Query 035848
Match_columns 244
No_of_seqs 160 out of 224
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 06:59:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035848.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035848hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07962 Swi3: Replication For 100.0 1.8E-35 3.9E-40 226.7 8.4 81 80-161 1-81 (83)
2 KOG3004 Meiotic chromosome se 100.0 5.4E-30 1.2E-34 235.0 9.4 99 64-163 48-146 (305)
3 PF00098 zf-CCHC: Zinc knuckle 98.5 5.3E-08 1.2E-12 56.1 1.6 17 10-26 2-18 (18)
4 KOG0109 RNA-binding protein LA 98.1 1.3E-06 2.9E-11 81.9 1.7 28 3-30 155-182 (346)
5 PF13696 zf-CCHC_2: Zinc knuck 97.5 3.6E-05 7.8E-10 50.6 0.9 21 7-27 7-27 (32)
6 PF13917 zf-CCHC_3: Zinc knuck 97.4 9.4E-05 2E-09 51.1 2.3 20 7-26 3-22 (42)
7 smart00343 ZnF_C2HC zinc finge 97.1 0.00018 4E-09 43.8 1.0 18 10-27 1-18 (26)
8 PF14787 zf-CCHC_5: GAG-polypr 97.1 0.00023 4.9E-09 48.0 1.2 22 8-29 2-23 (36)
9 COG5082 AIR1 Arginine methyltr 95.7 0.0043 9.3E-08 55.1 1.1 19 9-27 98-117 (190)
10 COG5082 AIR1 Arginine methyltr 95.6 0.0055 1.2E-07 54.4 1.4 21 5-25 57-77 (190)
11 PTZ00368 universal minicircle 95.1 0.014 3E-07 48.1 2.4 20 8-27 27-46 (148)
12 KOG4400 E3 ubiquitin ligase in 95.1 0.0087 1.9E-07 53.7 1.2 19 9-27 144-162 (261)
13 PF14392 zf-CCHC_4: Zinc knuck 95.0 0.0079 1.7E-07 41.8 0.4 20 7-26 30-49 (49)
14 COG5222 Uncharacterized conser 94.9 0.012 2.5E-07 56.3 1.5 23 8-30 176-198 (427)
15 PTZ00368 universal minicircle 94.5 0.018 3.8E-07 47.5 1.5 19 9-27 1-19 (148)
16 KOG4400 E3 ubiquitin ligase in 92.2 0.08 1.7E-06 47.5 1.8 24 7-30 163-186 (261)
17 PF15288 zf-CCHC_6: Zinc knuck 89.0 0.35 7.5E-06 33.4 2.2 21 9-29 2-24 (40)
18 KOG0314 Predicted E3 ubiquitin 81.6 0.87 1.9E-05 45.3 1.9 25 6-30 156-180 (448)
19 KOG0107 Alternative splicing f 77.7 1.1 2.3E-05 40.2 1.1 18 9-26 101-118 (195)
20 KOG3116 Predicted C3H1-type Zn 65.0 1.6 3.4E-05 38.3 -0.7 22 8-29 27-48 (177)
21 KOG0119 Splicing factor 1/bran 63.5 3.6 7.8E-05 41.8 1.3 18 10-27 287-304 (554)
22 PF00446 GnRH: Gonadotropin-re 61.6 2 4.2E-05 21.9 -0.5 9 123-131 1-9 (10)
23 KOG2044 5'-3' exonuclease HKE1 54.7 5.5 0.00012 42.6 0.9 23 5-27 257-279 (931)
24 PRK04016 DNA-directed RNA poly 46.1 8.5 0.00018 28.9 0.5 11 7-17 3-13 (62)
25 PLN00032 DNA-directed RNA poly 45.9 8.7 0.00019 29.6 0.6 10 8-17 4-13 (71)
26 PF01194 RNA_pol_N: RNA polyme 45.1 10 0.00022 28.3 0.8 10 8-17 4-13 (60)
27 PF00531 Death: Death domain; 41.7 61 0.0013 23.1 4.5 41 114-154 39-79 (83)
28 COG1644 RPB10 DNA-directed RNA 37.1 14 0.0003 28.0 0.4 10 8-17 4-13 (63)
29 PF08844 DUF1815: Domain of un 34.9 16 0.00036 29.9 0.6 14 6-19 30-45 (105)
30 KOG3004 Meiotic chromosome se 33.0 9.7 0.00021 36.4 -1.1 182 4-225 64-247 (305)
31 KOG2673 Uncharacterized conser 32.9 24 0.00052 35.7 1.5 20 11-30 131-150 (485)
32 PRK14383 hypothetical protein; 30.1 2.4E+02 0.0052 22.3 6.4 44 115-158 8-58 (84)
33 PF03462 PCRF: PCRF domain; I 29.9 43 0.00092 26.9 2.3 22 108-129 57-79 (115)
34 KOG3497 DNA-directed RNA polym 29.3 19 0.0004 27.5 0.1 8 9-16 5-12 (69)
35 PLN03148 Blue copper-like prot 29.1 39 0.00085 29.6 2.0 17 9-30 97-113 (167)
36 COG1859 KptA RNA:NAD 2'-phosph 27.8 68 0.0015 29.3 3.4 72 78-153 24-97 (211)
37 KOG0122 Translation initiation 26.6 53 0.0011 31.0 2.5 21 8-29 119-139 (270)
38 cd03144 GATase1_ScBLP_like Typ 25.7 1.5E+02 0.0032 24.3 4.7 28 127-155 47-74 (114)
39 KOG3794 CBF1-interacting corep 23.7 44 0.00095 33.5 1.5 31 7-37 123-155 (453)
40 smart00647 IBR In Between Ring 23.1 50 0.0011 22.5 1.3 16 9-24 49-64 (64)
41 PF01885 PTS_2-RNA: RNA 2'-pho 22.0 1.6E+02 0.0034 25.8 4.5 56 90-149 10-65 (186)
42 PF07580 Peptidase_M26_C: M26 21.5 85 0.0018 33.5 3.1 122 91-237 116-251 (737)
43 KOG0584 Serine/threonine prote 21.4 48 0.001 34.7 1.3 65 117-182 102-178 (632)
44 COG3946 VirJ Type IV secretory 20.9 64 0.0014 32.6 2.0 28 109-136 306-336 (456)
45 PF09297 zf-NADH-PPase: NADH p 20.5 22 0.00048 22.4 -0.8 18 9-26 4-26 (32)
No 1
>PF07962 Swi3: Replication Fork Protection Component Swi3; InterPro: IPR012923 Replication fork pausing is required to initiate recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1. Together they define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks []. This complex is required for accurate replication, fork protection and replication checkpoint signalling [, ].; GO: 0006974 response to DNA damage stimulus, 0007049 cell cycle, 0048478 replication fork protection, 0005634 nucleus
Probab=100.00 E-value=1.8e-35 Score=226.73 Aligned_cols=81 Identities=38% Similarity=0.800 Sum_probs=79.7
Q ss_pred CcCcccccCCCChHHHHHhccccccccCCCchHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhhcchHHHHHHHHHH
Q 035848 80 KLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLR 159 (244)
Q Consensus 80 KLd~eRLls~kGLp~Llr~fpk~~KfKGKGHE~~DL~~LL~~YQ~WaH~LfPK~~F~Dfi~rVEkLG~kk~Vk~~lrelR 159 (244)
|||++||+|++|||+|+++| ++++|+|||||++||.+||++||+|||+||||++|+|||++||+||++++||+||++||
T Consensus 1 KLd~~rL~~~~Glp~l~~~~-k~~k~kgkghE~~dL~~ll~~Yq~W~h~LfPk~~F~d~i~~vE~LG~~k~v~~~~~~lr 79 (83)
T PF07962_consen 1 KLDEERLLSPKGLPYLRKNF-KKFKFKGKGHEYEDLRRLLQFYQLWAHRLFPKASFEDFIERVEKLGKKKRVRNYRRELR 79 (83)
T ss_pred CCCHHHccCCCCHHHHHHHH-HHcCcCCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 89999999999999999999 99999999999999999999999999999999999999999999999999999999999
Q ss_pred HH
Q 035848 160 DR 161 (244)
Q Consensus 160 ~~ 161 (244)
++
T Consensus 80 ~~ 81 (83)
T PF07962_consen 80 EE 81 (83)
T ss_pred hh
Confidence 85
No 2
>KOG3004 consensus Meiotic chromosome segregation protein [Cell cycle control, cell division, chromosome partitioning]
Probab=99.96 E-value=5.4e-30 Score=235.05 Aligned_cols=99 Identities=29% Similarity=0.549 Sum_probs=93.6
Q ss_pred ccCcCCCCccCCCCCCCcCcccccCCCChHHHHHhccccccccCCCchHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHH
Q 035848 64 AIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVE 143 (244)
Q Consensus 64 ~~~~~~kkkk~Rr~rpKLd~eRLls~kGLp~Llr~fpk~~KfKGKGHE~~DL~~LL~~YQ~WaH~LfPK~~F~Dfi~rVE 143 (244)
+...+++|+.+|++++||++++|+|++|||+ +|++++++||+|||||+.||..||++||+|+|+||||++|+|||.+||
T Consensus 48 ~k~l~~rKR~~~~~~~~lsa~~L~s~~Gip~-lR~~~k~~k~kgKg~e~~dL~~llr~y~~WgH~lfPk~kf~D~i~~~e 126 (305)
T KOG3004|consen 48 PKDLRGRKRAVRVKSPKLSAETLISEKGIPA-LRDCFKKAKFKGKGHEYIDLKELLRSYQHWGHELFPKAKFDDFINRVE 126 (305)
T ss_pred ccccccccccccccccccchhhhcCccCchH-HHHHHhhcCcCCCCCcccCHHHHHHHHHHHHHhhcccchhHHHHHHHH
Confidence 6667888999999999999999999999999 666679999999999999999999999999999999999999999999
Q ss_pred HhhcchHHHHHHHHHHHHhh
Q 035848 144 QVAASRRVKMCIRDLRDRVA 163 (244)
Q Consensus 144 kLG~kk~Vk~~lrelR~~~~ 163 (244)
+||+++.||++|..||++++
T Consensus 127 tLGk~r~vkv~~~r~rLg~~ 146 (305)
T KOG3004|consen 127 TLGKKREVKVDLLRYRLGYF 146 (305)
T ss_pred hhccccchhhhhhHHHhccC
Confidence 99999999999999999774
No 3
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=98.49 E-value=5.3e-08 Score=56.06 Aligned_cols=17 Identities=65% Similarity=1.660 Sum_probs=16.0
Q ss_pred cccccCCCCccCCCCCC
Q 035848 10 GCFKCGRPGHWSRDCPS 26 (244)
Q Consensus 10 ~Cy~CG~~GHwardCp~ 26 (244)
.||+||+.||+|+|||.
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 69999999999999984
No 4
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=98.08 E-value=1.3e-06 Score=81.87 Aligned_cols=28 Identities=36% Similarity=1.196 Sum_probs=25.9
Q ss_pred CCCCCCCcccccCCCCccCCCCCCCCCC
Q 035848 3 NAKAAPTGCFKCGRPGHWSRDCPSSSSS 30 (244)
Q Consensus 3 p~~~~~~~Cy~CG~~GHwardCp~~~~~ 30 (244)
|+|+.+.+||+|||.||||.+||.+..+
T Consensus 155 pgmgDq~~cyrcGkeghwskEcP~~~~~ 182 (346)
T KOG0109|consen 155 PGMGDQSGCYRCGKEGHWSKECPVDRTG 182 (346)
T ss_pred CCCCCHHHheeccccccccccCCccCCC
Confidence 8999999999999999999999997653
No 5
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=97.49 E-value=3.6e-05 Score=50.58 Aligned_cols=21 Identities=43% Similarity=1.257 Sum_probs=18.4
Q ss_pred CCCcccccCCCCccCCCCCCC
Q 035848 7 APTGCFKCGRPGHWSRDCPSS 27 (244)
Q Consensus 7 ~~~~Cy~CG~~GHwardCp~~ 27 (244)
..-.|+.|++.|||.+|||..
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~~ 27 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPTN 27 (32)
T ss_pred CCCEeecCCCCCccHhHCCCC
Confidence 445799999999999999974
No 6
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=97.43 E-value=9.4e-05 Score=51.13 Aligned_cols=20 Identities=50% Similarity=1.345 Sum_probs=18.0
Q ss_pred CCCcccccCCCCccCCCCCC
Q 035848 7 APTGCFKCGRPGHWSRDCPS 26 (244)
Q Consensus 7 ~~~~Cy~CG~~GHwardCp~ 26 (244)
....|.+||+.|||+.+|+.
T Consensus 3 ~~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 3 ARVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCCcCcccCCCCcchhhCCC
Confidence 45789999999999999995
No 7
>smart00343 ZnF_C2HC zinc finger.
Probab=97.12 E-value=0.00018 Score=43.78 Aligned_cols=18 Identities=50% Similarity=1.437 Sum_probs=16.1
Q ss_pred cccccCCCCccCCCCCCC
Q 035848 10 GCFKCGRPGHWSRDCPSS 27 (244)
Q Consensus 10 ~Cy~CG~~GHwardCp~~ 27 (244)
.||+||+.||++++||..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 499999999999999843
No 8
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=97.09 E-value=0.00023 Score=48.02 Aligned_cols=22 Identities=36% Similarity=0.987 Sum_probs=13.2
Q ss_pred CCcccccCCCCccCCCCCCCCC
Q 035848 8 PTGCFKCGRPGHWSRDCPSSSS 29 (244)
Q Consensus 8 ~~~Cy~CG~~GHwardCp~~~~ 29 (244)
+..|.+|||-.|||+||-.-..
T Consensus 2 ~~~CprC~kg~Hwa~~C~sk~d 23 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECRSKTD 23 (36)
T ss_dssp --C-TTTSSSCS-TTT---TCC
T ss_pred CccCcccCCCcchhhhhhhhhc
Confidence 5789999999999999976543
No 9
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=95.69 E-value=0.0043 Score=55.09 Aligned_cols=19 Identities=58% Similarity=1.400 Sum_probs=16.5
Q ss_pred CcccccCCCCccCCCC-CCC
Q 035848 9 TGCFKCGRPGHWSRDC-PSS 27 (244)
Q Consensus 9 ~~Cy~CG~~GHwardC-p~~ 27 (244)
..||+||+.||++||| |+.
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~~ 117 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPSK 117 (190)
T ss_pred cccccccccCccccccCccc
Confidence 6799999999999999 553
No 10
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=95.59 E-value=0.0055 Score=54.40 Aligned_cols=21 Identities=48% Similarity=1.217 Sum_probs=19.0
Q ss_pred CCCCCcccccCCCCccCCCCC
Q 035848 5 KAAPTGCFKCGRPGHWSRDCP 25 (244)
Q Consensus 5 ~~~~~~Cy~CG~~GHwardCp 25 (244)
+.+...||+||+-||.+||||
T Consensus 57 ~~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 57 REENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred cccccccchhcccCcccccCC
Confidence 456778999999999999999
No 11
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=95.15 E-value=0.014 Score=48.06 Aligned_cols=20 Identities=60% Similarity=1.469 Sum_probs=13.7
Q ss_pred CCcccccCCCCccCCCCCCC
Q 035848 8 PTGCFKCGRPGHWSRDCPSS 27 (244)
Q Consensus 8 ~~~Cy~CG~~GHwardCp~~ 27 (244)
...||+||+.||+|++||..
T Consensus 27 ~~~C~~Cg~~GH~~~~Cp~~ 46 (148)
T PTZ00368 27 ARPCYKCGEPGHLSRECPSA 46 (148)
T ss_pred CccCccCCCCCcCcccCcCC
Confidence 45677777777777777654
No 12
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=95.12 E-value=0.0087 Score=53.68 Aligned_cols=19 Identities=47% Similarity=1.263 Sum_probs=17.2
Q ss_pred CcccccCCCCccCCCCCCC
Q 035848 9 TGCFKCGRPGHWSRDCPSS 27 (244)
Q Consensus 9 ~~Cy~CG~~GHwardCp~~ 27 (244)
..||+||+.|||+++||.+
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred CccCCCCcCCcchhhCCCC
Confidence 5699999999999999965
No 13
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=94.97 E-value=0.0079 Score=41.83 Aligned_cols=20 Identities=50% Similarity=1.243 Sum_probs=17.5
Q ss_pred CCCcccccCCCCccCCCCCC
Q 035848 7 APTGCFKCGRPGHWSRDCPS 26 (244)
Q Consensus 7 ~~~~Cy~CG~~GHwardCp~ 26 (244)
-+.-|++||.-||..++||.
T Consensus 30 lp~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 30 LPRFCFHCGRIGHSDKECPK 49 (49)
T ss_pred cChhhcCCCCcCcCHhHcCC
Confidence 35679999999999999983
No 14
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.93 E-value=0.012 Score=56.34 Aligned_cols=23 Identities=35% Similarity=1.198 Sum_probs=19.6
Q ss_pred CCcccccCCCCccCCCCCCCCCC
Q 035848 8 PTGCFKCGRPGHWSRDCPSSSSS 30 (244)
Q Consensus 8 ~~~Cy~CG~~GHwardCp~~~~~ 30 (244)
.-.||+||+.|||-..||-++..
T Consensus 176 gY~CyRCGqkgHwIqnCpTN~Dp 198 (427)
T COG5222 176 GYVCYRCGQKGHWIQNCPTNQDP 198 (427)
T ss_pred ceeEEecCCCCchhhcCCCCCCC
Confidence 35799999999999999987643
No 15
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=94.54 E-value=0.018 Score=47.49 Aligned_cols=19 Identities=53% Similarity=1.268 Sum_probs=17.3
Q ss_pred CcccccCCCCccCCCCCCC
Q 035848 9 TGCFKCGRPGHWSRDCPSS 27 (244)
Q Consensus 9 ~~Cy~CG~~GHwardCp~~ 27 (244)
+.||+||+.||+|++||..
T Consensus 1 ~~C~~C~~~GH~~~~c~~~ 19 (148)
T PTZ00368 1 MVCYRCGGVGHQSRECPNS 19 (148)
T ss_pred CcCCCCCCCCcCcccCcCC
Confidence 4799999999999999974
No 16
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=92.16 E-value=0.08 Score=47.54 Aligned_cols=24 Identities=54% Similarity=1.111 Sum_probs=21.4
Q ss_pred CCCcccccCCCCccCCCCCCCCCC
Q 035848 7 APTGCFKCGRPGHWSRDCPSSSSS 30 (244)
Q Consensus 7 ~~~~Cy~CG~~GHwardCp~~~~~ 30 (244)
....||.||+.||+++|||..+..
T Consensus 163 ~~~~c~~c~~~~h~~~~C~~~~~~ 186 (261)
T KOG4400|consen 163 KGGTCFRCGKVGHGSRDCPSKQKS 186 (261)
T ss_pred CCCccccCCCcceecccCCccccc
Confidence 478999999999999999998754
No 17
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=89.00 E-value=0.35 Score=33.42 Aligned_cols=21 Identities=33% Similarity=0.762 Sum_probs=17.6
Q ss_pred CcccccCCCCccC--CCCCCCCC
Q 035848 9 TGCFKCGRPGHWS--RDCPSSSS 29 (244)
Q Consensus 9 ~~Cy~CG~~GHwa--rdCp~~~~ 29 (244)
..|.+||.-||.+ +.||.-..
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~ 24 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCW 24 (40)
T ss_pred ccccccccccccccCccCCCCCC
Confidence 3699999999998 78998753
No 18
>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.59 E-value=0.87 Score=45.28 Aligned_cols=25 Identities=40% Similarity=0.997 Sum_probs=21.1
Q ss_pred CCCCcccccCCCCccCCCCCCCCCC
Q 035848 6 AAPTGCFKCGRPGHWSRDCPSSSSS 30 (244)
Q Consensus 6 ~~~~~Cy~CG~~GHwardCp~~~~~ 30 (244)
...-.||+|+.+|||...||.....
T Consensus 156 ppsy~c~rc~~~g~wikacptv~~~ 180 (448)
T KOG0314|consen 156 PPSYKCVKCPTPGPWIKACPTVSGS 180 (448)
T ss_pred CCCcceecCCCCCccceeccccCCc
Confidence 3456799999999999999987654
No 19
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=77.66 E-value=1.1 Score=40.21 Aligned_cols=18 Identities=39% Similarity=1.112 Sum_probs=16.4
Q ss_pred CcccccCCCCccCCCCCC
Q 035848 9 TGCFKCGRPGHWSRDCPS 26 (244)
Q Consensus 9 ~~Cy~CG~~GHwardCp~ 26 (244)
..||.||..|||.|.|-.
T Consensus 101 ~~~~r~G~rg~~~r~~~~ 118 (195)
T KOG0107|consen 101 GFCYRCGERGHIGRNCKD 118 (195)
T ss_pred cccccCCCcccccccccc
Confidence 449999999999999987
No 20
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=65.01 E-value=1.6 Score=38.31 Aligned_cols=22 Identities=32% Similarity=0.939 Sum_probs=18.8
Q ss_pred CCcccccCCCCccCCCCCCCCC
Q 035848 8 PTGCFKCGRPGHWSRDCPSSSS 29 (244)
Q Consensus 8 ~~~Cy~CG~~GHwardCp~~~~ 29 (244)
.-.|-+|=+.|||..+|.....
T Consensus 27 ~~rCQKClq~GHWtYECk~kRk 48 (177)
T KOG3116|consen 27 SARCQKCLQAGHWTYECKNKRK 48 (177)
T ss_pred chhHHHHHhhccceeeecCcee
Confidence 3479999999999999987654
No 21
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=63.53 E-value=3.6 Score=41.79 Aligned_cols=18 Identities=44% Similarity=0.811 Sum_probs=17.4
Q ss_pred cccccCCCCccCCCCCCC
Q 035848 10 GCFKCGRPGHWSRDCPSS 27 (244)
Q Consensus 10 ~Cy~CG~~GHwardCp~~ 27 (244)
.|..||--||.++||+..
T Consensus 287 ~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 287 VCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccCCcccccccCCCc
Confidence 899999999999999997
No 22
>PF00446 GnRH: Gonadotropin-releasing hormone; InterPro: IPR002012 The gonadotropin-releasing hormones (GnRH) (gonadoliberin) [] are a family of peptides that play a pivotal role in reproduction. The main function of GnRH is to act on the pituitary to stimulate the synthesis and secretion of luteinizing and follicle-stimulating hormones, but GnRH also acts on the brain, retina, sympathetic nervous system, gonads and placenta in certain species. There seems to be at least three forms of GnRH. The second form is expressed in midbrain and seems to be widespread. The third form has only been found so far in fish. GnRH is a C-terminal amidated decapeptide processed from a larger precursor protein. Four of the ten residues are perfectly conserved in all species where GnRH has been sequenced.; GO: 0005179 hormone activity, 0007275 multicellular organismal development, 0005576 extracellular region
Probab=61.56 E-value=2 Score=21.88 Aligned_cols=9 Identities=22% Similarity=0.660 Sum_probs=8.1
Q ss_pred HHHHhccCC
Q 035848 123 SEWHSHLLP 131 (244)
Q Consensus 123 Q~WaH~LfP 131 (244)
|+|.|.++|
T Consensus 1 QHwS~~w~P 9 (10)
T PF00446_consen 1 QHWSHGWKP 9 (10)
T ss_pred CccccccCC
Confidence 789999988
No 23
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=54.72 E-value=5.5 Score=42.64 Aligned_cols=23 Identities=39% Similarity=1.006 Sum_probs=19.2
Q ss_pred CCCCCcccccCCCCccCCCCCCC
Q 035848 5 KAAPTGCFKCGRPGHWSRDCPSS 27 (244)
Q Consensus 5 ~~~~~~Cy~CG~~GHwardCp~~ 27 (244)
.+.+..|+.||+-||-+.||..-
T Consensus 257 P~~~~~C~~cgq~gh~~~dc~g~ 279 (931)
T KOG2044|consen 257 PNKPRRCFLCGQTGHEAKDCEGK 279 (931)
T ss_pred CCCcccchhhcccCCcHhhcCCc
Confidence 34566699999999999999754
No 24
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=46.08 E-value=8.5 Score=28.91 Aligned_cols=11 Identities=45% Similarity=1.313 Sum_probs=7.8
Q ss_pred CCCcccccCCC
Q 035848 7 APTGCFKCGRP 17 (244)
Q Consensus 7 ~~~~Cy~CG~~ 17 (244)
-|..||+|||.
T Consensus 3 iPvRCFTCGkv 13 (62)
T PRK04016 3 IPVRCFTCGKV 13 (62)
T ss_pred CCeEecCCCCC
Confidence 35678888875
No 25
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=45.92 E-value=8.7 Score=29.62 Aligned_cols=10 Identities=50% Similarity=1.471 Sum_probs=6.8
Q ss_pred CCcccccCCC
Q 035848 8 PTGCFKCGRP 17 (244)
Q Consensus 8 ~~~Cy~CG~~ 17 (244)
|..||+|||.
T Consensus 4 PVRCFTCGkv 13 (71)
T PLN00032 4 PVRCFTCGKV 13 (71)
T ss_pred ceeecCCCCC
Confidence 5567777765
No 26
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=45.10 E-value=10 Score=28.26 Aligned_cols=10 Identities=50% Similarity=1.471 Sum_probs=6.1
Q ss_pred CCcccccCCC
Q 035848 8 PTGCFKCGRP 17 (244)
Q Consensus 8 ~~~Cy~CG~~ 17 (244)
|..||+||+.
T Consensus 4 PVRCFTCGkv 13 (60)
T PF01194_consen 4 PVRCFTCGKV 13 (60)
T ss_dssp SSS-STTTSB
T ss_pred ceecCCCCCC
Confidence 5567777764
No 27
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=41.74 E-value=61 Score=23.11 Aligned_cols=41 Identities=7% Similarity=0.188 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhhcchHHHHH
Q 035848 114 DLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMC 154 (244)
Q Consensus 114 DL~~LL~~YQ~WaH~LfPK~~F~Dfi~rVEkLG~kk~Vk~~ 154 (244)
.-...+++.+.|..+--|.++.+..+..+++.|....+...
T Consensus 39 ~~~~~~~~L~~W~~~~~~~at~~~L~~aL~~~~~~d~~~~i 79 (83)
T PF00531_consen 39 LREQTYEMLQRWRQREGPNATVDQLIQALRDIGRNDLAEKI 79 (83)
T ss_dssp HHHHHHHHHHHHHHHHGSTSSHHHHHHHHHHTTHHHHHHHH
T ss_pred hHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHCCcHHHHHHH
Confidence 34678899999999999999999999999999998866443
No 28
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=37.12 E-value=14 Score=27.99 Aligned_cols=10 Identities=50% Similarity=1.471 Sum_probs=6.3
Q ss_pred CCcccccCCC
Q 035848 8 PTGCFKCGRP 17 (244)
Q Consensus 8 ~~~Cy~CG~~ 17 (244)
|-.||.||++
T Consensus 4 PiRCFsCGkv 13 (63)
T COG1644 4 PVRCFSCGKV 13 (63)
T ss_pred ceEeecCCCC
Confidence 4567777764
No 29
>PF08844 DUF1815: Domain of unknown function (DUF1815); InterPro: IPR014943 This entry is about 100 amino acids in length and is functionally uncharacterised.
Probab=34.95 E-value=16 Score=29.86 Aligned_cols=14 Identities=29% Similarity=0.797 Sum_probs=9.2
Q ss_pred CCCCccccc--CCCCc
Q 035848 6 AAPTGCFKC--GRPGH 19 (244)
Q Consensus 6 ~~~~~Cy~C--G~~GH 19 (244)
+-.-.||.| |+.+|
T Consensus 30 G~~AsCYtC~dG~~~~ 45 (105)
T PF08844_consen 30 GYLASCYTCGDGRDMN 45 (105)
T ss_pred CceeEEEecCCCCCCC
Confidence 445579999 55544
No 30
>KOG3004 consensus Meiotic chromosome segregation protein [Cell cycle control, cell division, chromosome partitioning]
Probab=32.95 E-value=9.7 Score=36.41 Aligned_cols=182 Identities=27% Similarity=0.302 Sum_probs=127.8
Q ss_pred CCCCCCcccccCCCCccCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCcccCCccCcCCCCccCCCCCCCcC
Q 035848 4 AKAAPTGCFKCGRPGHWSRDCPSSSSSAPSN-SNFPSNNTASGGGGGGSGVGDGGVSVSKSAIGVKEKPKKLPRSRPKLT 82 (244)
Q Consensus 4 ~~~~~~~Cy~CG~~GHwardCp~~~~~~~~~-~~~p~~p~p~~~g~~~~~~~~~~~~ge~~~~~~~~kkkk~Rr~rpKLd 82 (244)
+-..+..|..||.|+ .|+|+..-+.++.- |..+...--.+-. -|+- ..-+..|-..+.+.+.+|.
T Consensus 64 ~lsa~~L~s~~Gip~--lR~~~k~~k~kgKg~e~~dL~~llr~y~------~WgH------~lfPk~kf~D~i~~~etLG 129 (305)
T KOG3004|consen 64 KLSAETLISEKGIPA--LRDCFKKAKFKGKGHEYIDLKELLRSYQ------HWGH------ELFPKAKFDDFINRVETLG 129 (305)
T ss_pred ccchhhhcCccCchH--HHHHHhhcCcCCCCCcccCHHHHHHHHH------HHHH------hhcccchhHHHHHHHHhhc
Confidence 445678999999999 99998765431111 0000000000000 0110 3556777788888999999
Q ss_pred cccccCCCChHHHHHhccccccccCCCchHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhhcchHHHHHHHHHHHHh
Q 035848 83 PDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRV 162 (244)
Q Consensus 83 ~eRLls~kGLp~Llr~fpk~~KfKGKGHE~~DL~~LL~~YQ~WaH~LfPK~~F~Dfi~rVEkLG~kk~Vk~~lrelR~~~ 162 (244)
..|++.-.++.|.+.++++ -.|+-.+-+.+++.. ++.+-+..++..|+..+|+.+
T Consensus 130 k~r~vkv~~~r~rLg~~~~---------------------~~~h~~~~~~~s~~~----~q~~as~~~~D~f~~dl~E~~ 184 (305)
T KOG3004|consen 130 KKREVKVDLLRYRLGYFPE---------------------NEEHEHLLLEYSPDH----VQHVASDEEVDPFIQDLRERV 184 (305)
T ss_pred cccchhhhhhHHHhccCcc---------------------chhhhhhhhhcCchh----hhhccccccccHHHHhhHhhh
Confidence 9999999999999998853 246667777777765 788888889999999999999
Q ss_pred hcCCCCCCCcCCcccCCCCCCCCCCccccccCCCCCCCCCCCCCCCCChh-HHHHHHHHHhhhc
Q 035848 163 ANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQPHQQDPASNVHAADDF-NDLFNKVYRTATE 225 (244)
Q Consensus 163 ~~G~d~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~d~~~~~~~~~~~ 225 (244)
+-+.++++..+--....+..+++-+.+.-. ........+..+.+++++. +.++++|++.+..
T Consensus 185 a~~~d~~~~~e~~~~~t~~~~~q~~de~~~-~e~~~~s~~~~~d~~a~~~~~~~~~ev~dee~~ 247 (305)
T KOG3004|consen 185 AVGVDPNKSYEKQEQSTAESDDQVADERRH-DEENINSKSVDADTNADAFEDSMVNEVFDEESK 247 (305)
T ss_pred hhccCCCccHHHHHHhhccccccccccccc-chhhccccCccccccccchhhhhhccccccccc
Confidence 999999998887777777777776555422 2233344455778888888 8999999987654
No 31
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=32.94 E-value=24 Score=35.71 Aligned_cols=20 Identities=45% Similarity=0.984 Sum_probs=18.1
Q ss_pred ccccCCCCccCCCCCCCCCC
Q 035848 11 CFKCGRPGHWSRDCPSSSSS 30 (244)
Q Consensus 11 Cy~CG~~GHwardCp~~~~~ 30 (244)
||+||-.-|--||||.+-++
T Consensus 131 CFNC~g~~hsLrdC~rp~d~ 150 (485)
T KOG2673|consen 131 CFNCGGTPHSLRDCPRPFDF 150 (485)
T ss_pred ccccCCCCCccccCCCcccc
Confidence 99999999999999997654
No 32
>PRK14383 hypothetical protein; Provisional
Probab=30.07 E-value=2.4e+02 Score=22.30 Aligned_cols=44 Identities=18% Similarity=0.166 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHhccCC--CCCH-----HHHHHHHHHhhcchHHHHHHHHH
Q 035848 115 LGHLIGLYSEWHSHLLP--YYSF-----DHFVSKVEQVAASRRVKMCIRDL 158 (244)
Q Consensus 115 L~~LL~~YQ~WaH~LfP--K~~F-----~Dfi~rVEkLG~kk~Vk~~lrel 158 (244)
|-.|+.+||.|-.-++| .-.| +..++.|++.|--+-.-..+.++
T Consensus 8 ~i~lI~~Yq~~iSpl~~~~~CRy~PTCS~Ya~~Ai~~~G~~kG~~l~~~Ri 58 (84)
T PRK14383 8 LVRAVRWYQRVLSPRKPAPTCRFSPTCSQYAVEAIERHGALKGGWLALWRV 58 (84)
T ss_pred HHHHHHHHHHHhCCcCCCCCCCcCccHHHHHHHHHHHhCcHHHHHHHHHHH
Confidence 45689999999998875 6666 68999999999888654444433
No 33
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors. Peptide chain release factors are important for protein synthesis since they direct the termination of translation in response to the peptide chain termination codons UAG and UAA. These are structurally distinct but both contain the PCRF domain [].; GO: 0016149 translation release factor activity, codon specific, 0006415 translational termination, 0005737 cytoplasm; PDB: 3D5A_X 3D5C_X 3MR8_V 3MS0_V 3F1G_X 3F1E_X 1ZBT_A 2IHR_1 2X9R_Y 2X9T_Y ....
Probab=29.95 E-value=43 Score=26.90 Aligned_cols=22 Identities=18% Similarity=0.324 Sum_probs=17.8
Q ss_pred CCchHHH-HHHHHHHHHHHHhcc
Q 035848 108 RGHEVSD-LGHLIGLYSEWHSHL 129 (244)
Q Consensus 108 KGHE~~D-L~~LL~~YQ~WaH~L 129 (244)
-|.|..+ ...|++||+.|+.+.
T Consensus 57 GG~EA~lfa~~L~~MY~~~a~~~ 79 (115)
T PF03462_consen 57 GGDEACLFAEELFRMYQRYAERR 79 (115)
T ss_dssp STHHHHHHHHHHHHHHHHHHHHT
T ss_pred CchHHHHHHHHHHHHHHHHHHHc
Confidence 4778877 677899999999863
No 34
>KOG3497 consensus DNA-directed RNA polymerase, subunit RPB10 [Transcription]
Probab=29.32 E-value=19 Score=27.46 Aligned_cols=8 Identities=50% Similarity=1.572 Sum_probs=3.7
Q ss_pred CcccccCC
Q 035848 9 TGCFKCGR 16 (244)
Q Consensus 9 ~~Cy~CG~ 16 (244)
-.||+|||
T Consensus 5 iRCFtCGK 12 (69)
T KOG3497|consen 5 IRCFTCGK 12 (69)
T ss_pred eEeeeccc
Confidence 34555544
No 35
>PLN03148 Blue copper-like protein; Provisional
Probab=29.05 E-value=39 Score=29.62 Aligned_cols=17 Identities=29% Similarity=0.626 Sum_probs=12.9
Q ss_pred CcccccCCCCccCCCCCCCCCC
Q 035848 9 TGCFKCGRPGHWSRDCPSSSSS 30 (244)
Q Consensus 9 ~~Cy~CG~~GHwardCp~~~~~ 30 (244)
..-|-|| .|| |-..++-
T Consensus 97 ~~YFIcg-~gh----C~~GmKl 113 (167)
T PLN03148 97 RYYFICG-NGQ----CFNGMKV 113 (167)
T ss_pred cEEEEcC-CCc----cccCCEE
Confidence 5678999 575 8888775
No 36
>COG1859 KptA RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]
Probab=27.83 E-value=68 Score=29.28 Aligned_cols=72 Identities=21% Similarity=0.206 Sum_probs=52.1
Q ss_pred CCCcCccccc-CCCChHHHHHhccccccccCCCchHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhhcch-HHHH
Q 035848 78 RPKLTPDLLL-SDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASR-RVKM 153 (244)
Q Consensus 78 rpKLd~eRLl-s~kGLp~Llr~fpk~~KfKGKGHE~~DL~~LL~~YQ~WaH~LfPK~~F~Dfi~rVEkLG~kk-~Vk~ 153 (244)
+..++..++. ..+=|.++|||+|..+.++=-.+=+.|++.|+...+.= |..++++.....|+..=++| +++.
T Consensus 24 ~~~~~~~~~~~~SK~lS~vLRH~p~~~gl~lD~~Gwa~i~~l~~~~~k~----~~~~~~~~l~~iV~~d~K~Rf~l~~ 97 (211)
T COG1859 24 KALLNEKERVKLSKFLSGVLRHFPEAIGLRLDEEGWADIDELLEGLRKA----GRWLTRELLLAVVATDDKGRFELKE 97 (211)
T ss_pred hhccCcchhhhHHHHHHHHHhcChHHcCeeeccccchhHHHHHHHHHhh----ccCCCHHHHHHHHhcCCCceeEecc
Confidence 4455543333 37889999999999887765555567777777776654 78889999999998887776 4544
No 37
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=26.56 E-value=53 Score=31.03 Aligned_cols=21 Identities=29% Similarity=0.948 Sum_probs=17.9
Q ss_pred CCcccccCCCCccCCCCCCCCC
Q 035848 8 PTGCFKCGRPGHWSRDCPSSSS 29 (244)
Q Consensus 8 ~~~Cy~CG~~GHwardCp~~~~ 29 (244)
-..|--| +--||+-+||.-.-
T Consensus 119 ~~~CR~C-~gdHwt~~CPyK~~ 139 (270)
T KOG0122|consen 119 IVACRIC-KGDHWTTNCPYKDT 139 (270)
T ss_pred eeeeeec-CCCeeeecCCchhh
Confidence 4579999 89999999998654
No 38
>cd03144 GATase1_ScBLP_like Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP). Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP). Biotin-apoprotein ligase modifies proteins by covalently attaching biotin. ScBLP is known to biotinylate acety-CoA carboxylase and pyruvate carboxylase. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, the Cys residue found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow in a typical GATase1 domain is conserved.
Probab=25.67 E-value=1.5e+02 Score=24.34 Aligned_cols=28 Identities=11% Similarity=0.144 Sum_probs=22.8
Q ss_pred hccCCCCCHHHHHHHHHHhhcchHHHHHH
Q 035848 127 SHLLPYYSFDHFVSKVEQVAASRRVKMCI 155 (244)
Q Consensus 127 H~LfPK~~F~Dfi~rVEkLG~kk~Vk~~l 155 (244)
.-++|--.|.++++.++..| ...++.++
T Consensus 47 ~lVlPGGa~~~~~~~L~~~g-~~~i~~~v 74 (114)
T cd03144 47 LLVVPGGADLPYCRALNGKG-NRRIRNFV 74 (114)
T ss_pred EEEECCCChHHHHHHHHhhC-cHHHHHHH
Confidence 46799999999999999988 66665554
No 39
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=23.69 E-value=44 Score=33.46 Aligned_cols=31 Identities=32% Similarity=0.668 Sum_probs=22.9
Q ss_pred CCCcccccCCCCccC--CCCCCCCCCCCCCCCC
Q 035848 7 APTGCFKCGRPGHWS--RDCPSSSSSAPSNSNF 37 (244)
Q Consensus 7 ~~~~Cy~CG~~GHwa--rdCp~~~~~~~~~~~~ 37 (244)
+-..|.+|++-||.. |+||.-..++.+++.+
T Consensus 123 RNVrC~kChkwGH~n~DreCplf~~~~~~~s~l 155 (453)
T KOG3794|consen 123 RNVRCLKCHKWGHINTDRECPLFGKSMNNASSL 155 (453)
T ss_pred eeeeEEeecccccccCCccCcchhhcccchhcc
Confidence 446799999999987 6799876664444444
No 40
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=23.09 E-value=50 Score=22.52 Aligned_cols=16 Identities=38% Similarity=0.887 Sum_probs=12.7
Q ss_pred CcccccCCCCccCCCC
Q 035848 9 TGCFKCGRPGHWSRDC 24 (244)
Q Consensus 9 ~~Cy~CG~~GHwardC 24 (244)
.-|++|+.+.|.--.|
T Consensus 49 ~fC~~C~~~~H~~~~C 64 (64)
T smart00647 49 SFCFRCKVPWHSPVSC 64 (64)
T ss_pred eECCCCCCcCCCCCCC
Confidence 4589999999976655
No 41
>PF01885 PTS_2-RNA: RNA 2'-phosphotransferase, Tpt1 / KptA family; InterPro: IPR002745 The final step of tRNA splicing in Saccharomyces cerevisiae (Baker's yeast) requires 2'-phosphotransferase (Tpt1) to transfer the 2'-phosphate from ligated tRNA to NAD, producing mature tRNA and ADP ribose-1' '-2' '-cyclic phosphate. Yeast and Mus musculus (Mouse) Tpt1 protein and bacterial KptA protein can catalyze the conversion of the generated intermediate to both product and the original substrate, these enzymes likely use the same reaction mechanism. Step 1 of this reaction is strikingly similar to the ADP-ribosylation of proteins catalyzed by a number of bacterial toxins. KptA, a functional Tpt1 protein homologue from Escherichia coli is strikingly similar to yeast Tpt1 in its kinetic parameters, although E. coli is not known to have a 2'-phosphorylated RNA substrate [,].; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 1WFX_A.
Probab=22.03 E-value=1.6e+02 Score=25.78 Aligned_cols=56 Identities=16% Similarity=0.119 Sum_probs=29.3
Q ss_pred CChHHHHHhccccccccCCCchHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhhcch
Q 035848 90 DGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASR 149 (244)
Q Consensus 90 kGLp~Llr~fpk~~KfKGKGHE~~DL~~LL~~YQ~WaH~LfPK~~F~Dfi~rVEkLG~kk 149 (244)
|=|-|||||.|.++.+.=.-+=+=++..||+..+. + +..+++++..+.|+.--++|
T Consensus 10 K~Ls~lLRH~p~~~gL~~d~~G~v~v~dLL~~~~~---~-~~~~t~~~i~~vV~~~~K~R 65 (186)
T PF01885_consen 10 KALSYLLRHGPEKEGLVMDPDGWVSVDDLLRALRF---K-GLWVTEEDIREVVETDDKQR 65 (186)
T ss_dssp HHHHHHHHT-TGGGT----TT--EEHHHHHHHHHH---T--TT--HHHHHHHHHH-SS--
T ss_pred HHHHHHhCCChhhcCCccCCCCCEeHHHHHHHHHH---c-CCCCCHHHHHHHHhhCCCCC
Confidence 45789999999887654222223344445544444 1 33379999999999876665
No 42
>PF07580 Peptidase_M26_C: M26 IgA1-specific Metallo-endopeptidase C-terminal region; InterPro: IPR011505 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry represents metallopeptidases belonging to MEROPS peptidase family M26 (IgA1-specific metallopeptidase, clan MA). They are extracellular enzymes, which cleave mammalian IgA. They are only found in Gram-positive bacteria and are often found associated with IPR001899 from INTERPRO; they may be attached to the cell wall. This entry also contains the metallopeptidases ZmpB and ZmpC from Streptococcus pneumoniae. These metallopeptidases are thought to contribute to the inflammatory response to Streptococcal infection [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0005576 extracellular region, 0005618 cell wall
Probab=21.45 E-value=85 Score=33.48 Aligned_cols=122 Identities=20% Similarity=0.254 Sum_probs=83.6
Q ss_pred ChHHHHHhccccccccC-------------CCchHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhhcchHHHHHHHH
Q 035848 91 GLGFVLRHFPRAFKYRG-------------RGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRD 157 (244)
Q Consensus 91 GLp~Llr~fpk~~KfKG-------------KGHE~~DL~~LL~~YQ~WaH~LfPK~~F~Dfi~rVEkLG~kk~Vk~~lre 157 (244)
||-||-|+. +|+|-+ -|...+-|.+|++.=..=-..|=++=+++.|-..|.+.-.+..|..+|.-
T Consensus 116 GLtYLnR~Y--~i~fgd~nikdlmlf~pdf~Gkn~s~LD~LI~lG~s~~~~Lk~~n~~~~y~~~la~~tg~~~L~~fLey 193 (737)
T PF07580_consen 116 GLTYLNRWY--NIKFGDTNIKDLMLFKPDFFGKNVSVLDRLIELGSSGENNLKGKNNVDTYNEVLAKNTGKGDLFDFLEY 193 (737)
T ss_pred HHHHHHHHh--CCCcCcccHHHhHhhCccccCCCccHHHHHHHhcccccccccccCcHHHHHHHHhhccCchhHHHHHHH
Confidence 899999875 444421 24488889999998877778999999999999999999999999999999
Q ss_pred HHHHhhcCCCCCC-CcCCcccCCCCCCCCCCccccccCCCCCCCCCCCCCCCCChhHHHHHHHHHhhhcchhHHHHHHHH
Q 035848 158 LRDRVANGGDPTK-LHEAAVEHDGPVDEQAPAEAMSSERQPHQQDPASNVHAADDFNDLFNKVYRTATEVSIFSNLILRL 236 (244)
Q Consensus 158 lR~~~~~G~d~~~-l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~ 236 (244)
.|.......|+.. +.+.+. +.-.|.+.+.++ +.+--..||++.+.-..+.++||-|
T Consensus 194 ~rklft~~~d~ndWFk~~tk---~yIvE~~S~~~e--------------------~~~k~~~vyd~l~~~~~~~~mILPL 250 (737)
T PF07580_consen 194 NRKLFTPDKDNNDWFKDATK---AYIVEKKSTIPE--------------------VKNKQYRVYDRLTNPSKYRKMILPL 250 (737)
T ss_pred HHHhcCCCCCHHHHHHHhCc---eEEEecCCCchh--------------------hhhcceehhhhcCCcchhhcccccc
Confidence 9986655555543 222222 222222222111 1111267888888777888888766
Q ss_pred H
Q 035848 237 F 237 (244)
Q Consensus 237 ~ 237 (244)
+
T Consensus 251 L 251 (737)
T PF07580_consen 251 L 251 (737)
T ss_pred c
Confidence 4
No 43
>KOG0584 consensus Serine/threonine protein kinase [General function prediction only]
Probab=21.42 E-value=48 Score=34.68 Aligned_cols=65 Identities=18% Similarity=0.289 Sum_probs=49.5
Q ss_pred HHHHHHHHHHh----------ccCCCCCHHHHHHHHHHhhcchHHHHHHHHH--HHHhhcCCCCCCCcCCcccCCCCC
Q 035848 117 HLIGLYSEWHS----------HLLPYYSFDHFVSKVEQVAASRRVKMCIRDL--RDRVANGGDPTKLHEAAVEHDGPV 182 (244)
Q Consensus 117 ~LL~~YQ~WaH----------~LfPK~~F~Dfi~rVEkLG~kk~Vk~~lrel--R~~~~~G~d~~~l~e~~~~~~~~~ 182 (244)
+||++|..|-. .||+..+++.+..+..++-=| .+|.|=|.+ =+.+.-+-|||.+|-|..-+-||-
T Consensus 102 NIirfy~SW~d~~n~~in~iTEL~TSGtLr~Y~kk~~~vn~k-aik~W~RQILkGL~yLHs~~PPIIHRDLKCDNIFi 178 (632)
T KOG0584|consen 102 NIIRFYDSWVDTDNKTINFITELFTSGTLREYRKKHRRVNIK-AIKSWCRQILKGLVYLHSQDPPIIHRDLKCDNIFV 178 (632)
T ss_pred ceeeeeeheecCCCceeeeeeecccCCcHHHHHHHhccCCHH-HHHHHHHHHHHHhhhhhcCCCCccccccccceEEE
Confidence 57899999975 489999999999998877554 555554444 223455678999999999888884
No 44
>COG3946 VirJ Type IV secretory pathway, VirJ component [Intracellular trafficking and secretion]
Probab=20.91 E-value=64 Score=32.55 Aligned_cols=28 Identities=39% Similarity=0.713 Sum_probs=20.7
Q ss_pred CchHHHHHHHHHHHHH-HHhc--cCCCCCHH
Q 035848 109 GHEVSDLGHLIGLYSE-WHSH--LLPYYSFD 136 (244)
Q Consensus 109 GHE~~DL~~LL~~YQ~-WaH~--LfPK~~F~ 136 (244)
-.-..||.+|+++|++ |.-. +.--|+|.
T Consensus 306 e~~a~Dl~r~i~~y~~~w~~~~~~liGySfG 336 (456)
T COG3946 306 EQIAADLSRLIRFYARRWGAKRVLLIGYSFG 336 (456)
T ss_pred HHHHHHHHHHHHHHHHhhCcceEEEEeeccc
Confidence 3347899999999998 9753 44566664
No 45
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=20.54 E-value=22 Score=22.40 Aligned_cols=18 Identities=56% Similarity=1.385 Sum_probs=10.1
Q ss_pred CcccccCCC-----CccCCCCCC
Q 035848 9 TGCFKCGRP-----GHWSRDCPS 26 (244)
Q Consensus 9 ~~Cy~CG~~-----GHwardCp~ 26 (244)
.-|-+||-+ +-|+|-||.
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~ 26 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPS 26 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESS
T ss_pred cccCcCCccccCCCCcCEeECCC
Confidence 468889875 458888875
Done!