Query 012298
Match_columns 466
No_of_seqs 33 out of 35
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 01:09:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012298hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13696 zf-CCHC_2: Zinc knuck 94.3 0.011 2.4E-07 42.5 -0.2 20 86-105 7-26 (32)
2 cd02395 SF1_like-KH Splicing f 93.9 0.027 5.8E-07 49.4 1.3 46 132-177 24-95 (120)
3 PF00098 zf-CCHC: Zinc knuckle 93.5 0.036 7.7E-07 34.9 1.0 17 89-105 2-18 (18)
4 cd02393 PNPase_KH Polynucleoti 86.1 0.34 7.5E-06 37.3 1.0 36 126-161 12-50 (61)
5 cd02394 vigilin_like_KH K homo 85.4 0.55 1.2E-05 35.1 1.8 34 126-159 10-50 (62)
6 smart00322 KH K homology RNA-b 85.2 0.52 1.1E-05 33.4 1.5 41 132-173 21-66 (69)
7 PF00013 KH_1: KH domain syndr 85.1 0.34 7.4E-06 36.0 0.5 34 125-158 9-48 (60)
8 PRK13763 putative RNA-processi 84.4 0.69 1.5E-05 42.6 2.3 44 132-176 113-156 (180)
9 TIGR03665 arCOG04150 arCOG0415 83.1 0.7 1.5E-05 42.2 1.8 51 126-176 8-64 (172)
10 PF13917 zf-CCHC_3: Zinc knuck 82.5 0.38 8.3E-06 36.3 -0.1 18 88-105 5-22 (42)
11 PF13014 KH_3: KH domain 80.7 1.2 2.7E-05 31.7 2.0 20 132-151 9-28 (43)
12 TIGR03665 arCOG04150 arCOG0415 80.1 0.97 2.1E-05 41.3 1.6 44 132-176 107-150 (172)
13 cd00105 KH-I K homology RNA-bi 78.7 1.7 3.7E-05 31.8 2.2 28 132-159 18-52 (64)
14 KOG2191 RNA-binding protein NO 74.2 2.8 6E-05 44.0 3.1 45 132-177 57-107 (402)
15 cd02396 PCBP_like_KH K homolog 71.4 2.6 5.6E-05 32.3 1.6 43 132-175 18-61 (65)
16 smart00343 ZnF_C2HC zinc finge 68.1 2.5 5.4E-05 27.7 0.8 19 89-107 1-19 (26)
17 PTZ00368 universal minicircle 67.4 2 4.4E-05 37.6 0.3 20 87-106 103-122 (148)
18 PF12353 eIF3g: Eukaryotic tra 66.0 2 4.4E-05 38.3 0.1 17 88-105 107-123 (128)
19 PTZ00368 universal minicircle 64.5 2.6 5.7E-05 36.9 0.5 19 88-106 1-19 (148)
20 TIGR02696 pppGpp_PNP guanosine 62.3 3.7 7.9E-05 46.0 1.2 50 127-176 589-641 (719)
21 PF07798 DUF1640: Protein of u 61.4 46 0.00099 30.5 7.9 64 317-380 85-155 (177)
22 PRK13763 putative RNA-processi 60.2 5.6 0.00012 36.7 1.8 51 126-176 13-70 (180)
23 KOG0119 Splicing factor 1/bran 58.7 3.4 7.4E-05 45.0 0.2 44 55-106 261-304 (554)
24 PF10154 DUF2362: Uncharacteri 54.4 46 0.00099 36.4 7.6 68 315-382 103-197 (510)
25 COG5082 AIR1 Arginine methyltr 54.3 5.4 0.00012 38.5 0.8 18 88-105 98-116 (190)
26 PF10668 Phage_terminase: Phag 48.7 10 0.00023 30.6 1.4 22 1-23 1-22 (60)
27 TIGR03591 polynuc_phos polyrib 47.9 9.6 0.00021 42.0 1.5 49 127-175 562-613 (684)
28 KOG4602 Nanos and related prot 41.7 11 0.00025 38.5 0.8 25 88-112 269-296 (318)
29 PF14392 zf-CCHC_4: Zinc knuck 41.6 10 0.00022 28.4 0.4 18 88-105 32-49 (49)
30 PF12037 DUF3523: Domain of un 41.5 1.7E+02 0.0036 30.0 8.8 75 294-370 26-120 (276)
31 KOG0119 Splicing factor 1/bran 38.6 16 0.00035 40.0 1.5 46 132-177 162-230 (554)
32 PF13801 Metal_resist: Heavy-m 38.3 82 0.0018 24.9 5.1 45 326-381 33-77 (125)
33 PF11931 DUF3449: Domain of un 38.2 12 0.00027 36.1 0.5 47 43-97 65-111 (196)
34 COG5222 Uncharacterized conser 36.2 11 0.00025 39.4 -0.1 23 86-108 175-197 (427)
35 PF13734 Inhibitor_I69: Spi pr 35.1 19 0.00042 31.1 1.1 12 151-162 51-62 (96)
36 PF15288 zf-CCHC_6: Zinc knuck 34.6 18 0.00038 27.6 0.7 18 88-105 2-21 (40)
37 PF09731 Mitofilin: Mitochondr 32.5 3.6E+02 0.0078 28.6 10.0 22 318-339 246-267 (582)
38 COG5082 AIR1 Arginine methyltr 32.0 19 0.00041 34.9 0.6 24 82-105 55-78 (190)
39 KOG4400 E3 ubiquitin ligase in 30.8 19 0.00042 34.4 0.5 18 89-106 145-162 (261)
40 PRK04163 exosome complex RNA-b 30.6 30 0.00065 33.3 1.7 47 127-173 156-205 (235)
41 PLN00207 polyribonucleotide nu 30.4 31 0.00068 39.8 2.1 50 126-175 695-748 (891)
42 KOG0122 Translation initiation 27.1 17 0.00037 36.9 -0.6 53 45-105 71-136 (270)
43 PF12925 APP_E2: E2 domain of 25.2 4E+02 0.0087 26.1 8.1 65 316-380 27-98 (193)
44 KOG2814 Transcription coactiva 24.9 39 0.00085 35.4 1.5 54 126-179 62-127 (345)
45 PF07795 DUF1635: Protein of u 24.3 7.2E+02 0.016 24.8 10.4 38 319-357 1-38 (214)
46 KOG2190 PolyC-binding proteins 23.7 55 0.0012 35.3 2.3 44 132-175 156-199 (485)
47 KOG0335 ATP-dependent RNA heli 22.1 49 0.0011 36.0 1.6 65 89-162 5-70 (482)
48 KOG0742 AAA+-type ATPase [Post 22.1 9E+02 0.019 27.3 10.8 32 313-344 87-118 (630)
49 KOG1588 RNA-binding protein Sa 21.6 37 0.0008 34.4 0.5 19 133-151 117-135 (259)
50 KOG3915 Transcription regulato 20.2 5.7E+02 0.012 28.8 8.9 56 316-371 499-557 (641)
No 1
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=94.32 E-value=0.011 Score=42.55 Aligned_cols=20 Identities=40% Similarity=1.169 Sum_probs=18.5
Q ss_pred hhhhHhhcCCCCccccCCCC
Q 012298 86 EEMICKICGESGHFTQGCPS 105 (466)
Q Consensus 86 eem~ckicge~ghf~qgcp~ 105 (466)
+..+|.+|+..|||-+-||.
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCCEeecCCCCCccHhHCCC
Confidence 45799999999999999998
No 2
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=93.89 E-value=0.027 Score=49.44 Aligned_cols=46 Identities=22% Similarity=0.503 Sum_probs=41.8
Q ss_pred hHHHHHHhhhccccccccccc------------------------eEEeccCc--ceeeecchhhHHHHHHh
Q 012298 132 TEKVIQRIEKDISCKIKMDEK------------------------FIIVSGKD--RLILSKGVDAVHKIIKE 177 (466)
Q Consensus 132 te~vi~~iEkd~gckikm~ek------------------------f~~vsgkD--Rl~l~kgvdaVhk~i~e 177 (466)
.+++|.+||+++||+|-+.++ .|.|++.| --.|.+++..|..|++.
T Consensus 24 gG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~~ 95 (120)
T cd02395 24 RGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLKP 95 (120)
T ss_pred CChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhcc
Confidence 789999999999999999875 79999999 89999999999998864
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=93.49 E-value=0.036 Score=34.92 Aligned_cols=17 Identities=47% Similarity=1.183 Sum_probs=15.6
Q ss_pred hHhhcCCCCccccCCCC
Q 012298 89 ICKICGESGHFTQGCPS 105 (466)
Q Consensus 89 ~ckicge~ghf~qgcp~ 105 (466)
+|-.||+.||++.-||.
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 58899999999999995
No 4
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=86.07 E-value=0.34 Score=37.35 Aligned_cols=36 Identities=19% Similarity=0.500 Sum_probs=27.5
Q ss_pred hhhhhh--hHHHHHHhhhccccccccccc-eEEeccCcc
Q 012298 126 HVRALF--TEKVIQRIEKDISCKIKMDEK-FIIVSGKDR 161 (466)
Q Consensus 126 ~vr~lf--te~vi~~iEkd~gckikm~ek-f~~vsgkDR 161 (466)
.+..+. ++.+|..|+..+||+|.+++. .|.|+|.|.
T Consensus 12 ~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~~~ 50 (61)
T cd02393 12 KIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDK 50 (61)
T ss_pred heeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCH
Confidence 344444 789999999999999999873 566666654
No 5
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.39 E-value=0.55 Score=35.07 Aligned_cols=34 Identities=21% Similarity=0.386 Sum_probs=27.7
Q ss_pred hhhhhh--hHHHHHHhhhcccccccccc-----ceEEeccC
Q 012298 126 HVRALF--TEKVIQRIEKDISCKIKMDE-----KFIIVSGK 159 (466)
Q Consensus 126 ~vr~lf--te~vi~~iEkd~gckikm~e-----kf~~vsgk 159 (466)
.+..++ .+..|..|++++||+|.+.. .+|.|+|+
T Consensus 10 ~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~ 50 (62)
T cd02394 10 LHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP 50 (62)
T ss_pred HhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC
Confidence 345555 67899999999999999977 57888887
No 6
>smart00322 KH K homology RNA-binding domain.
Probab=85.18 E-value=0.52 Score=33.41 Aligned_cols=41 Identities=20% Similarity=0.390 Sum_probs=30.3
Q ss_pred hHHHHHHhhhcccccccccc-----ceEEeccCcceeeecchhhHHH
Q 012298 132 TEKVIQRIEKDISCKIKMDE-----KFIIVSGKDRLILSKGVDAVHK 173 (466)
Q Consensus 132 te~vi~~iEkd~gckikm~e-----kf~~vsgkDRl~l~kgvdaVhk 173 (466)
.++.|+.|++.+||+|.+.. ..+.|.|. ..-+....+++.+
T Consensus 21 ~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~ 66 (69)
T smart00322 21 GGSTIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILE 66 (69)
T ss_pred CchHHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHH
Confidence 67899999999999998877 67888887 3444444444443
No 7
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=85.05 E-value=0.34 Score=35.96 Aligned_cols=34 Identities=24% Similarity=0.465 Sum_probs=26.4
Q ss_pred chhhhhh--hHHHHHHhhhccccccccccc----eEEecc
Q 012298 125 KHVRALF--TEKVIQRIEKDISCKIKMDEK----FIIVSG 158 (466)
Q Consensus 125 k~vr~lf--te~vi~~iEkd~gckikm~ek----f~~vsg 158 (466)
..+..++ .+..|..||+++||+|.+.++ .|.|+|
T Consensus 9 ~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G 48 (60)
T PF00013_consen 9 SLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG 48 (60)
T ss_dssp HHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE
T ss_pred HHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe
Confidence 3444555 788999999999999999874 666666
No 8
>PRK13763 putative RNA-processing protein; Provisional
Probab=84.38 E-value=0.69 Score=42.62 Aligned_cols=44 Identities=20% Similarity=0.222 Sum_probs=38.6
Q ss_pred hHHHHHHhhhccccccccccceEEeccCcceeeecchhhHHHHHH
Q 012298 132 TEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIK 176 (466)
Q Consensus 132 te~vi~~iEkd~gckikm~ekf~~vsgkDRl~l~kgvdaVhk~i~ 176 (466)
.+++|..||..+||+|-++++.|.|.| |-.-+....++|..||+
T Consensus 113 ~G~~~k~ie~~t~~~i~i~~~~v~i~G-~~~~~~~A~~~I~~li~ 156 (180)
T PRK13763 113 GGKTRRIIEELTGVDISVYGKTVAIIG-DPEQVEIAREAIEMLIE 156 (180)
T ss_pred CcHHHHHHHHHHCcEEEEcCCEEEEEe-CHHHHHHHHHHHHHHHc
Confidence 678999999999999999999999998 77777777888888883
No 9
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=83.11 E-value=0.7 Score=42.19 Aligned_cols=51 Identities=20% Similarity=0.326 Sum_probs=43.7
Q ss_pred hhhhhh--hHHHHHHhhhccccccccccc--eEEe--ccCcceeeecchhhHHHHHH
Q 012298 126 HVRALF--TEKVIQRIEKDISCKIKMDEK--FIIV--SGKDRLILSKGVDAVHKIIK 176 (466)
Q Consensus 126 ~vr~lf--te~vi~~iEkd~gckikm~ek--f~~v--sgkDRl~l~kgvdaVhk~i~ 176 (466)
.|.++. ++++|..|++.+||+|.|+++ -|.| .+.|-..+.|+.+.|..+..
T Consensus 8 kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~ 64 (172)
T TIGR03665 8 RIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred HhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 455555 799999999999999999985 8888 88999999999999988654
No 10
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=82.45 E-value=0.38 Score=36.29 Aligned_cols=18 Identities=44% Similarity=1.224 Sum_probs=16.9
Q ss_pred hhHhhcCCCCccccCCCC
Q 012298 88 MICKICGESGHFTQGCPS 105 (466)
Q Consensus 88 m~ckicge~ghf~qgcp~ 105 (466)
-+|.-||+.||+|-=||.
T Consensus 5 ~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 5 VRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CcCcccCCCCcchhhCCC
Confidence 479999999999999997
No 11
>PF13014 KH_3: KH domain
Probab=80.70 E-value=1.2 Score=31.67 Aligned_cols=20 Identities=20% Similarity=0.380 Sum_probs=18.2
Q ss_pred hHHHHHHhhhcccccccccc
Q 012298 132 TEKVIQRIEKDISCKIKMDE 151 (466)
Q Consensus 132 te~vi~~iEkd~gckikm~e 151 (466)
.+.+|..|++++||+|++..
T Consensus 9 ~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 9 GGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CChHHHHHHHHhCcEEEECC
Confidence 46889999999999999887
No 12
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=80.14 E-value=0.97 Score=41.30 Aligned_cols=44 Identities=20% Similarity=0.191 Sum_probs=38.2
Q ss_pred hHHHHHHhhhccccccccccceEEeccCcceeeecchhhHHHHHH
Q 012298 132 TEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKIIK 176 (466)
Q Consensus 132 te~vi~~iEkd~gckikm~ekf~~vsgkDRl~l~kgvdaVhk~i~ 176 (466)
.+++|..||..+||+|-+.++.|.|+| +---+.....+|..||+
T Consensus 107 ~G~t~~~ie~~t~~~i~i~~~~v~i~G-~~~~~~~A~~~i~~li~ 150 (172)
T TIGR03665 107 GGKTRRIIEELTGVSISVYGKTVGIIG-DPEQVQIAREAIEMLIE 150 (172)
T ss_pred CcHHHHHHHHHHCCeEEEcCCEEEEEC-CHHHHHHHHHHHHHHHc
Confidence 678999999999999999999999999 66666677778888883
No 13
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=78.67 E-value=1.7 Score=31.79 Aligned_cols=28 Identities=21% Similarity=0.507 Sum_probs=23.0
Q ss_pred hHHHHHHhhhccccccccccc-------eEEeccC
Q 012298 132 TEKVIQRIEKDISCKIKMDEK-------FIIVSGK 159 (466)
Q Consensus 132 te~vi~~iEkd~gckikm~ek-------f~~vsgk 159 (466)
.+.+|+.|+..+||+|.+.+. .|.|+|.
T Consensus 18 ~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~ 52 (64)
T cd00105 18 GGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT 52 (64)
T ss_pred CCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC
Confidence 789999999999999999763 4555665
No 14
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=74.22 E-value=2.8 Score=43.97 Aligned_cols=45 Identities=27% Similarity=0.559 Sum_probs=35.0
Q ss_pred hHHHHHHhhhccccccccccc--eEEeccCcceeeecc----hhhHHHHHHh
Q 012298 132 TEKVIQRIEKDISCKIKMDEK--FIIVSGKDRLILSKG----VDAVHKIIKE 177 (466)
Q Consensus 132 te~vi~~iEkd~gckikm~ek--f~~vsgkDRl~l~kg----vdaVhk~i~e 177 (466)
++.+|-++.||+||+|||--. |+ -.-.+|++|-+| +-|||.+|.+
T Consensus 57 GG~ti~~lqk~tgariklSks~dfy-PGTTeRvcli~Gt~eai~av~efI~d 107 (402)
T KOG2191|consen 57 GGQTIVQLQKETGARIKLSKSKDFY-PGTTERVCLIQGTVEALNAVHEFIAD 107 (402)
T ss_pred chHHHHHHHhccCcEEEeccccccC-CCccceEEEEeccHHHHHHHHHHHHH
Confidence 688999999999999999753 32 233588888775 6788888764
No 15
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=71.44 E-value=2.6 Score=32.34 Aligned_cols=43 Identities=21% Similarity=0.426 Sum_probs=32.0
Q ss_pred hHHHHHHhhhccccccccccceEEeccCcceeeecc-hhhHHHHH
Q 012298 132 TEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKG-VDAVHKII 175 (466)
Q Consensus 132 te~vi~~iEkd~gckikm~ekf~~vsgkDRl~l~kg-vdaVhk~i 175 (466)
.+..|..|+.++||+|.+.+... .+..+|++.-.| +++|.+.+
T Consensus 18 ~G~~i~~i~~~tga~I~i~~~~~-~~~~~r~v~I~G~~~~v~~A~ 61 (65)
T cd02396 18 GGSTIKEIREETGAKIRVSKSVL-PGSTERVVTISGKPSAVQKAL 61 (65)
T ss_pred CcHHHHHHHHHHCCEEEEcCCCC-CCCCceEEEEEeCHHHHHHHH
Confidence 67899999999999999987654 567777766554 35555543
No 16
>smart00343 ZnF_C2HC zinc finger.
Probab=68.07 E-value=2.5 Score=27.70 Aligned_cols=19 Identities=37% Similarity=0.964 Sum_probs=16.2
Q ss_pred hHhhcCCCCccccCCCCcc
Q 012298 89 ICKICGESGHFTQGCPSTL 107 (466)
Q Consensus 89 ~ckicge~ghf~qgcp~tL 107 (466)
.|..||..||+.+-||...
T Consensus 1 ~C~~CG~~GH~~~~C~~~~ 19 (26)
T smart00343 1 KCYNCGKEGHIARDCPKXX 19 (26)
T ss_pred CCccCCCCCcchhhCCccc
Confidence 3889999999999999543
No 17
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=67.39 E-value=2 Score=37.61 Aligned_cols=20 Identities=35% Similarity=0.988 Sum_probs=14.9
Q ss_pred hhhHhhcCCCCccccCCCCc
Q 012298 87 EMICKICGESGHFTQGCPST 106 (466)
Q Consensus 87 em~ckicge~ghf~qgcp~t 106 (466)
..+|.+||+.||++.-||..
T Consensus 103 ~~~C~~Cg~~gH~~~~C~~~ 122 (148)
T PTZ00368 103 RRACYNCGGEGHISRDCPNA 122 (148)
T ss_pred chhhcccCcCCcchhcCCCc
Confidence 45788888888888888764
No 18
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=65.98 E-value=2 Score=38.26 Aligned_cols=17 Identities=41% Similarity=1.116 Sum_probs=15.5
Q ss_pred hhHhhcCCCCccccCCCC
Q 012298 88 MICKICGESGHFTQGCPS 105 (466)
Q Consensus 88 m~ckicge~ghf~qgcp~ 105 (466)
+.|.||+ -.|||-=||-
T Consensus 107 v~CR~Ck-GdH~T~~CPy 123 (128)
T PF12353_consen 107 VKCRICK-GDHWTSKCPY 123 (128)
T ss_pred EEeCCCC-CCcccccCCc
Confidence 7899997 8999999994
No 19
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=64.50 E-value=2.6 Score=36.88 Aligned_cols=19 Identities=42% Similarity=1.129 Sum_probs=17.7
Q ss_pred hhHhhcCCCCccccCCCCc
Q 012298 88 MICKICGESGHFTQGCPST 106 (466)
Q Consensus 88 m~ckicge~ghf~qgcp~t 106 (466)
|+|-.||+.||+..-||..
T Consensus 1 ~~C~~C~~~GH~~~~c~~~ 19 (148)
T PTZ00368 1 MVCYRCGGVGHQSRECPNS 19 (148)
T ss_pred CcCCCCCCCCcCcccCcCC
Confidence 8999999999999999973
No 20
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=62.25 E-value=3.7 Score=46.01 Aligned_cols=50 Identities=12% Similarity=0.305 Sum_probs=43.7
Q ss_pred hhhhh--hHHHHHHhhhccccccccccc-eEEeccCcceeeecchhhHHHHHH
Q 012298 127 VRALF--TEKVIQRIEKDISCKIKMDEK-FIIVSGKDRLILSKGVDAVHKIIK 176 (466)
Q Consensus 127 vr~lf--te~vi~~iEkd~gckikm~ek-f~~vsgkDRl~l~kgvdaVhk~i~ 176 (466)
+++++ ++++|..|..++||+|.+++. -|.|+++|.-.+.|..+.|..++.
T Consensus 589 i~~vIG~gGk~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 589 IGEVIGPKGKMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred hhheeCCCcHhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 45555 899999999999999999885 888999999999999988888775
No 21
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=61.35 E-value=46 Score=30.53 Aligned_cols=64 Identities=16% Similarity=0.185 Sum_probs=44.2
Q ss_pred CCCcHHHHHHHHHHHHHHhhhhcchhh-------hHhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Q 012298 317 FPKTLDELELDYTREAMELGRIRDKEE-------DEENYKHRETIREMRESYMKKLTQVRAMHAKQWEEFL 380 (466)
Q Consensus 317 ~PqTlEeLE~eF~dEameL~KerddeE-------DeENaRHRE~IreIne~Y~eKL~aLRa~hAkrrEEFL 380 (466)
|-.-+|.|++++.+||.+|-.+.--+= -+|...+.-+|.+++..--..++.||+.-+.-+-+-|
T Consensus 85 L~~eie~l~~~L~~ei~~l~a~~klD~n~eK~~~r~e~~~~~~ki~e~~~ki~~ei~~lr~~iE~~K~~~l 155 (177)
T PF07798_consen 85 LQREIEKLRQELREEINKLRAEVKLDLNLEKGRIREEQAKQELKIQELNNKIDTEIANLRTEIESLKWDTL 155 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445678899999999988776443221 2344555557888888888899999988776444433
No 22
>PRK13763 putative RNA-processing protein; Provisional
Probab=60.19 E-value=5.6 Score=36.74 Aligned_cols=51 Identities=25% Similarity=0.423 Sum_probs=41.5
Q ss_pred hhhhhh--hHHHHHHhhhccccccccccc--eEEec---cCcceeeecchhhHHHHHH
Q 012298 126 HVRALF--TEKVIQRIEKDISCKIKMDEK--FIIVS---GKDRLILSKGVDAVHKIIK 176 (466)
Q Consensus 126 ~vr~lf--te~vi~~iEkd~gckikm~ek--f~~vs---gkDRl~l~kgvdaVhk~i~ 176 (466)
.+..+. .+++|..|++.+||+|.|++. -|.|. +.|...+-|+.+.|..++.
T Consensus 13 kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 13 RIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred HhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 344554 689999999999999999986 55565 6799999999999888764
No 23
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=58.69 E-value=3.4 Score=44.97 Aligned_cols=44 Identities=27% Similarity=0.537 Sum_probs=34.4
Q ss_pred CCCCCcccchhhhHHHHhhHHHHHhhhhhhhhhhhHhhcCCCCccccCCCCc
Q 012298 55 NAVPTDFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESGHFTQGCPST 106 (466)
Q Consensus 55 navptdftsreakvweak~ka~ernwkkrkeeem~ckicge~ghf~qgcp~t 106 (466)
|+++|..-+-+-|-|+--.. --||+. .|+|||--|||+-+|+.-
T Consensus 261 ~~~c~~cg~~~H~q~~cp~r--~~~~~n------~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 261 NRACRNCGSTGHKQYDCPGR--IPNTTN------VCKICGPLGHISIDCKVN 304 (554)
T ss_pred cccccccCCCccccccCCcc--cccccc------cccccCCcccccccCCCc
Confidence 47777778888888876655 347765 799999999999999864
No 24
>PF10154 DUF2362: Uncharacterized conserved protein (DUF2362); InterPro: IPR019311 This is a family of proteins conserved from nematodes to humans. The function is not known.
Probab=54.40 E-value=46 Score=36.37 Aligned_cols=68 Identities=21% Similarity=0.340 Sum_probs=53.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHhhhhcchhh---------------------------hHhhhhhHHHHHHHHHHHHHHHHH
Q 012298 315 PAFPKTLDELELDYTREAMELGRIRDKEE---------------------------DEENYKHRETIREMRESYMKKLTQ 367 (466)
Q Consensus 315 ~~~PqTlEeLE~eF~dEameL~KerddeE---------------------------DeENaRHRE~IreIne~Y~eKL~a 367 (466)
++.-.||=.||..|...+.+|.+.+|.+= ..-.++|-|.++.|..+|...|.+
T Consensus 103 SpaletLL~LE~~Ya~~vseli~~Rd~el~kl~~rq~~Eme~a~q~Lg~~ltd~dIN~laaqH~Ee~q~ie~kw~seL~~ 182 (510)
T PF10154_consen 103 SPALETLLQLEHNYAKAVSELIQARDQELKKLQERQTEEMEKAMQKLGISLTDRDINHLAAQHFEEQQRIESKWSSELKA 182 (510)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456777899999999999999998652 133578999999999999999999
Q ss_pred HHHHhhhhHHHHHhH
Q 012298 368 VRAMHAKQWEEFLQL 382 (466)
Q Consensus 368 LRa~hAkrrEEFL~~ 382 (466)
|+..|-+.--+|+..
T Consensus 183 L~~~QK~EYRewV~~ 197 (510)
T PF10154_consen 183 LKETQKQEYREWVMR 197 (510)
T ss_pred HHHHHHHHHHHHHHH
Confidence 988876665566644
No 25
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=54.32 E-value=5.4 Score=38.49 Aligned_cols=18 Identities=50% Similarity=1.208 Sum_probs=13.3
Q ss_pred hhHhhcCCCCccccCC-CC
Q 012298 88 MICKICGESGHFTQGC-PS 105 (466)
Q Consensus 88 m~ckicge~ghf~qgc-p~ 105 (466)
-+|.+||+-||+.--| |+
T Consensus 98 ~~C~~Cg~~GH~~~dC~P~ 116 (190)
T COG5082 98 KKCYNCGETGHLSRDCNPS 116 (190)
T ss_pred cccccccccCccccccCcc
Confidence 4677888888888878 44
No 26
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=48.67 E-value=10 Score=30.57 Aligned_cols=22 Identities=45% Similarity=0.889 Sum_probs=18.3
Q ss_pred CCCCCCCCCChhHHHHHHhhcCC
Q 012298 1 MAKRPDPDDDDDFSELYKEYTGP 23 (466)
Q Consensus 1 ma~~~~pd~dd~f~evykeytgp 23 (466)
||+..+|+.|--| |||+++.|=
T Consensus 1 M~r~Rsp~rdkA~-e~y~~~~g~ 22 (60)
T PF10668_consen 1 MARKRSPNRDKAF-EIYKESNGK 22 (60)
T ss_pred CCCCCCcCHHHHH-HHHHHhCCC
Confidence 9999999876666 799998774
No 27
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=47.92 E-value=9.6 Score=42.00 Aligned_cols=49 Identities=18% Similarity=0.386 Sum_probs=37.9
Q ss_pred hhhhh--hHHHHHHhhhccccccccccc-eEEeccCcceeeecchhhHHHHH
Q 012298 127 VRALF--TEKVIQRIEKDISCKIKMDEK-FIIVSGKDRLILSKGVDAVHKII 175 (466)
Q Consensus 127 vr~lf--te~vi~~iEkd~gckikm~ek-f~~vsgkDRl~l~kgvdaVhk~i 175 (466)
|.++. ++++|..|+.++||+|-+++. -|.|++.|...+.|...-+..++
T Consensus 562 I~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~ 613 (684)
T TIGR03591 562 IRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGIT 613 (684)
T ss_pred HHhhcCCCcHHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhh
Confidence 44555 899999999999999999864 78888888777666655555543
No 28
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=41.69 E-value=11 Score=38.50 Aligned_cols=25 Identities=36% Similarity=0.968 Sum_probs=20.9
Q ss_pred hhHhhcCCCC---ccccCCCCccccCCc
Q 012298 88 MICKICGESG---HFTQGCPSTLGANRK 112 (466)
Q Consensus 88 m~ckicge~g---hf~qgcp~tLGanrk 112 (466)
|.|.|||-+| |-..=||.+.|.--.
T Consensus 269 YVCPiCGATgDnAHTiKyCPl~~~~~~s 296 (318)
T KOG4602|consen 269 YVCPICGATGDNAHTIKYCPLAFGDDTS 296 (318)
T ss_pred hcCccccccCCcccceecccccCCCCcc
Confidence 9999998665 899999999886543
No 29
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=41.64 E-value=10 Score=28.42 Aligned_cols=18 Identities=39% Similarity=0.957 Sum_probs=16.4
Q ss_pred hhHhhcCCCCccccCCCC
Q 012298 88 MICKICGESGHFTQGCPS 105 (466)
Q Consensus 88 m~ckicge~ghf~qgcp~ 105 (466)
.+|..||--||-.+-||.
T Consensus 32 ~~C~~C~~~gH~~~~C~k 49 (49)
T PF14392_consen 32 RFCFHCGRIGHSDKECPK 49 (49)
T ss_pred hhhcCCCCcCcCHhHcCC
Confidence 589999999999999983
No 30
>PF12037 DUF3523: Domain of unknown function (DUF3523); InterPro: IPR021911 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with PF00004 from PFAM. This domain has a conserved LER sequence motif.
Probab=41.55 E-value=1.7e+02 Score=30.01 Aligned_cols=75 Identities=19% Similarity=0.248 Sum_probs=42.3
Q ss_pred CCCCCccccCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHHHhhhhcchhhhHhhhhh--------------------HHH
Q 012298 294 NDGWDIERRGSDMQSGHQFEYPAFPKTLDELELDYTREAMELGRIRDKEEDEENYKH--------------------RET 353 (466)
Q Consensus 294 ~d~wd~Er~~sDm~~~~~fE~~~~PqTlEeLE~eF~dEameL~KerddeEDeENaRH--------------------RE~ 353 (466)
..++|++.-+--... -.+.++.|..=+-||+-=+.|.++.+..+.+....|-+.. .-.
T Consensus 26 ~~~FDP~aLERaAkA--lrel~~S~~Ak~afel~k~QE~TkQ~E~~ak~~e~ea~~~q~~~e~~rv~~EE~Rkt~~~q~q 103 (276)
T PF12037_consen 26 ASGFDPEALERAAKA--LRELNSSPHAKKAFELMKKQEETKQAELQAKIAEYEAAQAQAEIERQRVEAEERRKTLQQQTQ 103 (276)
T ss_pred cCCCCcHHHHHHHHH--HHHHhcChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455443323333 4556777888888888878887776665555444443333 333
Q ss_pred HHHHHHHHHHHHHHHHH
Q 012298 354 IREMRESYMKKLTQVRA 370 (466)
Q Consensus 354 IreIne~Y~eKL~aLRa 370 (466)
....+.+|+.+|+.-|-
T Consensus 104 ~~~q~aqY~D~LaRkR~ 120 (276)
T PF12037_consen 104 QKQQRAQYEDELARKRY 120 (276)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 44455566666665554
No 31
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=38.58 E-value=16 Score=40.01 Aligned_cols=46 Identities=17% Similarity=0.395 Sum_probs=36.4
Q ss_pred hHHHHHHhhhccccccccccc-----------------------eEEeccCcceeeecchhhHHHHHHh
Q 012298 132 TEKVIQRIEKDISCKIKMDEK-----------------------FIIVSGKDRLILSKGVDAVHKIIKE 177 (466)
Q Consensus 132 te~vi~~iEkd~gckikm~ek-----------------------f~~vsgkDRl~l~kgvdaVhk~i~e 177 (466)
-+.+..+|||++||||-+-.| ...||+-+--.|.|++..|.+||+.
T Consensus 162 RG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 162 RGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred CccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 567888999999999977552 4456677777788899999999974
No 32
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=38.34 E-value=82 Score=24.87 Aligned_cols=45 Identities=9% Similarity=0.209 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhhhcchhhhHhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHh
Q 012298 326 LDYTREAMELGRIRDKEEDEENYKHRETIREMRESYMKKLTQVRAMHAKQWEEFLQ 381 (466)
Q Consensus 326 ~eF~dEameL~KerddeEDeENaRHRE~IreIne~Y~eKL~aLRa~hAkrrEEFL~ 381 (466)
..+..+...|+.+| ++.|++|...|.+++..||......|.++..
T Consensus 33 ~~~~~~~l~Lt~eQ-----------~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~ 77 (125)
T PF13801_consen 33 HPMLADMLNLTPEQ-----------QAKLRALMDEFRQEMRALRQELRAARQELRA 77 (125)
T ss_dssp HHHHHHHS-TTHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chhhhhhcCCCHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555566666665 4456666666666666666666666666543
No 33
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=38.20 E-value=12 Score=36.07 Aligned_cols=47 Identities=28% Similarity=0.550 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCcccchhhhHHHHhhHHHHHhhhhhhhhhhhHhhcCCCC
Q 012298 43 AGSDEEEEPRDPNAVPTDFTSREAKVWEAKSKATERNWKKRKEEEMICKICGESG 97 (466)
Q Consensus 43 ~~sdeeee~~dpnavptdftsreakvweak~ka~ernwkkrkeeem~ckicge~g 97 (466)
+.+|+++..-+|.-+|-++...-.-.|--|-.-.- -+..|.|||-..
T Consensus 65 ~~~~~~~~~~np~~lPLG~DGkPIPyWLYKLhGL~--------~ey~CEICGN~~ 111 (196)
T PF11931_consen 65 SDDDEEEKIYNPLNLPLGWDGKPIPYWLYKLHGLG--------VEYKCEICGNQS 111 (196)
T ss_dssp -------------------------------------------------------
T ss_pred cccccccccCCcccCCCCCCCCcccHHHHHHhCCC--------CeeeeEeCCCcc
Confidence 34444556678999999999999999998876543 248899999764
No 34
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=36.22 E-value=11 Score=39.37 Aligned_cols=23 Identities=35% Similarity=0.967 Sum_probs=19.5
Q ss_pred hhhhHhhcCCCCccccCCCCccc
Q 012298 86 EEMICKICGESGHFTQGCPSTLG 108 (466)
Q Consensus 86 eem~ckicge~ghf~qgcp~tLG 108 (466)
+-.+|=-||..||.-|.||+---
T Consensus 175 pgY~CyRCGqkgHwIqnCpTN~D 197 (427)
T COG5222 175 PGYVCYRCGQKGHWIQNCPTNQD 197 (427)
T ss_pred CceeEEecCCCCchhhcCCCCCC
Confidence 34689999999999999998543
No 35
>PF13734 Inhibitor_I69: Spi protease inhibitor; PDB: 1PVJ_A 1DKI_D 2UZJ_A 2JTC_A 4D8E_A 4D8I_A 4D8B_A.
Probab=35.09 E-value=19 Score=31.12 Aligned_cols=12 Identities=58% Similarity=1.085 Sum_probs=10.0
Q ss_pred cceEEeccCcce
Q 012298 151 EKFIIVSGKDRL 162 (466)
Q Consensus 151 ekf~~vsgkDRl 162 (466)
.-||||||-||+
T Consensus 51 ~GFVIVSgDdr~ 62 (96)
T PF13734_consen 51 KGFVIVSGDDRM 62 (96)
T ss_dssp S-EEEEESBTTS
T ss_pred CEEEEEECCCCc
Confidence 359999999997
No 36
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=34.63 E-value=18 Score=27.59 Aligned_cols=18 Identities=44% Similarity=1.090 Sum_probs=15.1
Q ss_pred hhHhhcCCCCccc--cCCCC
Q 012298 88 MICKICGESGHFT--QGCPS 105 (466)
Q Consensus 88 m~ckicge~ghf~--qgcp~ 105 (466)
+.|+-||.-||.. .-||.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred ccccccccccccccCccCCC
Confidence 5699999999987 67875
No 37
>PF09731 Mitofilin: Mitochondrial inner membrane protein; InterPro: IPR019133 Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex []. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence (residues 1-43) rich in positive-charged and hydroxylated residues and a membrane anchor domain (residues 47-66). In addition, it has three centrally located coiled coil domains (residues 200-240,280-310 and 400-420) []. ; GO: 0031305 integral to mitochondrial inner membrane
Probab=32.46 E-value=3.6e+02 Score=28.65 Aligned_cols=22 Identities=14% Similarity=0.036 Sum_probs=13.0
Q ss_pred CCcHHHHHHHHHHHHHHhhhhc
Q 012298 318 PKTLDELELDYTREAMELGRIR 339 (466)
Q Consensus 318 PqTlEeLE~eF~dEameL~Ker 339 (466)
.-.+..|-..++.+|..|.+..
T Consensus 246 ~~~~~~~i~~a~~~i~~L~~~l 267 (582)
T PF09731_consen 246 ESDLNSLIAHAKERIDALQKEL 267 (582)
T ss_pred ccccHHHHHHHHHHHHHHHHHH
Confidence 3455666666666666666533
No 38
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=32.00 E-value=19 Score=34.94 Aligned_cols=24 Identities=38% Similarity=0.967 Sum_probs=22.1
Q ss_pred hhhhhhhhHhhcCCCCccccCCCC
Q 012298 82 KRKEEEMICKICGESGHFTQGCPS 105 (466)
Q Consensus 82 krkeeem~ckicge~ghf~qgcp~ 105 (466)
...|+.-.|-+||+.||..+-||.
T Consensus 55 ~~~~~~~~C~nCg~~GH~~~DCP~ 78 (190)
T COG5082 55 AIREENPVCFNCGQNGHLRRDCPH 78 (190)
T ss_pred cccccccccchhcccCcccccCCh
Confidence 678899999999999999999993
No 39
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=30.78 E-value=19 Score=34.43 Aligned_cols=18 Identities=44% Similarity=1.171 Sum_probs=16.4
Q ss_pred hHhhcCCCCccccCCCCc
Q 012298 89 ICKICGESGHFTQGCPST 106 (466)
Q Consensus 89 ~ckicge~ghf~qgcp~t 106 (466)
.|=.||+.|||+-.||..
T Consensus 145 ~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 145 KCYSCGEQGHISDDCPEN 162 (261)
T ss_pred ccCCCCcCCcchhhCCCC
Confidence 499999999999999965
No 40
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=30.57 E-value=30 Score=33.26 Aligned_cols=47 Identities=19% Similarity=0.371 Sum_probs=37.2
Q ss_pred hhhhh--hHHHHHHhhhccccccccccc-eEEeccCcceeeecchhhHHH
Q 012298 127 VRALF--TEKVIQRIEKDISCKIKMDEK-FIIVSGKDRLILSKGVDAVHK 173 (466)
Q Consensus 127 vr~lf--te~vi~~iEkd~gckikm~ek-f~~vsgkDRl~l~kgvdaVhk 173 (466)
++.|+ ++++|..|.+.+||+|-+.+. .|.|++++--.+.+...++..
T Consensus 156 i~~lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~~~~~~~~~a~~~I~~ 205 (235)
T PRK04163 156 VPRVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKK 205 (235)
T ss_pred HHhhcCCCChhHhhhhhhhCcEEEEcCCcEEEEeeCCHHHHHHHHHHHHH
Confidence 44554 578999999999999999865 999999998766666666555
No 41
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=30.39 E-value=31 Score=39.84 Aligned_cols=50 Identities=16% Similarity=0.278 Sum_probs=39.8
Q ss_pred hhhhhh--hHHHHHHhhhccccc-cccccc-eEEeccCcceeeecchhhHHHHH
Q 012298 126 HVRALF--TEKVIQRIEKDISCK-IKMDEK-FIIVSGKDRLILSKGVDAVHKII 175 (466)
Q Consensus 126 ~vr~lf--te~vi~~iEkd~gck-ikm~ek-f~~vsgkDRl~l~kgvdaVhk~i 175 (466)
.|++++ ++++|..|..++|++ |.+++. -|.|.++|..-|.+..+.+..++
T Consensus 695 ki~~vIG~GGktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~ 748 (891)
T PLN00207 695 KVNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISSLT 748 (891)
T ss_pred HHHHHhcCCchhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHHh
Confidence 456666 899999999999999 999886 56788888887777666666655
No 42
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=27.11 E-value=17 Score=36.89 Aligned_cols=53 Identities=30% Similarity=0.595 Sum_probs=31.6
Q ss_pred CCCCCCCCCCCCCCCcccchhhhHHHHhhHHHHHhhhhhhhhh-------------hhHhhcCCCCccccCCCC
Q 012298 45 SDEEEEPRDPNAVPTDFTSREAKVWEAKSKATERNWKKRKEEE-------------MICKICGESGHFTQGCPS 105 (466)
Q Consensus 45 sdeeee~~dpnavptdftsreakvweak~ka~ernwkkrkeee-------------m~ckicge~ghf~qgcp~ 105 (466)
-|+.-+++-|+++-|--|. |. .----|||..-.|.+ |.|.|| .-.|+|--||-
T Consensus 71 G~~~~~~~Gp~~~Tt~v~E-eI------~l~~~~~~~~~~~~~~~~d~~s~~g~~~~~CR~C-~gdHwt~~CPy 136 (270)
T KOG0122|consen 71 GDSKGEPAGPSVATTRVTE-EI------ELRFIRSPTFEEEQDIQEDKASKLGKSIVACRIC-KGDHWTTNCPY 136 (270)
T ss_pred ccccCCCCCCceeeEeccc-ce------eEEeccCcccchhhhhhhcchhhcccceeeeeec-CCCeeeecCCc
Confidence 3455577778877654331 11 011125554333332 689999 78899999993
No 43
>PF12925 APP_E2: E2 domain of amyloid precursor protein; InterPro: IPR024329 Amyloid-beta precursor protein (APP, or A4) is associated with Alzheimer's disease (AD), because one of its breakdown products, amyloid-beta (A-beta), aggregates to form amyloid or senile plaques [, ]. Mutations in APP or in proteins that process APP have been linked with early-onset, familial AD. Individuals with Down's syndrome carry an extra copy of chromosome 21, which contains the APP gene, and almost invariably develop amyloid plaques and Alzheimer's symptoms. APP is important for the neurogenesis and neuronal regeneration, either through the intact protein, or through its many breakdown products []. APP consists of a large N-terminal extracellular region containing heparin-binding and copper-binding sites, a short hydrophobic transmembrane domain, and a short C-terminal intracellular domain. The N-terminal region is similar in structure to cysteine-rich growth factors and appears to function as a cell surface receptor, contributing to neurite growth, neuronal adhesion, axonogenesis and cell mobility []. APP acts as a kinesin I membrane receptor to mediate the axonal transport of beta-secretase and presenilin 1. The N-terminal domain can regulate neurite outgrowth through its binding to heparin and collagen I and IV, which are components of the extracellular matrix. APP is also coupled to apoptosis-inducing pathways, and is involved in copper homeostasis/oxidative stress through copper ion reduction, where copper-metallated APP induces neuronal death []. The C-terminal intracellular domain appears to be involved in transcription regulation through protein-protein interactions. APP can promote transcription activation through binding to APBB1/Tip60, and may bind to the adaptor protein FE65 to transactivate a wide variety of different promoters. APP can be processed by different sets of enzymes: In the non-amyloidogenic (non-plaque-forming) pathway, APP is cleaved by alpha-secretase to yield a soluble N-terminal sAPP-alpha (neuroprotective) and a membrane-bound CTF-alpha. CTF-alpha is broken-down by presenilin-containing gamma-secretase to yield soluble p3 and membrane-bound AICD (nuclear signalling). In the amyloidogenic pathway (plaque-forming), APP is broken down by beta-secretase to yield soluble sAPP-beta and membrane-bound CTF-beta. CTF-beta is broken down by gamma-secretase to yield soluble amyloid-beta and membrane-bound AICD. Amyloid-beta is required for neuronal function, but can aggregate to form amyloid plaques that seem to disrupt brain cells by clogging points of cell-cell contact. The E2 domain is the largest of the conserved domains in the amyloidogenic glycoproteins. The structure of E2 consists of two coiled-coil sub-structures connected through a continuous helix, and bears an unexpected resemblance to the spectrin family of protein structures. E2 can reversibly dimerise in solution, and the dimerisation occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. The high degree of conservation of residues at the putative dimer interface suggests that the E2 dimer observed in the crystal could be physiologically relevant. Heparin sulphate proteoglycans, the putative ligands for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface [].; PDB: 3K6B_A 3K66_A 1TKN_A 3NYL_A 3NYJ_A 3UMH_A 3UMK_A 3UMI_A 3QMK_B 3PMR_B ....
Probab=25.16 E-value=4e+02 Score=26.07 Aligned_cols=65 Identities=12% Similarity=0.204 Sum_probs=51.3
Q ss_pred CCCCcHHHHHHHHHHHHHHhhhhcchhhhHhhhhhHHH-------HHHHHHHHHHHHHHHHHHhhhhHHHHH
Q 012298 316 AFPKTLDELELDYTREAMELGRIRDKEEDEENYKHRET-------IREMRESYMKKLTQVRAMHAKQWEEFL 380 (466)
Q Consensus 316 ~~PqTlEeLE~eF~dEameL~KerddeEDeENaRHRE~-------IreIne~Y~eKL~aLRa~hAkrrEEFL 380 (466)
.|-+--+.||...+.=+.+++|+-.++|+-=+.-+.-- =.+|+..||+++.+|--..+.-|....
T Consensus 27 ~f~~Ak~rLe~~hr~r~~~VmkeW~eaE~~~~~l~~~DPk~Ae~~k~~m~~rFQ~~v~aLE~e~~~er~qL~ 98 (193)
T PF12925_consen 27 RFKEAKERLEEKHRERMTKVMKEWSEAEERYKELPKADPKKAEQFKKEMTQRFQKTVQALEQEAAAERQQLV 98 (193)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455678999999999999999999988655444433 568999999999999988887776544
No 44
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=24.91 E-value=39 Score=35.44 Aligned_cols=54 Identities=20% Similarity=0.340 Sum_probs=41.7
Q ss_pred hhhhhhhHHHHH-------Hhhhcccccccccc-----ceEEeccCcceeeecchhhHHHHHHhhc
Q 012298 126 HVRALFTEKVIQ-------RIEKDISCKIKMDE-----KFIIVSGKDRLILSKGVDAVHKIIKEEG 179 (466)
Q Consensus 126 ~vr~lfte~vi~-------~iEkd~gckikm~e-----kf~~vsgkDRl~l~kgvdaVhk~i~e~~ 179 (466)
+|++.|-+.||. +||++++|+|.+-- .-|+++|.-|=.|-+.-+-++++|.+.+
T Consensus 62 ~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 62 LVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred hhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 466777665554 89999999998854 3678888888888888888999997743
No 45
>PF07795 DUF1635: Protein of unknown function (DUF1635); InterPro: IPR012862 The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.
Probab=24.34 E-value=7.2e+02 Score=24.82 Aligned_cols=38 Identities=24% Similarity=0.359 Sum_probs=27.3
Q ss_pred CcHHHHHHHHHHHHHHhhhhcchhhhHhhhhhHHHHHHH
Q 012298 319 KTLDELELDYTREAMELGRIRDKEEDEENYKHRETIREM 357 (466)
Q Consensus 319 qTlEeLE~eF~dEameL~KerddeEDeENaRHRE~IreI 357 (466)
+|+|||=+..+-=-|||..-+.. -.||--||.|.|..+
T Consensus 1 ~s~EELRq~Ll~TTlELE~~k~~-A~EElRk~eeqi~~L 38 (214)
T PF07795_consen 1 ESMEELRQKLLYTTLELEATKME-ANEELRKREEQIAHL 38 (214)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 57899999999988898765433 256666777666543
No 46
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=23.66 E-value=55 Score=35.28 Aligned_cols=44 Identities=23% Similarity=0.357 Sum_probs=30.3
Q ss_pred hHHHHHHhhhccccccccccceEEeccCcceeeecchhhHHHHH
Q 012298 132 TEKVIQRIEKDISCKIKMDEKFIIVSGKDRLILSKGVDAVHKII 175 (466)
Q Consensus 132 te~vi~~iEkd~gckikm~ekf~~vsgkDRl~l~kgvdaVhk~i 175 (466)
.+++|+.|..++||+|++-..+|--|.--.+.|+==++||+|.|
T Consensus 156 ~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al 199 (485)
T KOG2190|consen 156 GGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKAL 199 (485)
T ss_pred CcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHH
Confidence 78999999999999999877755444433344444455555544
No 47
>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=22.14 E-value=49 Score=36.00 Aligned_cols=65 Identities=17% Similarity=0.236 Sum_probs=50.7
Q ss_pred hHhhcCCCCccccCCCCccccCCchhHHHHhhhcccchhhhhhhHHHHHHhhhccccccccccceEE-eccCcce
Q 012298 89 ICKICGESGHFTQGCPSTLGANRKSQDFFERVAARDKHVRALFTEKVIQRIEKDISCKIKMDEKFII-VSGKDRL 162 (466)
Q Consensus 89 ~ckicge~ghf~qgcp~tLGanrks~dffeRv~ardk~vr~lfte~vi~~iEkd~gckikm~ekf~~-vsgkDRl 162 (466)
.|.-|++.||++..|..-+ +...+.+.++.|....-.-+.|.. .++|-++.=.+.++. +||.|=.
T Consensus 5 ~~~~~~~~~~~~~~~~~~~--~~~~~~k~~~~~~~~~~~~~~~~~-------~~~~~nfd~~~~i~v~~~G~~~p 70 (482)
T KOG0335|consen 5 SGRNCGEGGPRPKHCGNST--MEEEKQKGKKGPLKAYLEQAFFLG-------ISTGINFDKYNDIPVKVSGRDVP 70 (482)
T ss_pred cccccCCCCCCCccccccc--ccccccccccCCcccchhhhhhhc-------cchhhccCCccceeeeccCCccC
Confidence 6888999999999999987 777888889999888887777766 566655544445544 8998874
No 48
>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=22.11 E-value=9e+02 Score=27.32 Aligned_cols=32 Identities=22% Similarity=0.235 Sum_probs=20.6
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHhhhhcchhhh
Q 012298 313 EYPAFPKTLDELELDYTREAMELGRIRDKEED 344 (466)
Q Consensus 313 E~~~~PqTlEeLE~eF~dEameL~KerddeED 344 (466)
|-++.|..-+.||+-=+.|.+.++.-+.+...
T Consensus 87 ein~s~~aK~vfel~r~qE~Trq~E~~~k~~~ 118 (630)
T KOG0742|consen 87 EINHSPYAKDVFELARMQEQTRQAEQQAKTKE 118 (630)
T ss_pred hhccCccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34667777777777777777766655444433
No 49
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=21.58 E-value=37 Score=34.37 Aligned_cols=19 Identities=26% Similarity=0.646 Sum_probs=15.0
Q ss_pred HHHHHHhhhcccccccccc
Q 012298 133 EKVIQRIEKDISCKIKMDE 151 (466)
Q Consensus 133 e~vi~~iEkd~gckikm~e 151 (466)
+-.+.+||+++||||-+-.
T Consensus 117 GnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 117 GNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred cchHHHHHHHHCCeEEEec
Confidence 4567899999999996543
No 50
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=20.24 E-value=5.7e+02 Score=28.79 Aligned_cols=56 Identities=25% Similarity=0.176 Sum_probs=43.2
Q ss_pred CCCCcHHHHHHHHHHHHHHhhhhcc---hhhhHhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 012298 316 AFPKTLDELELDYTREAMELGRIRD---KEEDEENYKHRETIREMRESYMKKLTQVRAM 371 (466)
Q Consensus 316 ~~PqTlEeLE~eF~dEameL~Kerd---deEDeENaRHRE~IreIne~Y~eKL~aLRa~ 371 (466)
+...||--=+|-.+.=||.+++.|. +-|-+|--.-+-.+|||+|...+.|+--|-.
T Consensus 499 SS~eTll~niq~llkva~dnar~qekQiq~Ek~ELkmd~lrerelreslekql~~Erkl 557 (641)
T KOG3915|consen 499 SSIETLLTNIQGLLKVAIDNARAQEKQIQLEKTELKMDFLRERELRESLEKQLAMERKL 557 (641)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445666668888888998888765 4578888888888999999999999864443
Done!