Query psy397
Match_columns 202
No_of_seqs 114 out of 308
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 21:58:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy397.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/397hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00071 40S ribosomal protein 100.0 1E-41 2.2E-46 274.7 12.6 98 7-104 3-101 (132)
2 KOG3424|consensus 100.0 2.9E-42 6.2E-47 276.9 9.1 101 6-106 1-101 (132)
3 PRK01178 rps24e 30S ribosomal 100.0 8.1E-40 1.8E-44 252.0 11.6 93 12-104 3-95 (99)
4 COG2004 RPS24A Ribosomal prote 100.0 8.4E-38 1.8E-42 244.9 10.9 92 10-101 2-93 (107)
5 PF01282 Ribosomal_S24e: Ribos 100.0 1.1E-32 2.3E-37 205.7 7.7 78 28-105 1-78 (84)
6 smart00360 RRM RNA recognition 61.2 35 0.00077 20.8 5.3 48 38-90 6-54 (71)
7 PF00076 RRM_1: RNA recognitio 59.7 35 0.00076 21.9 5.1 47 38-90 8-55 (70)
8 PF00276 Ribosomal_L23: Riboso 49.1 33 0.00071 25.9 4.1 57 20-80 14-76 (91)
9 PF04432 FrhB_FdhB_C: Coenzyme 46.1 43 0.00093 26.8 4.6 53 15-67 20-72 (161)
10 TIGR00608 radc DNA repair prot 45.7 36 0.00079 29.6 4.4 53 10-62 144-204 (218)
11 CHL00030 rpl23 ribosomal prote 45.0 32 0.00069 26.6 3.6 35 20-58 14-48 (93)
12 PF12436 USP7_ICP0_bdg: ICP0-b 42.3 29 0.00063 30.2 3.3 55 19-73 170-233 (249)
13 PRK00024 hypothetical protein; 40.1 47 0.001 28.8 4.2 53 10-62 150-210 (224)
14 PRK06425 histidinol-phosphate 38.0 39 0.00084 29.4 3.4 27 38-64 38-64 (332)
15 PRK10513 sugar phosphate phosp 37.0 43 0.00094 27.9 3.5 33 29-64 187-219 (270)
16 PRK05738 rplW 50S ribosomal pr 36.1 78 0.0017 24.1 4.4 36 20-59 14-50 (92)
17 PRK15126 thiamin pyrimidine py 36.0 43 0.00093 28.2 3.3 33 29-64 179-211 (272)
18 cd08071 MPN_DUF2466 Mov34/MPN/ 36.0 82 0.0018 24.4 4.6 38 25-62 60-104 (113)
19 PRK10976 putative hydrolase; P 35.5 46 0.001 27.7 3.4 33 29-64 181-213 (266)
20 PRK12280 rplW 50S ribosomal pr 35.3 47 0.001 28.2 3.4 36 19-58 16-51 (158)
21 TIGR03636 L23_arch archaeal ri 34.8 1.6E+02 0.0034 22.1 5.8 56 21-84 9-65 (77)
22 PRK01688 histidinol-phosphate 34.3 35 0.00076 29.9 2.6 27 38-64 55-81 (351)
23 PRK14548 50S ribosomal protein 33.4 1.3E+02 0.0028 22.9 5.2 60 18-85 13-73 (84)
24 TIGR01482 SPP-subfamily Sucros 33.3 62 0.0013 25.9 3.7 33 29-64 140-172 (225)
25 PF04002 RadC: RadC-like JAB d 31.9 65 0.0014 25.1 3.5 36 27-62 67-109 (123)
26 PF09581 Spore_III_AF: Stage I 30.7 30 0.00066 28.0 1.5 24 40-63 164-187 (188)
27 COG0245 IspF 2C-methyl-D-eryth 29.9 1E+02 0.0022 26.4 4.6 39 29-68 97-135 (159)
28 PF14560 Ubiquitin_2: Ubiquiti 29.7 1.5E+02 0.0032 21.4 4.9 27 38-64 22-48 (87)
29 COG2003 RadC DNA repair protei 29.6 72 0.0016 28.6 3.8 37 30-67 171-210 (224)
30 KOG1051|consensus 29.5 92 0.002 33.0 5.0 92 17-124 236-332 (898)
31 TIGR01485 SPP_plant-cyano sucr 28.9 1.1E+02 0.0023 25.7 4.5 32 30-64 159-190 (249)
32 PRK05387 histidinol-phosphate 28.9 48 0.001 28.5 2.5 25 40-64 60-84 (353)
33 PF08766 DEK_C: DEK C terminal 28.9 43 0.00093 22.7 1.8 22 36-57 17-38 (54)
34 PRK00084 ispF 2-C-methyl-D-ery 28.6 91 0.002 26.5 4.1 38 29-67 99-136 (159)
35 KOG3969|consensus 28.5 59 0.0013 30.6 3.1 56 42-97 218-288 (310)
36 PLN03026 histidinol-phosphate 28.2 63 0.0014 28.9 3.2 26 39-64 85-110 (380)
37 PRK04781 histidinol-phosphate 28.1 53 0.0012 29.1 2.7 26 39-64 58-83 (364)
38 PRK01158 phosphoglycolate phos 28.0 77 0.0017 25.5 3.4 33 29-64 148-180 (230)
39 PRK14807 histidinol-phosphate 27.4 74 0.0016 27.8 3.5 26 39-64 58-83 (351)
40 cd01804 midnolin_N Ubiquitin-l 27.2 1.8E+02 0.0039 20.8 4.9 25 38-62 20-44 (78)
41 cd08059 MPN_prok_mb Mpr1p, Pad 25.7 45 0.00099 24.4 1.6 18 29-46 60-78 (101)
42 PHA01976 helix-turn-helix prot 25.6 55 0.0012 21.9 1.9 24 36-60 38-61 (67)
43 PRK07392 threonine-phosphate d 25.5 70 0.0015 28.0 3.0 25 40-64 57-81 (360)
44 cd01791 Ubl5 UBL5 ubiquitin-li 25.2 1.1E+02 0.0024 22.0 3.5 25 38-62 20-44 (73)
45 PLN03134 glycine-rich RNA-bind 25.0 1.3E+02 0.0029 24.0 4.3 47 38-89 44-91 (144)
46 COG0561 Cof Predicted hydrolas 24.9 88 0.0019 26.1 3.3 32 30-64 181-212 (264)
47 PF11013 DUF2851: Protein of u 24.8 20 0.00043 33.9 -0.6 12 180-191 61-72 (377)
48 cd00554 MECDP_synthase MECDP_s 24.6 1.3E+02 0.0028 25.4 4.3 36 28-64 95-130 (153)
49 TIGR01141 hisC histidinol-phos 24.3 74 0.0016 27.3 2.8 27 38-64 52-78 (346)
50 PTZ00397 macrophage migration 24.1 89 0.0019 23.7 3.0 35 29-63 60-99 (116)
51 PRK14809 histidinol-phosphate 24.0 93 0.002 27.1 3.4 25 40-64 65-89 (357)
52 PRK06358 threonine-phosphate d 23.6 82 0.0018 27.7 3.0 25 40-64 54-78 (354)
53 PRK08056 threonine-phosphate d 23.2 75 0.0016 27.8 2.7 25 40-64 55-79 (356)
54 PRK04635 histidinol-phosphate 23.1 74 0.0016 27.8 2.7 24 41-64 61-84 (354)
55 TIGR03576 pyridox_MJ0158 pyrid 23.1 69 0.0015 28.8 2.5 27 38-64 52-78 (346)
56 COG0710 AroD 3-dehydroquinate 23.1 1.4E+02 0.0029 26.7 4.3 33 29-61 119-151 (231)
57 PRK08153 histidinol-phosphate 22.6 63 0.0014 28.6 2.2 25 40-64 67-91 (369)
58 TIGR00151 ispF 2C-methyl-D-ery 22.0 1.5E+02 0.0032 25.1 4.1 36 28-64 95-130 (155)
59 PRK10530 pyridoxal phosphate ( 21.8 1.1E+02 0.0024 25.2 3.3 32 30-64 191-222 (272)
60 PRK09105 putative aminotransfe 21.8 86 0.0019 28.0 2.8 24 41-64 79-102 (370)
61 TIGR01484 HAD-SF-IIB HAD-super 21.4 1.5E+02 0.0032 23.6 3.8 33 29-64 154-186 (204)
62 PRK03967 histidinol-phosphate 21.4 1.2E+02 0.0025 26.6 3.5 25 40-64 55-79 (337)
63 TIGR00099 Cof-subfamily Cof su 21.1 1.1E+02 0.0023 25.5 3.1 33 29-64 179-211 (256)
64 PRK03321 putative aminotransfe 21.1 85 0.0019 27.1 2.6 26 39-64 56-81 (352)
65 PF01863 DUF45: Protein of unk 20.9 1.1E+02 0.0023 24.7 3.0 29 48-76 120-148 (205)
66 smart00362 RRM_2 RNA recogniti 20.6 2.1E+02 0.0046 17.3 4.1 45 39-90 10-55 (72)
67 PRK01533 histidinol-phosphate 20.6 1.2E+02 0.0026 27.1 3.5 25 40-64 64-88 (366)
68 PF02542 YgbB: YgbB family; I 20.6 89 0.0019 26.5 2.5 28 37-64 104-131 (157)
69 PF12327 FtsZ_C: FtsZ family, 20.4 78 0.0017 23.8 2.0 51 15-66 21-76 (95)
70 PF08282 Hydrolase_3: haloacid 20.4 1.7E+02 0.0036 22.9 3.9 33 29-64 177-209 (254)
71 PF00046 Homeobox: Homeobox do 20.1 30 0.00065 22.7 -0.3 23 37-60 22-44 (57)
72 TIGR01140 L_thr_O3P_dcar L-thr 20.1 1.1E+02 0.0023 26.6 3.0 27 38-64 45-71 (330)
No 1
>PTZ00071 40S ribosomal protein S24; Provisional
Probab=100.00 E-value=1e-41 Score=274.72 Aligned_cols=98 Identities=55% Similarity=0.939 Sum_probs=95.0
Q ss_pred CCeEEEEeecceeccCccceeEEEEEEcCCCCCCCHHHHHHHHHhHhC-CCCCeEEEeceeecCCCCEEEEEEEEeCCHH
Q psy397 7 ASTVTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFK-SKPENIFAFGFQTNFGGGKSTGFALIYDSID 85 (202)
Q Consensus 7 ~~~vTIrtRKf~eNpLL~RREv~fdV~HpGkaTPSRkEIreKLAamln-vd~dlVVVfg~kT~FGgGkStGfA~IYDS~E 85 (202)
.++|||+|++|++||||+|||++|+|.|||+|||||+||+++||+||+ +|+++|||++|+|+||+|+|+|||+||||.|
T Consensus 3 ~~~~~ir~rk~~~NpLL~RkE~~~~v~Hpg~~TpSr~eirekLA~~~~v~d~~~Vvv~~~~T~fG~g~StG~a~IYds~e 82 (132)
T PTZ00071 3 KAEFTVRTRKFLVNPLLNRKQFVVEVLHPGKGTVSKKDIKEKLAKQYKVADARTIVLFGFKTKFGGGKTTGFGLIYDNLA 82 (132)
T ss_pred CccEEEEEeeeeeccCcCcEEEEEEEEeCCCCCCCHHHHHHHHHHHhCCCCCCEEEEEccEecCCCceEEEEEEEECCHH
Confidence 346999999999999999999999999999999999999999999999 7999999999999999999999999999999
Q ss_pred HHHhcCcceeeeeCCccce
Q psy397 86 LAKKFEPKYRLQRVSTKSL 104 (202)
Q Consensus 86 ~aKK~EPKyrL~Rngl~ek 104 (202)
+|++|||+|+|+|||+.++
T Consensus 83 ~~kk~Epk~~l~Rngl~~~ 101 (132)
T PTZ00071 83 ALKKFEPKYRLIRLGLIKK 101 (132)
T ss_pred HHHhhCchheeeecCcccc
Confidence 9999999999999999865
No 2
>KOG3424|consensus
Probab=100.00 E-value=2.9e-42 Score=276.91 Aligned_cols=101 Identities=67% Similarity=1.107 Sum_probs=98.7
Q ss_pred cCCeEEEEeecceeccCccceeEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCEEEEEEEEeCCHH
Q psy397 6 SASTVTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALIYDSID 85 (202)
Q Consensus 6 ~~~~vTIrtRKf~eNpLL~RREv~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGkStGfA~IYDS~E 85 (202)
++++|||||||||+|+||+|+|++++|+|||+||||++|||||||+||+++||+|+||+|+|+||+|+|+|||+||||.|
T Consensus 1 ~~~~vtirtrk~~tNrLL~RKqmvvdvlHPG~a~vsK~EirEKla~mYkt~~d~V~vfgfrt~~GggkstgfalIYdsve 80 (132)
T KOG3424|consen 1 MSDAVTIRTRKFMTNRLLSRKQMVVDVLHPGKANVSKTEIREKLAKMYKTTPDAVFVFGFRTHFGGGKSTGFALIYDSVE 80 (132)
T ss_pred CCccEEEehhhhhhhhhhhhhheeEEEecCCCCCCCHHHHHHHHHHHhcCCcceEEEEEeeeccCCcccceeeeeeehHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCcceeeeeCCccceee
Q psy397 86 LAKKFEPKYRLQRVSTKSLLV 106 (202)
Q Consensus 86 ~aKK~EPKyrL~Rngl~ek~~ 106 (202)
.+++|||+|||+|+|+.|+..
T Consensus 81 ~akkfEpkyrl~r~gl~e~~k 101 (132)
T KOG3424|consen 81 YAKKFEPKYRLVRLGLAEKIK 101 (132)
T ss_pred HHHhcCcceeeeecccccccc
Confidence 999999999999999999873
No 3
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=100.00 E-value=8.1e-40 Score=252.04 Aligned_cols=93 Identities=35% Similarity=0.596 Sum_probs=90.1
Q ss_pred EEeecceeccCccceeEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCEEEEEEEEeCCHHHHHhcC
Q psy397 12 IKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALIYDSIDLAKKFE 91 (202)
Q Consensus 12 IrtRKf~eNpLL~RREv~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGkStGfA~IYDS~E~aKK~E 91 (202)
+.+-++++||||+|||++|+|.|||+|||||+||++|||+|||+++++|||++|+|+||+|+|+|||+||||.|+|++||
T Consensus 3 i~I~~~~~N~LL~Rke~~~~v~h~g~~tpsr~eirekLa~~~~~~~~~vvv~~~~t~fG~g~s~G~a~IYds~e~~kk~E 82 (99)
T PRK01178 3 IKIISDKENPLLGRREIKFEVYHEGSATPSRKDVRKKLAAMLNADKELVVVRKIKTEYGMGKSKGYAKVYDDKERARKIE 82 (99)
T ss_pred EEEEEeeecCCcCcEEEEEEEEeCCCCCCCHHHHHHHHHHHHCcCCCEEEEEccCccCCCceEEEEEEEECCHHHHHhhC
Confidence 56778899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeeeeCCccce
Q psy397 92 PKYRLQRVSTKSL 104 (202)
Q Consensus 92 PKyrL~Rngl~ek 104 (202)
|+|+|+|||+.++
T Consensus 83 pk~~l~Rn~~~~~ 95 (99)
T PRK01178 83 PKYILERNKIEEE 95 (99)
T ss_pred chheeeecCcccc
Confidence 9999999999764
No 4
>COG2004 RPS24A Ribosomal protein S24E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.4e-38 Score=244.87 Aligned_cols=92 Identities=40% Similarity=0.633 Sum_probs=90.8
Q ss_pred EEEEeecceeccCccceeEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCEEEEEEEEeCCHHHHHh
Q psy397 10 VTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALIYDSIDLAKK 89 (202)
Q Consensus 10 vTIrtRKf~eNpLL~RREv~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGkStGfA~IYDS~E~aKK 89 (202)
++|+|+++++||||+|||+.|+|.|||++||||+|||+|||++||+|+++|+|++++|+||+|+|+|||+||||.+.|++
T Consensus 2 ~ei~I~~~r~NpLL~RkEi~~~v~h~g~~TPSr~evrekla~~l~~d~e~VvV~~ikt~fG~~~s~g~akIY~s~e~~~~ 81 (107)
T COG2004 2 MEIKILEKRDNPLLKRKEIVFVVYHEGSPTPSRKEVREKLAAMLGADKELVVVDYIKTEFGKGRSKGYAKIYDSVERAKK 81 (107)
T ss_pred ceEEeehcccCccccceEEEEEEEeCCCCCCCHHHHHHHHHHHHCCCcceEEEEehhhhcCCcceeEEEEEECCHHHHHh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcceeeeeCCc
Q psy397 90 FEPKYRLQRVST 101 (202)
Q Consensus 90 ~EPKyrL~Rngl 101 (202)
|||+|+|.||+.
T Consensus 82 iEp~yiL~Rn~~ 93 (107)
T COG2004 82 IEPEYILERNGG 93 (107)
T ss_pred cCcceEEEeccc
Confidence 999999999987
No 5
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=99.98 E-value=1.1e-32 Score=205.66 Aligned_cols=78 Identities=56% Similarity=0.954 Sum_probs=72.3
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCEEEEEEEEeCCHHHHHhcCcceeeeeCCcccee
Q psy397 28 MVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALIYDSIDLAKKFEPKYRLQRVSTKSLL 105 (202)
Q Consensus 28 v~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGkStGfA~IYDS~E~aKK~EPKyrL~Rngl~ek~ 105 (202)
|+|+|.|||+|||||+||+++||+|||+|+++|||++|+|+||+|+|+|||+||||.|+|+++||+|+|+||++.++.
T Consensus 1 ~~~~v~h~g~~Tpsr~ei~~klA~~~~~~~~~ivv~~~~t~fG~~~s~g~a~IYd~~e~~kk~Ep~~~l~R~~~~e~~ 78 (84)
T PF01282_consen 1 MVFEVLHPGKPTPSRKEIREKLAAMLNVDPDLIVVFGIKTEFGGGKSTGFAKIYDSAEALKKFEPKYRLKRNGLEEKK 78 (84)
T ss_dssp EEEEEE-SSSSS--HHHHHHHHHHHHTSTGCCEEEEEEEESSSSSEEEEEEEEESSHHHHHHHSTHHHHHHTTSSSS-
T ss_pred CEEEEECCCCCCCCHHHHHHHHHHHhCCCCCeEEEeccEecCCCceEEEEEEEeCCHHHHHHhCcHHHhHhcCccccc
Confidence 689999999999999999999999999999999999999999999999999999999999999999999999988763
No 6
>smart00360 RRM RNA recognition motif.
Probab=61.23 E-value=35 Score=20.83 Aligned_cols=48 Identities=33% Similarity=0.553 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCEEEEEEEE-eCCHHHHHhc
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALI-YDSIDLAKKF 90 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGkStGfA~I-YDS~E~aKK~ 90 (202)
...+.++|++.+. .+|.- ..+ .+......+++.|+|.| |++.+.+++.
T Consensus 6 ~~~~~~~l~~~f~-~~g~v-~~~---~i~~~~~~~~~~~~a~v~f~~~~~a~~a 54 (71)
T smart00360 6 PDVTEEELRELFS-KFGKI-ESV---RLVRDKDTGKSKGFAFVEFESEEDAEKA 54 (71)
T ss_pred cccCHHHHHHHHH-hhCCE-eEE---EEEeCCCCCCCCceEEEEeCCHHHHHHH
Confidence 3467889988875 55621 222 33344446778888887 7888877654
No 7
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=59.69 E-value=35 Score=21.86 Aligned_cols=47 Identities=30% Similarity=0.518 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCEEEEEEEE-eCCHHHHHhc
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALI-YDSIDLAKKF 90 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGkStGfA~I-YDS~E~aKK~ 90 (202)
+..+.+||++.+.. +|.-... .+.+. +.+...|+|.| |++.+.+++.
T Consensus 8 ~~~t~~~l~~~f~~-~g~i~~~----~~~~~-~~~~~~~~a~V~F~~~~~a~~a 55 (70)
T PF00076_consen 8 PDVTEEELRDFFSQ-FGKIESI----KVMRN-SSGKSKGYAFVEFESEEDAEKA 55 (70)
T ss_dssp TTSSHHHHHHHHHT-TSTEEEE----EEEEE-TTSSEEEEEEEEESSHHHHHHH
T ss_pred CcCCHHHHHHHHHH-hhhcccc----ccccc-ccccccceEEEEEcCHHHHHHH
Confidence 45678899988876 5543222 22222 77777777766 7777777653
No 8
>PF00276 Ribosomal_L23: Ribosomal protein L23; InterPro: IPR013025 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found in both eukaryotic L25 and prokaryotic and eukaryotic L23 proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3DF4_T 3DF2_T 4A1E_R 4A1A_R 4A1C_R 4A17_R 2HGU_W 2HGQ_W 1N88_A 2HGJ_W ....
Probab=49.14 E-value=33 Score=25.85 Aligned_cols=57 Identities=26% Similarity=0.399 Sum_probs=36.6
Q ss_pred ccCccc-eeEEEEEEcCCCCCCCHHHHHHHHHhHhCCC---CCeEEEeceeecCCC--CEEEEEEEE
Q psy397 20 NRLLGR-KQMVVDVLHPGKPSVKKTDIREKLSKMFKSK---PENIFAFGFQTNFGG--GKSTGFALI 80 (202)
Q Consensus 20 NpLL~R-REv~fdV~HpGkaTPSRkEIreKLAamlnvd---~dlVVVfg~kT~FGg--GkStGfA~I 80 (202)
..+++. .++.|.|. +..++.||++.|-+.||++ .+...+.|=..++|. |+..+|=+.
T Consensus 14 ~~~~~~~n~~tF~V~----~~atK~~Ik~aie~iy~V~V~~Vnt~~~~gk~kR~g~~~g~~~~~KKa 76 (91)
T PF00276_consen 14 MKLLENPNQYTFEVD----PRATKTEIKEAIEKIYGVKVKKVNTMNYPGKKKRKGKFVGKTKDYKKA 76 (91)
T ss_dssp HHHHHHSSEEEEEET----TTSTHHHHHHHHHHHHTSEEEEEEEEEETSEEEESSSCEEEE-EEEEE
T ss_pred HHhhhcCCEEEEEEe----CCCCHHHHHHHHHhhcCCCeeEEEEeEeCCCceEeCCccccCCCcEEE
Confidence 344555 77888763 4578999999999999995 344455544455665 444444333
No 9
>PF04432 FrhB_FdhB_C: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus; InterPro: IPR007525 Coenzyme F420 hydrogenase (1.12.99.1 from EC) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C-termini of F420 hydrogenase and dehydrogenase beta subunits [, ]. The C terminus of Methanobacterium formicicum formate dehydrogenase beta chain (1.2.1.2 from EC, P06130 from SWISSPROT) is also represented in this entry []. This region is often found in association with the 4Fe-4S binding domain, fer4 (IPR001450 from INTERPRO), and the N terminus IPR007516 from INTERPRO.
Probab=46.08 E-value=43 Score=26.84 Aligned_cols=53 Identities=19% Similarity=0.308 Sum_probs=37.7
Q ss_pred ecceeccCccceeEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEeceee
Q psy397 15 RKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQT 67 (202)
Q Consensus 15 RKf~eNpLL~RREv~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg~kT 67 (202)
|++..++..+|.++.+.|--.-.++||.+-.++.|+.+++.+++.|.=+.++.
T Consensus 20 ~~~~~~~~~~~~~~~~~igl~C~g~~s~~~~~~~l~~~~~~~~~~v~~~~~r~ 72 (161)
T PF04432_consen 20 RKLLKRNYENRDEIVYTIGLFCHGVPSPKKLRKYLEEQLGIKPDDVKKFDFRD 72 (161)
T ss_pred HHHHhhCcccCcceEEEEeEECCCCCCHHHHHHHHHHHhCCChhheeEEEEeC
Confidence 34444444444445555555556899999999999999999988877777776
No 10
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=45.70 E-value=36 Score=29.58 Aligned_cols=53 Identities=21% Similarity=0.403 Sum_probs=31.8
Q ss_pred EEEEeecceeccCccc-eeEEEEEEcC-CCCCCCHHHHH-----HHHHhHhCCC-CCeEEE
Q psy397 10 VTIKTRKYMTNRLLGR-KQMVVDVLHP-GKPSVKKTDIR-----EKLSKMFKSK-PENIFA 62 (202)
Q Consensus 10 vTIrtRKf~eNpLL~R-REv~fdV~Hp-GkaTPSRkEIr-----eKLAamlnvd-~dlVVV 62 (202)
..+..|..+.--|... .-+.+.=.|| |.+|||++|+. .+.++.+|+. -|-++|
T Consensus 144 ~~v~pReI~~~Al~~~A~~vIlaHNHPSG~~~PS~~Di~~T~~l~~a~~~lgI~llDHiIv 204 (218)
T TIGR00608 144 VPVHPREIFKEALKLSASALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLII 204 (218)
T ss_pred EEEcHHHHHHHHHHhhCCeEEEEeecCCCCCCCCHHHHHHHHHHHHHHHhCCCEEeeEEEE
Confidence 4455555544433332 2344445677 79999999986 3445566765 566666
No 11
>CHL00030 rpl23 ribosomal protein L23
Probab=44.98 E-value=32 Score=26.60 Aligned_cols=35 Identities=31% Similarity=0.357 Sum_probs=27.1
Q ss_pred ccCccceeEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCC
Q psy397 20 NRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPE 58 (202)
Q Consensus 20 NpLL~RREv~fdV~HpGkaTPSRkEIreKLAamlnvd~d 58 (202)
..|+...++.|.|. +..++.||++.+-++||+...
T Consensus 14 ~~l~e~n~y~F~V~----~~anK~eIK~avE~lf~VkV~ 48 (93)
T CHL00030 14 IRLLEKNQYTFDVD----SGSTKTEIKHWIELFFGVKVI 48 (93)
T ss_pred HHhhHCCEEEEEEC----CCCCHHHHHHHHHHHhCCeEE
Confidence 34556678888875 447899999999999999643
No 12
>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.
Probab=42.29 E-value=29 Score=30.23 Aligned_cols=55 Identities=16% Similarity=0.213 Sum_probs=34.0
Q ss_pred eccCccceeEEEEEEcCCC---------CCCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCE
Q psy397 19 TNRLLGRKQMVVDVLHPGK---------PSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGK 73 (202)
Q Consensus 19 eNpLL~RREv~fdV~HpGk---------aTPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGk 73 (202)
.+-|++|.++.|.=.+... ..=+=.|+.+++|+.+|+||+.+=++......|+.+
T Consensus 170 y~~l~nrv~V~f~~~~~~~~~~F~l~ls~~~tY~~la~~Va~~l~~dP~~lr~~~~~~~~~~P~ 233 (249)
T PF12436_consen 170 YDFLYNRVEVEFKPKDNPNDPEFTLWLSKKMTYDQLAEKVAEHLNVDPEHLRFFTVNPYSGKPK 233 (249)
T ss_dssp HHHHHHEEEEEEEETTSTT---EEEEEETT--HHHHHHHHHHHHTS-GGGEEEE---TTS-S--
T ss_pred HHHHhCeEEEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHCCChHHEEEEEeccCCCCCC
Confidence 3456777777766443321 223568999999999999999999999887666655
No 13
>PRK00024 hypothetical protein; Reviewed
Probab=40.07 E-value=47 Score=28.80 Aligned_cols=53 Identities=17% Similarity=0.360 Sum_probs=31.7
Q ss_pred EEEEeecceeccCccc-eeEEEEEEcC-CCCCCCHHHHH-----HHHHhHhCCC-CCeEEE
Q psy397 10 VTIKTRKYMTNRLLGR-KQMVVDVLHP-GKPSVKKTDIR-----EKLSKMFKSK-PENIFA 62 (202)
Q Consensus 10 vTIrtRKf~eNpLL~R-REv~fdV~Hp-GkaTPSRkEIr-----eKLAamlnvd-~dlVVV 62 (202)
..+..|..+.--|... .-+.+.=.|| |.++||++|+. .+.++++|+. -|-++|
T Consensus 150 ~~v~pRei~~~Al~~~A~~iIl~HNHPSG~~~PS~~D~~~T~~l~~a~~~l~I~llDHiIv 210 (224)
T PRK00024 150 SIVHPREIVKRALKLNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIII 210 (224)
T ss_pred EEEcHHHHHHHHHHhhccceEEEecCCCCCCCCCHHHHHHHHHHHHHHHhCCCEEeeEEEE
Confidence 4455555444433322 2344445677 69999999986 3455667775 566666
No 14
>PRK06425 histidinol-phosphate aminotransferase; Validated
Probab=38.03 E-value=39 Score=29.37 Aligned_cols=27 Identities=15% Similarity=0.223 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
|-|...+++++||+.+++++++|++..
T Consensus 38 p~~~~~~lr~~ia~~~~~~~~~I~it~ 64 (332)
T PRK06425 38 PEISYTDIEDQIKIYTQGLKIKVLIGP 64 (332)
T ss_pred cCcCHHHHHHHHHHHhCCCcceEEECC
Confidence 457889999999999999999988753
No 15
>PRK10513 sugar phosphate phosphatase; Provisional
Probab=37.05 E-value=43 Score=27.86 Aligned_cols=33 Identities=27% Similarity=0.463 Sum_probs=27.6
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.++|.++| .||..--+.|++.+|.+++.++.+|
T Consensus 187 ~~eI~~~g---vsKg~al~~l~~~~gi~~~~v~afG 219 (270)
T PRK10513 187 FLEILDKR---VNKGTGVKSLAEHLGIKPEEVMAIG 219 (270)
T ss_pred eEEEeCCC---CChHHHHHHHHHHhCCCHHHEEEEC
Confidence 46777777 8999999999999999988887764
No 16
>PRK05738 rplW 50S ribosomal protein L23; Reviewed
Probab=36.06 E-value=78 Score=24.08 Aligned_cols=36 Identities=28% Similarity=0.517 Sum_probs=26.8
Q ss_pred ccCcc-ceeEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCe
Q psy397 20 NRLLG-RKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPEN 59 (202)
Q Consensus 20 NpLL~-RREv~fdV~HpGkaTPSRkEIreKLAamlnvd~dl 59 (202)
+.|+. ..++.|.|. +..++.||++.+-++||+++..
T Consensus 14 ~~~~e~~n~~~F~V~----~~a~K~eIK~aie~lf~VkV~~ 50 (92)
T PRK05738 14 TLLMEKQNKYVFEVA----PDATKPEIKAAVEKLFGVKVES 50 (92)
T ss_pred HHhHHhCCEEEEEEC----CCCCHHHHHHHHHHHcCCceeE
Confidence 33444 467787764 4578999999999999997443
No 17
>PRK15126 thiamin pyrimidine pyrophosphate hydrolase; Provisional
Probab=36.04 E-value=43 Score=28.16 Aligned_cols=33 Identities=27% Similarity=0.357 Sum_probs=27.0
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.++|.++| .||..--+.|++.+|.+++.++.+|
T Consensus 179 ~~eI~~~g---~sKg~al~~l~~~~gi~~~~v~afG 211 (272)
T PRK15126 179 CLEVLPVG---CNKGAALAVLSQHLGLSLADCMAFG 211 (272)
T ss_pred EEEeecCC---CChHHHHHHHHHHhCCCHHHeEEec
Confidence 45677766 7899999999999999988887654
No 18
>cd08071 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.
Probab=35.95 E-value=82 Score=24.39 Aligned_cols=38 Identities=18% Similarity=0.482 Sum_probs=26.6
Q ss_pred ceeEEEEEEcC-CCCCCCHHHHH-----HHHHhHhCCC-CCeEEE
Q psy397 25 RKQMVVDVLHP-GKPSVKKTDIR-----EKLSKMFKSK-PENIFA 62 (202)
Q Consensus 25 RREv~fdV~Hp-GkaTPSRkEIr-----eKLAamlnvd-~dlVVV 62 (202)
-..+.+.=.|| |.++||.+|+. .+.++++|+. -|-++|
T Consensus 60 A~~vil~HNHPsG~~~PS~~D~~~T~~l~~~~~~l~i~llDHiIi 104 (113)
T cd08071 60 AAAIILAHNHPSGDPTPSREDIELTKRLKEAGELLGIRLLDHIIV 104 (113)
T ss_pred hheEEEEeeCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEeeEEEE
Confidence 44566667888 68899999875 4455667775 566666
No 19
>PRK10976 putative hydrolase; Provisional
Probab=35.50 E-value=46 Score=27.72 Aligned_cols=33 Identities=27% Similarity=0.424 Sum_probs=25.9
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.++|.++| .+|..--+.|++.+|.+++.++.+|
T Consensus 181 ~~eI~~~g---vsKg~al~~l~~~lgi~~~~viafG 213 (266)
T PRK10976 181 CLEVMAGG---VSKGHALEAVAKKLGYSLKDCIAFG 213 (266)
T ss_pred eEEEEcCC---CChHHHHHHHHHHcCCCHHHeEEEc
Confidence 35666666 7889999999999999888887654
No 20
>PRK12280 rplW 50S ribosomal protein L23; Reviewed
Probab=35.30 E-value=47 Score=28.22 Aligned_cols=36 Identities=19% Similarity=0.298 Sum_probs=28.0
Q ss_pred eccCccceeEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCC
Q psy397 19 TNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPE 58 (202)
Q Consensus 19 eNpLL~RREv~fdV~HpGkaTPSRkEIreKLAamlnvd~d 58 (202)
.+.|+.+.++.|.|.- ..++.||++.+-.+||+.+.
T Consensus 16 s~~l~e~N~ytF~V~~----~anK~eIK~AVE~iF~VkV~ 51 (158)
T PRK12280 16 SYSLMSKNVYTFKVDR----RANKIEIKKAVEFIFKVKVL 51 (158)
T ss_pred HHhhhhCCEEEEEECC----CCCHHHHHHHHHHHhCCceE
Confidence 3445666788888754 46899999999999999643
No 21
>TIGR03636 L23_arch archaeal ribosomal protein L23. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts.
Probab=34.82 E-value=1.6e+02 Score=22.07 Aligned_cols=56 Identities=20% Similarity=0.360 Sum_probs=35.5
Q ss_pred cCccc-eeEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCEEEEEEEEeCCH
Q psy397 21 RLLGR-KQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALIYDSI 84 (202)
Q Consensus 21 pLL~R-REv~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGkStGfA~IYDS~ 84 (202)
.|+.+ +++.|.|.- ..+|.||++.+-++||++...|=. +... ++.-.+|....+..
T Consensus 9 ~~~e~~n~y~F~V~~----~anK~eIK~avE~lf~VkV~~Vnt--~~~~--~~~KKA~VtL~~g~ 65 (77)
T TIGR03636 9 NLIEKENKLTFIVDR----KATKGDIKRAVEKLFDVKVEKVNT--LITP--RGEKKAYVKLAEEY 65 (77)
T ss_pred HHHHhCCEEEEEECC----CCCHHHHHHHHHHHhCCceEEEEe--EEcC--CCceEEEEEECCCC
Confidence 34554 688888854 367999999999999996544433 3222 33444555554443
No 22
>PRK01688 histidinol-phosphate aminotransferase; Provisional
Probab=34.32 E-value=35 Score=29.95 Aligned_cols=27 Identities=19% Similarity=0.325 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
|-|...++++++|+.+|+++++|++.+
T Consensus 55 p~~~~~~l~~~~a~~~g~~~~~I~~~~ 81 (351)
T PRK01688 55 PECQPKAVIENYAAYAGVKPEQVLVSR 81 (351)
T ss_pred CCCChHHHHHHHHHHhCCCHHHEEEcC
Confidence 345668999999999999999998865
No 23
>PRK14548 50S ribosomal protein L23P; Provisional
Probab=33.36 E-value=1.3e+02 Score=22.90 Aligned_cols=60 Identities=18% Similarity=0.321 Sum_probs=38.5
Q ss_pred eeccCccc-eeEEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCEEEEEEEEeCCHH
Q psy397 18 MTNRLLGR-KQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALIYDSID 85 (202)
Q Consensus 18 ~eNpLL~R-REv~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGkStGfA~IYDS~E 85 (202)
+.+.|+.+ .++.|.|. +..++.||++.+-++||++...| ..+.+. .+.-.+|....+..+
T Consensus 13 K~~~~~e~~n~y~F~V~----~~anK~eIK~AvE~lf~VkV~~V--nT~~~~--~~~KKA~V~L~~g~~ 73 (84)
T PRK14548 13 KAMNLIEKENKLTFIVD----RRATKPDIKRAVEELFDVKVEKV--NTLITP--KGEKKAYVKLAEEYD 73 (84)
T ss_pred HHHHHHHhCCEEEEEEC----CCCCHHHHHHHHHHHhCCceEEE--EeEEcC--CCcEEEEEEeCCCCc
Confidence 33445553 68888874 45789999999999999964443 333333 344555555555443
No 24
>TIGR01482 SPP-subfamily Sucrose-phosphate phosphatase subfamily. catalyze the same reaction as SPP.
Probab=33.29 E-value=62 Score=25.93 Aligned_cols=33 Identities=27% Similarity=0.397 Sum_probs=25.3
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.+++.++| .+|..--++|++.+|.+++.++.+|
T Consensus 140 ~~ei~~~~---~~K~~~i~~l~~~~~i~~~~~i~~G 172 (225)
T TIGR01482 140 DIHILPQG---VNKGVAVKKLKEKLGIKPGETLVCG 172 (225)
T ss_pred EEEEeeCC---CCHHHHHHHHHHHhCCCHHHEEEEC
Confidence 45666665 7888888999999999887776554
No 25
>PF04002 RadC: RadC-like JAB domain; InterPro: IPR001405 This family was named initially with reference to the Escherichia coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions []. However the relevant mutation has subsequently been shown to be in recG, not radC []. In addition all attempts to characterise a radiation-related function for RadC in Streptococcus pneumoniae failed, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair [].; PDB: 2QLC_A.
Probab=31.86 E-value=65 Score=25.11 Aligned_cols=36 Identities=22% Similarity=0.503 Sum_probs=19.9
Q ss_pred eEEEEEEcC-CCCCCCHHHHH-----HHHHhHhCCC-CCeEEE
Q psy397 27 QMVVDVLHP-GKPSVKKTDIR-----EKLSKMFKSK-PENIFA 62 (202)
Q Consensus 27 Ev~fdV~Hp-GkaTPSRkEIr-----eKLAamlnvd-~dlVVV 62 (202)
-+.+-=.|| |.++||.+|+. .+.++.+++. -|-++|
T Consensus 67 ~vIl~HNHPsG~~~PS~~D~~~T~~L~~~~~~l~I~llDHiIv 109 (123)
T PF04002_consen 67 SVILAHNHPSGDPEPSDADIALTRRLKKAARLLGIELLDHIIV 109 (123)
T ss_dssp EEEEEEE-TTS--S--HHHHHHHHHHHHHHHHHT-EEEEEEEE
T ss_pred eEEEEEEcCCCCCCCCHhHHHHHHHHHHHHHHcCCeeeeEEEE
Confidence 355556788 78999999983 4556667776 566665
No 26
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=30.70 E-value=30 Score=28.03 Aligned_cols=24 Identities=21% Similarity=0.511 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHhHhCCCCCeEEEe
Q psy397 40 VKKTDIREKLSKMFKSKPENIFAF 63 (202)
Q Consensus 40 PSRkEIreKLAamlnvd~dlVVVf 63 (202)
...++|++.||+.||+++++|-|.
T Consensus 164 ~~~~~i~~~la~~~~i~~~~I~V~ 187 (188)
T PF09581_consen 164 EEEEEIKQYLADFYGISPEQIKVY 187 (188)
T ss_pred HHHHHHHHHHHHHhCCCHHHeEEe
Confidence 446789999999999999999774
No 27
>COG0245 IspF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid metabolism]
Probab=29.86 E-value=1e+02 Score=26.45 Aligned_cols=39 Identities=13% Similarity=0.179 Sum_probs=30.9
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEeceeec
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTN 68 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg~kT~ 68 (202)
.+...-| |-.|-|.++|+.||+.+++++++|-|.-=.|+
T Consensus 97 tii~~~P-K~~P~~~amr~~ia~~L~i~~~~invKatT~E 135 (159)
T COG0245 97 TIIAQRP-KLGPYREAMRANIAELLGIPVDRINVKATTTE 135 (159)
T ss_pred EEEEecC-cccchHHHHHHHHHHHhCCCchheEEEEeccC
Confidence 4444455 47899999999999999999999988754443
No 28
>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A.
Probab=29.74 E-value=1.5e+02 Score=21.35 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.+-+-.|+|++|.+.+|++++..-+.-
T Consensus 22 ~~~Tv~eLK~kl~~~~Gi~~~~m~L~l 48 (87)
T PF14560_consen 22 KSITVSELKQKLEKLTGIPPSDMRLQL 48 (87)
T ss_dssp TTSBHHHHHHHHHHHHTS-TTTEEEEE
T ss_pred CCCCHHHHHHHHHHHhCCCcccEEEEE
Confidence 456789999999999999988777754
No 29
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=29.62 E-value=72 Score=28.57 Aligned_cols=37 Identities=24% Similarity=0.239 Sum_probs=23.0
Q ss_pred EEEEcC-CCCCCCHHHHH--HHHHhHhCCCCCeEEEeceee
Q psy397 30 VDVLHP-GKPSVKKTDIR--EKLSKMFKSKPENIFAFGFQT 67 (202)
Q Consensus 30 fdV~Hp-GkaTPSRkEIr--eKLAamlnvd~dlVVVfg~kT 67 (202)
+-=.|| |.+|||++|+. ++|++..+. -+-.+++-+-.
T Consensus 171 laHNHPSGd~~PS~aD~~iT~rl~~a~~l-l~I~vLDHiIi 210 (224)
T COG2003 171 LAHNHPSGDPTPSRADILITERLKEAGKL-LGIRLLDHIII 210 (224)
T ss_pred eeccCCCCCCCcCHHHHHHHHHHHHHHHh-cCceeeeeEEe
Confidence 334677 79999999874 566665544 23344444444
No 30
>KOG1051|consensus
Probab=29.54 E-value=92 Score=32.98 Aligned_cols=92 Identities=22% Similarity=0.298 Sum_probs=66.6
Q ss_pred ceeccCccceeEEEEEEcCCCCCCCHHHHHHHHHhHhC----C-CCCeEEEeceeecCCCCEEEEEEEEeCCHHHHHhcC
Q psy397 17 YMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFK----S-KPENIFAFGFQTNFGGGKSTGFALIYDSIDLAKKFE 91 (202)
Q Consensus 17 f~eNpLL~RREv~fdV~HpGkaTPSRkEIreKLAamln----v-d~dlVVVfg~kT~FGgGkStGfA~IYDS~E~aKK~E 91 (202)
+.-++|..++=+.+++-.-..++..|.|+.++|=...+ . ..=.+++..+++--|.|.+ |...+.+.++.
T Consensus 236 ~vp~~l~~~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfigelh~lvg~g~~------~~~~d~~nlLk 309 (898)
T KOG1051|consen 236 DVPETLKDKKLIALDFGSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLGELHWLVGSGSN------YGAIDAANLLK 309 (898)
T ss_pred CCCccccccceEEEEhhhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEecceeeeecCCCc------chHHHHHHhhH
Confidence 34445566666666666556788999999999977775 3 2335677899999999988 44778888877
Q ss_pred cceeeeeCCccceeeeeeeeecccccccccccc
Q psy397 92 PKYRLQRVSTKSLLVLIIATIGITSCQEAEHKI 124 (202)
Q Consensus 92 PKyrL~Rngl~ek~~~~~~~~~~~~~~~~~~~~ 124 (202)
|. |+|++ +-.||-|+|||-..-|
T Consensus 310 p~--L~rg~--------l~~IGatT~e~Y~k~i 332 (898)
T KOG1051|consen 310 PL--LARGG--------LWCIGATTLETYRKCI 332 (898)
T ss_pred HH--HhcCC--------eEEEecccHHHHHHHH
Confidence 64 67777 5678888888875443
No 31
>TIGR01485 SPP_plant-cyano sucrose-6F-phosphate phosphohydrolase. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
Probab=28.91 E-value=1.1e+02 Score=25.66 Aligned_cols=32 Identities=22% Similarity=0.372 Sum_probs=24.4
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 30 VDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 30 fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+++.++| .+|.+--+.|++++|.+++.++.+|
T Consensus 159 ldi~~~~---~~K~~al~~l~~~~~i~~~~~i~~G 190 (249)
T TIGR01485 159 LDILPQG---SGKGQALQYLLQKLAMEPSQTLVCG 190 (249)
T ss_pred EEEEeCC---CChHHHHHHHHHHcCCCccCEEEEE
Confidence 4566655 6777778999999999887777765
No 32
>PRK05387 histidinol-phosphate aminotransferase; Provisional
Probab=28.91 E-value=48 Score=28.49 Aligned_cols=25 Identities=16% Similarity=0.402 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 40 VKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 40 PSRkEIreKLAamlnvd~dlVVVfg 64 (202)
|.-.++|+.+|+.+++++++|++..
T Consensus 60 ~~~~~lr~aia~~~~~~~~~I~it~ 84 (353)
T PRK05387 60 PNADALRQAIAAYYGLDPEQVFVGN 84 (353)
T ss_pred CcHHHHHHHHHHHhCCCHHHEEEcC
Confidence 4457999999999999999888865
No 33
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=28.90 E-value=43 Score=22.74 Aligned_cols=22 Identities=27% Similarity=0.398 Sum_probs=14.6
Q ss_pred CCCCCCHHHHHHHHHhHhCCCC
Q psy397 36 GKPSVKKTDIREKLSKMFKSKP 57 (202)
Q Consensus 36 GkaTPSRkEIreKLAamlnvd~ 57 (202)
+-.|.+.++||+.|.+.||+|-
T Consensus 17 dl~~vT~k~vr~~Le~~~~~dL 38 (54)
T PF08766_consen 17 DLDTVTKKQVREQLEERFGVDL 38 (54)
T ss_dssp -GGG--HHHHHHHHHHH-SS--
T ss_pred CHhHhhHHHHHHHHHHHHCCCc
Confidence 4468899999999999999873
No 34
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=28.58 E-value=91 Score=26.48 Aligned_cols=38 Identities=11% Similarity=0.142 Sum_probs=29.8
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEeceee
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQT 67 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg~kT 67 (202)
.+....| +=.|-|.++|+.||+.++.++++|-|.-=.|
T Consensus 99 tii~e~P-Ki~p~~~~m~~~la~~L~i~~~~V~iKatT~ 136 (159)
T PRK00084 99 TIIAQRP-KMAPHIEEMRANIAEDLGIPLDDVNVKATTT 136 (159)
T ss_pred EEEcCCC-cchHHHHHHHHHHHHHhCCCcceEEEEEecC
Confidence 4444455 4789999999999999999999998865433
No 35
>KOG3969|consensus
Probab=28.50 E-value=59 Score=30.55 Aligned_cols=56 Identities=16% Similarity=0.373 Sum_probs=45.7
Q ss_pred HHHHHHHHHhHhCCCCCeEEEe---------------ceeecCCCCEEEEEEEEeCCHHHHHhcCcceeee
Q psy397 42 KTDIREKLSKMFKSKPENIFAF---------------GFQTNFGGGKSTGFALIYDSIDLAKKFEPKYRLQ 97 (202)
Q Consensus 42 RkEIreKLAamlnvd~dlVVVf---------------g~kT~FGgGkStGfA~IYDS~E~aKK~EPKyrL~ 97 (202)
|..+++.+.+.||+++|.+.++ +++-.-|.|.+.|.|..-|+.=..-.+-|+|--+
T Consensus 218 r~k~~~~i~~~y~v~~dqlrmf~HYqPSyYHlHVHi~nik~~~~~~~~~~rAilLddVI~nL~~~P~~Y~k 288 (310)
T KOG3969|consen 218 RNKSREAIPQRYGVDPDQLRMFFHYQPSYYHLHVHIVNIKHDHAPGSGCGRAILLDDVIENLELDPEGYKK 288 (310)
T ss_pred HHHHHHHHHHHhCCCchhEEEEEEecCceEEEEEEEEeccCCCCCCccccceeeHHHHHHHhccChHhhhh
Confidence 6778899999999999988664 4555569999999999999987777778876544
No 36
>PLN03026 histidinol-phosphate aminotransferase; Provisional
Probab=28.22 E-value=63 Score=28.86 Aligned_cols=26 Identities=19% Similarity=0.153 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 39 SVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 39 TPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.|.-.++|++||+.+++++++|++.+
T Consensus 85 ~~~~~~lr~~ia~~~~~~~~~I~~t~ 110 (380)
T PLN03026 85 DPESRRLRAALAEDSGLESENILVGC 110 (380)
T ss_pred CCCHHHHHHHHHHHhCcChhhEEEcC
Confidence 35578999999999999999887743
No 37
>PRK04781 histidinol-phosphate aminotransferase; Provisional
Probab=28.08 E-value=53 Score=29.05 Aligned_cols=26 Identities=15% Similarity=0.360 Sum_probs=22.0
Q ss_pred CCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 39 SVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 39 TPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.|...++|+.||+.+|+++++|++..
T Consensus 58 ~~~~~~lr~~ia~~~~~~~~~I~~t~ 83 (364)
T PRK04781 58 DPQPPGLRSALAALYGCAPEQLLIGR 83 (364)
T ss_pred CCCHHHHHHHHHHHhCcChHHEEEeC
Confidence 45578999999999999998888754
No 38
>PRK01158 phosphoglycolate phosphatase; Provisional
Probab=27.99 E-value=77 Score=25.54 Aligned_cols=33 Identities=30% Similarity=0.544 Sum_probs=25.0
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.+++.++| .+|..--+.|++.+|.+++.++.+|
T Consensus 148 ~~ei~~~~---~~Kg~al~~l~~~~~i~~~~~i~~G 180 (230)
T PRK01158 148 AIHIKSPG---VNKGTGLKKLAELMGIDPEEVAAIG 180 (230)
T ss_pred EEEEeeCC---CChHHHHHHHHHHhCCCHHHEEEEC
Confidence 35666655 7888888899999999877776654
No 39
>PRK14807 histidinol-phosphate aminotransferase; Provisional
Probab=27.42 E-value=74 Score=27.79 Aligned_cols=26 Identities=27% Similarity=0.423 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 39 SVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 39 TPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.|.-.++|+++|+.+++++++|++.+
T Consensus 58 ~~~~~~lr~~ia~~~~~~~~~i~it~ 83 (351)
T PRK14807 58 DPTAEKLREELARYCSVVPTNIFVGN 83 (351)
T ss_pred CccHHHHHHHHHHHhCCCcccEEEec
Confidence 45678999999999999988887764
No 40
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=27.23 E-value=1.8e+02 Score=20.75 Aligned_cols=25 Identities=16% Similarity=0.335 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEE
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFA 62 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVV 62 (202)
++-+-.|+|+++|+..+.+++..-+
T Consensus 20 ~~~TV~~LK~~I~~~~~~~~~~qrL 44 (78)
T cd01804 20 PDETVEGLKKRISQRLKVPKERLAL 44 (78)
T ss_pred CcCHHHHHHHHHHHHhCCChHHEEE
Confidence 4567899999999999987665443
No 41
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=25.74 E-value=45 Score=24.38 Aligned_cols=18 Identities=22% Similarity=0.296 Sum_probs=13.4
Q ss_pred EEEEEcC-CCCCCCHHHHH
Q psy397 29 VVDVLHP-GKPSVKKTDIR 46 (202)
Q Consensus 29 ~fdV~Hp-GkaTPSRkEIr 46 (202)
.+-=.|| |.+.||.+|++
T Consensus 60 ~i~HsHP~g~~~PS~~D~~ 78 (101)
T cd08059 60 GLVHSHPSGSCRPSEADLS 78 (101)
T ss_pred EEEecCcCCCCCCCHHHHH
Confidence 3334567 78999999986
No 42
>PHA01976 helix-turn-helix protein
Probab=25.60 E-value=55 Score=21.92 Aligned_cols=24 Identities=8% Similarity=0.065 Sum_probs=17.6
Q ss_pred CCCCCCHHHHHHHHHhHhCCCCCeE
Q psy397 36 GKPSVKKTDIREKLSKMFKSKPENI 60 (202)
Q Consensus 36 GkaTPSRkEIreKLAamlnvd~dlV 60 (202)
|+..|+...+ .+||+.||++++.+
T Consensus 38 g~~~p~~~~l-~~ia~~l~v~~~~l 61 (67)
T PHA01976 38 DKRLPNLKTL-LRLADALGVTLDWL 61 (67)
T ss_pred CCCCCCHHHH-HHHHHHHCcCHHHH
Confidence 5556765555 79999999987643
No 43
>PRK07392 threonine-phosphate decarboxylase; Validated
Probab=25.53 E-value=70 Score=27.97 Aligned_cols=25 Identities=20% Similarity=0.222 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 40 VKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 40 PSRkEIreKLAamlnvd~dlVVVfg 64 (202)
|.-.++|+.||+.+++++++|++..
T Consensus 57 ~~~~~Lr~aia~~~~v~~~~I~it~ 81 (360)
T PRK07392 57 PDYRELRLALAQHHQLPPEWILPGN 81 (360)
T ss_pred cCHHHHHHHHHHHhCcChhhEEECC
Confidence 4456999999999999999998865
No 44
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=25.17 E-value=1.1e+02 Score=21.96 Aligned_cols=25 Identities=20% Similarity=0.397 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEE
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFA 62 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVV 62 (202)
++.+-.|+|+++|+..|.+++..-+
T Consensus 20 ~~~TV~~LK~~I~~~~~~~~~~qrL 44 (73)
T cd01791 20 PDDTIGDLKKLIAAQTGTRPEKIVL 44 (73)
T ss_pred CCCcHHHHHHHHHHHhCCChHHEEE
Confidence 6788999999999999998776644
No 45
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=24.97 E-value=1.3e+02 Score=23.99 Aligned_cols=47 Identities=17% Similarity=0.365 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCEEEEEEEE-eCCHHHHHh
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALI-YDSIDLAKK 89 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGkStGfA~I-YDS~E~aKK 89 (202)
.+.+.++|++-+.+ ++.=.+..++.+-.| +++.|||.| |.+.+.+++
T Consensus 44 ~~~te~~L~~~F~~-~G~I~~v~i~~d~~t----g~~kGfaFV~F~~~e~A~~ 91 (144)
T PLN03134 44 WGTDDASLRDAFAH-FGDVVDAKVIVDRET----GRSRGFGFVNFNDEGAATA 91 (144)
T ss_pred CCCCHHHHHHHHhc-CCCeEEEEEEecCCC----CCcceEEEEEECCHHHHHH
Confidence 45678888888854 664334444444444 555566664 555555544
No 46
>COG0561 Cof Predicted hydrolases of the HAD superfamily [General function prediction only]
Probab=24.91 E-value=88 Score=26.08 Aligned_cols=32 Identities=34% Similarity=0.554 Sum_probs=26.7
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 30 VDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 30 fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
++|.+.| .+|..--+.|++.+|.+++.++.||
T Consensus 181 lei~~~g---~~K~~al~~l~~~lgi~~~~v~afG 212 (264)
T COG0561 181 LDITPKG---VSKGYALQRLAKLLGIKLEEVIAFG 212 (264)
T ss_pred EEEecCC---CchHHHHHHHHHHhCCCHHHeEEeC
Confidence 6677766 8999999999999999988777663
No 47
>PF11013 DUF2851: Protein of unknown function (DUF2851); InterPro: IPR021272 This bacterial family of proteins has no known function.
Probab=24.77 E-value=20 Score=33.90 Aligned_cols=12 Identities=58% Similarity=1.118 Sum_probs=10.5
Q ss_pred ceeecCceeeee
Q psy397 180 SYHCKGSDWYLH 191 (202)
Q Consensus 180 ~~~~~~~~~~~~ 191 (202)
--|++.||||.|
T Consensus 61 EiH~~sSDW~~H 72 (377)
T PF11013_consen 61 EIHLKSSDWYRH 72 (377)
T ss_pred EEEcchhhHhhc
Confidence 469999999977
No 48
>cd00554 MECDP_synthase MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea. MECDP_synthase forms a homotrimer, carrying three active sites, each of which is formed in a cleft between pairs of subunits.
Probab=24.64 E-value=1.3e+02 Score=25.37 Aligned_cols=36 Identities=17% Similarity=0.266 Sum_probs=28.9
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 28 MVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 28 v~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+.+....| |=.|=|.++++.||+.++.+++.|-|.-
T Consensus 95 ~tii~e~P-Ki~p~~~~m~~~ls~~L~~~~~~V~iKa 130 (153)
T cd00554 95 ITIIAERP-KISPYREAMRANLAELLGIPPSRVNIKA 130 (153)
T ss_pred EEEEecCC-cchHHHHHHHHHHHHHhCCCCceEEEEE
Confidence 34445555 4789999999999999999999988864
No 49
>TIGR01141 hisC histidinol-phosphate aminotransferase. Histidinol-phosphate aminotransferase is a pyridoxal-phosphate dependent enzyme.
Probab=24.31 E-value=74 Score=27.27 Aligned_cols=27 Identities=19% Similarity=0.459 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+.|.-.++|+.+|+.+++++++|++..
T Consensus 52 ~~~~~~~lr~~ia~~~~~~~~~i~~~~ 78 (346)
T TIGR01141 52 PDPDPAELKQALADYYGVDPEQILLGN 78 (346)
T ss_pred CCCCHHHHHHHHHHHhCcChHHEEEcC
Confidence 345668999999999999888777643
No 50
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=24.12 E-value=89 Score=23.68 Aligned_cols=35 Identities=26% Similarity=0.276 Sum_probs=23.1
Q ss_pred EEEEEcCCCCCCCH-----HHHHHHHHhHhCCCCCeEEEe
Q psy397 29 VVDVLHPGKPSVKK-----TDIREKLSKMFKSKPENIFAF 63 (202)
Q Consensus 29 ~fdV~HpGkaTPSR-----kEIreKLAamlnvd~dlVVVf 63 (202)
.+.|.--|..++.. ++|-+.|++.+|+++++|+|.
T Consensus 60 ~v~i~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~rv~I~ 99 (116)
T PTZ00397 60 FVRVTSIGGISRSNNSSIAAAITKILASHLKVKSERVYIE 99 (116)
T ss_pred EEEEEEecCCCHHHHHHHHHHHHHHHHHHhCcCcccEEEE
Confidence 44555445455542 246667778899999999874
No 51
>PRK14809 histidinol-phosphate aminotransferase; Provisional
Probab=24.04 E-value=93 Score=27.09 Aligned_cols=25 Identities=16% Similarity=0.413 Sum_probs=21.3
Q ss_pred CCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 40 VKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 40 PSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+...++|+.+|+.+++++++|++..
T Consensus 65 ~~~~~lr~~ia~~~~~~~~~I~it~ 89 (357)
T PRK14809 65 ASHADLTAALADRWDVSPEQVWLAN 89 (357)
T ss_pred CCHHHHHHHHHHHhCCCcceEEECC
Confidence 4577999999999999999887754
No 52
>PRK06358 threonine-phosphate decarboxylase; Provisional
Probab=23.62 E-value=82 Score=27.71 Aligned_cols=25 Identities=12% Similarity=0.191 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 40 VKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 40 PSRkEIreKLAamlnvd~dlVVVfg 64 (202)
|.-.++|+++|+.+++++++|++..
T Consensus 54 ~~~~~lr~~ia~~~~~~~~~i~it~ 78 (354)
T PRK06358 54 PDYLELRKRIASFEQLDLENVILGN 78 (354)
T ss_pred ccHHHHHHHHHHHhCCChhhEEECC
Confidence 4567999999999999999988754
No 53
>PRK08056 threonine-phosphate decarboxylase; Provisional
Probab=23.20 E-value=75 Score=27.81 Aligned_cols=25 Identities=16% Similarity=0.191 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 40 VKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 40 PSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+.-.++|+.+|+.+++++++|++..
T Consensus 55 ~~~~~lr~~ia~~~~~~~~~i~it~ 79 (356)
T PRK08056 55 VEYRHLHQALARHHQVPASWILAGN 79 (356)
T ss_pred ccHHHHHHHHHHHhCcChhhEEECC
Confidence 4578999999999999999988743
No 54
>PRK04635 histidinol-phosphate aminotransferase; Provisional
Probab=23.10 E-value=74 Score=27.82 Aligned_cols=24 Identities=17% Similarity=0.225 Sum_probs=21.0
Q ss_pred CHHHHHHHHHhHhCCCCCeEEEec
Q psy397 41 KKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 41 SRkEIreKLAamlnvd~dlVVVfg 64 (202)
...++++++|+.+|+++++|++..
T Consensus 61 ~~~~Lr~aia~~~~~~~~~I~it~ 84 (354)
T PRK04635 61 QPPELINAYSAYAGVAPEQILTSR 84 (354)
T ss_pred CHHHHHHHHHHHhCcCHHHEEEeC
Confidence 468999999999999999998854
No 55
>TIGR03576 pyridox_MJ0158 pyridoxal phosphate enzyme, MJ0158 family. Members of this archaeal protein family are pyridoxal phosphate enzymes of unknown function. Sequence similarity to SelA, a bacterial enzyme of selenocysteine biosynthesis, has led to some members being misannotated as functionally equivalent, but selenocysteine is made on tRNA in Archaea by a two-step process that does not involve a SelA homolog.
Probab=23.09 E-value=69 Score=28.75 Aligned_cols=27 Identities=19% Similarity=0.367 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.++-..++.++||+.+|++++.+++++
T Consensus 52 ~~~~~~~Le~~lA~~~g~~~e~ilv~~ 78 (346)
T TIGR03576 52 PAIFEEKVQELGREHLGGPEEKILVFN 78 (346)
T ss_pred CHHHHHHHHHHHHHHcCCCcceEEEEC
Confidence 678889999999999999888888875
No 56
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=23.06 E-value=1.4e+02 Score=26.67 Aligned_cols=33 Identities=21% Similarity=0.162 Sum_probs=27.8
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEE
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIF 61 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVV 61 (202)
.+.=+|.=..|||.+++.+.+.+|...++|.+=
T Consensus 119 vI~SyH~F~~TP~~~~i~~~l~km~~~~aDivK 151 (231)
T COG0710 119 VIVSYHDFEKTPPLEEIIERLDKMESLGADIVK 151 (231)
T ss_pred EEEEeccCCCCCcHHHHHHHHHHHHhhCCCeEE
Confidence 556688888999999999999999988776553
No 57
>PRK08153 histidinol-phosphate aminotransferase; Provisional
Probab=22.60 E-value=63 Score=28.57 Aligned_cols=25 Identities=28% Similarity=0.369 Sum_probs=21.2
Q ss_pred CCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 40 VKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 40 PSRkEIreKLAamlnvd~dlVVVfg 64 (202)
|...++|++||+.+++++++|++..
T Consensus 67 ~~~~~Lr~~ia~~~~~~~~~I~it~ 91 (369)
T PRK08153 67 PENHDLRHALAAHHGVAPENIMVGE 91 (369)
T ss_pred CccHHHHHHHHHHhCCCHHHEEEcC
Confidence 3467999999999999988888765
No 58
>TIGR00151 ispF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes.
Probab=22.02 E-value=1.5e+02 Score=25.12 Aligned_cols=36 Identities=11% Similarity=0.191 Sum_probs=28.5
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 28 MVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 28 v~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+.+....| +=.|=|.++++.||+.++.+++.|-|.-
T Consensus 95 ~tii~e~P-Ki~p~~~~m~~~la~~L~~~~~~V~iKa 130 (155)
T TIGR00151 95 ITIIAQRP-KLLPHIPAMRENIAELLGIPLDSVNVKA 130 (155)
T ss_pred EEEEcCCC-cchHHHHHHHHHHHHHhCCCcceEEEEE
Confidence 34444455 4689999999999999999988888764
No 59
>PRK10530 pyridoxal phosphate (PLP) phosphatase; Provisional
Probab=21.83 E-value=1.1e+02 Score=25.24 Aligned_cols=32 Identities=25% Similarity=0.289 Sum_probs=24.8
Q ss_pred EEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 30 VDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 30 fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+++..+| .+|..--+++++.+|.+++.++.+|
T Consensus 191 ~ei~~~~---~~K~~~l~~l~~~~gi~~~e~i~~G 222 (272)
T PRK10530 191 VDIARKG---NSKGKRLTQWVEAQGWSMKNVVAFG 222 (272)
T ss_pred EEEecCC---CChHHHHHHHHHHcCCCHHHeEEeC
Confidence 5666665 5688888999999999887777664
No 60
>PRK09105 putative aminotransferase; Provisional
Probab=21.80 E-value=86 Score=27.97 Aligned_cols=24 Identities=13% Similarity=0.279 Sum_probs=20.9
Q ss_pred CHHHHHHHHHhHhCCCCCeEEEec
Q psy397 41 KKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 41 SRkEIreKLAamlnvd~dlVVVfg 64 (202)
...++|+.+|+.+|+++++|++..
T Consensus 79 ~~~~Lr~aia~~~~v~~e~I~it~ 102 (370)
T PRK09105 79 LEDDLRTLFAAQEGLPADHVMAYA 102 (370)
T ss_pred hHHHHHHHHHHHhCcChhhEEEcC
Confidence 478999999999999999998754
No 61
>TIGR01484 HAD-SF-IIB HAD-superfamily hydrolase, subfamily IIB. The IIB subfamily consists of Trehalose-6-phosphatase (TIGR00685), plant and cyanobacterial Sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase (pfam03332), a large subfamily ("Cof-like hydrolases", TIGR00099) containing many closely related bacterial sequences, a hypothetical equivalog containing the E. coli YedP protein, as well as two small clusters containing sequences whose relationship to the other groups is unclear.
Probab=21.43 E-value=1.5e+02 Score=23.61 Aligned_cols=33 Identities=36% Similarity=0.544 Sum_probs=25.0
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.++|..+| .+|.+.-+.+++.++.+++.++.+|
T Consensus 154 ~~ev~p~~---~~K~~~~~~~~~~~~~~~~~~~~~G 186 (204)
T TIGR01484 154 DLEVLPAG---VDKGSALQALLKELNGKRDEILAFG 186 (204)
T ss_pred EEEEecCC---CChHHHHHHHHHHhCCCHHHEEEEc
Confidence 44566544 7899999999999998877776654
No 62
>PRK03967 histidinol-phosphate aminotransferase; Provisional
Probab=21.39 E-value=1.2e+02 Score=26.56 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=21.3
Q ss_pred CCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 40 VKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 40 PSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+.-.++|+.+|+.+++++++|++..
T Consensus 55 ~g~~~lr~~ia~~~~~~~~~I~~t~ 79 (337)
T PRK03967 55 ITSDPLREAIAEFYGLDAENIAVGN 79 (337)
T ss_pred CCHHHHHHHHHHHhCcCcceEEEcC
Confidence 4568999999999999999987754
No 63
>TIGR00099 Cof-subfamily Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily. The members of this subfamily are restricted almost exclusively to bacteria (one sequences from S. pombe scores above trusted, while another is between trusted and noise). It is notable that no archaea are found in this group, the closest relations to the archaea found here being two Deinococcus sequences.
Probab=21.13 E-value=1.1e+02 Score=25.47 Aligned_cols=33 Identities=24% Similarity=0.457 Sum_probs=25.8
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.++|.++| .+|..--+++++.+|.+++.++.+|
T Consensus 179 ~leI~~~~---~~K~~~i~~~~~~~~~~~~~~~~~G 211 (256)
T TIGR00099 179 SIEITAKG---VSKGSALQSLAEALGISLEDVIAFG 211 (256)
T ss_pred eEEecCCC---CChHHHHHHHHHHcCCCHHHEEEeC
Confidence 34566655 7899999999999999888877664
No 64
>PRK03321 putative aminotransferase; Provisional
Probab=21.06 E-value=85 Score=27.12 Aligned_cols=26 Identities=15% Similarity=0.268 Sum_probs=21.9
Q ss_pred CCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 39 SVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 39 TPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.+...++++.+|+.+++++++|++..
T Consensus 56 ~~g~~~lr~~ia~~~~~~~~~I~~~~ 81 (352)
T PRK03321 56 DMGAVELRAALAEHLGVPPEHVAVGC 81 (352)
T ss_pred CCcHHHHHHHHHHHhCcCHHHEEECC
Confidence 45678999999999999998888754
No 65
>PF01863 DUF45: Protein of unknown function DUF45; InterPro: IPR002725 Members of this family are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines.
Probab=20.86 E-value=1.1e+02 Score=24.71 Aligned_cols=29 Identities=24% Similarity=0.363 Sum_probs=23.8
Q ss_pred HHHhHhCCCCCeEEEeceeecCCCCEEEE
Q psy397 48 KLSKMFKSKPENIFAFGFQTNFGGGKSTG 76 (202)
Q Consensus 48 KLAamlnvd~dlVVVfg~kT~FGgGkStG 76 (202)
..++.+|+.+..|.|..++|+.|.-.++|
T Consensus 120 ~~~~~~~~~~~~i~ir~~ksrWGsc~~~~ 148 (205)
T PF01863_consen 120 KYAKKLGLPPPKIKIRDMKSRWGSCSSKG 148 (205)
T ss_pred HHHHHcCCCcceEEEeehhhccccCCCCC
Confidence 34778899999999999999999874333
No 66
>smart00362 RRM_2 RNA recognition motif.
Probab=20.61 E-value=2.1e+02 Score=17.33 Aligned_cols=45 Identities=31% Similarity=0.461 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHHhHhCCCCCeEEEeceeecCCCCEEEEEEEE-eCCHHHHHhc
Q psy397 39 SVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALI-YDSIDLAKKF 90 (202)
Q Consensus 39 TPSRkEIreKLAamlnvd~dlVVVfg~kT~FGgGkStGfA~I-YDS~E~aKK~ 90 (202)
.-+..||++-+. .+|.-.+..+ .... | ...|+|.| |++.+.+++.
T Consensus 10 ~~~~~~l~~~~~-~~g~v~~~~~---~~~~-~--~~~~~~~v~f~~~~~a~~a 55 (72)
T smart00362 10 DVTEEDLKELFS-KFGPIESVKI---PKDT-G--KSKGFAFVEFESEEDAEKA 55 (72)
T ss_pred cCCHHHHHHHHH-hcCCEEEEEE---ecCC-C--CCCceEEEEeCCHHHHHHH
Confidence 456788988774 5553222111 1222 4 44455544 5666665543
No 67
>PRK01533 histidinol-phosphate aminotransferase; Validated
Probab=20.59 E-value=1.2e+02 Score=27.07 Aligned_cols=25 Identities=16% Similarity=0.239 Sum_probs=21.1
Q ss_pred CCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 40 VKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 40 PSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+.-.++|+.||+.+++++++|++..
T Consensus 64 ~g~~~Lr~aia~~~~~~~~~I~vt~ 88 (366)
T PRK01533 64 GGATTLRQTIANKLHVKMEQVLCGS 88 (366)
T ss_pred CCHHHHHHHHHHHhCCCcceEEECC
Confidence 3457899999999999999998754
No 68
>PF02542 YgbB: YgbB family; InterPro: IPR003526 MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[]. A number of proteins from eukaryotes and prokaryotes share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme of this type [].; GO: 0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity, 0016114 terpenoid biosynthetic process; PDB: 3T80_B 3GHZ_A 2PMP_A 3F6M_A 3FPI_A 3RE3_A 1T0A_C 1W57_A 1W55_A 3B6N_A ....
Probab=20.56 E-value=89 Score=26.50 Aligned_cols=28 Identities=25% Similarity=0.354 Sum_probs=23.9
Q ss_pred CCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 37 KPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 37 kaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+=.|=+.++++.||+.++.++++|-|.-
T Consensus 104 Ki~p~~~~m~~~la~~L~~~~~~V~iKa 131 (157)
T PF02542_consen 104 KISPYRPAMRENLAKLLGIPPDRVNIKA 131 (157)
T ss_dssp TTGGGHHHHHHHHHHHHTS-GGGEEEEE
T ss_pred ccHHHHHHHHHHHHHHhCCCcceEEEEE
Confidence 4689999999999999999999987753
No 69
>PF12327 FtsZ_C: FtsZ family, C-terminal domain; InterPro: IPR024757 The FtsZ family of proteins are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin []. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea []. This entry represents a domain of FtsZ. In most FtsZ proteins is found in the C terminus, except in some alphaproteobacteria proteins where there is an extension C-terminal domain TIGR03483 from TIGRFAMs.; PDB: 2RHO_B 2RHJ_A 2VXY_A 2RHL_B 2RHH_A 2VAM_A 1W5F_B 2R75_1 2R6R_1 1RQ7_A ....
Probab=20.43 E-value=78 Score=23.84 Aligned_cols=51 Identities=18% Similarity=0.328 Sum_probs=31.1
Q ss_pred ecceeccCccceeE----EEEEEcCCCCCCCHHHHHHHHHhHhC-CCCCeEEEecee
Q psy397 15 RKYMTNRLLGRKQM----VVDVLHPGKPSVKKTDIREKLSKMFK-SKPENIFAFGFQ 66 (202)
Q Consensus 15 RKf~eNpLL~RREv----~fdV~HpGkaTPSRkEIreKLAamln-vd~dlVVVfg~k 66 (202)
.+-++||||+ .++ .+-|.-.|.+.++-.|+.+..-.... ++++.-+++|..
T Consensus 21 ~~Al~spLl~-~~i~~A~~vLvni~~~~d~~l~ev~~~~~~i~~~~~~~a~ii~G~~ 76 (95)
T PF12327_consen 21 EQALNSPLLD-VDIKGAKGVLVNITGGPDLSLSEVNEAMEIIREKADPDANIIWGAS 76 (95)
T ss_dssp HHHHTSTTST-S-GGG-SEEEEEEEE-TTS-HHHHHHHHHHHHHHSSTTSEEEEEEE
T ss_pred HHHHhCcccc-CChHHhceEEEEEEcCCCCCHHHHHHHHHHHHHHhhcCceEEEEEE
Confidence 4567899998 544 33344456688999998887755532 356666666654
No 70
>PF08282 Hydrolase_3: haloacid dehalogenase-like hydrolase; InterPro: IPR013200 The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification []. This HAD domain is found in several distinct enzymes including: Phospholipid-transporting ATPase 1 (3.6.3.1 from EC), a putative lipid-flipping enzyme involved in cold tolerance in Arabidopsis [] 3-deoxy-D-manno-octulosonate (KDO) 8-phosphate phosphatase (3.1.3.45 from EC), which catalyses the final step in the biosynthesis of KDO - a component of lipopolysaccharide in Gram-negative bacteria [] Mannosyl-3-phosphoglycerate phosphatase (3.1.3.70 from EC), which hydrolyzes mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate [] Phosphoglycolate phopshatase (3.1.3.18 from EC), which catalyses the dephosphorylation of 2-phosphoglycolate [] ; PDB: 2B30_B 3R4C_A 1XVI_B 3IJ5_B 3MMZ_C 3L7Y_A 1XPJ_C 1RLT_B 1RLM_B 2HF2_A ....
Probab=20.43 E-value=1.7e+02 Score=22.90 Aligned_cols=33 Identities=30% Similarity=0.504 Sum_probs=26.6
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 29 VVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 29 ~fdV~HpGkaTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
.++|...| .||..--++|++.+|.+++.++.+|
T Consensus 177 ~lei~~~~---vsK~~ai~~l~~~~~i~~~~~~~~G 209 (254)
T PF08282_consen 177 FLEITPKG---VSKGSAIKYLLEYLGISPEDIIAFG 209 (254)
T ss_dssp EEEEEETT---SSHHHHHHHHHHHHTTSGGGEEEEE
T ss_pred ceEEeeCC---CCHHHHHHHHhhhcccccceeEEee
Confidence 45666666 8999999999999999888777653
No 71
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=20.10 E-value=30 Score=22.65 Aligned_cols=23 Identities=26% Similarity=0.421 Sum_probs=17.6
Q ss_pred CCCCCHHHHHHHHHhHhCCCCCeE
Q psy397 37 KPSVKKTDIREKLSKMFKSKPENI 60 (202)
Q Consensus 37 kaTPSRkEIreKLAamlnvd~dlV 60 (202)
.+.|+.++ ++.||+.+|++++.|
T Consensus 22 ~~~p~~~~-~~~la~~l~l~~~~V 44 (57)
T PF00046_consen 22 NPYPSKEE-REELAKELGLTERQV 44 (57)
T ss_dssp SSSCHHHH-HHHHHHHHTSSHHHH
T ss_pred hccccccc-ccccccccccccccc
Confidence 46787777 678999999986654
No 72
>TIGR01140 L_thr_O3P_dcar L-threonine-O-3-phosphate decarboxylase. This family contains pyridoxal phosphate-binding class II aminotransferases (see PFAM:PF00222) closely related to, yet distinct from, histidinol-phosphate aminotransferase (HisC). It is found in cobalamin biosynthesis operons in Salmonella typhimurium and Bacillus halodurans (each of which also has HisC) and has been shown to have L-threonine-O-3-phosphate decarboxylase activity in Salmonella. Although the gene symbol cobD was assigned in Salmonella, cobD in other contexts refers to a different cobalamin biosynthesis enzyme, modeled by pfam03186 and called cbiB in Salmonella.
Probab=20.09 E-value=1.1e+02 Score=26.61 Aligned_cols=27 Identities=7% Similarity=0.284 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHHHhHhCCCCCeEEEec
Q psy397 38 PSVKKTDIREKLSKMFKSKPENIFAFG 64 (202)
Q Consensus 38 aTPSRkEIreKLAamlnvd~dlVVVfg 64 (202)
+.|.-.++|+.+|+.+|+++++|++..
T Consensus 45 ~~~~~~~lr~~la~~~~~~~~~i~~t~ 71 (330)
T TIGR01140 45 PDPEYDELRAAAAAYYGLPAASVLPVN 71 (330)
T ss_pred CCccHHHHHHHHHHHhCCChhhEEECC
Confidence 556679999999999999888877654
Done!