Query 032398
Match_columns 141
No_of_seqs 130 out of 297
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 13:34:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032398.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032398hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3152 TBP-binding protein, a 99.7 1.3E-18 2.8E-23 147.1 4.3 58 84-141 54-111 (278)
2 PF00076 RRM_1: RNA recognitio 98.2 1.2E-06 2.7E-11 54.6 3.3 32 107-138 1-32 (70)
3 PF14259 RRM_6: RNA recognitio 98.0 5.5E-06 1.2E-10 53.0 3.6 33 107-139 1-33 (70)
4 KOG4208 Nucleolar RNA-binding 98.0 3.3E-06 7.2E-11 70.2 3.0 40 100-139 45-85 (214)
5 smart00362 RRM_2 RNA recogniti 98.0 1.3E-05 2.8E-10 48.2 4.0 33 107-139 2-34 (72)
6 cd00590 RRM RRM (RNA recogniti 97.7 5.2E-05 1.1E-09 45.7 3.9 34 106-139 1-34 (74)
7 TIGR01661 ELAV_HUD_SF ELAV/HuD 97.3 0.00029 6.3E-09 57.1 4.1 34 106-139 271-304 (352)
8 PLN03134 glycine-rich RNA-bind 97.2 0.00036 7.8E-09 52.9 3.9 37 102-138 32-68 (144)
9 smart00360 RRM RNA recognition 97.1 0.00062 1.3E-08 40.5 3.0 31 109-139 1-31 (71)
10 COG0724 RNA-binding proteins ( 97.0 0.0011 2.5E-08 47.6 4.1 36 104-139 115-150 (306)
11 TIGR01649 hnRNP-L_PTB hnRNP-L/ 96.7 0.002 4.4E-08 56.4 4.1 35 104-138 275-310 (481)
12 TIGR01622 SF-CC1 splicing fact 96.6 0.003 6.5E-08 53.4 4.3 35 104-138 186-220 (457)
13 TIGR01642 U2AF_lg U2 snRNP aux 96.3 0.0041 8.9E-08 53.2 3.9 35 104-138 295-329 (509)
14 KOG0148 Apoptosis-promoting RN 96.3 0.0035 7.7E-08 54.8 3.5 41 99-139 159-199 (321)
15 TIGR01659 sex-lethal sex-letha 96.3 0.0046 9.9E-08 53.3 4.1 36 103-138 106-141 (346)
16 KOG0113 U1 small nuclear ribon 96.3 0.0035 7.6E-08 55.2 3.4 34 106-139 103-136 (335)
17 TIGR01659 sex-lethal sex-letha 96.3 0.0043 9.3E-08 53.4 3.7 36 104-139 193-228 (346)
18 TIGR01661 ELAV_HUD_SF ELAV/HuD 96.1 0.007 1.5E-07 49.1 3.9 34 105-138 90-123 (352)
19 TIGR01645 half-pint poly-U bin 96.1 0.0058 1.3E-07 57.0 3.8 36 104-139 204-239 (612)
20 TIGR01628 PABP-1234 polyadenyl 96.0 0.014 3E-07 51.4 5.5 37 103-139 284-320 (562)
21 TIGR01622 SF-CC1 splicing fact 96.0 0.0083 1.8E-07 50.8 4.0 35 104-138 89-123 (457)
22 TIGR01645 half-pint poly-U bin 96.0 0.027 5.8E-07 52.7 7.6 37 102-138 105-141 (612)
23 TIGR01649 hnRNP-L_PTB hnRNP-L/ 95.9 0.01 2.2E-07 52.1 4.0 35 105-139 97-131 (481)
24 KOG0122 Translation initiation 95.5 0.012 2.7E-07 50.6 3.2 36 104-139 189-224 (270)
25 PLN03213 repressor of silencin 95.2 0.022 4.7E-07 53.8 4.0 37 104-140 10-46 (759)
26 TIGR01628 PABP-1234 polyadenyl 95.2 0.025 5.3E-07 49.8 4.1 36 104-139 178-213 (562)
27 TIGR01648 hnRNP-R-Q heterogene 95.1 0.024 5.2E-07 52.6 4.0 34 105-138 59-92 (578)
28 KOG0144 RNA-binding protein CU 94.6 0.028 6E-07 51.9 3.1 33 107-139 37-69 (510)
29 TIGR01648 hnRNP-R-Q heterogene 94.5 0.042 9.2E-07 51.0 4.0 35 103-137 232-268 (578)
30 KOG0114 Predicted RNA-binding 94.4 0.053 1.1E-06 42.2 3.6 36 103-138 17-52 (124)
31 KOG0121 Nuclear cap-binding pr 94.2 0.048 1E-06 43.7 3.1 36 101-136 33-68 (153)
32 KOG0127 Nucleolar protein fibr 93.9 0.035 7.6E-07 52.5 2.1 36 102-137 290-325 (678)
33 KOG0126 Predicted RNA-binding 93.9 0.014 3E-07 48.9 -0.5 38 102-139 33-70 (219)
34 KOG0145 RNA-binding protein EL 93.7 0.041 8.9E-07 48.5 2.1 30 103-132 126-155 (360)
35 PF13893 RRM_5: RNA recognitio 93.6 0.055 1.2E-06 33.6 2.1 19 121-139 1-19 (56)
36 KOG0107 Alternative splicing f 93.2 0.11 2.4E-06 43.1 3.8 35 106-140 12-46 (195)
37 KOG4205 RNA-binding protein mu 92.4 0.12 2.5E-06 44.9 2.9 31 105-135 98-128 (311)
38 KOG0116 RasGAP SH3 binding pro 91.7 0.15 3.3E-06 45.9 3.0 34 105-138 289-322 (419)
39 KOG0149 Predicted RNA-binding 91.5 0.15 3.3E-06 43.6 2.6 31 106-136 14-44 (247)
40 KOG0125 Ataxin 2-binding prote 91.4 0.13 2.9E-06 46.1 2.2 36 101-136 93-128 (376)
41 TIGR01642 U2AF_lg U2 snRNP aux 90.9 0.29 6.3E-06 42.0 3.8 25 104-128 175-199 (509)
42 KOG0117 Heterogeneous nuclear 90.7 0.17 3.6E-06 46.9 2.3 35 102-136 257-291 (506)
43 KOG0144 RNA-binding protein CU 88.9 0.18 3.9E-06 46.7 1.0 34 107-140 127-160 (510)
44 KOG0533 RRM motif-containing p 88.4 0.57 1.2E-05 39.6 3.6 37 102-138 81-117 (243)
45 KOG1548 Transcription elongati 85.9 0.47 1E-05 42.8 1.8 30 104-133 134-163 (382)
46 KOG0117 Heterogeneous nuclear 85.7 0.7 1.5E-05 43.0 2.9 34 106-139 85-118 (506)
47 PF14605 Nup35_RRM_2: Nup53/35 85.2 0.89 1.9E-05 29.5 2.5 31 107-138 4-34 (53)
48 KOG0124 Polypyrimidine tract-b 84.6 0.97 2.1E-05 41.8 3.3 38 102-139 208-245 (544)
49 KOG0132 RNA polymerase II C-te 84.0 1 2.2E-05 44.3 3.3 35 104-138 421-455 (894)
50 KOG0108 mRNA cleavage and poly 83.9 1.2 2.6E-05 40.4 3.5 33 105-137 19-51 (435)
51 PF15513 DUF4651: Domain of un 80.7 1.4 3.1E-05 30.7 2.2 20 119-138 9-28 (62)
52 PF08777 RRM_3: RNA binding mo 79.8 1.8 3.8E-05 31.6 2.6 34 106-139 3-36 (105)
53 KOG0130 RNA-binding protein RB 78.8 2.2 4.8E-05 34.7 3.1 33 105-137 73-105 (170)
54 KOG0110 RNA-binding protein (R 77.8 2.3 5E-05 41.2 3.3 34 103-136 384-417 (725)
55 KOG0123 Polyadenylate-binding 74.5 4 8.8E-05 35.8 3.8 39 101-139 267-305 (369)
56 KOG4660 Protein Mei2, essentia 73.4 2.8 6.1E-05 39.5 2.7 41 99-139 70-110 (549)
57 KOG0153 Predicted RNA-binding 73.1 3.8 8.2E-05 37.1 3.3 72 68-139 186-263 (377)
58 PF08675 RNA_bind: RNA binding 72.4 4.6 9.9E-05 29.9 3.0 35 101-136 6-40 (87)
59 smart00361 RRM_1 RNA recogniti 68.4 5.1 0.00011 26.1 2.4 18 118-135 2-23 (70)
60 KOG0147 Transcriptional coacti 66.3 3.2 6.8E-05 39.2 1.4 38 102-139 275-313 (549)
61 KOG0124 Polypyrimidine tract-b 64.1 3.6 7.7E-05 38.2 1.3 34 104-137 113-146 (544)
62 PF04940 BLUF: Sensors of blue 63.6 4.9 0.00011 28.6 1.7 22 106-127 4-25 (93)
63 KOG4207 Predicted splicing fac 63.0 7.8 0.00017 33.4 3.0 30 110-139 19-48 (256)
64 KOG0129 Predicted RNA-binding 62.5 5.4 0.00012 37.5 2.2 26 106-131 261-286 (520)
65 KOG0123 Polyadenylate-binding 62.0 8.6 0.00019 33.8 3.2 38 102-139 74-111 (369)
66 KOG0151 Predicted splicing reg 61.1 7.5 0.00016 38.4 2.9 30 106-135 176-205 (877)
67 cd00842 MPP_ASMase acid sphing 59.7 11 0.00024 30.4 3.2 39 92-130 200-248 (296)
68 KOG0145 RNA-binding protein EL 58.4 11 0.00023 33.8 3.1 33 107-139 44-76 (360)
69 PF03721 UDPG_MGDP_dh_N: UDP-g 46.0 12 0.00026 29.4 1.4 27 104-130 114-140 (185)
70 cd00027 BRCT Breast Cancer Sup 43.4 35 0.00075 19.9 2.9 25 106-130 3-27 (72)
71 KOG0148 Apoptosis-promoting RN 43.1 21 0.00045 31.9 2.5 36 104-139 62-97 (321)
72 cd01789 Alp11_N Ubiquitin-like 41.5 29 0.00062 24.0 2.6 28 110-137 17-46 (84)
73 cd07970 OBF_DNA_ligase_LigC Th 41.3 22 0.00048 26.4 2.1 22 106-128 31-52 (122)
74 COG2441 Predicted butyrate kin 38.3 24 0.00052 31.9 2.2 35 102-136 272-312 (374)
75 KOG2891 Surface glycoprotein [ 38.1 23 0.0005 32.1 2.1 38 99-136 144-193 (445)
76 PF06297 PET: PET Domain; Int 38.1 27 0.00058 26.3 2.1 24 107-130 19-42 (106)
77 PF06481 COX_ARM: COX Aromatic 37.2 14 0.0003 23.5 0.4 28 99-126 17-44 (47)
78 PF14581 SseB_C: SseB protein 37.1 9 0.00019 27.1 -0.5 20 118-137 21-40 (108)
79 COG5175 MOT2 Transcriptional r 35.3 34 0.00073 31.7 2.7 37 103-139 113-155 (480)
80 PHA01782 hypothetical protein 33.3 28 0.0006 28.8 1.7 23 110-132 61-83 (177)
81 KOG0115 RNA-binding protein p5 31.7 33 0.00072 30.1 2.0 32 105-136 32-63 (275)
82 KOG0120 Splicing factor U2AF, 29.8 35 0.00077 31.9 2.0 34 104-137 289-322 (500)
83 KOG4661 Hsp27-ERE-TATA-binding 29.3 36 0.00079 33.5 2.0 31 106-136 407-437 (940)
84 PF13433 Peripla_BP_5: Peripla 28.8 39 0.00084 30.2 2.0 40 100-140 104-143 (363)
85 PF06753 Bradykinin: Bradykini 28.6 27 0.00058 19.5 0.6 11 109-119 1-11 (19)
86 KOG0131 Splicing factor 3b, su 28.1 40 0.00086 28.5 1.8 30 104-133 96-125 (203)
87 PF11608 Limkain-b1: Limkain b 27.2 62 0.0013 24.2 2.5 22 106-127 4-25 (90)
88 KOG4210 Nuclear localization s 26.9 48 0.001 28.2 2.1 38 101-138 181-219 (285)
89 KOG0146 RNA-binding protein ET 26.6 44 0.00096 30.1 1.9 33 106-138 287-321 (371)
90 KOG4483 Uncharacterized conser 25.7 47 0.001 31.2 2.0 30 102-131 389-418 (528)
91 PF12949 HeH: HeH/LEM domain; 25.4 44 0.00095 20.7 1.2 17 113-129 1-17 (35)
92 PF02668 TauD: Taurine catabol 25.2 78 0.0017 24.1 2.8 28 102-131 34-61 (258)
93 PF05172 Nup35_RRM: Nup53/35/4 24.9 53 0.0012 24.2 1.8 28 106-135 9-36 (100)
94 KOG1457 RNA binding protein (c 24.2 61 0.0013 28.5 2.3 35 104-138 210-244 (284)
95 cd01393 recA_like RecA is a b 24.2 1.1E+02 0.0025 23.2 3.6 34 103-137 53-91 (226)
96 KOG0112 Large RNA-binding prot 23.6 36 0.00077 34.4 0.8 35 103-137 371-405 (975)
97 COG0724 RNA-binding proteins ( 23.5 1.1E+02 0.0023 21.9 3.1 39 100-138 221-259 (306)
98 PF04355 SmpA_OmlA: SmpA / Oml 22.7 59 0.0013 21.2 1.5 19 109-127 9-27 (71)
99 KOG0127 Nucleolar protein fibr 22.5 81 0.0017 30.7 2.9 33 106-138 119-151 (678)
100 cd00080 HhH2_motif Helix-hairp 22.2 32 0.00069 23.5 0.2 30 106-136 21-50 (75)
101 PF00837 T4_deiodinase: Iodoth 21.6 1E+02 0.0022 26.4 3.0 26 103-128 210-236 (237)
102 KOG1190 Polypyrimidine tract-b 21.6 83 0.0018 29.6 2.7 34 103-136 27-60 (492)
103 KOG0146 RNA-binding protein ET 21.3 56 0.0012 29.4 1.6 33 106-138 21-53 (371)
104 TIGR03767 P_acnes_RR metalloph 21.3 2.1E+02 0.0046 26.9 5.3 46 90-135 324-385 (496)
105 COG0106 HisA Phosphoribosylfor 20.9 1.1E+02 0.0023 26.3 3.0 29 106-137 100-128 (241)
106 PF05189 RTC_insert: RNA 3'-te 20.7 62 0.0013 22.9 1.4 34 103-136 9-45 (103)
107 PF12385 Peptidase_C70: Papain 20.4 76 0.0016 26.0 2.0 20 112-131 90-111 (166)
108 PF09992 DUF2233: Predicted pe 20.4 89 0.0019 23.3 2.3 34 103-136 99-136 (170)
109 KOG0110 RNA-binding protein (R 20.3 53 0.0012 32.3 1.3 33 104-136 613-645 (725)
No 1
>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]
Probab=99.74 E-value=1.3e-18 Score=147.12 Aligned_cols=58 Identities=55% Similarity=0.884 Sum_probs=47.5
Q ss_pred hhhhhhhHHHHHHHHhhcCCcceEEecCCCCCCCHHHHHHHhhccCccceEEeccCCC
Q 032398 84 SIVKSKKKQRLLEEAAKADRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPEDP 141 (141)
Q Consensus 84 ~~~kkkkkK~L~~~~~k~~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pEd~ 141 (141)
+..+.++...+....++..++||||||||||+|+|.+||+||++||+||||||+||+.
T Consensus 54 ~~l~~~k~~~~~~a~~kkrk~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~ 111 (278)
T KOG3152|consen 54 KELKEKKLTELSEAKAKKRKTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDD 111 (278)
T ss_pred hhhhhhhhcccchhhhhhccceEEEeccCCCccCHHHHHHHHHhccccceEEecchhh
Confidence 3344444445555555566999999999999999999999999999999999999973
No 2
>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=98.23 E-value=1.2e-06 Score=54.56 Aligned_cols=32 Identities=28% Similarity=0.608 Sum_probs=30.7
Q ss_pred EEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 107 CYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 107 IYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
|||+.||+.+++..|+++|++||.|..+.+.+
T Consensus 1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~ 32 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMR 32 (70)
T ss_dssp EEEESETTTSSHHHHHHHHHTTSTEEEEEEEE
T ss_pred cEEcCCCCcCCHHHHHHHHHHhhhcccccccc
Confidence 79999999999999999999999999998876
No 3
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=98.04 E-value=5.5e-06 Score=52.96 Aligned_cols=33 Identities=24% Similarity=0.613 Sum_probs=29.4
Q ss_pred EEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 107 CYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 107 IYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
|||++||+.+++..|+.+|++||.|.+|++...
T Consensus 1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~ 33 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKN 33 (70)
T ss_dssp EEEESSTTT--HHHHHHHCTTSSBEEEEEEEES
T ss_pred CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEee
Confidence 799999999999999999999999999999765
No 4
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]
Probab=98.03 E-value=3.3e-06 Score=70.15 Aligned_cols=40 Identities=20% Similarity=0.457 Sum_probs=37.1
Q ss_pred hcCCcceEEecCCCCCCCHHHHHHHhhcc-CccceEEeccC
Q 032398 100 KADRCGICYLSRIPAHMDPVKLRQILSQY-GEIQRIYLAPE 139 (141)
Q Consensus 100 k~~k~GVIYLSrIPpgM~p~kLR~~fsqf-GeV~RIyL~pE 139 (141)
.....||+|+.|||++|++.++..||.|| |.|+|++|+|.
T Consensus 45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRn 85 (214)
T KOG4208|consen 45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRN 85 (214)
T ss_pred ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecc
Confidence 34679999999999999999999999999 99999999885
No 5
>smart00362 RRM_2 RNA recognition motif.
Probab=97.96 E-value=1.3e-05 Score=48.17 Aligned_cols=33 Identities=15% Similarity=0.573 Sum_probs=30.9
Q ss_pred EEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 107 CYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 107 IYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
|||+.||+.++...|+++|++||.|.++++.+.
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~ 34 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKD 34 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecC
Confidence 899999999999999999999999999988754
No 6
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=97.73 E-value=5.2e-05 Score=45.75 Aligned_cols=34 Identities=15% Similarity=0.576 Sum_probs=31.6
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.|||+.||+.+.+..|+++|.+||.|.++++.+.
T Consensus 1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~ 34 (74)
T cd00590 1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRD 34 (74)
T ss_pred CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeC
Confidence 4899999999999999999999999999998764
No 7
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=97.29 E-value=0.00029 Score=57.07 Aligned_cols=34 Identities=15% Similarity=0.409 Sum_probs=31.8
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
+|||++||+..++..|+++|++||.|.++++...
T Consensus 271 ~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d 304 (352)
T TIGR01661 271 CIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRD 304 (352)
T ss_pred EEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEc
Confidence 5999999999999999999999999999998653
No 8
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=97.24 E-value=0.00036 Score=52.88 Aligned_cols=37 Identities=11% Similarity=0.217 Sum_probs=33.3
Q ss_pred CCcceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 102 DRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 102 ~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
..+..|||+.||+.+++..|+++|++||.|.++.+..
T Consensus 32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~ 68 (144)
T PLN03134 32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIV 68 (144)
T ss_pred CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEe
Confidence 3455799999999999999999999999999999864
No 9
>smart00360 RRM RNA recognition motif.
Probab=97.08 E-value=0.00062 Score=40.48 Aligned_cols=31 Identities=23% Similarity=0.629 Sum_probs=28.1
Q ss_pred ecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 109 LSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 109 LSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
|+.||..++...|+++|++||.|.++.+.+.
T Consensus 1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~ 31 (71)
T smart00360 1 VGNLPPDVTEEELRELFSKFGKIESVRLVRD 31 (71)
T ss_pred CCCCCcccCHHHHHHHHHhhCCEeEEEEEeC
Confidence 5789999999999999999999999988653
No 10
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=96.97 E-value=0.0011 Score=47.56 Aligned_cols=36 Identities=17% Similarity=0.528 Sum_probs=33.4
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
...|||+.||..+++..|+.+|.+||.|.+|++...
T Consensus 115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d 150 (306)
T COG0724 115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRD 150 (306)
T ss_pred CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeec
Confidence 589999999999999999999999999999988653
No 11
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=96.67 E-value=0.002 Score=56.43 Aligned_cols=35 Identities=14% Similarity=0.352 Sum_probs=32.1
Q ss_pred cceEEecCCCC-CCCHHHHHHHhhccCccceEEecc
Q 032398 104 CGICYLSRIPA-HMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 104 ~GVIYLSrIPp-gM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
..+|||+.||+ .+++..|+.+|++||.|.+|.+.+
T Consensus 275 ~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~ 310 (481)
T TIGR01649 275 GSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMK 310 (481)
T ss_pred CCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEe
Confidence 35999999998 699999999999999999999865
No 12
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=96.56 E-value=0.003 Score=53.44 Aligned_cols=35 Identities=23% Similarity=0.427 Sum_probs=32.6
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
+-.|||+.||+.+++..|+++|++||.|..|.|.+
T Consensus 186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~ 220 (457)
T TIGR01622 186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHR 220 (457)
T ss_pred CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEE
Confidence 46899999999999999999999999999998875
No 13
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=96.35 E-value=0.0041 Score=53.20 Aligned_cols=35 Identities=14% Similarity=0.456 Sum_probs=32.1
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
+-.|||+.||..+++..|+++|++||.|..+.|..
T Consensus 295 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~ 329 (509)
T TIGR01642 295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIK 329 (509)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEe
Confidence 45799999999999999999999999999988864
No 14
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=96.33 E-value=0.0035 Score=54.82 Aligned_cols=41 Identities=20% Similarity=0.340 Sum_probs=35.5
Q ss_pred hhcCCcceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 99 AKADRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 99 ~k~~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
+.....--||+|.|++++++..||+.|++||.|.-||+.+.
T Consensus 159 Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~ 199 (321)
T KOG0148|consen 159 QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD 199 (321)
T ss_pred cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc
Confidence 34445568999999999999999999999999999998764
No 15
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=96.32 E-value=0.0046 Score=53.26 Aligned_cols=36 Identities=14% Similarity=0.194 Sum_probs=32.7
Q ss_pred CcceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 103 RCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
..-.|||+.||+.+++..|+++|++||.|..|+|..
T Consensus 106 ~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~ 141 (346)
T TIGR01659 106 SGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMR 141 (346)
T ss_pred CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEe
Confidence 345899999999999999999999999999998854
No 16
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=96.32 E-value=0.0035 Score=55.18 Aligned_cols=34 Identities=29% Similarity=0.547 Sum_probs=32.0
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.+|||||+...++++|+..|+.||.|.||+|...
T Consensus 103 TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d 136 (335)
T KOG0113|consen 103 TLFVARLNYDTSESKLRREFEKYGPIKRIRLVRD 136 (335)
T ss_pred eeeeeeccccccHHHHHHHHHhcCcceeEEEeee
Confidence 5899999999999999999999999999999764
No 17
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=96.29 E-value=0.0043 Score=53.42 Aligned_cols=36 Identities=19% Similarity=0.411 Sum_probs=32.3
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.--|||+.||+.+++..|+++|++||+|.++.+.+.
T Consensus 193 ~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d 228 (346)
T TIGR01659 193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRD 228 (346)
T ss_pred cceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeec
Confidence 345999999999999999999999999999988653
No 18
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=96.11 E-value=0.007 Score=49.09 Aligned_cols=34 Identities=26% Similarity=0.455 Sum_probs=31.0
Q ss_pred ceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 105 GICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 105 GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
-.|||+.||+.+++..|+.+|++||.|.++.+..
T Consensus 90 ~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~ 123 (352)
T TIGR01661 90 ANLYVSGLPKTMTQHELESIFSPFGQIITSRILS 123 (352)
T ss_pred ceEEECCccccCCHHHHHHHHhccCCEEEEEEEe
Confidence 3699999999999999999999999998888754
No 19
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=96.09 E-value=0.0058 Score=57.04 Aligned_cols=36 Identities=17% Similarity=0.433 Sum_probs=33.3
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
...|||+.||+.+++..|+++|++||.|.+++|.+.
T Consensus 204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D 239 (612)
T TIGR01645 204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARA 239 (612)
T ss_pred cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEec
Confidence 457999999999999999999999999999999764
No 20
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=96.01 E-value=0.014 Score=51.40 Aligned_cols=37 Identities=22% Similarity=0.333 Sum_probs=32.8
Q ss_pred CcceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 103 RCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
..--|||+.||+.+++..||++|++||.|..+++...
T Consensus 284 ~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d 320 (562)
T TIGR01628 284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD 320 (562)
T ss_pred CCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC
Confidence 4456999999999999999999999999999888653
No 21
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=96.00 E-value=0.0083 Score=50.79 Aligned_cols=35 Identities=9% Similarity=0.203 Sum_probs=32.2
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
.-.|||+.||+.+++..|+.+|++||.|..|+|..
T Consensus 89 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~ 123 (457)
T TIGR01622 89 DRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIK 123 (457)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEee
Confidence 44799999999999999999999999999999854
No 22
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=95.98 E-value=0.027 Score=52.73 Aligned_cols=37 Identities=16% Similarity=0.290 Sum_probs=34.1
Q ss_pred CCcceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 102 DRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 102 ~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
....-||||.||..+++..|+++|++||.|.+|++..
T Consensus 105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~ 141 (612)
T TIGR01645 105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSW 141 (612)
T ss_pred cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEee
Confidence 4567899999999999999999999999999999864
No 23
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=95.85 E-value=0.01 Score=52.13 Aligned_cols=35 Identities=20% Similarity=0.155 Sum_probs=32.1
Q ss_pred ceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 105 GICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 105 GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
-.|||+.||..+++..|+++|+.||.|.+|.+.+.
T Consensus 97 ~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~ 131 (481)
T TIGR01649 97 LRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTK 131 (481)
T ss_pred EEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEec
Confidence 36899999999999999999999999999998654
No 24
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=95.52 E-value=0.012 Score=50.60 Aligned_cols=36 Identities=22% Similarity=0.491 Sum_probs=33.4
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.-.|-|++||-.|++..|+.||-.||.|.||||++.
T Consensus 189 ~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylard 224 (270)
T KOG0122|consen 189 EATVRVTNLSEDMREDDLEELFRPFGPITRVYLARD 224 (270)
T ss_pred cceeEEecCccccChhHHHHHhhccCccceeEEEEc
Confidence 346999999999999999999999999999999875
No 25
>PLN03213 repressor of silencing 3; Provisional
Probab=95.20 E-value=0.022 Score=53.81 Aligned_cols=37 Identities=11% Similarity=0.112 Sum_probs=33.8
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEeccCC
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPED 140 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pEd 140 (141)
.=-||||.|+...+..-|+..|++||.|.+|+|.|+.
T Consensus 10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRET 46 (759)
T PLN03213 10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTK 46 (759)
T ss_pred ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeccc
Confidence 3459999999999999999999999999999998763
No 26
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=95.18 E-value=0.025 Score=49.82 Aligned_cols=36 Identities=19% Similarity=0.433 Sum_probs=32.3
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.--|||+.||+.+++..|+.+|++||.|..+.+.+.
T Consensus 178 ~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~ 213 (562)
T TIGR01628 178 FTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD 213 (562)
T ss_pred CCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEEC
Confidence 345999999999999999999999999999988653
No 27
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=95.11 E-value=0.024 Score=52.57 Aligned_cols=34 Identities=18% Similarity=0.308 Sum_probs=31.4
Q ss_pred ceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 105 GICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 105 GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
--|||++||+.+++..|+.+|++||.|..++|..
T Consensus 59 ~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~ 92 (578)
T TIGR01648 59 CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMM 92 (578)
T ss_pred CEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEE
Confidence 3599999999999999999999999999998854
No 28
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=94.65 E-value=0.028 Score=51.85 Aligned_cols=33 Identities=24% Similarity=0.586 Sum_probs=30.5
Q ss_pred EEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 107 CYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 107 IYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.|+|.||..|++..||.||++||.|.-|-|-+.
T Consensus 37 lfVgqIprt~sE~dlr~lFe~yg~V~einl~kD 69 (510)
T KOG0144|consen 37 LFVGQIPRTASEKDLRELFEKYGNVYEINLIKD 69 (510)
T ss_pred heeccCCccccHHHHHHHHHHhCceeEEEeecc
Confidence 699999999999999999999999999987653
No 29
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=94.53 E-value=0.042 Score=50.98 Aligned_cols=35 Identities=14% Similarity=0.370 Sum_probs=31.9
Q ss_pred CcceEEecCCCCCCCHHHHHHHhhcc--CccceEEec
Q 032398 103 RCGICYLSRIPAHMDPVKLRQILSQY--GEIQRIYLA 137 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p~kLR~~fsqf--GeV~RIyL~ 137 (141)
..-+|||+.||..+++..|+++|++| |.|.||.+.
T Consensus 232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~ 268 (578)
T TIGR01648 232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI 268 (578)
T ss_pred cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee
Confidence 34689999999999999999999999 999999764
No 30
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=94.37 E-value=0.053 Score=42.20 Aligned_cols=36 Identities=19% Similarity=0.499 Sum_probs=33.1
Q ss_pred CcceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 103 RCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
..-|+||-+||-..+...|..+|..||.|..|++--
T Consensus 17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~ 52 (124)
T KOG0114|consen 17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN 52 (124)
T ss_pred hheeEEEecCCccccHHHHHHHhhcccceEEEEecC
Confidence 467999999999999999999999999999999853
No 31
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=94.19 E-value=0.048 Score=43.70 Aligned_cols=36 Identities=17% Similarity=0.395 Sum_probs=32.9
Q ss_pred cCCcceEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 101 ADRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 101 ~~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
..++-.||+|+|.-+-++.+|.++||..|+|.||-+
T Consensus 33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiM 68 (153)
T KOG0121|consen 33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIM 68 (153)
T ss_pred HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEe
Confidence 456889999999999999999999999999999864
No 32
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=93.87 E-value=0.035 Score=52.51 Aligned_cols=36 Identities=14% Similarity=0.388 Sum_probs=31.4
Q ss_pred CCcceEEecCCCCCCCHHHHHHHhhccCccceEEec
Q 032398 102 DRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLA 137 (141)
Q Consensus 102 ~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~ 137 (141)
.---+|||-+||-.-++..|.+.|++||+|.-+.|.
T Consensus 290 ~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV 325 (678)
T KOG0127|consen 290 TEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIV 325 (678)
T ss_pred cccceEEEecCCccccHHHHHHHHHhhccceeEEEE
Confidence 334689999999999999999999999999876653
No 33
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=93.87 E-value=0.014 Score=48.93 Aligned_cols=38 Identities=26% Similarity=0.467 Sum_probs=35.2
Q ss_pred CCcceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 102 DRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 102 ~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
..+..||||.||.-+++.-|--.|||||+|--|-|.|.
T Consensus 33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRD 70 (219)
T KOG0126|consen 33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRD 70 (219)
T ss_pred ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEec
Confidence 45789999999999999999999999999999999874
No 34
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=93.71 E-value=0.041 Score=48.54 Aligned_cols=30 Identities=33% Similarity=0.546 Sum_probs=27.0
Q ss_pred CcceEEecCCCCCCCHHHHHHHhhccCccc
Q 032398 103 RCGICYLSRIPAHMDPVKLRQILSQYGEIQ 132 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~ 132 (141)
+-.-+|+|-||+.|+-..|.++|++||.|-
T Consensus 126 k~aNLYvSGlPktMtqkelE~iFs~fGrII 155 (360)
T KOG0145|consen 126 KDANLYVSGLPKTMTQKELEQIFSPFGRII 155 (360)
T ss_pred cccceEEecCCccchHHHHHHHHHHhhhhh
Confidence 455689999999999999999999999873
No 35
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=93.64 E-value=0.055 Score=33.63 Aligned_cols=19 Identities=26% Similarity=0.663 Sum_probs=16.1
Q ss_pred HHHHhhccCccceEEeccC
Q 032398 121 LRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 121 LR~~fsqfGeV~RIyL~pE 139 (141)
|+.+|++||+|.+|.+.+.
T Consensus 1 L~~~f~~fG~V~~i~~~~~ 19 (56)
T PF13893_consen 1 LYKLFSKFGEVKKIKIFKK 19 (56)
T ss_dssp HHHHHTTTS-EEEEEEETT
T ss_pred ChHHhCCcccEEEEEEEeC
Confidence 6899999999999998775
No 36
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=93.25 E-value=0.11 Score=43.08 Aligned_cols=35 Identities=17% Similarity=0.463 Sum_probs=32.5
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEeccCC
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPED 140 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pEd 140 (141)
-||+|+||..-+...|-..|+.||.|.-|++++.-
T Consensus 12 kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP 46 (195)
T KOG0107|consen 12 KVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP 46 (195)
T ss_pred eEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC
Confidence 49999999999999999999999999999998743
No 37
>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]
Probab=92.38 E-value=0.12 Score=44.91 Aligned_cols=31 Identities=10% Similarity=0.409 Sum_probs=28.4
Q ss_pred ceEEecCCCCCCCHHHHHHHhhccCccceEE
Q 032398 105 GICYLSRIPAHMDPVKLRQILSQYGEIQRIY 135 (141)
Q Consensus 105 GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIy 135 (141)
=.|+++.||++..+..+|.||.|||.|.++=
T Consensus 98 kkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~ 128 (311)
T KOG4205|consen 98 KKIFVGGLPPDTTEEDFKDYFEQFGKVADVV 128 (311)
T ss_pred eEEEecCcCCCCchHHHhhhhhccceeEeeE
Confidence 3899999999999999999999999888763
No 38
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=91.72 E-value=0.15 Score=45.93 Aligned_cols=34 Identities=18% Similarity=0.393 Sum_probs=31.0
Q ss_pred ceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 105 GICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 105 GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
+-||+..||+.-.+..|.+.|.+||.|...+++.
T Consensus 289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~v 322 (419)
T KOG0116|consen 289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQV 322 (419)
T ss_pred cceEeecCCCCCCHHHHHHHHhhcccccccceEE
Confidence 3499999999999999999999999999888764
No 39
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=91.46 E-value=0.15 Score=43.56 Aligned_cols=31 Identities=19% Similarity=0.355 Sum_probs=27.2
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
-||+|-||-.-.-.-||.||.|||+|--.-+
T Consensus 14 KifVggL~w~T~~~~l~~yFeqfGeI~eavv 44 (247)
T KOG0149|consen 14 KIFVGGLAWETHKETLRRYFEQFGEIVEAVV 44 (247)
T ss_pred EEEEcCcccccchHHHHHHHHHhCceEEEEE
Confidence 4899999999999999999999999865433
No 40
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=91.36 E-value=0.13 Score=46.09 Aligned_cols=36 Identities=19% Similarity=0.365 Sum_probs=31.8
Q ss_pred cCCcceEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 101 ADRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 101 ~~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
...+--+|+|+||=.|...-||.+|.+||.|--|-+
T Consensus 93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEI 128 (376)
T KOG0125|consen 93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEI 128 (376)
T ss_pred CCCCceeEeecCCccccCccHHHHHHhhCceeeEEE
Confidence 456778999999999999999999999999987654
No 41
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=90.91 E-value=0.29 Score=41.99 Aligned_cols=25 Identities=12% Similarity=0.246 Sum_probs=22.9
Q ss_pred cceEEecCCCCCCCHHHHHHHhhcc
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQY 128 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqf 128 (141)
.-.||||.||+.+++..|+.+|++|
T Consensus 175 ~r~lyVgnLp~~~t~~~l~~~F~~~ 199 (509)
T TIGR01642 175 ARRLYVGGIPPEFVEEAVVDFFNDL 199 (509)
T ss_pred ccEEEEeCCCCCCCHHHHHHHHHHH
Confidence 3469999999999999999999996
No 42
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=90.73 E-value=0.17 Score=46.89 Aligned_cols=35 Identities=11% Similarity=0.454 Sum_probs=31.6
Q ss_pred CCcceEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 102 DRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 102 ~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
.+--|+||-+||-.-++.+|+.+|++||.|.||.-
T Consensus 257 s~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk 291 (506)
T KOG0117|consen 257 SKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKK 291 (506)
T ss_pred hheeeeeeeccchhhhHHHHHHHHHhccceEEeec
Confidence 34569999999999999999999999999999854
No 43
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=88.90 E-value=0.18 Score=46.68 Aligned_cols=34 Identities=18% Similarity=0.496 Sum_probs=31.5
Q ss_pred EEecCCCCCCCHHHHHHHhhccCccceEEeccCC
Q 032398 107 CYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPED 140 (141)
Q Consensus 107 IYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pEd 140 (141)
+|||.|++.-++..+|++|++||.|.-+|+-|.+
T Consensus 127 LFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~ 160 (510)
T KOG0144|consen 127 LFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP 160 (510)
T ss_pred hhhhhccccccHHHHHHHHHhhCccchhhheecc
Confidence 5999999999999999999999999999987753
No 44
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=88.42 E-value=0.57 Score=39.56 Aligned_cols=37 Identities=19% Similarity=0.434 Sum_probs=33.1
Q ss_pred CCcceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 102 DRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 102 ~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
.++.-|||+.+|.+....-|+++|.+||.+.|+.|..
T Consensus 81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy 117 (243)
T KOG0533|consen 81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHY 117 (243)
T ss_pred CCcceeeeecCCcCcchHHHHHHHHHhccceEEeecc
Confidence 3457799999999999999999999999999998864
No 45
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=85.87 E-value=0.47 Score=42.80 Aligned_cols=30 Identities=23% Similarity=0.429 Sum_probs=27.0
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccce
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQR 133 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~R 133 (141)
.--||||.||...+...+-++|+.||-|-|
T Consensus 134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~ 163 (382)
T KOG1548|consen 134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMR 163 (382)
T ss_pred CceEEecCCCCcccHHHHHHHHHhcceEec
Confidence 345999999999999999999999998864
No 46
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=85.70 E-value=0.7 Score=42.95 Aligned_cols=34 Identities=18% Similarity=0.357 Sum_probs=31.6
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
=||||.||..+++..|+-+|..-|+|--++|-.+
T Consensus 85 EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD 118 (506)
T KOG0117|consen 85 EVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMD 118 (506)
T ss_pred eEEecCCCccccchhhHHHHHhccceeeEEEeec
Confidence 5999999999999999999999999999998654
No 47
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=85.22 E-value=0.89 Score=29.50 Aligned_cols=31 Identities=23% Similarity=0.493 Sum_probs=23.1
Q ss_pred EEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 107 CYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 107 IYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
|-++=.|+++.. .++.+|++||+|.++++.+
T Consensus 4 I~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~ 34 (53)
T PF14605_consen 4 ISVSGFPPDLAE-EVLEHFASFGEIVDIYVPE 34 (53)
T ss_pred EEEEeECchHHH-HHHHHHHhcCCEEEEEcCC
Confidence 456666777664 4556888999999999873
No 48
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=84.64 E-value=0.97 Score=41.75 Aligned_cols=38 Identities=16% Similarity=0.438 Sum_probs=33.7
Q ss_pred CCcceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 102 DRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 102 ~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.+---||++.|.|.+.+.-|++.|..||+|-.--|++.
T Consensus 208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~ 245 (544)
T KOG0124|consen 208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARA 245 (544)
T ss_pred HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeecc
Confidence 34456999999999999999999999999999888764
No 49
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=83.96 E-value=1 Score=44.32 Aligned_cols=35 Identities=29% Similarity=0.586 Sum_probs=31.9
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
+-.+|||.||..|++.-|+.+|..||+|.+|-|.+
T Consensus 421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~ 455 (894)
T KOG0132|consen 421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP 455 (894)
T ss_pred eeeeeeccccchhhHHHHHHHHHhcccceeEeecc
Confidence 45679999999999999999999999999998864
No 50
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=83.86 E-value=1.2 Score=40.41 Aligned_cols=33 Identities=21% Similarity=0.313 Sum_probs=31.3
Q ss_pred ceEEecCCCCCCCHHHHHHHhhccCccceEEec
Q 032398 105 GICYLSRIPAHMDPVKLRQILSQYGEIQRIYLA 137 (141)
Q Consensus 105 GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~ 137 (141)
..||+|+||.-+.+.+|..+|+..|.|--++|.
T Consensus 19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v 51 (435)
T KOG0108|consen 19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLV 51 (435)
T ss_pred cceEecCCCCcccHHHHHHHHhccCccceeeec
Confidence 799999999999999999999999999988875
No 51
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=80.71 E-value=1.4 Score=30.70 Aligned_cols=20 Identities=45% Similarity=0.851 Sum_probs=18.3
Q ss_pred HHHHHHhhccCccceEEecc
Q 032398 119 VKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 119 ~kLR~~fsqfGeV~RIyL~p 138 (141)
..||++||+.|+|.=+|+.+
T Consensus 9 ~~iR~~fs~lG~I~vLYvn~ 28 (62)
T PF15513_consen 9 AEIRQFFSQLGEIAVLYVNP 28 (62)
T ss_pred HHHHHHHHhcCcEEEEEEcc
Confidence 57999999999999999976
No 52
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=79.85 E-value=1.8 Score=31.62 Aligned_cols=34 Identities=18% Similarity=0.322 Sum_probs=22.0
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
||+|+-++....-..|+..|++||.|.-|-+++-
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G 36 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG 36 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC
Confidence 7888889999999999999999999998877654
No 53
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=78.85 E-value=2.2 Score=34.74 Aligned_cols=33 Identities=21% Similarity=0.421 Sum_probs=30.9
Q ss_pred ceEEecCCCCCCCHHHHHHHhhccCccceEEec
Q 032398 105 GICYLSRIPAHMDPVKLRQILSQYGEIQRIYLA 137 (141)
Q Consensus 105 GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~ 137 (141)
=||+++.|.+--++..|...|.-||+|..|+|.
T Consensus 73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLN 105 (170)
T KOG0130|consen 73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLN 105 (170)
T ss_pred EEEEEeccCcchhHHHHHHHHhhcccccceeec
Confidence 378999999999999999999999999999985
No 54
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=77.77 E-value=2.3 Score=41.22 Aligned_cols=34 Identities=24% Similarity=0.417 Sum_probs=31.0
Q ss_pred CcceEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 103 RCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
-.-||.++.||.+-.+..+...|..||.|+||-|
T Consensus 384 s~~vil~kNlpa~t~~~elt~~F~~fG~i~rvll 417 (725)
T KOG0110|consen 384 SDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLL 417 (725)
T ss_pred hcceeeeccCccccccHHHHHHhhcccccceeec
Confidence 3578999999999999999999999999999943
No 55
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=74.49 E-value=4 Score=35.82 Aligned_cols=39 Identities=23% Similarity=0.388 Sum_probs=34.9
Q ss_pred cCCcceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 101 ADRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 101 ~~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
......+|+..++..+....|+.+|+.||+|+.++|.-.
T Consensus 267 ~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~ 305 (369)
T KOG0123|consen 267 SLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVD 305 (369)
T ss_pred cccccccccccCccccchhHHHHHHhcccceeeEEEEec
Confidence 456778999999999999999999999999999998753
No 56
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=73.35 E-value=2.8 Score=39.50 Aligned_cols=41 Identities=27% Similarity=0.411 Sum_probs=36.1
Q ss_pred hhcCCcceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 99 AKADRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 99 ~k~~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.+....|.+.|=.||+......|+.+|+.||+|.-|+-.|.
T Consensus 70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~ 110 (549)
T KOG4660|consen 70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN 110 (549)
T ss_pred cccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc
Confidence 34678999999999999999999999999999988776553
No 57
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=73.08 E-value=3.8 Score=37.11 Aligned_cols=72 Identities=17% Similarity=0.210 Sum_probs=46.5
Q ss_pred hhchhhhhchhhhhhh---hhhhhhhHHHHHH--HH-hhcCCcceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 68 EEGKQEELNLKKRRSQ---SIVKSKKKQRLLE--EA-AKADRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 68 ~ed~q~~~N~~~dks~---~~~kkkkkK~L~~--~~-~k~~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.+|....-|+++...+ +...+-.+.+... .. ..-..--.+||+.+=+...+..||..|-|||+|.-|.+.++
T Consensus 186 ~d~~L~~qni~dryyg~ndPva~kil~ra~~~~~lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~ 263 (377)
T KOG0153|consen 186 PDDPLSLQNIKDRYYGLNDPVALKILNRAGSAGTLEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR 263 (377)
T ss_pred CCcchhhcccccccccccChHHHHHHhhcccccccCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc
Confidence 3555666677666554 2222222211110 00 12234567999999889999999999999999999988765
No 58
>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN). ; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.
Probab=72.37 E-value=4.6 Score=29.94 Aligned_cols=35 Identities=20% Similarity=0.415 Sum_probs=25.3
Q ss_pred cCCcceEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 101 ADRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 101 ~~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
.....|.||+ .|+-..-..|.++|+.||.|.=-+|
T Consensus 6 P~RdHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi 40 (87)
T PF08675_consen 6 PSRDHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWI 40 (87)
T ss_dssp -SGCCEEEEE---TT--HHHHHHHCCCCCCEEEEEE
T ss_pred CCcceEEEEe-CchHhhhhhHHHHhccCCcEEEEEE
Confidence 3457888998 9999999999999999999865544
No 59
>smart00361 RRM_1 RNA recognition motif.
Probab=68.40 E-value=5.1 Score=26.14 Aligned_cols=18 Identities=22% Similarity=0.451 Sum_probs=15.0
Q ss_pred HHHHHHHhh----ccCccceEE
Q 032398 118 PVKLRQILS----QYGEIQRIY 135 (141)
Q Consensus 118 p~kLR~~fs----qfGeV~RIy 135 (141)
+..|+.+|+ +||.|++|+
T Consensus 2 ~~~l~~~~~~~~~~fG~v~~v~ 23 (70)
T smart00361 2 DEDFEREFSEEEEYFGEVGKIN 23 (70)
T ss_pred chhHHHHHHHHHHhcCCeeEEE
Confidence 356788888 999999985
No 60
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=66.26 E-value=3.2 Score=39.20 Aligned_cols=38 Identities=18% Similarity=0.333 Sum_probs=33.4
Q ss_pred CCcce-EEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 102 DRCGI-CYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 102 ~k~GV-IYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.-|.+ +|+|.|...|.+..||.+|..||.|.-|-|...
T Consensus 275 ~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d 313 (549)
T KOG0147|consen 275 TGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKD 313 (549)
T ss_pred ccchhhhhhcccccCchHHHHhhhccCcccceeeeeccc
Confidence 34556 899999999999999999999999999988653
No 61
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=64.15 E-value=3.6 Score=38.19 Aligned_cols=34 Identities=18% Similarity=0.390 Sum_probs=30.7
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEec
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLA 137 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~ 137 (141)
.--||+|.|---+.+..||..|..||.|.-|-++
T Consensus 113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMS 146 (544)
T KOG0124|consen 113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMS 146 (544)
T ss_pred hHheeeeeeEEEechHHHHhhccCCCCcceeecc
Confidence 4569999999999999999999999999988664
No 62
>PF04940 BLUF: Sensors of blue-light using FAD; InterPro: IPR007024 An FAD-binding domain, BLUF, exemplified by the N terminus of the AppA protein, (Q53119 from SWISSPROT), from Rhodobacter sphaeroides, is present in various proteins, primarily from Bacteria. The BLUF domain is involved in sensing blue-light (and possibly redox) using FAD and is similar to the flavin-binding PAS domains and cryptochromes. The predicted secondary structure reveals that the BLUF domain is a novel FAD-binding fold [].; PDB: 2IYG_A 2IYI_B 1X0P_A 2HFN_G 3MZI_A 2HFO_E 3GFZ_A 3GG1_B 2KB2_A 3GFY_A ....
Probab=63.60 E-value=4.9 Score=28.64 Aligned_cols=22 Identities=27% Similarity=0.532 Sum_probs=18.5
Q ss_pred eEEecCCCCCCCHHHHHHHhhc
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQ 127 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsq 127 (141)
+||+|+++..|.+..|.+++.+
T Consensus 4 l~Y~S~~~~~~~~~~~~~Il~~ 25 (93)
T PF04940_consen 4 LIYVSTASEDLSPEDLADILRS 25 (93)
T ss_dssp EEEEEEE-TTS-HHHHHHHHHH
T ss_pred EEEEEccCCCCCHHHHHHHHHH
Confidence 7999999999999999999875
No 63
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=63.02 E-value=7.8 Score=33.43 Aligned_cols=30 Identities=20% Similarity=0.629 Sum_probs=25.3
Q ss_pred cCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 110 SRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 110 SrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
=+|-..-.|..||..|.+||.|+-||+-++
T Consensus 19 dNLTyRTspd~LrrvFekYG~vgDVyIPrd 48 (256)
T KOG4207|consen 19 DNLTYRTSPDDLRRVFEKYGRVGDVYIPRD 48 (256)
T ss_pred cceeccCCHHHHHHHHHHhCcccceecccc
Confidence 356666789999999999999999998654
No 64
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=62.54 E-value=5.4 Score=37.47 Aligned_cols=26 Identities=12% Similarity=0.465 Sum_probs=24.4
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCcc
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEI 131 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV 131 (141)
=|++|-||++|++..|-..|-+||.|
T Consensus 261 KVFvGGlp~dise~~i~~~F~~FGs~ 286 (520)
T KOG0129|consen 261 KVFVGGLPWDITEAQINASFGQFGSV 286 (520)
T ss_pred ceeecCCCccccHHHHHhhcccccce
Confidence 48999999999999999999999976
No 65
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=61.98 E-value=8.6 Score=33.80 Aligned_cols=38 Identities=16% Similarity=0.364 Sum_probs=33.3
Q ss_pred CCcceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 102 DRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 102 ~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
..+-.|||-.+|+.++-..|...||.||+|.-+.|...
T Consensus 74 rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~ 111 (369)
T KOG0123|consen 74 RDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATD 111 (369)
T ss_pred cCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEc
Confidence 34555999999999999999999999999998888653
No 66
>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]
Probab=61.12 E-value=7.5 Score=38.37 Aligned_cols=30 Identities=13% Similarity=0.329 Sum_probs=27.0
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEE
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIY 135 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIy 135 (141)
=+|+|+|+|.|.+..|...|..||.|--|.
T Consensus 176 Nlyv~Nlnpsv~E~~ll~tfGrfgPlasvK 205 (877)
T KOG0151|consen 176 NLYVGNLNPSVDENFLLRTFGRFGPLASVK 205 (877)
T ss_pred ceeeecCCccccHHHHHHHhcccCccccee
Confidence 489999999999999999999999986544
No 67
>cd00842 MPP_ASMase acid sphingomyelinase and related proteins, metallophosphatase domain. Acid sphingomyelinase (ASMase) is a ubiquitously expressed phosphodiesterase which hydrolyzes sphingomyelin in acid pH conditions to form ceramide, a bioactive second messenger, as part of the sphingomyelin signaling pathway. ASMase is localized at the noncytosolic leaflet of biomembranes (for example the luminal leaflet of endosomes, lysosomes and phagosomes, and the extracellular leaflet of plasma membranes). ASMase-deficient humans develop Niemann-Pick disease. This disease is characterized by lysosomal storage of sphingomyelin in all tissues. Although ASMase-deficient mice are resistant to stress-induced apoptosis, they have greater susceptibility to bacterial infection. The latter correlates with defective phagolysosomal fusion and antibacterial killing activity in ASMase-deficient macrophages. ASMase belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but
Probab=59.65 E-value=11 Score=30.42 Aligned_cols=39 Identities=23% Similarity=0.400 Sum_probs=26.6
Q ss_pred HHHHHHHhhc--CCcceEEecCCCCCCCH--------HHHHHHhhccCc
Q 032398 92 QRLLEEAAKA--DRCGICYLSRIPAHMDP--------VKLRQILSQYGE 130 (141)
Q Consensus 92 K~L~~~~~k~--~k~GVIYLSrIPpgM~p--------~kLR~~fsqfGe 130 (141)
..|.+..+.. ...-||-++||||+... ..+.+++.+|..
T Consensus 200 ~WL~~~L~~a~~~~~~v~I~~HiPp~~~~~~~~~~~~~~~~~ii~~y~~ 248 (296)
T cd00842 200 QWLEDELQEAEQAGEKVWIIGHIPPGVNSYDTLENWSERYLQIINRYSD 248 (296)
T ss_pred HHHHHHHHHHHHCCCeEEEEeccCCCCcccccchHHHHHHHHHHHHHHH
Confidence 3444444333 23458889999999752 578899999975
No 68
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=58.38 E-value=11 Score=33.80 Aligned_cols=33 Identities=24% Similarity=0.450 Sum_probs=29.2
Q ss_pred EEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 107 CYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 107 IYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
+-+--+|..|+...+|++|+--|+|.-..|.|.
T Consensus 44 LIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRD 76 (360)
T KOG0145|consen 44 LIVNYLPQNMTQDELRSLFGSIGEIESCKLVRD 76 (360)
T ss_pred eeeeecccccCHHHHHHHhhcccceeeeeeeec
Confidence 345668999999999999999999999999875
No 69
>PF03721 UDPG_MGDP_dh_N: UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain; InterPro: IPR001732 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the N-terminal NAD(+)-binding domain. Structural studies indicate that this domain forms an alpha-beta structure containing the six-stranded parallel beta sheet characteristic of the dinucleotide binding Rossman fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3OJO_A 3OJL_A 1MV8_B 1MUU_A 1MFZ_C 3GG2_D 1DLJ_A 1DLI_A 3G79_B 2Y0E_D ....
Probab=45.98 E-value=12 Score=29.35 Aligned_cols=27 Identities=19% Similarity=0.156 Sum_probs=24.0
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCc
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGE 130 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGe 130 (141)
.=||+=|++|||.+...++.+|.+++.
T Consensus 114 ~lvV~~STvppGtt~~~~~~ile~~~~ 140 (185)
T PF03721_consen 114 DLVVIESTVPPGTTEELLKPILEKRSG 140 (185)
T ss_dssp EEEEESSSSSTTHHHHHHHHHHHHHCC
T ss_pred ceEEEccEEEEeeehHhhhhhhhhhcc
Confidence 456888999999999999999999885
No 70
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=43.43 E-value=35 Score=19.94 Aligned_cols=25 Identities=8% Similarity=0.194 Sum_probs=21.4
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCc
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGE 130 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGe 130 (141)
.+||+..++......|.+++..+|-
T Consensus 3 ~~~i~g~~~~~~~~~l~~~i~~~Gg 27 (72)
T cd00027 3 TFVITGDLPSEERDELKELIEKLGG 27 (72)
T ss_pred EEEEEecCCCcCHHHHHHHHHHcCC
Confidence 4788888778999999999999985
No 71
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=43.09 E-value=21 Score=31.86 Aligned_cols=36 Identities=17% Similarity=0.376 Sum_probs=31.8
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEeccC
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pE 139 (141)
.=-|+++-+-+-..-..||+.|..||+|.--++.|.
T Consensus 62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD 97 (321)
T KOG0148|consen 62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRD 97 (321)
T ss_pred ceeEEehhcchhcchHHHHHHhccccccccceEeec
Confidence 445899999999999999999999999998887764
No 72
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=41.53 E-value=29 Score=24.01 Aligned_cols=28 Identities=14% Similarity=0.237 Sum_probs=22.4
Q ss_pred cCCCCCCCHHHHHHHhhc-cCc-cceEEec
Q 032398 110 SRIPAHMDPVKLRQILSQ-YGE-IQRIYLA 137 (141)
Q Consensus 110 SrIPpgM~p~kLR~~fsq-fGe-V~RIyL~ 137 (141)
-|+|+.|+..+|++.+.. ||. ...++|+
T Consensus 17 kr~~~~~Tv~~lK~kl~~~~G~~~~~mrL~ 46 (84)
T cd01789 17 KKYSRGLTIAELKKKLELVVGTPASSMRLQ 46 (84)
T ss_pred EecCCCCcHHHHHHHHHHHHCCCccceEEE
Confidence 369999999999999988 565 6666664
No 73
>cd07970 OBF_DNA_ligase_LigC The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigC and similar ba
Probab=41.34 E-value=22 Score=26.41 Aligned_cols=22 Identities=9% Similarity=0.202 Sum_probs=19.4
Q ss_pred eEEecCCCCCCCHHHHHHHhhcc
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQY 128 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqf 128 (141)
.+|+|++ -+|+...+++++...
T Consensus 31 l~yvG~v-tGf~~~~~~~L~~~l 52 (122)
T cd07970 31 LRHVGRT-SPLAAAERRELAELL 52 (122)
T ss_pred EEEEEEE-CCCCHHHHHHHHHHH
Confidence 8999999 899999999887754
No 74
>COG2441 Predicted butyrate kinase [Energy production and conversion]
Probab=38.30 E-value=24 Score=31.88 Aligned_cols=35 Identities=34% Similarity=0.406 Sum_probs=27.1
Q ss_pred CCcceEEec----CCCCCCCH--HHHHHHhhccCccceEEe
Q 032398 102 DRCGICYLS----RIPAHMDP--VKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 102 ~k~GVIYLS----rIPpgM~p--~kLR~~fsqfGeV~RIyL 136 (141)
..|--|||| |||.+|.. .+||..||.||.--+|++
T Consensus 272 ~~pd~iylSGrf~~~~~~~~dv~~~l~d~~s~~g~~~evr~ 312 (374)
T COG2441 272 TYPDAIYLSGRFSRIPRFFSDVKEKLRDAFSSYGFGIEVRK 312 (374)
T ss_pred cCcceEEEeeecccccchhhHHHHHHHHHHhhcCccceeeh
Confidence 344457765 89998886 789999999998666654
No 75
>KOG2891 consensus Surface glycoprotein [General function prediction only]
Probab=38.12 E-value=23 Score=32.14 Aligned_cols=38 Identities=24% Similarity=0.450 Sum_probs=29.8
Q ss_pred hhcCCcceEEecCCCCCC------------CHHHHHHHhhccCccceEEe
Q 032398 99 AKADRCGICYLSRIPAHM------------DPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 99 ~k~~k~GVIYLSrIPpgM------------~p~kLR~~fsqfGeV~RIyL 136 (141)
..-..|-.|||.+||-.. .+..||..|..||.|..|-+
T Consensus 144 kpgerpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdi 193 (445)
T KOG2891|consen 144 KPGERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDI 193 (445)
T ss_pred CCCCCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCC
Confidence 345678899999999543 35789999999999987643
No 76
>PF06297 PET: PET Domain; InterPro: IPR010442 The PET domain is a ~110 amino acid motif in the N-terminal part of LIM domain proteins. The domain was described in Drosophila proteins involved in cell differentiation and is named after Prickle, Espinas and Testin. PET domain proteins contain about three zinc-binding LIM domains (see PDOC00382 from INTERPRO, IPR001781 from INTERPRO) and are found among metazoans. The PET domain has been suggested to play a role in protein-protein interactions with proteins involved in planar polarity signalling or organisation of the cytoskeleton []. Some proteins known to contain a PET domain: Mammalian testin protein (Q9UGI8 from SWISSPROT), which may function as a tumour suppressor. Mammalian LIM domain only protein 6 (LMO6/Prickle3, O43900 from SWISSPROT). Fruit fly prickle (A1Z6W3 from SWISSPROT) and espinas (Q9U1I1 from SWISSPROT) proteins encoded by the tissue polarity gene prickle (pk), involved in the control of orientation of bristles and hairs. Mammalian prickle-like proteins 1 (Q96MT3 from SWISSPROT) and 2 (Q7Z3G6 from SWISSPROT). ; GO: 0008270 zinc ion binding
Probab=38.08 E-value=27 Score=26.31 Aligned_cols=24 Identities=21% Similarity=0.267 Sum_probs=20.2
Q ss_pred EEecCCCCCCCHHHHHHHhhccCc
Q 032398 107 CYLSRIPAHMDPVKLRQILSQYGE 130 (141)
Q Consensus 107 IYLSrIPpgM~p~kLR~~fsqfGe 130 (141)
+=..=+|||+++..+..||+...+
T Consensus 19 ~~Y~WvPpgl~~~~v~~Ym~~LP~ 42 (106)
T PF06297_consen 19 EEYAWVPPGLSPELVEQYMSCLPE 42 (106)
T ss_pred ceeeecCCCCChHHHHHHHHhCCC
Confidence 345679999999999999998764
No 77
>PF06481 COX_ARM: COX Aromatic Rich Motif; InterPro: IPR010514 COX2 (Cytochrome O ubiquinol OXidase 2) is a major component of the respiratory complex during vegetative growth. It transfers electrons from a quinol to the binuclear centre of the catalytic subunit 1. The function of this region is not known.; GO: 0008827 cytochrome o ubiquinol oxidase activity, 0022900 electron transport chain, 0055114 oxidation-reduction process, 0016021 integral to membrane; PDB: 1CYX_A 1CYW_A 1FFT_G.
Probab=37.25 E-value=14 Score=23.53 Aligned_cols=28 Identities=7% Similarity=0.148 Sum_probs=18.2
Q ss_pred hhcCCcceEEecCCCCCCCHHHHHHHhh
Q 032398 99 AKADRCGICYLSRIPAHMDPVKLRQILS 126 (141)
Q Consensus 99 ~k~~k~GVIYLSrIPpgM~p~kLR~~fs 126 (141)
+....--|-|+|.++|+|+..-|..++.
T Consensus 17 ~PS~~~pv~yfssv~p~LF~~Iv~k~~~ 44 (47)
T PF06481_consen 17 KPSENNPVTYFSSVEPGLFDDIVMKYMG 44 (47)
T ss_dssp SS-SS--SEEES-B-TTHHHHHHHHTT-
T ss_pred CcCcCCCceeeccCCHHHHHHHHHHhcc
Confidence 4455677899999999999988887764
No 78
>PF14581 SseB_C: SseB protein C-terminal domain
Probab=37.11 E-value=9 Score=27.08 Aligned_cols=20 Identities=25% Similarity=0.368 Sum_probs=17.5
Q ss_pred HHHHHHHhhccCccceEEec
Q 032398 118 PVKLRQILSQYGEIQRIYLA 137 (141)
Q Consensus 118 p~kLR~~fsqfGeV~RIyL~ 137 (141)
...|.+||++++.|.+.||.
T Consensus 21 ~~aL~~~~~~~~~V~~Ayl~ 40 (108)
T PF14581_consen 21 LAALSEYFKQHKNVRAAYLA 40 (108)
T ss_pred HHHHHHHHhhCccHHHhHHH
Confidence 36789999999999999985
No 79
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=35.28 E-value=34 Score=31.67 Aligned_cols=37 Identities=24% Similarity=0.542 Sum_probs=27.9
Q ss_pred CcceEEecCCCCCCCH------HHHHHHhhccCccceEEeccC
Q 032398 103 RCGICYLSRIPAHMDP------VKLRQILSQYGEIQRIYLAPE 139 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p------~kLR~~fsqfGeV~RIyL~pE 139 (141)
....||+--|||-.-- .+=-+||.|||.|..|-+.+.
T Consensus 113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkk 155 (480)
T COG5175 113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKK 155 (480)
T ss_pred ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEeccc
Confidence 4567899999886643 234689999999999977543
No 80
>PHA01782 hypothetical protein
Probab=33.30 E-value=28 Score=28.81 Aligned_cols=23 Identities=22% Similarity=0.424 Sum_probs=20.9
Q ss_pred cCCCCCCCHHHHHHHhhccCccc
Q 032398 110 SRIPAHMDPVKLRQILSQYGEIQ 132 (141)
Q Consensus 110 SrIPpgM~p~kLR~~fsqfGeV~ 132 (141)
--+|.|+.-.-|+++|..||.|.
T Consensus 61 ~aMPKGsRrnAL~~wlv~~Gkv~ 83 (177)
T PHA01782 61 EAMPKGSRRNALAEWLVKFGKVQ 83 (177)
T ss_pred HHccccchhhHHHHHHHHhCCcc
Confidence 35899999999999999999984
No 81
>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]
Probab=31.70 E-value=33 Score=30.09 Aligned_cols=32 Identities=19% Similarity=0.272 Sum_probs=28.9
Q ss_pred ceEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 105 GICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 105 GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
-.+|+-.++++-.-..+.+-|++||+|.|--.
T Consensus 32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~ 63 (275)
T KOG0115|consen 32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVA 63 (275)
T ss_pred ceEEEEecchhhhhHHHHHhhhhcCccchhee
Confidence 68999999999999999999999999987433
No 82
>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]
Probab=29.85 E-value=35 Score=31.92 Aligned_cols=34 Identities=12% Similarity=0.395 Sum_probs=29.8
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEec
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLA 137 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~ 137 (141)
+-=||+|-||-.+++.++++++.-||.+.-+.|.
T Consensus 289 ~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv 322 (500)
T KOG0120|consen 289 PNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLV 322 (500)
T ss_pred cchhhhccCcCccCHHHHHHHHHhcccchhheee
Confidence 3348999999999999999999999998877664
No 83
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=29.30 E-value=36 Score=33.51 Aligned_cols=31 Identities=16% Similarity=0.406 Sum_probs=26.2
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
-+|+|-|...-..+-|+.|||+||.|--..+
T Consensus 407 NlWVSGLSstTRAtDLKnlFSKyGKVvGAKV 437 (940)
T KOG4661|consen 407 NLWVSGLSSTTRATDLKNLFSKYGKVVGAKV 437 (940)
T ss_pred ceeeeccccchhhhHHHHHHHHhcceeceee
Confidence 4789999998899999999999999854443
No 84
>PF13433 Peripla_BP_5: Periplasmic binding protein domain; PDB: 1QNL_A 1QO0_A 1PEA_A.
Probab=28.83 E-value=39 Score=30.25 Aligned_cols=40 Identities=20% Similarity=0.311 Sum_probs=27.4
Q ss_pred hcCCcceEEecCCCCCCCHHHHHHHhhccCccceEEeccCC
Q 032398 100 KADRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAPED 140 (141)
Q Consensus 100 k~~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~pEd 140 (141)
-+.-+-|||.|-.|..--..-++-++.+|| ..|+||.-.|
T Consensus 104 ~E~S~nviYtGa~PNQ~~~pl~~~~~~~~G-~~r~~lvGSd 143 (363)
T PF13433_consen 104 FECSPNVIYTGAAPNQQLLPLIDYLLENFG-AKRFYLVGSD 143 (363)
T ss_dssp ----TTEEE-S--GGGTHHHHHHHHHHHS---SEEEEEEES
T ss_pred ccCCCceEEcCCCchhhHHHHHHHHHhccC-CceEEEecCC
Confidence 345789999999999888899999999999 8899996443
No 85
>PF06753 Bradykinin: Bradykinin; InterPro: IPR009608 This family consists of several bradykinin sequences. The skins of anuran amphibians, in addition to mucus glands, contain highly specialised poison glands, which, in reaction to stress or attack, exude a complex noxious cocktail of biologically active molecules. These secretions often contain a plethora of peptides among which bradykinin or structural variants have been identified [].; GO: 0005179 hormone activity, 0006950 response to stress, 0005576 extracellular region
Probab=28.56 E-value=27 Score=19.47 Aligned_cols=11 Identities=36% Similarity=0.676 Sum_probs=8.7
Q ss_pred ecCCCCCCCHH
Q 032398 109 LSRIPAHMDPV 119 (141)
Q Consensus 109 LSrIPpgM~p~ 119 (141)
|-|.||||.|-
T Consensus 1 lqr~p~gftpf 11 (19)
T PF06753_consen 1 LQRRPPGFTPF 11 (19)
T ss_pred CCccCCCCCcc
Confidence 45889999884
No 86
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=28.15 E-value=40 Score=28.47 Aligned_cols=30 Identities=13% Similarity=0.264 Sum_probs=26.7
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccce
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQR 133 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~R 133 (141)
.-=++++.+-|...+..|...||.||.|-+
T Consensus 96 ganlfvgNLd~~vDe~~L~dtFsafG~l~~ 125 (203)
T KOG0131|consen 96 GANLFVGNLDPEVDEKLLYDTFSAFGVLIS 125 (203)
T ss_pred cccccccccCcchhHHHHHHHHHhcccccc
Confidence 346899999999999999999999998754
No 87
>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.
Probab=27.22 E-value=62 Score=24.22 Aligned_cols=22 Identities=32% Similarity=0.696 Sum_probs=16.2
Q ss_pred eEEecCCCCCCCHHHHHHHhhc
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQ 127 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsq 127 (141)
.+|+++||..-.+..++..|.|
T Consensus 4 ~L~V~NLP~~~d~~~I~~RL~q 25 (90)
T PF11608_consen 4 LLYVSNLPTNKDPSSIKNRLRQ 25 (90)
T ss_dssp EEEEES--TTS-HHHHHHHHHH
T ss_pred EEEEecCCCCCCHHHHHHHHHH
Confidence 6899999999999888877775
No 88
>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]
Probab=26.89 E-value=48 Score=28.25 Aligned_cols=38 Identities=13% Similarity=0.272 Sum_probs=33.6
Q ss_pred cCCcceEE-ecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 101 ADRCGICY-LSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 101 ~~k~GVIY-LSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
...++.|| ++.+|--+....|+.+|..+|.|.++++-.
T Consensus 181 ~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~ 219 (285)
T KOG4210|consen 181 SGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPT 219 (285)
T ss_pred cCccccceeecccccccchHHHhhhccCcCcceeeccCC
Confidence 34577888 899999999999999999999999999854
No 89
>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]
Probab=26.60 E-value=44 Score=30.07 Aligned_cols=33 Identities=15% Similarity=0.484 Sum_probs=27.9
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccc--eEEecc
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQ--RIYLAP 138 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~--RIyL~p 138 (141)
-+||=|||.-|.-+.|-++|-.||-|- +||+-|
T Consensus 287 NlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDR 321 (371)
T KOG0146|consen 287 NLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDR 321 (371)
T ss_pred eEEEEeCchhhccHHHHHHhccccceeeeeeeehh
Confidence 578889999999999999999999984 455544
No 90
>KOG4483 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.66 E-value=47 Score=31.24 Aligned_cols=30 Identities=13% Similarity=0.194 Sum_probs=26.7
Q ss_pred CCcceEEecCCCCCCCHHHHHHHhhccCcc
Q 032398 102 DRCGICYLSRIPAHMDPVKLRQILSQYGEI 131 (141)
Q Consensus 102 ~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV 131 (141)
.-+-||-|...|+.|.-.-|-..|++||.=
T Consensus 389 dlpHVlEIydfp~efkteDll~~f~~yq~k 418 (528)
T KOG4483|consen 389 DLPHVLEIYDFPDEFKTEDLLKAFETYQNK 418 (528)
T ss_pred cccceeEeccCchhhccHHHHHHHHHhhcC
Confidence 467899999999999999999999999863
No 91
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=25.36 E-value=44 Score=20.69 Aligned_cols=17 Identities=29% Similarity=0.636 Sum_probs=13.4
Q ss_pred CCCCCHHHHHHHhhccC
Q 032398 113 PAHMDPVKLRQILSQYG 129 (141)
Q Consensus 113 PpgM~p~kLR~~fsqfG 129 (141)
|..|+..+||.+|..+|
T Consensus 1 p~sltV~~Lk~iL~~~~ 17 (35)
T PF12949_consen 1 PKSLTVAQLKRILDEHG 17 (35)
T ss_dssp STT--SHHHHHHHHHHT
T ss_pred CCcCcHHHHHHHHHHcC
Confidence 66789999999999888
No 92
>PF02668 TauD: Taurine catabolism dioxygenase TauD, TfdA family; InterPro: IPR003819 This family consists of TauD/TfdA taurine catabolism dioxygenases. The Escherichia coli tauD gene is required for the utilization of taurine (2-aminoethanesulphonic acid) as a sulphur source and is expressed only under conditions of sulphate starvation. TauD is an alpha-ketoglutarate-dependent dioxygenase catalyzing the oxygenolytic release of sulphite from taurine []. The 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. (strain RASC) also belongs to this family []. TfdA from Ralstonia eutropha (Alcaligenes eutrophus) is a 2,4-D monooxygenase [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3SWT_B 3R1J_A 1GVG_A 1DRT_A 1DS1_A 1DS0_A 1DRY_A 3V15_A 3PVJ_D 3V17_A ....
Probab=25.21 E-value=78 Score=24.15 Aligned_cols=28 Identities=25% Similarity=0.579 Sum_probs=25.4
Q ss_pred CCcceEEecCCCCCCCHHHHHHHhhccCcc
Q 032398 102 DRCGICYLSRIPAHMDPVKLRQILSQYGEI 131 (141)
Q Consensus 102 ~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV 131 (141)
...|+|.|..+| +++..+.++.++||.|
T Consensus 34 ~~~G~vvlrg~~--~~~~~~~~~~~~~G~~ 61 (258)
T PF02668_consen 34 AEYGFVVLRGFP--LDPEQFEALASRLGPL 61 (258)
T ss_dssp HHHSEEEEESCT--SSHHHHHHHHHHHSEB
T ss_pred hcccEEEEcCCC--CCHHHHHHHHHhhCcc
Confidence 458999999999 4999999999999977
No 93
>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []. This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.
Probab=24.92 E-value=53 Score=24.16 Aligned_cols=28 Identities=14% Similarity=0.389 Sum_probs=17.7
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEE
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIY 135 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIy 135 (141)
|+-+| -||. .-..+-++|++||+|-..+
T Consensus 9 VtVFG-fp~~-~~~~Vl~~F~~~G~Ile~~ 36 (100)
T PF05172_consen 9 VTVFG-FPPS-ASNQVLRHFSSFGTILEHF 36 (100)
T ss_dssp EEEE----GG-GHHHHHHHHHCCS-EECEE
T ss_pred EEEEc-cCHH-HHHHHHHHHHhcceEEEee
Confidence 44444 5665 4567788999999998776
No 94
>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]
Probab=24.22 E-value=61 Score=28.48 Aligned_cols=35 Identities=17% Similarity=0.449 Sum_probs=30.9
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
...+||.++-|-.++..||++|+.|--..|++|..
T Consensus 210 cstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~ 244 (284)
T KOG1457|consen 210 CSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA 244 (284)
T ss_pred hhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec
Confidence 44689999999999999999999999888888754
No 95
>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.
Probab=24.18 E-value=1.1e+02 Score=23.17 Aligned_cols=34 Identities=24% Similarity=0.507 Sum_probs=25.4
Q ss_pred CcceEEecCCCCCCCHHHHHHHhhccCc-----cceEEec
Q 032398 103 RCGICYLSRIPAHMDPVKLRQILSQYGE-----IQRIYLA 137 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p~kLR~~fsqfGe-----V~RIyL~ 137 (141)
..+||||+.-- .|.+.+|++++..++. ..||++.
T Consensus 53 ~~~v~yi~~e~-~~~~~rl~~~~~~~~~~~~~~~~~i~~~ 91 (226)
T cd01393 53 EGKVVYIDTEG-AFRPERLVQLAVRFGLDPEEVLDNIYVA 91 (226)
T ss_pred cceEEEEecCC-CCCHHHHHHHHHHhccchhhhhccEEEE
Confidence 37899999853 4788999999888764 4666654
No 96
>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=23.60 E-value=36 Score=34.41 Aligned_cols=35 Identities=9% Similarity=0.348 Sum_probs=31.3
Q ss_pred CcceEEecCCCCCCCHHHHHHHhhccCccceEEec
Q 032398 103 RCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLA 137 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~ 137 (141)
-+-.+++|+++..+...+||..|..||.|.+|-+-
T Consensus 371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiK 405 (975)
T KOG0112|consen 371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIK 405 (975)
T ss_pred hhhhhhhcCcccchhhhhhhhhhhhhccccccccc
Confidence 35578999999999999999999999999998653
No 97
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=23.49 E-value=1.1e+02 Score=21.92 Aligned_cols=39 Identities=21% Similarity=0.422 Sum_probs=33.4
Q ss_pred hcCCcceEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 100 KADRCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 100 k~~k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
.......+|++.+|..+....+..+|..+|.+.++.+..
T Consensus 221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 259 (306)
T COG0724 221 LLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPP 259 (306)
T ss_pred cccccceeeccccccccchhHHHHhccccccceeeeccC
Confidence 345678899999999999999999999999997766543
No 98
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=22.68 E-value=59 Score=21.24 Aligned_cols=19 Identities=26% Similarity=0.438 Sum_probs=16.0
Q ss_pred ecCCCCCCCHHHHHHHhhc
Q 032398 109 LSRIPAHMDPVKLRQILSQ 127 (141)
Q Consensus 109 LSrIPpgM~p~kLR~~fsq 127 (141)
|+.|-+||+..+++.+|..
T Consensus 9 ~~~i~~GmTk~qV~~lLG~ 27 (71)
T PF04355_consen 9 LAQIKPGMTKDQVRALLGS 27 (71)
T ss_dssp HTTT-TTSBHHHHHHHHTS
T ss_pred HHhhcCCCCHHHHHHhcCC
Confidence 5688999999999999976
No 99
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=22.54 E-value=81 Score=30.72 Aligned_cols=33 Identities=15% Similarity=0.406 Sum_probs=29.0
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
-+-|-++|=.-.+..|+.+||+||.|--|++-+
T Consensus 119 rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~ 151 (678)
T KOG0127|consen 119 RLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPR 151 (678)
T ss_pred eEEeecCCcccCcHHHHHHHhhcceEEEEEccc
Confidence 456889999999999999999999999888753
No 100
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=22.18 E-value=32 Score=23.50 Aligned_cols=30 Identities=17% Similarity=0.443 Sum_probs=24.6
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
.=|+..|| |+.+..-..++.+||.+..++-
T Consensus 21 ~D~i~gv~-giG~k~A~~ll~~~~~~~~~~~ 50 (75)
T cd00080 21 SDNIPGVP-GIGPKTALKLLKEYGSLENLLE 50 (75)
T ss_pred cccCCCCC-cccHHHHHHHHHHhCCHHHHHH
Confidence 56677665 5999999999999999877654
No 101
>PF00837 T4_deiodinase: Iodothyronine deiodinase; InterPro: IPR000643 Iodothyronine deiodinase (1.97.1.10 from EC) (DI) [] is the vertebrate enzyme responsible for the deiodination of the prohormone thyroxine (T4 or 3,5,3',5'-tetraiodothyronine) into the biologically active hormone T3 (3,5,3'-triiodothyronine) and of T3 into the inactive metabolite T2 (3,3'-diiodothyronine). All known DI are proteins of about 250 residues that contain a selenocysteine at their active site. Three types of DI are known, type II is essential for providing the brain with the appropriate levels of T3 during the critical period of development, and type III is essential for the regulation of thyroid hormone inactivation during embryological development.; GO: 0004800 thyroxine 5'-deiodinase activity, 0055114 oxidation-reduction process
Probab=21.60 E-value=1e+02 Score=26.36 Aligned_cols=26 Identities=27% Similarity=0.455 Sum_probs=21.3
Q ss_pred CcceEEecCC-CCCCCHHHHHHHhhcc
Q 032398 103 RCGICYLSRI-PAHMDPVKLRQILSQY 128 (141)
Q Consensus 103 k~GVIYLSrI-PpgM~p~kLR~~fsqf 128 (141)
..-|+|.|.. |-++.+..||++|.+|
T Consensus 210 ~gkv~Y~Gg~GP~~y~~~e~r~~L~~~ 236 (237)
T PF00837_consen 210 DGKVVYKGGPGPFGYSPEELREWLEKY 236 (237)
T ss_pred CCEEEEeCCCCCCcCCHHHHHHHHHhc
Confidence 4458999955 6678899999999987
No 102
>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]
Probab=21.58 E-value=83 Score=29.60 Aligned_cols=34 Identities=12% Similarity=0.300 Sum_probs=31.2
Q ss_pred CcceEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 103 RCGICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
.+-||-|..||.--.+..+-+++-+||.|+.+-.
T Consensus 27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~ 60 (492)
T KOG1190|consen 27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLM 60 (492)
T ss_pred CcceeEeccCCccccHHHHHHhcccccceeeeee
Confidence 5679999999999999999999999999998754
No 103
>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]
Probab=21.31 E-value=56 Score=29.43 Aligned_cols=33 Identities=9% Similarity=0.299 Sum_probs=28.7
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEecc
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYLAP 138 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~p 138 (141)
-+|||.+-+--.+..+|.+|+.||.|.-.-+.+
T Consensus 21 klfvgml~kqq~e~dvrrlf~pfG~~~e~tvlr 53 (371)
T KOG0146|consen 21 KLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLR 53 (371)
T ss_pred hhhhhhhcccccHHHHHHHhcccCCcceeEEec
Confidence 478899989899999999999999998876654
No 104
>TIGR03767 P_acnes_RR metallophosphoesterase, PPA1498 family. This model describes a small collection of probable metallophosphoresterases, related to pfam00149 but with long inserts separating some of the shared motifs such that the homology is apparent only through multiple sequence alignment. Members of this protein family, in general, have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region modeled by this alignment. Members include YP_056203.1 from Propionibacterium acnes KPA171202.
Probab=21.29 E-value=2.1e+02 Score=26.91 Aligned_cols=46 Identities=7% Similarity=-0.015 Sum_probs=32.0
Q ss_pred hHHHHHHHHhhcCCcceEEecCCCCC----------------CCHHHHHHHhhccCccceEE
Q 032398 90 KKQRLLEEAAKADRCGICYLSRIPAH----------------MDPVKLRQILSQYGEIQRIY 135 (141)
Q Consensus 90 kkK~L~~~~~k~~k~GVIYLSrIPpg----------------M~p~kLR~~fsqfGeV~RIy 135 (141)
+=..|.+..++...+-||.++|+|+. .+..+|.++|.+|..|..|+
T Consensus 324 QL~WLeqeLa~a~~k~VVVf~HHPp~s~g~~~~Dp~~pg~~~~n~~eLldLL~~ypnV~aVf 385 (496)
T TIGR03767 324 QFKWIKDTLRASSDTLFVLFSHHTSWSMVNELTDPVDPGEKRHLGTELVSLLLEHPNVLAWV 385 (496)
T ss_pred HHHHHHHHHhcCCCCCEEEEECCCCccccccccccccccccccCHHHHHHHHhcCCCceEEE
Confidence 33456665555555669999999952 22468999999998787654
No 105
>COG0106 HisA Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]
Probab=20.88 E-value=1.1e+02 Score=26.27 Aligned_cols=29 Identities=21% Similarity=0.430 Sum_probs=25.2
Q ss_pred eEEecCCCCCCCHHHHHHHhhccCccceEEec
Q 032398 106 ICYLSRIPAHMDPVKLRQILSQYGEIQRIYLA 137 (141)
Q Consensus 106 VIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL~ 137 (141)
-|-||+.+ ..+|..+++++..|| +||.++
T Consensus 100 rViiGt~a-v~~p~~v~~~~~~~g--~rivv~ 128 (241)
T COG0106 100 RVIIGTAA-VKNPDLVKELCEEYG--DRIVVA 128 (241)
T ss_pred EEEEecce-ecCHHHHHHHHHHcC--CcEEEE
Confidence 35578988 699999999999999 898875
No 106
>PF05189 RTC_insert: RNA 3'-terminal phosphate cyclase (RTC), insert domain; InterPro: IPR013796 RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. RNA 3'-terminal phosphate cyclase (6.5.1.4 from EC) [, ] catalyses the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA. ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate These enzymes might be responsible for production of the cyclic phosphate RNA ends that are known to be required by many RNA ligases in both prokaryotes and eukaryotes. RNA cyclase is a protein of from 36 to 42 kDa. The best conserved region is a glycine-rich stretch of residues located in the central part of the sequence and which is reminiscent of various ATP, GTP or AMP glycine-rich loops. The crystal structure of RNA 3'-terminal phosphate cyclase shows that each molecule consists of two domains. The larger domain contains three repeats of a folding unit comprising two parallel alpha helices and a four-stranded beta sheet; this fold was previously identified in translation initiation factor 3 (IF3). The large domain is similar to one of the two domains of 5-enolpyruvylshikimate-3-phosphate synthase and UDP-N-acetylglucosamine enolpyruvyl transferase. The smaller domain uses a similar secondary structure element with different topology, observed in many other proteins such as thioredoxin []. Although the active site of this enzyme could not be unambiguously assigned, it can be mapped to a region surrounding His309, an adenylate acceptor, in which a number of amino acids are highly conserved in the enzyme from different sources []. This entry contains the insert-domain of approximately 100 amino acids.; PDB: 3TV1_B 3KGD_D 1QMI_D 1QMH_B 3TUX_A 3TUT_A 3TW3_A 3PQV_A.
Probab=20.67 E-value=62 Score=22.86 Aligned_cols=34 Identities=24% Similarity=0.354 Sum_probs=23.8
Q ss_pred CcceEEecCCCCCCCHHH---HHHHhhccCccceEEe
Q 032398 103 RCGICYLSRIPAHMDPVK---LRQILSQYGEIQRIYL 136 (141)
Q Consensus 103 k~GVIYLSrIPpgM~p~k---LR~~fsqfGeV~RIyL 136 (141)
-+|+.|.++||+.+-..+ .++.|.+|+.=-.|+.
T Consensus 9 i~g~a~~a~lp~~va~R~~~~a~~~L~~~~~~v~i~~ 45 (103)
T PF05189_consen 9 IRGIAFVAGLPSSVAERMANAARKRLNWYGPDVEIET 45 (103)
T ss_dssp EEEEEEEESS-CHHHHHHHHHHHHHHCTTCSEEEEEE
T ss_pred EEEEEEEcCCCHHHHHHHHHHHHHHhhhhCCCeEEEE
Confidence 589999999999887644 4566666765455554
No 107
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=20.42 E-value=76 Score=26.04 Aligned_cols=20 Identities=30% Similarity=0.556 Sum_probs=18.0
Q ss_pred CCC--CCCHHHHHHHhhccCcc
Q 032398 112 IPA--HMDPVKLRQILSQYGEI 131 (141)
Q Consensus 112 IPp--gM~p~kLR~~fsqfGeV 131 (141)
.|+ .+++..++.+|.+||.|
T Consensus 90 ~P~~~~~t~e~~~~LL~~yGPL 111 (166)
T PF12385_consen 90 EPANASYTAEGLANLLREYGPL 111 (166)
T ss_pred CCcccccCHHHHHHHHHHcCCe
Confidence 566 89999999999999987
No 108
>PF09992 DUF2233: Predicted periplasmic protein (DUF2233); InterPro: IPR018711 This entry contains proteins that catalyze the second step in the formation of the mannose 6-phosphate targeting signal on lysosomal enzyme oligosaccharides, this is achieved by removing GlcNAc residues from GlcNAc-alpha-P-mannose moieties, which are formed in the first step.; PDB: 3OHG_A.
Probab=20.37 E-value=89 Score=23.26 Aligned_cols=34 Identities=29% Similarity=0.295 Sum_probs=23.5
Q ss_pred CcceEEecCCC----CCCCHHHHHHHhhccCccceEEe
Q 032398 103 RCGICYLSRIP----AHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 103 k~GVIYLSrIP----pgM~p~kLR~~fsqfGeV~RIyL 136 (141)
+.|-++|-.+. .+|+..+|.++|.++|-..-|+|
T Consensus 99 ~~g~l~l~~vdg~~~~g~tl~ela~~l~~lG~~~AinL 136 (170)
T PF09992_consen 99 ADGKLLLIVVDGRQSAGMTLDELAQLLKSLGCVDAINL 136 (170)
T ss_dssp TTSEEEEEEE----S--B-HHHHHHHHHHHT-SEEEE-
T ss_pred CCCcEEEEEEcCCcCCCCCHHHHHHHHHHcCcCeEEEe
Confidence 56767776676 79999999999999998887776
No 109
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=20.33 E-value=53 Score=32.25 Aligned_cols=33 Identities=15% Similarity=0.406 Sum_probs=29.9
Q ss_pred cceEEecCCCCCCCHHHHHHHhhccCccceEEe
Q 032398 104 CGICYLSRIPAHMDPVKLRQILSQYGEIQRIYL 136 (141)
Q Consensus 104 ~GVIYLSrIPpgM~p~kLR~~fsqfGeV~RIyL 136 (141)
.+=|.|-.||-.-.-..+|.||+.||.|--|+|
T Consensus 613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRl 645 (725)
T KOG0110|consen 613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRL 645 (725)
T ss_pred cceeeeeccchHHHHHHHHHHHhcccceeeecc
Confidence 567899999999899999999999999988877
Done!