Query 048268
Match_columns 244
No_of_seqs 139 out of 172
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 07:57:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048268.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048268hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03120 nucleic acid binding 100.0 2.4E-75 5.3E-80 526.4 17.8 234 1-241 25-259 (260)
2 PLN03121 nucleic acid binding 100.0 4.5E-70 9.7E-75 487.4 13.8 208 1-216 26-243 (243)
3 PF13893 RRM_5: RNA recognitio 97.5 0.00011 2.3E-09 50.7 3.2 49 1-55 5-54 (56)
4 PF00076 RRM_1: RNA recognitio 96.8 0.00087 1.9E-08 46.3 2.1 51 1-53 19-70 (70)
5 PLN03134 glycine-rich RNA-bind 96.1 0.0099 2.1E-07 49.5 4.9 54 1-58 55-112 (144)
6 PLN03120 nucleic acid binding 96.0 0.0088 1.9E-07 55.2 4.4 64 99-162 134-209 (260)
7 smart00360 RRM RNA recognition 95.9 0.0093 2E-07 39.7 3.2 53 1-55 17-71 (71)
8 PF14259 RRM_6: RNA recognitio 95.3 0.018 4E-07 40.4 3.2 49 1-53 19-70 (70)
9 smart00362 RRM_2 RNA recogniti 95.3 0.022 4.8E-07 38.0 3.4 50 1-54 20-71 (72)
10 PLN03121 nucleic acid binding 95.1 0.027 5.9E-07 51.6 4.4 51 97-147 145-198 (243)
11 TIGR01661 ELAV_HUD_SF ELAV/HuD 95.1 0.016 3.6E-07 52.7 3.1 53 1-57 24-80 (352)
12 smart00361 RRM_1 RNA recogniti 95.1 0.029 6.2E-07 40.6 3.6 51 3-54 15-69 (70)
13 TIGR01661 ELAV_HUD_SF ELAV/HuD 95.0 0.019 4.2E-07 52.2 3.2 53 1-57 290-346 (352)
14 TIGR01659 sex-lethal sex-letha 94.2 0.031 6.8E-07 53.0 2.6 53 1-57 128-184 (346)
15 TIGR01622 SF-CC1 splicing fact 93.8 0.054 1.2E-06 51.3 3.4 53 1-57 110-165 (457)
16 cd00590 RRM RRM (RNA recogniti 93.8 0.078 1.7E-06 35.5 3.2 51 1-55 20-73 (74)
17 TIGR01622 SF-CC1 splicing fact 93.7 0.17 3.7E-06 48.0 6.5 57 1-61 207-267 (457)
18 TIGR01642 U2AF_lg U2 snRNP aux 92.8 0.1 2.3E-06 50.0 3.6 53 1-57 440-499 (509)
19 KOG4676 Splicing factor, argin 92.8 0.14 3E-06 50.2 4.4 63 1-63 28-92 (479)
20 TIGR01649 hnRNP-L_PTB hnRNP-L/ 92.7 0.093 2E-06 51.2 3.2 51 1-57 297-348 (481)
21 TIGR01649 hnRNP-L_PTB hnRNP-L/ 92.6 0.097 2.1E-06 51.0 3.1 50 1-55 117-169 (481)
22 TIGR01628 PABP-1234 polyadenyl 92.5 0.1 2.2E-06 51.3 3.0 52 1-56 21-76 (562)
23 KOG4209 Splicing factor RNPS1, 92.1 0.13 2.9E-06 46.4 3.1 55 1-57 122-177 (231)
24 TIGR01645 half-pint poly-U bin 92.1 0.13 2.8E-06 52.7 3.3 54 1-58 128-185 (612)
25 TIGR01648 hnRNP-R-Q heterogene 91.8 0.14 3E-06 52.0 3.3 48 1-57 254-304 (578)
26 TIGR01642 U2AF_lg U2 snRNP aux 90.9 0.22 4.7E-06 47.8 3.5 53 1-57 316-372 (509)
27 TIGR01628 PABP-1234 polyadenyl 90.7 0.22 4.8E-06 48.9 3.4 54 1-57 306-361 (562)
28 TIGR01659 sex-lethal sex-letha 89.1 0.39 8.4E-06 45.6 3.5 55 1-59 214-274 (346)
29 PF14605 Nup35_RRM_2: Nup53/35 87.9 0.29 6.2E-06 34.4 1.4 33 1-40 21-53 (53)
30 KOG0107 Alternative splicing f 87.6 0.61 1.3E-05 41.4 3.5 50 1-56 31-81 (195)
31 TIGR01645 half-pint poly-U bin 87.0 0.97 2.1E-05 46.4 5.0 54 1-58 225-282 (612)
32 PLN03213 repressor of silencin 87.0 0.58 1.3E-05 47.4 3.4 52 1-57 31-85 (759)
33 KOG0123 Polyadenylate-binding 86.3 0.66 1.4E-05 44.6 3.3 53 1-57 97-150 (369)
34 COG0724 RNA-binding proteins ( 82.1 1.8 3.8E-05 35.5 3.6 57 1-58 136-193 (306)
35 PF05172 Nup35_RRM: Nup53/35/4 78.7 1.9 4.1E-05 34.4 2.7 54 1-57 26-89 (100)
36 TIGR01648 hnRNP-R-Q heterogene 75.8 1.8 4E-05 44.1 2.3 52 1-55 79-133 (578)
37 KOG0121 Nuclear cap-binding pr 74.0 4.5 9.7E-05 34.7 3.8 60 1-62 57-118 (153)
38 PF01296 Galanin: Galanin; In 73.1 0.55 1.2E-05 29.9 -1.4 25 96-120 5-29 (29)
39 KOG0130 RNA-binding protein RB 70.3 2.7 5.9E-05 36.3 1.7 55 1-57 93-149 (170)
40 KOG0415 Predicted peptidyl pro 67.7 4 8.7E-05 40.0 2.4 51 1-55 260-314 (479)
41 KOG0113 U1 small nuclear ribon 65.0 5.1 0.00011 38.3 2.5 51 1-55 122-176 (335)
42 KOG0147 Transcriptional coacti 61.1 6.9 0.00015 39.8 2.8 52 1-56 200-254 (549)
43 KOG0126 Predicted RNA-binding 59.8 7.7 0.00017 35.0 2.6 59 1-63 56-118 (219)
44 PF08952 DUF1866: Domain of un 57.6 10 0.00023 32.5 2.9 33 25-57 72-104 (146)
45 KOG4206 Spliceosomal protein s 56.9 6.7 0.00015 35.7 1.7 51 1-55 34-85 (221)
46 KOG0124 Polypyrimidine tract-b 52.7 18 0.00038 35.9 3.9 56 1-60 134-193 (544)
47 KOG0105 Alternative splicing f 44.2 18 0.00039 32.9 2.3 56 1-60 27-83 (241)
48 KOG0131 Splicing factor 3b, su 43.8 18 0.0004 32.5 2.3 53 1-55 117-172 (203)
49 KOG0127 Nucleolar protein fibr 40.0 33 0.00071 35.5 3.7 53 1-55 138-191 (678)
50 KOG0125 Ataxin 2-binding prote 39.1 26 0.00056 34.1 2.7 51 4-57 120-171 (376)
51 smart00071 Galanin Galanin. Ga 38.4 6 0.00013 31.8 -1.4 28 95-122 16-43 (103)
52 KOG1996 mRNA splicing factor [ 36.8 31 0.00068 33.2 2.9 51 4-55 310-362 (378)
53 KOG4454 RNA binding protein (R 36.8 28 0.0006 32.3 2.4 38 20-57 46-84 (267)
54 KOG0148 Apoptosis-promoting RN 36.6 40 0.00087 32.1 3.5 31 25-55 202-233 (321)
55 KOG0123 Polyadenylate-binding 36.5 38 0.00083 32.6 3.5 51 1-55 19-70 (369)
56 KOG4207 Predicted splicing fac 33.1 40 0.00087 31.1 2.8 52 2-57 35-90 (256)
57 KOG0114 Predicted RNA-binding 33.0 56 0.0012 27.2 3.4 51 3-57 41-92 (124)
58 KOG0110 RNA-binding protein (R 29.5 50 0.0011 34.9 3.2 56 1-58 536-596 (725)
59 KOG0108 mRNA cleavage and poly 29.2 74 0.0016 31.7 4.2 55 2-60 40-98 (435)
60 KOG0117 Heterogeneous nuclear 27.0 60 0.0013 32.8 3.1 52 3-54 103-158 (506)
61 PF11985 DUF3486: Protein of u 27.0 4E+02 0.0086 22.7 9.1 20 90-109 31-54 (180)
62 KOG0117 Heterogeneous nuclear 26.5 61 0.0013 32.8 3.0 47 2-57 281-328 (506)
63 KOG0153 Predicted RNA-binding 24.8 59 0.0013 31.8 2.6 49 2-58 250-300 (377)
64 PF08543 Phos_pyr_kin: Phospho 24.6 80 0.0017 27.9 3.2 24 89-113 204-227 (246)
65 KOG3430 Dynein light chain typ 24.0 1.2E+02 0.0026 24.2 3.7 33 105-137 20-54 (90)
66 COG0351 ThiD Hydroxymethylpyri 23.9 81 0.0018 29.4 3.2 24 89-113 215-238 (263)
67 COG5175 MOT2 Transcriptional r 23.6 69 0.0015 31.6 2.8 54 1-55 141-198 (480)
68 KOG1548 Transcription elongati 23.1 1E+02 0.0022 30.2 3.8 50 4-58 300-350 (382)
69 PF03912 Psb28: Psb28 protein; 21.2 75 0.0016 26.1 2.1 30 10-39 11-41 (108)
70 KOG0127 Nucleolar protein fibr 20.7 89 0.0019 32.5 3.0 56 1-58 313-376 (678)
71 PLN00039 photosystem II reacti 20.6 71 0.0015 26.4 1.9 28 11-38 14-42 (111)
72 PF15023 DUF4523: Protein of u 20.3 67 0.0015 28.1 1.8 42 2-51 112-153 (166)
No 1
>PLN03120 nucleic acid binding protein; Provisional
Probab=100.00 E-value=2.4e-75 Score=526.36 Aligned_cols=234 Identities=65% Similarity=0.891 Sum_probs=212.6
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhhhccCceecCceEEEecCCCCCCCCCCCCCcccccCCCCCC
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVLLSGATIVDQSVTIELDPDYKPPATASVTSTARENKNEGG 80 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALLLnGAtL~d~~V~Vt~~~~~~~~~~~~~~~~~~~~~~qe~ 80 (244)
|||||+|.+|. |.++.+..+.|||||+++.++++||||||++|+|+.|+|+++++|..|+......+.... ...
T Consensus 25 FS~~G~I~~V~----I~~d~~~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~~~p~~~~~~~~~~~~--~~~ 98 (260)
T PLN03120 25 FSFSGDIEYVE----MQSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDYQLPPEALAPLSSNSP--ASG 98 (260)
T ss_pred HHhcCCeEEEE----EeecCCCCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCCCCCcccccccccccC--CCC
Confidence 89999999996 667777789999999999999999999999999999999999999988776443211111 111
Q ss_pred CccccchHHHHHHHHHhccccccHHHHHHHHHHhhhcCccHHHHHHHHhhhhhcccccccccchhhhhhHHhhccccccc
Q 048268 81 TESVVHKAEDVVSTMLAKGFILGKDAVGKAKAFDEKHRFTSTATATVASLDQKIGFTEKISAGTTLVNDKVREMDEKFHV 160 (244)
Q Consensus 81 kp~a~~~a~~IvA~mLAkGYvLgddAi~KA~~fDekhgiSs~f~a~v~slD~k~glteKi~~g~s~vn~k~k~vDeky~V 160 (244)
...+++++++||++||||||+||||||+|||+||||||||++|+++|.+||+||||||||+.|+++||+++|+|||||||
T Consensus 99 ~~~~~~~a~~vva~mLAkGy~l~~dA~~kAk~fDekH~~ss~a~a~v~~~d~k~gltek~~~g~~~v~~~~k~vDeky~v 178 (260)
T PLN03120 99 AESAVKKAEDVVSSMLAKGFILGKDAVNKAKAFDEKHQLTSTASAKVASLDKKIGLSEKLSAGTAVVNEKVKEVDQKYQV 178 (260)
T ss_pred ccchhhHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhhchHHHHHHHHHhhhhhcCcccccccchHHHHHHHHhhhhhhch
Confidence 12478999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHhhHHHHHHHHHHhhhhhhccccCceeeechhhhhhHHHHHHHHhhhhhhhhhHHH-HHHHhhhhhccCccccccCCCC
Q 048268 161 SEKTKSAFSAAEQTVSNAGSAIMKNRYVLTGASWVTGAFNRVTKAAGEVSEKTREKV-LAEEEETRKADGYSQVSDTEFP 239 (244)
Q Consensus 161 SektksA~~aaeq~~~~agsai~~n~Yvs~Ga~wvs~a~~~~akaa~~~~~~~~ek~-~~~~~~~~~~~~~~~~~~~~~~ 239 (244)
|++|++|+.++||+++++|+|||+||||++||+||||||+||||||.|+|+||+||| ++|+++ .-+++|+++|++|+|
T Consensus 179 s~kt~sa~~~~~~~~~~a~sai~~~~y~~~ga~w~~~a~~~~a~aa~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~ 257 (260)
T PLN03120 179 SEKTKSALAAAEQKVSSAGSAIMKNRYVLTGASWVTGAFNKVAKAAEEVGQKTKEKVGAAEEEQ-QVVDAYANIHLSESP 257 (260)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhcCcccccchHHHHHHHHHHHHHHHHHhhhhHHHHhhhhhhc-ccccccceeecCCCC
Confidence 999999999999999999999999999999999999999999999999999999999 666665 238889999999999
Q ss_pred cC
Q 048268 240 RS 241 (244)
Q Consensus 240 ~~ 241 (244)
++
T Consensus 258 ~~ 259 (260)
T PLN03120 258 KA 259 (260)
T ss_pred CC
Confidence 86
No 2
>PLN03121 nucleic acid binding protein; Provisional
Probab=100.00 E-value=4.5e-70 Score=487.43 Aligned_cols=208 Identities=43% Similarity=0.582 Sum_probs=189.2
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhhhccCceecCceEEEecCCCCCCCCCCCCCcc-cccCCC--
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVLLSGATIVDQSVTIELDPDYKPPATASVTST-ARENKN-- 77 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALLLnGAtL~d~~V~Vt~~~~~~~~~~~~~~~~-~~~~~~-- 77 (244)
|||||+|.+|. |+++++..+.|||+|+++++++|||||||++|+|++|+|+++++|..+++.+..+. ..++++
T Consensus 26 FS~~G~I~~V~----I~~D~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~y~~~~~~~~~~~~~~~~~~~~ 101 (243)
T PLN03121 26 FSHCGAIEHVE----IIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQYEDEFDFWNRPSWDTEDISTH 101 (243)
T ss_pred HHhcCCeEEEE----EecCCCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcccccCcccccCccccccccccc
Confidence 99999999996 88888889999999999999999999999999999999999999999876533221 111111
Q ss_pred ------CCCCc-cccchHHHHHHHHHhccccccHHHHHHHHHHhhhcCccHHHHHHHHhhhhhcccccccccchhhhhhH
Q 048268 78 ------EGGTE-SVVHKAEDVVSTMLAKGFILGKDAVGKAKAFDEKHRFTSTATATVASLDQKIGFTEKISAGTTLVNDK 150 (244)
Q Consensus 78 ------qe~kp-~a~~~a~~IvA~mLAkGYvLgddAi~KA~~fDekhgiSs~f~a~v~slD~k~glteKi~~g~s~vn~k 150 (244)
.-..| .++++|++||++||||||+||+|||+|||+|||+||||+++.++|.+||+|+||||||++|+ ++
T Consensus 102 ~~~~~~~~~~p~~a~~~aq~Vv~tmLAkGyvLgkda~~KAkafDE~h~lss~a~a~v~~~d~~iglt~k~~~g~----~~ 177 (243)
T PLN03121 102 NYETNQFASTPGEAVTVAQEVVKTMLAKGYVLGKDALSKAKAFDESHQVSATAAAKVAELSKRIGLTDKIFAGM----EA 177 (243)
T ss_pred cccccccCCCchhhHHHHHHHHHHHHHhcchhhHHHHHHHHHHHHhcCccHhhhhhhhhhhhhccchhhhhhhH----HH
Confidence 11123 48999999999999999999999999999999999999999999999999999999999999 77
Q ss_pred HhhccccccchHhhHHHHHHHHHHhhhhhhccccCceeeechhhhhhHHHHHHHHhhhhhhhhhHH
Q 048268 151 VREMDEKFHVSEKTKSAFSAAEQTVSNAGSAIMKNRYVLTGASWVTGAFNRVTKAAGEVSEKTREK 216 (244)
Q Consensus 151 ~k~vDeky~VSektksA~~aaeq~~~~agsai~~n~Yvs~Ga~wvs~a~~~~akaa~~~~~~~~ek 216 (244)
+|+||||||||++||+|+.++||+++.+|++||+||||++||+||||||+||||||+|+|++++++
T Consensus 178 vk~vDeky~vs~~tksA~~aa~~~~~~a~sai~~~~Y~~~Ga~w~sga~~~~akaa~~~g~~~~~~ 243 (243)
T PLN03121 178 VRSVDEKYHVSEFTKSAATATGRTAAAAANAVVNSSYFSKGALWVSDALTRAAKAAADLGAHGSNQ 243 (243)
T ss_pred HHhhhhhhhhHHHHHHHHHHHHHHHHHhhhhhhhcchhhcchHHHHHHHHHHHHHHHHhhccccCC
Confidence 999999999999999999999999999999999999999999999999999999999999999863
No 3
>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=97.48 E-value=0.00011 Score=50.67 Aligned_cols=49 Identities=22% Similarity=0.342 Sum_probs=41.0
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhhh-ccCceecCceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVL-LSGATIVDQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt 55 (244)
||=+|+|.+|.. .+.. ...|+|+|.++..|+.|+- |||..+.|.+|.|.
T Consensus 5 f~~fG~V~~i~~----~~~~--~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~ 54 (56)
T PF13893_consen 5 FSKFGEVKKIKI----FKKK--RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVS 54 (56)
T ss_dssp HTTTS-EEEEEE----ETTS--TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEE
T ss_pred hCCcccEEEEEE----EeCC--CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence 677899999973 3333 5789999999999999996 99999999999985
No 4
>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=96.76 E-value=0.00087 Score=46.34 Aligned_cols=51 Identities=24% Similarity=0.313 Sum_probs=41.4
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhhh-ccCceecCceEE
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVL-LSGATIVDQSVT 53 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~ 53 (244)
|+-||+|..+.... -+.+.....|+|+|+++..++.||- |+|-.|.|..|+
T Consensus 19 f~~~g~i~~~~~~~--~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir 70 (70)
T PF00076_consen 19 FSQFGKIESIKVMR--NSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR 70 (70)
T ss_dssp HHTTSTEEEEEEEE--ETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred HHHhhhcccccccc--cccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence 56789998886421 1344567899999999999999999 999999998874
No 5
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=96.10 E-value=0.0099 Score=49.49 Aligned_cols=54 Identities=15% Similarity=0.287 Sum_probs=43.1
Q ss_pred CcccccccceecccccccC--CC-CceEEEEEEeCCchhhhhhh-ccCceecCceEEEecCC
Q 048268 1 MSLWGQLSKILRNSFPLCD--NE-RSQIARVVFKDPQGAETAVL-LSGATIVDQSVTIELDP 58 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~--~~-~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt~~~ 58 (244)
|+=||.|.++.. ..+ .+ .-..|+|+|+++.+++.||- |||..|.|..|.|..+.
T Consensus 55 F~~~G~I~~v~i----~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~ 112 (144)
T PLN03134 55 FAHFGDVVDAKV----IVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN 112 (144)
T ss_pred HhcCCCeEEEEE----EecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence 455899999863 322 23 34589999999999999995 99999999999998654
No 6
>PLN03120 nucleic acid binding protein; Provisional
Probab=95.98 E-value=0.0088 Score=55.20 Aligned_cols=64 Identities=22% Similarity=0.324 Sum_probs=47.5
Q ss_pred cccccHHHHHHHHHHhhhcCccHHHH-------HHHHhhhhhcccccccccchhhhhhHHhh-----ccccccchH
Q 048268 99 GFILGKDAVGKAKAFDEKHRFTSTAT-------ATVASLDQKIGFTEKISAGTTLVNDKVRE-----MDEKFHVSE 162 (244)
Q Consensus 99 GYvLgddAi~KA~~fDekhgiSs~f~-------a~v~slD~k~glteKi~~g~s~vn~k~k~-----vDeky~VSe 162 (244)
-.-|+-.+..+...||+|+|||.++. .++.++|+|||+|||......+..+++.. +..+|=.+.
T Consensus 134 kH~~ss~a~a~v~~~d~k~gltek~~~g~~~v~~~~k~vDeky~vs~kt~sa~~~~~~~~~~a~sai~~~~y~~~g 209 (260)
T PLN03120 134 KHQLTSTASAKVASLDKKIGLSEKLSAGTAVVNEKVKEVDQKYQVSEKTKSALAAAEQKVSSAGSAIMKNRYVLTG 209 (260)
T ss_pred hhchHHHHHHHHHhhhhhcCcccccccchHHHHHHHHhhhhhhchhHHHHHHHHHHHHHHHHHHHHHhcCcccccc
Confidence 34456778888999999999999865 68999999999999977666655444432 455564433
No 7
>smart00360 RRM RNA recognition motif.
Probab=95.88 E-value=0.0093 Score=39.66 Aligned_cols=53 Identities=21% Similarity=0.307 Sum_probs=39.0
Q ss_pred CcccccccceecccccccCCC-CceEEEEEEeCCchhhhhh-hccCceecCceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDNE-RSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~-~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt 55 (244)
|+-||.|..+... .....+ ....|+|+|.++..++-|+ .|+|..+.|..|.|.
T Consensus 17 f~~~g~v~~~~i~--~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~ 71 (71)
T smart00360 17 FSKFGKIESVRLV--RDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK 71 (71)
T ss_pred HHhhCCEeEEEEE--eCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence 4557888888632 112222 3458999999999999998 678899999998873
No 8
>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=95.33 E-value=0.018 Score=40.45 Aligned_cols=49 Identities=20% Similarity=0.273 Sum_probs=38.8
Q ss_pred CcccccccceecccccccC--CCCceEEEEEEeCCchhhhhhhccC-ceecCceEE
Q 048268 1 MSLWGQLSKILRNSFPLCD--NERSQIARVVFKDPQGAETAVLLSG-ATIVDQSVT 53 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~--~~~sq~A~VtFe~~~Aa~TALLLnG-AtL~d~~V~ 53 (244)
|+-||.|..|. +..+ +.....|+|+|.++..++.|+-+.+ -.|.|..|.
T Consensus 19 f~~~g~v~~v~----~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~ 70 (70)
T PF14259_consen 19 FSRFGPVEKVR----LIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR 70 (70)
T ss_dssp CTTSSBEEEEE----EEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred HHhcCCcceEE----EEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence 67789988886 3333 3457899999999999999999888 777777763
No 9
>smart00362 RRM_2 RNA recognition motif.
Probab=95.30 E-value=0.022 Score=38.03 Aligned_cols=50 Identities=22% Similarity=0.349 Sum_probs=38.2
Q ss_pred CcccccccceecccccccC-CCCceEEEEEEeCCchhhhhhh-ccCceecCceEEE
Q 048268 1 MSLWGQLSKILRNSFPLCD-NERSQIARVVFKDPQGAETAVL-LSGATIVDQSVTI 54 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~-~~~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~V 54 (244)
|.-+|.|..+. +.++ +.....++|+|.++..++.|+. |+|..+.|..|.|
T Consensus 20 ~~~~g~v~~~~----~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v 71 (72)
T smart00362 20 FSKFGPIESVK----IPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV 71 (72)
T ss_pred HHhcCCEEEEE----EecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence 34578887775 3333 3345689999999999999986 6779999988877
No 10
>PLN03121 nucleic acid binding protein; Provisional
Probab=95.15 E-value=0.027 Score=51.56 Aligned_cols=51 Identities=18% Similarity=0.212 Sum_probs=41.9
Q ss_pred hccccccHHHHHHHHHHhhhcCccHHHH---HHHHhhhhhcccccccccchhhh
Q 048268 97 AKGFILGKDAVGKAKAFDEKHRFTSTAT---ATVASLDQKIGFTEKISAGTTLV 147 (244)
Q Consensus 97 AkGYvLgddAi~KA~~fDekhgiSs~f~---a~v~slD~k~glteKi~~g~s~v 147 (244)
-.-+.|+-.|-.|.-+||+|.|||.++. ..|.++|+|||++|+......+.
T Consensus 145 DE~h~lss~a~a~v~~~d~~iglt~k~~~g~~~vk~vDeky~vs~~tksA~~aa 198 (243)
T PLN03121 145 DESHQVSATAAAKVAELSKRIGLTDKIFAGMEAVRSVDEKYHVSEFTKSAATAT 198 (243)
T ss_pred HHhcCccHhhhhhhhhhhhhccchhhhhhhHHHHHhhhhhhhhHHHHHHHHHHH
Confidence 3446688899999999999999999995 68899999999999755444433
No 11
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=95.14 E-value=0.016 Score=52.65 Aligned_cols=53 Identities=19% Similarity=0.310 Sum_probs=43.2
Q ss_pred CcccccccceecccccccCC--C-CceEEEEEEeCCchhhhhh-hccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCDN--E-RSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~--~-~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~ 57 (244)
|+=||.|.+|. ++++. + .-.-|+|+|.++..++.|| .|||..|.|..|.|...
T Consensus 24 F~~~G~i~~v~----i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a 80 (352)
T TIGR01661 24 FTSIGEIESCK----LVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA 80 (352)
T ss_pred HHccCCEEEEE----EEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEee
Confidence 67799999986 44432 2 2358999999999999999 69999999999999643
No 12
>smart00361 RRM_1 RNA recognition motif.
Probab=95.08 E-value=0.029 Score=40.57 Aligned_cols=51 Identities=20% Similarity=0.320 Sum_probs=38.0
Q ss_pred ccccccceecccccccC---CCCceEEEEEEeCCchhhhhhh-ccCceecCceEEE
Q 048268 3 LWGQLSKILRNSFPLCD---NERSQIARVVFKDPQGAETAVL-LSGATIVDQSVTI 54 (244)
Q Consensus 3 FcGkI~si~~~~el~~~---~~~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~V 54 (244)
-+|.|.+|... .+-+. +..-.-++|+|+++..+..|+- |||..+.|..|.+
T Consensus 15 ~fG~v~~v~~v-~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~ 69 (70)
T smart00361 15 YFGEVGKINKI-YIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA 69 (70)
T ss_pred hcCCeeEEEEE-EeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence 57889988411 12222 2234569999999999999987 8999999999876
No 13
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=95.03 E-value=0.019 Score=52.17 Aligned_cols=53 Identities=17% Similarity=0.300 Sum_probs=42.4
Q ss_pred CcccccccceecccccccC--CC-CceEEEEEEeCCchhhhhhh-ccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCD--NE-RSQIARVVFKDPQGAETAVL-LSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~--~~-~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt~~ 57 (244)
|+=||.|.++.+ +.+ .+ .-..|+|+|+++..|..|+. |||..|.|..|.|.-.
T Consensus 290 F~~fG~v~~v~i----~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~ 346 (352)
T TIGR01661 290 FGPFGAVQNVKI----IRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK 346 (352)
T ss_pred HHhCCCeEEEEE----eEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence 566899999873 333 23 33479999999999999986 9999999999999744
No 14
>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=94.23 E-value=0.031 Score=52.95 Aligned_cols=53 Identities=19% Similarity=0.251 Sum_probs=42.5
Q ss_pred CcccccccceecccccccC--CCCc-eEEEEEEeCCchhhhhh-hccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCD--NERS-QIARVVFKDPQGAETAV-LLSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~--~~~s-q~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~ 57 (244)
|+=||.|.++. ++++ .+++ ..|+|+|+++..++.|| -|+|..|.+..|.|..+
T Consensus 128 F~~~G~V~~v~----i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a 184 (346)
T TIGR01659 128 FRTIGPINTCR----IMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA 184 (346)
T ss_pred HHhcCCEEEEE----EEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence 56789999886 3333 2333 46999999999999999 59999999999999743
No 15
>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=93.83 E-value=0.054 Score=51.34 Aligned_cols=53 Identities=19% Similarity=0.329 Sum_probs=43.7
Q ss_pred CcccccccceecccccccC---CCCceEEEEEEeCCchhhhhhhccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCD---NERSQIARVVFKDPQGAETAVLLSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~---~~~sq~A~VtFe~~~Aa~TALLLnGAtL~d~~V~Vt~~ 57 (244)
|+=||+|.+|.. +.+ +..-..|||+|.++..++-||-|+|..|.|..|.|...
T Consensus 110 F~~~G~v~~v~i----~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~ 165 (457)
T TIGR01622 110 FSKVGKVRDVQC----IKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSS 165 (457)
T ss_pred HHhcCCeeEEEE----eecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeec
Confidence 667899998863 332 22356899999999999999999999999999999753
No 16
>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=93.79 E-value=0.078 Score=35.51 Aligned_cols=51 Identities=24% Similarity=0.380 Sum_probs=37.7
Q ss_pred CcccccccceecccccccCC--CCceEEEEEEeCCchhhhhhhc-cCceecCceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDN--ERSQIARVVFKDPQGAETAVLL-SGATIVDQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~--~~sq~A~VtFe~~~Aa~TALLL-nGAtL~d~~V~Vt 55 (244)
|..||.|..+. +..+. .....++|+|.++..+..|+.. +|..+.|..|.|.
T Consensus 20 ~~~~g~i~~~~----~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~ 73 (74)
T cd00590 20 FSKFGKVESVR----IVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVE 73 (74)
T ss_pred HHhcCCEEEEE----EeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEe
Confidence 45678888876 33333 2356899999999999999974 4555888888874
No 17
>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=93.69 E-value=0.17 Score=47.97 Aligned_cols=57 Identities=14% Similarity=0.321 Sum_probs=44.8
Q ss_pred CcccccccceecccccccCC--C-CceEEEEEEeCCchhhhhh-hccCceecCceEEEecCCCCC
Q 048268 1 MSLWGQLSKILRNSFPLCDN--E-RSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELDPDYK 61 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~--~-~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~~~~~ 61 (244)
|+=||.|.+|. +..+. + ....|+|+|.++..+..|| .|||..|.|..|.|..+.+..
T Consensus 207 f~~~G~i~~v~----~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~ 267 (457)
T TIGR01622 207 FEPFGDIEDVQ----LHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDST 267 (457)
T ss_pred HHhcCCeEEEE----EEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCC
Confidence 56689999886 33332 2 2357999999999999999 599999999999998765443
No 18
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=92.80 E-value=0.1 Score=50.02 Aligned_cols=53 Identities=21% Similarity=0.251 Sum_probs=41.7
Q ss_pred CcccccccceecccccccC--C---C-CceEEEEEEeCCchhhhhhh-ccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCD--N---E-RSQIARVVFKDPQGAETAVL-LSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~--~---~-~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt~~ 57 (244)
|+-||.|.+|.+ .+. + + .-..++|+|+++..|+.|+. |||..|.|..|.|+-.
T Consensus 440 f~~~G~v~~v~i----~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~ 499 (509)
T TIGR01642 440 FSKYGPLINIVI----PRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFY 499 (509)
T ss_pred HHhcCCeeEEEe----eccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence 566899998863 222 1 1 12579999999999999996 9999999999999754
No 19
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=92.79 E-value=0.14 Score=50.17 Aligned_cols=63 Identities=21% Similarity=0.161 Sum_probs=51.6
Q ss_pred Ccccccccceec--ccccccCCCCceEEEEEEeCCchhhhhhhccCceecCceEEEecCCCCCCC
Q 048268 1 MSLWGQLSKILR--NSFPLCDNERSQIARVVFKDPQGAETAVLLSGATIVDQSVTIELDPDYKPP 63 (244)
Q Consensus 1 FSFcGkI~si~~--~~el~~~~~~sq~A~VtFe~~~Aa~TALLLnGAtL~d~~V~Vt~~~~~~~~ 63 (244)
|-|.|||..|.+ ++.-+..+...+++||-|-|++-+..|-+|++...+|-.+.|-|+++...|
T Consensus 28 Fg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~~~~~p 92 (479)
T KOG4676|consen 28 FGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYGDEVIP 92 (479)
T ss_pred HhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecCCCCCc
Confidence 789999998853 222334456789999999999999999999999999999999888765554
No 20
>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=92.74 E-value=0.093 Score=51.16 Aligned_cols=51 Identities=16% Similarity=0.380 Sum_probs=42.7
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhhh-ccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVL-LSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt~~ 57 (244)
|+=||.|.+|.. .++ ....|+|+|+++..|..||- |||..|.|..|.|...
T Consensus 297 F~~yG~V~~vki----~~~--~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s 348 (481)
T TIGR01649 297 FCVYGNVERVKF----MKN--KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPS 348 (481)
T ss_pred HHhcCCeEEEEE----EeC--CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence 677999999973 222 23589999999999999995 9999999999999743
No 21
>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=92.57 E-value=0.097 Score=51.04 Aligned_cols=50 Identities=28% Similarity=0.420 Sum_probs=39.0
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhhh-ccCceecCc--eEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVL-LSGATIVDQ--SVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~--~V~Vt 55 (244)
|+=||+|.+|. +.++.+. ..|+|.|+++..|.-|+. |||..|.+. .|.|.
T Consensus 117 F~~~G~V~~v~----i~~~~~~-~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~ 169 (481)
T TIGR01649 117 FNPYGKVLRIV----TFTKNNV-FQALVEFESVNSAQHAKAALNGADIYNGCCTLKIE 169 (481)
T ss_pred HhccCCEEEEE----EEecCCc-eEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEE
Confidence 67799999996 3344433 369999999999999996 999999764 45553
No 22
>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=92.45 E-value=0.1 Score=51.31 Aligned_cols=52 Identities=17% Similarity=0.224 Sum_probs=42.5
Q ss_pred CcccccccceecccccccCCC---CceEEEEEEeCCchhhhhh-hccCceecCceEEEec
Q 048268 1 MSLWGQLSKILRNSFPLCDNE---RSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIEL 56 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~---~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~ 56 (244)
|+=||.|.+|. ++++.. ....|||+|.++..|+.|| .||+..|.|..|.|..
T Consensus 21 F~~~G~v~~v~----v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~ 76 (562)
T TIGR01628 21 FKPFGPVLSVR----VCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMW 76 (562)
T ss_pred HHhcCCEEEEE----EEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeec
Confidence 56689999886 455432 2358999999999999999 7999999999999963
No 23
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=92.08 E-value=0.13 Score=46.43 Aligned_cols=55 Identities=18% Similarity=0.177 Sum_probs=43.1
Q ss_pred CcccccccceecccccccCCC-CceEEEEEEeCCchhhhhhhccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCDNE-RSQIARVVFKDPQGAETAVLLSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~-~sq~A~VtFe~~~Aa~TALLLnGAtL~d~~V~Vt~~ 57 (244)
|.=||.|.-+... .-+..+ .-..|||.|.+..+.+.||.|+|..|.+..|.|+..
T Consensus 122 f~~Cg~i~~~ti~--~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~ 177 (231)
T KOG4209|consen 122 FESCGGINRVTVP--KDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLK 177 (231)
T ss_pred eeccCCccceeee--ccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeee
Confidence 5569999876532 112222 345899999999999999999999999999999844
No 24
>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=92.06 E-value=0.13 Score=52.66 Aligned_cols=54 Identities=17% Similarity=0.297 Sum_probs=43.5
Q ss_pred CcccccccceecccccccC--CC-CceEEEEEEeCCchhhhhh-hccCceecCceEEEecCC
Q 048268 1 MSLWGQLSKILRNSFPLCD--NE-RSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELDP 58 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~--~~-~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~~ 58 (244)
|+-||.|.+|.. ..+ .+ .-.-+||+|+++.+++.|+ -|||..|.|..|.|....
T Consensus 128 F~~fG~I~sV~I----~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~ 185 (612)
T TIGR01645 128 FDPFGPIKSINM----SWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS 185 (612)
T ss_pred HHccCCEEEEEE----eecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence 677999999973 333 23 3347999999999999999 499999999999997443
No 25
>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=91.85 E-value=0.14 Score=52.00 Aligned_cols=48 Identities=23% Similarity=0.411 Sum_probs=40.4
Q ss_pred Cccc--ccccceecccccccCCCCceEEEEEEeCCchhhhhhh-ccCceecCceEEEecC
Q 048268 1 MSLW--GQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVL-LSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFc--GkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt~~ 57 (244)
|+=| |+|.+|.. ++ .-|+|+|+++..|+.|+. |||..|.|..|.|..+
T Consensus 254 F~~f~~G~I~rV~~----~r-----gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A 304 (578)
T TIGR01648 254 FSEFKPGKVERVKK----IR-----DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA 304 (578)
T ss_pred HHhcCCCceEEEEe----ec-----CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence 4556 99999863 22 269999999999999997 9999999999999844
No 26
>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=0.22 Score=47.84 Aligned_cols=53 Identities=21% Similarity=0.322 Sum_probs=42.4
Q ss_pred CcccccccceecccccccC---CCCceEEEEEEeCCchhhhhh-hccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCD---NERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~---~~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~ 57 (244)
|+-||.|..+.. +.+ +.....|+|+|+++..+.-|+ .|||..|.|..|.|..+
T Consensus 316 f~~~G~i~~~~~----~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a 372 (509)
T TIGR01642 316 LESFGDLKAFNL----IKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA 372 (509)
T ss_pred HHhcCCeeEEEE----EecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence 556899988863 332 223458999999999999999 59999999999999755
No 27
>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=90.72 E-value=0.22 Score=48.95 Aligned_cols=54 Identities=20% Similarity=0.304 Sum_probs=43.6
Q ss_pred CcccccccceecccccccCCCC-ceEEEEEEeCCchhhhhhh-ccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCDNER-SQIARVVFKDPQGAETAVL-LSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~-sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt~~ 57 (244)
|+=||.|.++.. +.+..+. ...++|+|.++..+..|+- |+|..|.|..|.|..+
T Consensus 306 F~~~G~i~~~~i---~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a 361 (562)
T TIGR01628 306 FSECGEITSAKV---MLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA 361 (562)
T ss_pred HHhcCCeEEEEE---EECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence 566899999974 3444333 4589999999999999994 9999999999999754
No 28
>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=89.12 E-value=0.39 Score=45.63 Aligned_cols=55 Identities=24% Similarity=0.308 Sum_probs=41.0
Q ss_pred CcccccccceecccccccC--CCC-ceEEEEEEeCCchhhhhhh-ccCceecC--ceEEEecCCC
Q 048268 1 MSLWGQLSKILRNSFPLCD--NER-SQIARVVFKDPQGAETAVL-LSGATIVD--QSVTIELDPD 59 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~--~~~-sq~A~VtFe~~~Aa~TALL-LnGAtL~d--~~V~Vt~~~~ 59 (244)
|+=||.|..+.. .++ .+. -..++|+|++...|+.||- |||..|.+ ..|.|..+..
T Consensus 214 F~~fG~V~~v~i----~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~ 274 (346)
T TIGR01659 214 FGKYGQIVQKNI----LRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEE 274 (346)
T ss_pred HHhcCCEEEEEE----eecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCc
Confidence 566899988763 333 233 2589999999999999997 89998876 5777765543
No 29
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=87.95 E-value=0.29 Score=34.45 Aligned_cols=33 Identities=21% Similarity=0.376 Sum_probs=27.5
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhh
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAV 40 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TAL 40 (244)
|+=||.|..+.. ++..-.+||.|+++.+++.||
T Consensus 21 F~~fGeI~~~~~-------~~~~~~~~l~y~~~~~ae~Al 53 (53)
T PF14605_consen 21 FASFGEIVDIYV-------PESTNWMYLKYKSRKDAEKAL 53 (53)
T ss_pred HHhcCCEEEEEc-------CCCCcEEEEEECCHHHHHhhC
Confidence 445999999864 256779999999999999997
No 30
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=87.63 E-value=0.61 Score=41.42 Aligned_cols=50 Identities=34% Similarity=0.500 Sum_probs=40.5
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhh-hccCceecCceEEEec
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIEL 56 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~ 56 (244)
|+.+|.|-+|-+- .+. .--|+|+|+|+--|+-|+ -|+|.+|.|..|.|..
T Consensus 31 F~~yG~lrsvWvA---rnP---PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~ 81 (195)
T KOG0107|consen 31 FSKYGPLRSVWVA---RNP---PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVEL 81 (195)
T ss_pred HHhcCcceeEEEe---ecC---CCceEEeccCcccHHHHHhhcCCccccCceEEEEe
Confidence 7888999888632 222 346999999999888887 6999999999999973
No 31
>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=87.02 E-value=0.97 Score=46.42 Aligned_cols=54 Identities=9% Similarity=0.078 Sum_probs=43.7
Q ss_pred CcccccccceecccccccCC--C-CceEEEEEEeCCchhhhhh-hccCceecCceEEEecCC
Q 048268 1 MSLWGQLSKILRNSFPLCDN--E-RSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELDP 58 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~--~-~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~~ 58 (244)
|+=||.|.++. +.++. + .-..++|+|++.+.+.-|+ -|||-.|+|+.|.|..+.
T Consensus 225 Fs~FG~I~svr----l~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi 282 (612)
T TIGR01645 225 FEAFGEIVKCQ----LARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV 282 (612)
T ss_pred HhhcCCeeEEE----EEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence 67799999986 44432 2 2347999999999999999 799999999999997543
No 32
>PLN03213 repressor of silencing 3; Provisional
Probab=86.97 E-value=0.58 Score=47.39 Aligned_cols=52 Identities=12% Similarity=0.126 Sum_probs=44.1
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCC--chhhhhhh-ccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDP--QGAETAVL-LSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~--~Aa~TALL-LnGAtL~d~~V~Vt~~ 57 (244)
|+=||.|.++. ++|+.| -.-|||+|..+ ..+..|+= |||+.+.|..|.|..+
T Consensus 31 FSeFGsVkdVE----IpRETG-RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA 85 (759)
T PLN03213 31 FSPMGTVDAVE----FVRTKG-RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA 85 (759)
T ss_pred HHhcCCeeEEE----EecccC-CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence 67789999996 568887 67999999998 56788875 9999999999999644
No 33
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=86.34 E-value=0.66 Score=44.59 Aligned_cols=53 Identities=21% Similarity=0.234 Sum_probs=44.7
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhh-hccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~ 57 (244)
||=+|+|-|..+ +.++++ ++..+|.|+++.+++.|+ +|||-.+.|..|-|-+.
T Consensus 97 f~~~g~ilS~kv---~~~~~g-~kg~FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~ 150 (369)
T KOG0123|consen 97 FSEFGNILSCKV---ATDENG-SKGYFVQFESEESAKKAIEKLNGMLLNGKKIYVGLF 150 (369)
T ss_pred HHhhcCeeEEEE---EEcCCC-ceeeEEEeCCHHHHHHHHHHhcCcccCCCeeEEeec
Confidence 677999999985 556666 666699999999999998 78999999999999644
No 34
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=82.10 E-value=1.8 Score=35.47 Aligned_cols=57 Identities=12% Similarity=0.147 Sum_probs=42.5
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhhhccC-ceecCceEEEecCC
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVLLSG-ATIVDQSVTIELDP 58 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALLLnG-AtL~d~~V~Vt~~~ 58 (244)
|.-||.|..|...... ..+-....|+|+|.++..+..|+...+ ..|.|..|.|....
T Consensus 136 F~~~g~~~~~~~~~d~-~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~ 193 (306)
T COG0724 136 FKKFGPVKRVRLVRDR-ETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ 193 (306)
T ss_pred HHhcCceeEEEeeecc-ccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence 5668999888643211 123445789999999999999986555 99999999998754
No 35
>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=78.67 E-value=1.9 Score=34.42 Aligned_cols=54 Identities=13% Similarity=0.220 Sum_probs=37.0
Q ss_pred CcccccccceecccccccC---------CCCceEEEEEEeCCchhhhhhhccCceecCceEE-EecC
Q 048268 1 MSLWGQLSKILRNSFPLCD---------NERSQIARVVFKDPQGAETAVLLSGATIVDQSVT-IELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~---------~~~sq~A~VtFe~~~Aa~TALLLnGAtL~d~~V~-Vt~~ 57 (244)
|+=||.|-+.. ++.++ .....=..|+|.++..|.-||.-||..|.|..+- |.+.
T Consensus 26 F~~~G~Ile~~---~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mvGV~~~ 89 (100)
T PF05172_consen 26 FSSFGTILEHF---EVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLMVGVKPC 89 (100)
T ss_dssp HHCCS-EECEE---GGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEEEEEEE-
T ss_pred HHhcceEEEee---cccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEEEEEEEc
Confidence 56789887664 12221 2334568999999999999999999999987554 4443
No 36
>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=75.77 E-value=1.8 Score=44.11 Aligned_cols=52 Identities=19% Similarity=0.145 Sum_probs=38.3
Q ss_pred CcccccccceecccccccCCCCc-eEEEEEEeCCchhhhhh-hccCceec-CceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDNERS-QIARVVFKDPQGAETAV-LLSGATIV-DQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~s-q~A~VtFe~~~Aa~TAL-LLnGAtL~-d~~V~Vt 55 (244)
|+=||.|.++.+ +.+..+.+ --|+|+|.++..++-|| .|||..|. +..|.|.
T Consensus 79 F~~~G~I~~vrl---~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~ 133 (578)
T TIGR01648 79 FEKAGPIYELRL---MMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC 133 (578)
T ss_pred HHhhCCEEEEEE---EECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence 566899998863 33333433 47999999999999999 58999986 4555553
No 37
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=73.98 E-value=4.5 Score=34.66 Aligned_cols=60 Identities=20% Similarity=0.312 Sum_probs=45.3
Q ss_pred CcccccccceecccccccCCCC-ceEEEEEEeCCchhhhhh-hccCceecCceEEEecCCCCCC
Q 048268 1 MSLWGQLSKILRNSFPLCDNER-SQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELDPDYKP 62 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~-sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~~~~~~ 62 (244)
||-||.|..|+-. |-+-.-. ----+|.|-...-++-|| -|||.-|++.+|.|.-...+.+
T Consensus 57 Fs~cG~irriiMG--Ldr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~GF~e 118 (153)
T KOG0121|consen 57 FSKCGDIRRIIMG--LDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAGFVE 118 (153)
T ss_pred HHhccchheeEec--cccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccccchh
Confidence 7899999999743 1121111 135789999999999998 5899999999999987666554
No 38
>PF01296 Galanin: Galanin; InterPro: IPR008174 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. Galanin is a 29 amino acid peptide processed from a larger precursor protein. Except in human, galanin is C-terminally amidated. Its sequence is highly conserved and the first 14 residues are identical in all currently known sequences.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=73.09 E-value=0.55 Score=29.87 Aligned_cols=25 Identities=28% Similarity=0.701 Sum_probs=22.2
Q ss_pred HhccccccHHHHHHHHHHhhhcCcc
Q 048268 96 LAKGFILGKDAVGKAKAFDEKHRFT 120 (244)
Q Consensus 96 LAkGYvLgddAi~KA~~fDekhgiS 120 (244)
-..||.||..||.-=+.|-+||||.
T Consensus 5 nsagyLlGPhaiD~HRSf~DK~Gla 29 (29)
T PF01296_consen 5 NSAGYLLGPHAIDNHRSFGDKHGLA 29 (29)
T ss_pred cccceEeccccccCccccccccCCC
Confidence 3569999999999999999999974
No 39
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=70.30 E-value=2.7 Score=36.27 Aligned_cols=55 Identities=22% Similarity=0.315 Sum_probs=40.3
Q ss_pred CcccccccceecccccccCCCCce-EEEEEEeCCchhhhhh-hccCceecCceEEEecC
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQ-IARVVFKDPQGAETAV-LLSGATIVDQSVTIELD 57 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq-~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~ 57 (244)
|+=+|.|+.|.+| |-|-.+..+ -|.|.++.-.-+..|+ -|||+.|.|+.|.|.=+
T Consensus 93 F~dyGeiKNihLN--LDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~ 149 (170)
T KOG0130|consen 93 FADYGEIKNIHLN--LDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC 149 (170)
T ss_pred Hhhcccccceeec--cccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence 5567999999988 555555443 4667777666555555 58999999999999644
No 40
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=67.67 E-value=4 Score=40.02 Aligned_cols=51 Identities=20% Similarity=0.364 Sum_probs=43.5
Q ss_pred CcccccccceecccccccC---CCCceEEEEEEeCCchhhhhhh-ccCceecCceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCD---NERSQIARVVFKDPQGAETAVL-LSGATIVDQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~---~~~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt 55 (244)
||=.|+|.+-. ++|+ +..-|-|+|.|++....+-|.. +.+..|+|..|+|.
T Consensus 260 FSrFG~i~sce----VIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD 314 (479)
T KOG0415|consen 260 FSRFGKIVSCE----VIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD 314 (479)
T ss_pred Hhhcccceeee----EEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence 78889999885 5554 3567999999999999999975 78999999999995
No 41
>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]
Probab=64.99 E-value=5.1 Score=38.28 Aligned_cols=51 Identities=16% Similarity=0.292 Sum_probs=38.2
Q ss_pred CcccccccceecccccccCC--CCc-eEEEEEEeCCchhhhhhhcc-CceecCceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDN--ERS-QIARVVFKDPQGAETAVLLS-GATIVDQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~--~~s-q~A~VtFe~~~Aa~TALLLn-GAtL~d~~V~Vt 55 (244)
|+++|.|+.|. |+++- +++ --|+|.|+++-.+++|-==. |-.|+|..|.|.
T Consensus 122 F~~YG~Ikrir----lV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD 176 (335)
T KOG0113|consen 122 FEKYGPIKRIR----LVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD 176 (335)
T ss_pred HHhcCcceeEE----EeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence 88999999996 66653 333 46999999999999998655 455566666663
No 42
>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]
Probab=61.13 E-value=6.9 Score=39.82 Aligned_cols=52 Identities=31% Similarity=0.452 Sum_probs=42.7
Q ss_pred CcccccccceecccccccCC--CC-ceEEEEEEeCCchhhhhhhccCceecCceEEEec
Q 048268 1 MSLWGQLSKILRNSFPLCDN--ER-SQIARVVFKDPQGAETAVLLSGATIVDQSVTIEL 56 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~--~~-sq~A~VtFe~~~Aa~TALLLnGAtL~d~~V~Vt~ 56 (244)
||-.|+|-.+. ++.+- .. --.+||.|-|++.+--|+-|+|..|.|.+|.|-+
T Consensus 200 Fs~~gkVrdVr----iI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~ 254 (549)
T KOG0147|consen 200 FSIVGKVRDVR----IIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQL 254 (549)
T ss_pred HHhhcCcceeE----eeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecc
Confidence 67778888885 44443 22 3589999999999999999999999999999953
No 43
>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=59.83 E-value=7.7 Score=34.97 Aligned_cols=59 Identities=25% Similarity=0.470 Sum_probs=46.9
Q ss_pred CcccccccceecccccccCC--CCc-eEEEEEEeCCchhhhhh-hccCceecCceEEEecCCCCCCC
Q 048268 1 MSLWGQLSKILRNSFPLCDN--ERS-QIARVVFKDPQGAETAV-LLSGATIVDQSVTIELDPDYKPP 63 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~--~~s-q~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~~~~~~~ 63 (244)
||=+|.|-.|+ |+|+. |++ .-|+..+||.-.---|+ =|||..|.|..|.|....+|..|
T Consensus 56 FSqyGe~vdin----LiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~Yk~p 118 (219)
T KOG0126|consen 56 FSQYGEIVDIN----LIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSNYKKP 118 (219)
T ss_pred eeccCceEEEE----EEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecccccCC
Confidence 88999999998 67765 333 46999999976544444 38999999999999998888765
No 44
>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function. ; PDB: 1UFW_A 2DNR_A.
Probab=57.61 E-value=10 Score=32.46 Aligned_cols=33 Identities=30% Similarity=0.444 Sum_probs=30.4
Q ss_pred EEEEEEeCCchhhhhhhccCceecCceEEEecC
Q 048268 25 IARVVFKDPQGAETAVLLSGATIVDQSVTIELD 57 (244)
Q Consensus 25 ~A~VtFe~~~Aa~TALLLnGAtL~d~~V~Vt~~ 57 (244)
.--|||.+-+.|=.||=|+|..|.|..|+|++-
T Consensus 72 ~mwVTF~dg~sALaals~dg~~v~g~~l~i~LK 104 (146)
T PF08952_consen 72 TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLK 104 (146)
T ss_dssp CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE-
T ss_pred eEEEEECccHHHHHHHccCCcEECCEEEEEEeC
Confidence 588999999999999999999999999999843
No 45
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=56.92 E-value=6.7 Score=35.74 Aligned_cols=51 Identities=25% Similarity=0.374 Sum_probs=42.1
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhh-hccCceecCceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt 55 (244)
||=.|+|.+|. ..+-..-.-.|.|+|++++++..|+ -|+|=-.-|.++.|-
T Consensus 34 FsqfG~ildI~----a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq 85 (221)
T KOG4206|consen 34 FSQFGKILDIS----AFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ 85 (221)
T ss_pred HHhhCCeEEEE----ecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence 67789999996 4455555667999999999999998 588888899988885
No 46
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=52.66 E-value=18 Score=35.90 Aligned_cols=56 Identities=16% Similarity=0.299 Sum_probs=44.0
Q ss_pred CcccccccceecccccccCC--CC-ceEEEEEEeCCchhhhhh-hccCceecCceEEEecCCCC
Q 048268 1 MSLWGQLSKILRNSFPLCDN--ER-SQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELDPDY 60 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~--~~-sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~~~~ 60 (244)
|-=.|-|+||+ |.-++ ++ -.-|+|.+|=|.|+.-|| -+||..|+|..|.|-...+.
T Consensus 134 F~PFGPIKSIn----MSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm 193 (544)
T KOG0124|consen 134 FDPFGPIKSIN----MSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM 193 (544)
T ss_pred ccCCCCcceee----cccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence 33469999997 55444 33 347999999999999998 58999999999999765554
No 47
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=44.17 E-value=18 Score=32.88 Aligned_cols=56 Identities=21% Similarity=0.242 Sum_probs=45.1
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhhhc-cCceecCceEEEecCCCC
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVLL-SGATIVDQSVTIELDPDY 60 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALLL-nGAtL~d~~V~Vt~~~~~ 60 (244)
|.=+|.|..|. |..-.+-..-|+|.|||+--++-|+-- +|=.+++-++.|.-+-..
T Consensus 27 FyKyg~i~~ie----LK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg 83 (241)
T KOG0105|consen 27 FYKYGRIREIE----LKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG 83 (241)
T ss_pred HhhhcceEEEE----eccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence 55679999996 556667788999999999999999974 677889999999855433
No 48
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=43.77 E-value=18 Score=32.50 Aligned_cols=53 Identities=11% Similarity=0.231 Sum_probs=37.4
Q ss_pred CcccccccceecccccccCC-CCce-EEEEEEeCCchhhhhhh-ccCceecCceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDN-ERSQ-IARVVFKDPQGAETAVL-LSGATIVDQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~-~~sq-~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt 55 (244)
||+.|.|-+- +.+ |..++ +..+ -++|.|.+..+...|+= +||--|.+.+|+|+
T Consensus 117 FsafG~l~~~-P~i-~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ 172 (203)
T KOG0131|consen 117 FSAFGVLISP-PKI-MRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVS 172 (203)
T ss_pred HHhccccccC-Ccc-cccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEE
Confidence 7889988764 111 33333 3444 79999999999999995 55555566778886
No 49
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=40.03 E-value=33 Score=35.54 Aligned_cols=53 Identities=26% Similarity=0.409 Sum_probs=42.0
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhh-hccCceecCceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt 55 (244)
||-.|++-.|.+. -..++.--.-|+|+|++-..++-|| -+||-.|+|.+|-|.
T Consensus 138 Fs~~G~V~Ei~IP--~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVD 191 (678)
T KOG0127|consen 138 FSNFGKVVEIVIP--RKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVD 191 (678)
T ss_pred HhhcceEEEEEcc--cCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEe
Confidence 6777888888753 2233344468999999999999998 589999999999995
No 50
>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]
Probab=39.15 E-value=26 Score=34.12 Aligned_cols=51 Identities=14% Similarity=0.281 Sum_probs=41.4
Q ss_pred cccccceecccccccCCCCceEEEEEEeCCchhhhhh-hccCceecCceEEEecC
Q 048268 4 WGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELD 57 (244)
Q Consensus 4 cGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~ 57 (244)
.|+|.++++ +-.+-|+----+|||+++.-++-|= =|+|..|.|..|.|-.+
T Consensus 120 fG~VldVEI---IfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A 171 (376)
T KOG0125|consen 120 FGKVLDVEI---IFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA 171 (376)
T ss_pred hCceeeEEE---EeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence 588888863 3445577778899999999999885 59999999999999644
No 51
>smart00071 Galanin Galanin. Galanin [1,2,3] is a neuropeptide that controls various biological activities: it regulates the release growth hormone, inhibits the release of insulin and somatostatin, contracts smooth muscle of the gastrointestinal and genitourinary tract and may be involved in the control of adrenal secretion
Probab=38.44 E-value=6 Score=31.82 Aligned_cols=28 Identities=29% Similarity=0.692 Sum_probs=24.3
Q ss_pred HHhccccccHHHHHHHHHHhhhcCccHH
Q 048268 95 MLAKGFILGKDAVGKAKAFDEKHRFTST 122 (244)
Q Consensus 95 mLAkGYvLgddAi~KA~~fDekhgiSs~ 122 (244)
+=..||.||..||.--+.|-+|||++.+
T Consensus 16 lnsagyllgp~aid~hrs~~dk~g~~gK 43 (103)
T smart00071 16 LNSAGYLLGPHAIDNHRSFHDKHGLTGK 43 (103)
T ss_pred eccCceeeCccccccccccccCCCcccc
Confidence 3456999999999999999999999865
No 52
>KOG1996 consensus mRNA splicing factor [RNA processing and modification]
Probab=36.84 E-value=31 Score=33.23 Aligned_cols=51 Identities=18% Similarity=0.180 Sum_probs=37.3
Q ss_pred cccccceeccccccc-CCCCceEEEEEEeCCchhhhh-hhccCceecCceEEEe
Q 048268 4 WGQLSKILRNSFPLC-DNERSQIARVVFKDPQGAETA-VLLSGATIVDQSVTIE 55 (244)
Q Consensus 4 cGkI~si~~~~el~~-~~~~sq~A~VtFe~~~Aa~TA-LLLnGAtL~d~~V~Vt 55 (244)
||+|..+.+.. +-+ .+...-..+|.|+.+..+--| +.|||--++|..|.-.
T Consensus 310 yg~V~~viife-ip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~ 362 (378)
T KOG1996|consen 310 YGKVGNVIIFE-IPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSAC 362 (378)
T ss_pred hcceeeEEEEe-cCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeehe
Confidence 89999887663 322 234566789999997655555 6799999999988764
No 53
>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]
Probab=36.75 E-value=28 Score=32.33 Aligned_cols=38 Identities=18% Similarity=0.285 Sum_probs=32.4
Q ss_pred CCCceEEEEEEeCCchhhhhh-hccCceecCceEEEecC
Q 048268 20 NERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELD 57 (244)
Q Consensus 20 ~~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~ 57 (244)
++..+-|||.|+++-.+--|. ||||-.|-+..+.|++-
T Consensus 46 d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r 84 (267)
T KOG4454|consen 46 DQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR 84 (267)
T ss_pred cCCCceeeeecccccchhhhhhhcccchhccchhhcccc
Confidence 355567999999999998886 78999999999999843
No 54
>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=36.63 E-value=40 Score=32.13 Aligned_cols=31 Identities=29% Similarity=0.263 Sum_probs=24.5
Q ss_pred EEEEEEeCCchhhhh-hhccCceecCceEEEe
Q 048268 25 IARVVFKDPQGAETA-VLLSGATIVDQSVTIE 55 (244)
Q Consensus 25 ~A~VtFe~~~Aa~TA-LLLnGAtL~d~~V~Vt 55 (244)
-|+|-|+...+|--| +-.||++|.|+.|.-.
T Consensus 202 YaFVrF~tkEaAahAIv~mNntei~G~~VkCs 233 (321)
T KOG0148|consen 202 YAFVRFETKEAAAHAIVQMNNTEIGGQLVRCS 233 (321)
T ss_pred eEEEEecchhhHHHHHHHhcCceeCceEEEEe
Confidence 489999876555555 5689999999999884
No 55
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=36.54 E-value=38 Score=32.65 Aligned_cols=51 Identities=24% Similarity=0.208 Sum_probs=42.7
Q ss_pred CcccccccceecccccccCCCCceEEEEEEeCCchhhhhhh-ccCceecCceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVL-LSGATIVDQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt 55 (244)
||=.|.+.||. ++|+-..-.-|||.|.+|.-++-||= ||...|-|.+|.|-
T Consensus 19 f~~~~~v~s~r----vc~d~tslgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim 70 (369)
T KOG0123|consen 19 FSPAGPVLSIR----VCRDATSLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIM 70 (369)
T ss_pred hcccCCceeEE----EeecCCccceEEEecCCHHHHHHHHHHcCCcccCCcEEEee
Confidence 66778898886 56655466789999999999999994 88888899999996
No 56
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=33.14 E-value=40 Score=31.10 Aligned_cols=52 Identities=21% Similarity=0.394 Sum_probs=40.6
Q ss_pred cccccccceecccccccCC---CCceEEEEEEeCCchhhhhh-hccCceecCceEEEecC
Q 048268 2 SLWGQLSKILRNSFPLCDN---ERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELD 57 (244)
Q Consensus 2 SFcGkI~si~~~~el~~~~---~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~ 57 (244)
-=||+|.+|-+ -++. +.-..|+|-|.+-.-|+-|| -|+|+.|+|..+.|.-+
T Consensus 35 ekYG~vgDVyI----Prdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a 90 (256)
T KOG4207|consen 35 EKYGRVGDVYI----PRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA 90 (256)
T ss_pred HHhCcccceec----ccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence 34899999953 2332 34568999999999999988 58999999999988643
No 57
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=32.98 E-value=56 Score=27.22 Aligned_cols=51 Identities=24% Similarity=0.242 Sum_probs=40.2
Q ss_pred ccccccceecccccccCCCCceEEEEEEeCCchhhhhh-hccCceecCceEEEecC
Q 048268 3 LWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELD 57 (244)
Q Consensus 3 FcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~ 57 (244)
=+|.|-.|.. =.+.+...+|+|.++|-+.|+.|+ -|+|=.+.+..+.|--+
T Consensus 41 kyg~IrQIRi----G~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy 92 (124)
T KOG0114|consen 41 KYGTIRQIRI----GNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY 92 (124)
T ss_pred cccceEEEEe----cCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence 3577777753 234467789999999999999998 58999999998888643
No 58
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=29.46 E-value=50 Score=34.87 Aligned_cols=56 Identities=18% Similarity=0.241 Sum_probs=43.0
Q ss_pred CcccccccceecccccccCCC----CceEEEEEEeCCchhhhhhhc-cCceecCceEEEecCC
Q 048268 1 MSLWGQLSKILRNSFPLCDNE----RSQIARVVFKDPQGAETAVLL-SGATIVDQSVTIELDP 58 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~----~sq~A~VtFe~~~Aa~TALLL-nGAtL~d~~V~Vt~~~ 58 (244)
|+-.|.|.+|... +.+++. +..-++|.|.++.-+..|+=. +|..|+|..|+|.-.+
T Consensus 536 F~k~G~VlS~~I~--kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~ 596 (725)
T KOG0110|consen 536 FSKQGTVLSIEIS--KKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE 596 (725)
T ss_pred HHhcCeEEEEEEe--ccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence 4557889888543 444443 247899999999999999855 8899999999987554
No 59
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=29.23 E-value=74 Score=31.66 Aligned_cols=55 Identities=20% Similarity=0.236 Sum_probs=40.4
Q ss_pred cccccccceecccccccCC--C-CceEEEEEEeCCchhhhhh-hccCceecCceEEEecCCCC
Q 048268 2 SLWGQLSKILRNSFPLCDN--E-RSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELDPDY 60 (244)
Q Consensus 2 SFcGkI~si~~~~el~~~~--~-~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~~~~ 60 (244)
|=.|.|-++. +..|. | -.--+++.|+++.-++.|+ .|||+++.|..+.|.-...+
T Consensus 40 ~~~g~v~s~~----~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~ 98 (435)
T KOG0108|consen 40 SGVGPVLSFR----LVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR 98 (435)
T ss_pred hccCccceee----ecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence 3356666665 44443 3 3467999999988888887 79999999999999754443
No 60
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=27.05 E-value=60 Score=32.84 Aligned_cols=52 Identities=19% Similarity=0.224 Sum_probs=33.9
Q ss_pred ccccccceeccccccc-CC-CCceEEEEEEeCCchhhhhh-hccCceec-CceEEE
Q 048268 3 LWGQLSKILRNSFPLC-DN-ERSQIARVVFKDPQGAETAV-LLSGATIV-DQSVTI 54 (244)
Q Consensus 3 FcGkI~si~~~~el~~-~~-~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~-d~~V~V 54 (244)
||++|..|-..=.|.+ .+ ..---|+|||.....|.-|+ +||+-+|- |..|.|
T Consensus 103 lfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igv 158 (506)
T KOG0117|consen 103 LFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGV 158 (506)
T ss_pred HHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEE
Confidence 6777777754433444 23 34457999999877776665 88988884 344433
No 61
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.99 E-value=4e+02 Score=22.69 Aligned_cols=20 Identities=20% Similarity=0.571 Sum_probs=18.1
Q ss_pred HHHHHHHhc----cccccHHHHHH
Q 048268 90 DVVSTMLAK----GFILGKDAVGK 109 (244)
Q Consensus 90 ~IvA~mLAk----GYvLgddAi~K 109 (244)
+|+++++.. ||.+|+.+|++
T Consensus 31 ei~~~~~~~~~~~g~~iSrSav~R 54 (180)
T PF11985_consen 31 EILAEWLEELAEEGYDISRSAVHR 54 (180)
T ss_pred HHHHHHHHhhhccCCCcCHHHHHH
Confidence 788999998 99999999987
No 62
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=26.48 E-value=61 Score=32.78 Aligned_cols=47 Identities=19% Similarity=0.330 Sum_probs=36.1
Q ss_pred cccccccceecccccccCCCCceEEEEEEeCCchhhhhh-hccCceecCceEEEecC
Q 048268 2 SLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELD 57 (244)
Q Consensus 2 SFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~ 57 (244)
+=.|+|..|.. ++| -|+|+|.+-..+--|+ -+||-.|+|+.|.||.+
T Consensus 281 ~~~G~veRVkk----~rD-----YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLA 328 (506)
T KOG0117|consen 281 NEFGKVERVKK----PRD-----YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLA 328 (506)
T ss_pred HhccceEEeec----ccc-----eeEEeecchHHHHHHHHHhcCceecCceEEEEec
Confidence 33488888863 233 6999998877666666 68999999999999855
No 63
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=24.81 E-value=59 Score=31.82 Aligned_cols=49 Identities=22% Similarity=0.190 Sum_probs=38.9
Q ss_pred cccccccceecccccccCCCCceEEEEEEeCCchhhhhh--hccCceecCceEEEecCC
Q 048268 2 SLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAV--LLSGATIVDQSVTIELDP 58 (244)
Q Consensus 2 SFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TAL--LLnGAtL~d~~V~Vt~~~ 58 (244)
-=||.|.+|... -.-+=|+|+|..-.|++-|. ++|...|.|.+|.|. |.
T Consensus 250 yqyGeirsi~~~-------~~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~-Wg 300 (377)
T KOG0153|consen 250 YQYGEIRSIRIL-------PRKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK-WG 300 (377)
T ss_pred hhcCCeeeEEee-------cccccceeeehhhHHHHHHHHhhcceeeecceEEEEE-eC
Confidence 348999999743 12347999999999999776 678888899999998 54
No 64
>PF08543 Phos_pyr_kin: Phosphomethylpyrimidine kinase; InterPro: IPR013749 This enzyme 2.7.4.7 from EC is part of the Thiamine pyrophosphate (TPP) synthesis pathway, TPP is an essential cofactor for many enzymes []. ; PDB: 2DDW_B 2DDO_B 2DDM_A 3IBQ_A 3H74_A 3HYO_A 1UB0_A 1VI9_D 1TD2_B 2PHP_D ....
Probab=24.57 E-value=80 Score=27.95 Aligned_cols=24 Identities=46% Similarity=0.747 Sum_probs=21.0
Q ss_pred HHHHHHHHhccccccHHHHHHHHHH
Q 048268 89 EDVVSTMLAKGFILGKDAVGKAKAF 113 (244)
Q Consensus 89 ~~IvA~mLAkGYvLgddAi~KA~~f 113 (244)
..+++.+|++||-| .+|+++|+.|
T Consensus 204 ss~laa~l~~g~~l-~~Av~~A~~~ 227 (246)
T PF08543_consen 204 SSALAAFLAKGYSL-EEAVEKAKNF 227 (246)
T ss_dssp HHHHHHHHHTTSSH-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCH-HHHHHHHHHH
Confidence 58889999999999 8899998874
No 65
>KOG3430 consensus Dynein light chain type 1 [Cytoskeleton]
Probab=23.96 E-value=1.2e+02 Score=24.22 Aligned_cols=33 Identities=27% Similarity=0.313 Sum_probs=20.2
Q ss_pred HHHHHHHHHhhhcC-ccHHHHHHHH-hhhhhcccc
Q 048268 105 DAVGKAKAFDEKHR-FTSTATATVA-SLDQKIGFT 137 (244)
Q Consensus 105 dAi~KA~~fDekhg-iSs~f~a~v~-slD~k~glt 137 (244)
+||.-|++-=+++. +......+|+ +||+|||.+
T Consensus 20 ~a~~~a~~al~~f~~~~k~iA~~iKkefDkkyG~~ 54 (90)
T KOG3430|consen 20 EAIELARQALEKFNVIEKDIAAFIKKEFDKKYGPT 54 (90)
T ss_pred HHHHHHHHHHHHcCCChHHHHHHHHHHHhhhcCCc
Confidence 45555555545555 5556666665 688888754
No 66
>COG0351 ThiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Coenzyme metabolism]
Probab=23.92 E-value=81 Score=29.43 Aligned_cols=24 Identities=46% Similarity=0.659 Sum_probs=20.5
Q ss_pred HHHHHHHHhccccccHHHHHHHHHH
Q 048268 89 EDVVSTMLAKGFILGKDAVGKAKAF 113 (244)
Q Consensus 89 ~~IvA~mLAkGYvLgddAi~KA~~f 113 (244)
+.-++..||+||-| .+|+.+||+|
T Consensus 215 SaAIaa~LA~G~~l-~~AV~~Ak~f 238 (263)
T COG0351 215 SAAIAANLAKGLSL-EEAVKKAKEF 238 (263)
T ss_pred HHHHHHHHHcCCCH-HHHHHHHHHH
Confidence 47788999999999 6789999875
No 67
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=23.61 E-value=69 Score=31.58 Aligned_cols=54 Identities=11% Similarity=0.241 Sum_probs=35.5
Q ss_pred CcccccccceecccccccCCCCc---eEEEEEEeCCchhhhhhh-ccCceecCceEEEe
Q 048268 1 MSLWGQLSKILRNSFPLCDNERS---QIARVVFKDPQGAETAVL-LSGATIVDQSVTIE 55 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~s---q~A~VtFe~~~Aa~TALL-LnGAtL~d~~V~Vt 55 (244)
|--+|+|.+|.+|-... +.+.+ --.||||....-|.+++- .+|..++|..+.-+
T Consensus 141 FGQyGkI~KIvvNkkt~-s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~lkat 198 (480)
T COG5175 141 FGQYGKIKKIVVNKKTS-SLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKAT 198 (480)
T ss_pred hhhccceeEEEeccccc-ccccccccceEEEEecchHHHHHHHHHhccccccCceEeee
Confidence 45579999998873222 22222 223999987777777664 56677777777765
No 68
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=23.12 E-value=1e+02 Score=30.22 Aligned_cols=50 Identities=18% Similarity=0.369 Sum_probs=39.0
Q ss_pred cccccceecccccccCCCCceEEEEEEeCCchhhhhh-hccCceecCceEEEecCC
Q 048268 4 WGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAV-LLSGATIVDQSVTIELDP 58 (244)
Q Consensus 4 cGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TAL-LLnGAtL~d~~V~Vt~~~ 58 (244)
||.|.+|.+ .+..--..+.|+|.++..|.-.+ +|+|--.+|+.|+-..+.
T Consensus 300 ~G~v~~vvv-----~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~D 350 (382)
T KOG1548|consen 300 FGQVRKVVV-----YDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWD 350 (382)
T ss_pred hCCcceEEE-----eccCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeC
Confidence 899999963 22233457999999999998887 678888899998887654
No 69
>PF03912 Psb28: Psb28 protein; InterPro: IPR005610 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein Psb28 (PsbW) found in PSII, where it is a subunit of the oxygen-evolving complex. Psb28 appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of Psb28, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 1 Psb28.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0016020 membrane; PDB: 2KVO_A.
Probab=21.21 E-value=75 Score=26.10 Aligned_cols=30 Identities=13% Similarity=0.206 Sum_probs=19.0
Q ss_pred eecccccccC-CCCceEEEEEEeCCchhhhh
Q 048268 10 ILRNSFPLCD-NERSQIARVVFKDPQGAETA 39 (244)
Q Consensus 10 i~~~~el~~~-~~~sq~A~VtFe~~~Aa~TA 39 (244)
+.|+|.|.|+ ++.+.+|..+|++|++.+--
T Consensus 11 ~~pdVrLtRsrdg~~g~a~f~F~~p~al~~~ 41 (108)
T PF03912_consen 11 VVPDVRLTRSRDGGTGTATFYFENPKALEKF 41 (108)
T ss_dssp ---EEEEEE-TTS-SEEEEEEEES-GGGTSS
T ss_pred cCCCeEEEEccCCCceEEEEEECCCcccccc
Confidence 3445556665 58899999999999997643
No 70
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=20.68 E-value=89 Score=32.53 Aligned_cols=56 Identities=16% Similarity=0.154 Sum_probs=39.7
Q ss_pred CcccccccceecccccccCCCC-ceEEEEEEeCCchhhhhhhcc----Cc---eecCceEEEecCC
Q 048268 1 MSLWGQLSKILRNSFPLCDNER-SQIARVVFKDPQGAETAVLLS----GA---TIVDQSVTIELDP 58 (244)
Q Consensus 1 FSFcGkI~si~~~~el~~~~~~-sq~A~VtFe~~~Aa~TALLLn----GA---tL~d~~V~Vt~~~ 58 (244)
||=.|.|....+- +-.+.+. -.+|+|.|+.+.++.-+|+-- |. .|+|..+.|+++-
T Consensus 313 fskFG~v~ya~iV--~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av 376 (678)
T KOG0127|consen 313 FSKFGEVKYAIIV--KDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAV 376 (678)
T ss_pred HHhhccceeEEEE--eccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeecc
Confidence 5567888887632 2223343 468999999999998888765 33 4788888998664
No 71
>PLN00039 photosystem II reaction center Psb28 protein; Provisional
Probab=20.64 E-value=71 Score=26.37 Aligned_cols=28 Identities=14% Similarity=0.150 Sum_probs=21.7
Q ss_pred ecccccccC-CCCceEEEEEEeCCchhhh
Q 048268 11 LRNSFPLCD-NERSQIARVVFKDPQGAET 38 (244)
Q Consensus 11 ~~~~el~~~-~~~sq~A~VtFe~~~Aa~T 38 (244)
.++|.|.|+ ++.+.+|...|++|++.+.
T Consensus 14 vp~VrLtRsrdg~~g~a~f~F~~p~~l~~ 42 (111)
T PLN00039 14 VPDVRLTRSRDGTNGTAIFVFDQPSVFDS 42 (111)
T ss_pred CCceEEEEccCCCccEEEEEECCchhhcc
Confidence 344556664 5889999999999999764
No 72
>PF15023 DUF4523: Protein of unknown function (DUF4523)
Probab=20.30 E-value=67 Score=28.07 Aligned_cols=42 Identities=29% Similarity=0.238 Sum_probs=30.0
Q ss_pred cccccccceecccccccCCCCceEEEEEEeCCchhhhhhhccCceecCce
Q 048268 2 SLWGQLSKILRNSFPLCDNERSQIARVVFKDPQGAETAVLLSGATIVDQS 51 (244)
Q Consensus 2 SFcGkI~si~~~~el~~~~~~sq~A~VtFe~~~Aa~TALLLnGAtL~d~~ 51 (244)
|--|-|.||..- .-|+|.|+|+|-..|=-|+=--+....|.-
T Consensus 112 s~fGpI~SVT~c--------GrqsavVvF~d~~SAC~Av~Af~s~~pgtm 153 (166)
T PF15023_consen 112 SVFGPIQSVTLC--------GRQSAVVVFKDITSACKAVSAFQSRAPGTM 153 (166)
T ss_pred HhcCCcceeeec--------CCceEEEEehhhHHHHHHHHhhcCCCCCce
Confidence 345888888642 268999999999998888765555444433
Done!