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=37.10 E-value=16 Score=25.52 Aligned_cols=23 Identities=26% Similarity=0.690 Sum_probs=15.7
Q ss_pred ceEEeccCccccCchhccccccC
Q 029229 11 AKMFCESDQASLCWDCDAKVHGA 33 (197)
Q Consensus 11 A~vyC~aD~A~LC~~CDa~VHsA 33 (197)
.++-|......+|..||.-||..
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 22
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.75 E-value=30 Score=30.69 Aligned_cols=35 Identities=23% Similarity=0.378 Sum_probs=21.0
Q ss_pred EEeccC--ccccCchhcccc-------------------ccCCCCCCcceeeeccc
Q 029229 13 MFCESD--QASLCWDCDAKV-------------------HGANFLVANHSRTLLCH 47 (197)
Q Consensus 13 vyC~aD--~A~LC~~CDa~V-------------------HsAN~La~rH~RvpLC~ 47 (197)
+.|+.+ .+..|+.|-..+ |.-+.+..||.|.+|-.
T Consensus 84 ~~Cr~CA~e~~vCAKC~ks~~~i~i~d~~p~~~E~~~l~~t~~n~ser~RRt~lR~ 139 (227)
T KOG3241|consen 84 KLCRGCAKEQKVCAKCCKSVDQILIRDIYPVEAEQKLLDETIKNASERDRRTLLRA 139 (227)
T ss_pred HhcccHHHHHHHHHHHhccHHHhhhcCCCCCcHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 556655 367788887532 22333556788877753
No 23
>KOG0699 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=33.84 E-value=22 Score=34.68 Aligned_cols=24 Identities=42% Similarity=0.723 Sum_probs=16.1
Q ss_pred CCCCCCCCCCCCCCCCCCCceeeC
Q 029229 103 EDDDDDDDDGGDEDEDEENQVVPW 126 (197)
Q Consensus 103 ~~~~~~~~~~~~~~~~~~nqvvpw 126 (197)
+++|++.+++.+++|..+-|.+|.
T Consensus 293 ed~Ded~e~e~ddEE~~e~~map~ 316 (542)
T KOG0699|consen 293 EDDDEDAEDEQDDEEMVEGSMAPL 316 (542)
T ss_pred cccccccccccchhhhhhhccccc
Confidence 334444555566777788899998
No 24
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=33.38 E-value=13 Score=42.08 Aligned_cols=43 Identities=28% Similarity=0.528 Sum_probs=32.0
Q ss_pred CCCCCCCC---CCceEEeccCccccCchhccccccCCCCCCcceeeec
Q 029229 1 MKKCELCG---SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45 (197)
Q Consensus 1 m~~Cd~C~---apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (197)
||.|+.-. ..|.|+|.-+. .||..||.-+|-. +-.+.|+|-.+
T Consensus 3322 ~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLH-rrtktH~~q~f 3367 (3738)
T KOG1428|consen 3322 MPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLH-RRTKTHQRQVF 3367 (3738)
T ss_pred CCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHH-hhccchhhhhh
Confidence 78899886 57789998777 9999999877732 12356888554
No 25
>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=29.72 E-value=43 Score=32.12 Aligned_cols=50 Identities=24% Similarity=0.535 Sum_probs=32.8
Q ss_pred ceEEeccCc-cccCchhccccccCCCCCCcceeeeccccccCCCCCccCCCCCCCccccCcccccC
Q 029229 11 AKMFCESDQ-ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGN 75 (197)
Q Consensus 11 A~vyC~aD~-A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s~~A~~~sG~C~~daasLC~sCd~~ 75 (197)
..++|+.+. ..-|..||...-. .++.+.+.|..|....+. -..|+.|...
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 457788884 7789999865532 245667889999864322 1357778554
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=28.26 E-value=47 Score=32.96 Aligned_cols=7 Identities=0% Similarity=-0.031 Sum_probs=2.8
Q ss_pred ceeeecc
Q 029229 40 HSRTLLC 46 (197)
Q Consensus 40 H~RvpLC 46 (197)
+.++.++
T Consensus 75 ~~~iyVi 81 (622)
T PF02724_consen 75 DVTIYVI 81 (622)
T ss_pred ceEEEEE
Confidence 3444443
No 27
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=28.21 E-value=41 Score=33.75 Aligned_cols=10 Identities=20% Similarity=0.740 Sum_probs=5.2
Q ss_pred cccccCCCCC
Q 029229 46 CHVCQSLTPW 55 (197)
Q Consensus 46 C~~C~s~~A~ 55 (197)
|+.|+....|
T Consensus 143 mD~cEn~~hw 152 (615)
T KOG3540|consen 143 MDQCENNQHW 152 (615)
T ss_pred cccccchHHH
Confidence 4556554443
No 28
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=26.96 E-value=43 Score=31.48 Aligned_cols=44 Identities=23% Similarity=0.511 Sum_probs=30.0
Q ss_pred CCCCCCCC-CC-ceEEeccCccccCchhccccccCCCCCCcceeeeccccccC
Q 029229 1 MKKCELCG-SP-AKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51 (197)
Q Consensus 1 m~~Cd~C~-ap-A~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s 51 (197)
|.+|-.|+ .. +.+ +.||..|....|. +--..+-..+.+|..|.+
T Consensus 6 ~~~C~~CGr~~~~~~------~~lC~dC~~~~~~-~~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 6 TILCVRCGRSVDPLI------DGLCGDCYVETTP-LIEIPDEVNVEVCRHCGA 51 (355)
T ss_pred ccEeccCCCcCchhh------ccccHHHHhccCc-cccCCCceEEEECCcCCC
Confidence 45788888 33 333 8999999999773 222345667778888885
No 29
>PLN02189 cellulose synthase
Probab=26.43 E-value=43 Score=35.85 Aligned_cols=30 Identities=17% Similarity=0.303 Sum_probs=17.4
Q ss_pred ccccccCCCCCcc----CCCCCCCccccCccccc
Q 029229 45 LCHVCQSLTPWNG----SGPKLGPTISVCNVCVG 74 (197)
Q Consensus 45 LC~~C~s~~A~~~----sG~C~~daasLC~sCd~ 74 (197)
+|.+|...-.... -..|..++-.+|..|.-
T Consensus 36 ~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye 69 (1040)
T PLN02189 36 VCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE 69 (1040)
T ss_pred cccccccccCcCCCCCEEEeeccCCCccccchhh
Confidence 6777774311111 12577777778887763
No 30
>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=26.14 E-value=31 Score=26.74 Aligned_cols=42 Identities=26% Similarity=0.700 Sum_probs=29.2
Q ss_pred CCCCCCCC------CceEEeccCccccCchhccccccCCCCCCcceeeeccccccC
Q 029229 2 KKCELCGS------PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51 (197)
Q Consensus 2 ~~Cd~C~a------pA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s 51 (197)
..|-.|+. .....|.......|..|... .+....|||-+|..
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 31
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.12 E-value=46 Score=33.47 Aligned_cols=49 Identities=18% Similarity=0.425 Sum_probs=32.8
Q ss_pred ceEEeccCc-cccCchhccccccCCCCCCcceeeeccccccCCCCCccCCCCCCCccccCcccccC
Q 029229 11 AKMFCESDQ-ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGN 75 (197)
Q Consensus 11 A~vyC~aD~-A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s~~A~~~sG~C~~daasLC~sCd~~ 75 (197)
..|+|+.+. ..-|..||..+-. .+..+.+.|..|..... -..|..|-..
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 467888884 7889999865532 13456788999986321 2357788554
No 32
>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=25.49 E-value=10 Score=25.04 Aligned_cols=28 Identities=25% Similarity=0.774 Sum_probs=12.0
Q ss_pred cccCc--hhcccccc---CCCCCCcceeeeccccc
Q 029229 20 ASLCW--DCDAKVHG---ANFLVANHSRTLLCHVC 49 (197)
Q Consensus 20 A~LC~--~CDa~VHs---AN~La~rH~RvpLC~~C 49 (197)
..+|. .|..++|. ++++ +|++.+.|..|
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 56677 69999995 3433 55555566655
No 33
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=25.12 E-value=58 Score=33.23 Aligned_cols=11 Identities=18% Similarity=0.407 Sum_probs=5.4
Q ss_pred CCCCceeeCCC
Q 029229 118 DEENQVVPWSS 128 (197)
Q Consensus 118 ~~~nqvvpws~ 128 (197)
++--||.--+.
T Consensus 438 ~e~~qI~D~T~ 448 (739)
T KOG2140|consen 438 EEKLQIIDMTE 448 (739)
T ss_pred cccceeecccc
Confidence 33556655443
No 34
>PLN02400 cellulose synthase
Probab=24.05 E-value=59 Score=34.98 Aligned_cols=30 Identities=17% Similarity=0.389 Sum_probs=18.6
Q ss_pred ccccccCCCCCccC----CCCCCCccccCccccc
Q 029229 45 LCHVCQSLTPWNGS----GPKLGPTISVCNVCVG 74 (197)
Q Consensus 45 LC~~C~s~~A~~~s----G~C~~daasLC~sCd~ 74 (197)
+|.+|...-..+.. ..|..++..+|..|.-
T Consensus 38 iCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE 71 (1085)
T PLN02400 38 ICQICGDDVGVTETGDVFVACNECAFPVCRPCYE 71 (1085)
T ss_pred eeeecccccCcCCCCCEEEEEccCCCccccchhh
Confidence 78888753221111 2578888888888863
No 35
>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=23.07 E-value=30 Score=21.52 Aligned_cols=23 Identities=43% Similarity=0.875 Sum_probs=16.0
Q ss_pred CCCCCCCCCceEEeccCccccCc
Q 029229 2 KKCELCGSPAKMFCESDQASLCW 24 (197)
Q Consensus 2 ~~Cd~C~apA~vyC~aD~A~LC~ 24 (197)
.+|.+|+.++.+-|....+.+|.
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 36888888888888888887775
No 36
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=22.85 E-value=57 Score=31.38 Aligned_cols=42 Identities=26% Similarity=0.430 Sum_probs=32.5
Q ss_pred CCCCCCCCCceEEeccC-ccccCchhccccccCCCCCCcceeeec
Q 029229 2 KKCELCGSPAKMFCESD-QASLCWDCDAKVHGANFLVANHSRTLL 45 (197)
Q Consensus 2 ~~Cd~C~apA~vyC~aD-~A~LC~~CDa~VHsAN~La~rH~RvpL 45 (197)
|.|+.|++--.-....| .++.|..|..-|- ++++++|.-+-|
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 68999994444444445 5799999999887 789999988776
No 37
>KOG4032 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.72 E-value=72 Score=27.84 Aligned_cols=10 Identities=30% Similarity=0.468 Sum_probs=4.1
Q ss_pred CCCCCCCcee
Q 029229 115 EDEDEENQVV 124 (197)
Q Consensus 115 ~~~~~~nqvv 124 (197)
++.+.+|+=+
T Consensus 147 ~evdae~~~~ 156 (184)
T KOG4032|consen 147 EEVDAEDDEA 156 (184)
T ss_pred hhhcccCCCC
Confidence 3344444433
No 38
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.56 E-value=65 Score=35.41 Aligned_cols=7 Identities=43% Similarity=1.540 Sum_probs=4.6
Q ss_pred CCCCCCC
Q 029229 2 KKCELCG 8 (197)
Q Consensus 2 ~~Cd~C~ 8 (197)
++|..|+
T Consensus 668 rkCPkCG 674 (1337)
T PRK14714 668 RRCPSCG 674 (1337)
T ss_pred EECCCCC
Confidence 4577777
No 39
>KOG0468 consensus U5 snRNP-specific protein [Translation, ribosomal structure and biogenesis]
Probab=21.24 E-value=68 Score=33.73 Aligned_cols=15 Identities=20% Similarity=0.406 Sum_probs=10.5
Q ss_pred CCCCCCCCCceeeCC
Q 029229 113 GDEDEDEENQVVPWS 127 (197)
Q Consensus 113 ~~~~~~~~nqvvpws 127 (197)
...|++..||||=-.
T Consensus 46 ~~~e~~~~~~vvLhe 60 (971)
T KOG0468|consen 46 DHNEDEPQNAVVLHE 60 (971)
T ss_pred ccccccccceeeecc
Confidence 445566789998655
No 40
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.16 E-value=80 Score=24.81 Aligned_cols=24 Identities=38% Similarity=0.753 Sum_probs=19.8
Q ss_pred CceEEeccCccccCchhc-cccccC
Q 029229 10 PAKMFCESDQASLCWDCD-AKVHGA 33 (197)
Q Consensus 10 pA~vyC~aD~A~LC~~CD-a~VHsA 33 (197)
...+||..+...+|..|. ...|..
T Consensus 95 ~~~~~c~~~~~~~c~~c~~~~~h~~ 119 (386)
T KOG2177|consen 95 ELKLFCEEDEKLLCVLCRESGEHRG 119 (386)
T ss_pred cceEEecccccccCCCCCCcccccC
Confidence 367999999999999998 666644
No 41
>KOG4032 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.02 E-value=82 Score=27.49 Aligned_cols=9 Identities=33% Similarity=0.520 Sum_probs=3.9
Q ss_pred CCCCCCCce
Q 029229 115 EDEDEENQV 123 (197)
Q Consensus 115 ~~~~~~nqv 123 (197)
.++..-++|
T Consensus 153 ~~~~~~~~~ 161 (184)
T KOG4032|consen 153 DDEAPSGPV 161 (184)
T ss_pred CCCCCCCCC
Confidence 334444444
No 42
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.26 E-value=78 Score=32.52 Aligned_cols=50 Identities=22% Similarity=0.553 Sum_probs=35.1
Q ss_pred ceEEeccCc-cccCchhccccccCCCCCCcceeeeccccccCCCCCccCCCCCCCccccCcccccC
Q 029229 11 AKMFCESDQ-ASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGN 75 (197)
Q Consensus 11 A~vyC~aD~-A~LC~~CDa~VHsAN~La~rH~RvpLC~~C~s~~A~~~sG~C~~daasLC~sCd~~ 75 (197)
..|.|+.+. ..=|..||...- ..++.+.+.|..|...... ..-|+.|-..
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 467888885 677999997653 3366789999999975321 3457778655
Done!