Query 009733
Match_columns 527
No_of_seqs 143 out of 230
Neff 3.7
Searched_HMMs 46136
Date Thu Mar 28 16:41:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009733.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009733hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03467 Smg4_UPF3: Smg-4/UPF3 100.0 3.2E-50 6.9E-55 376.9 7.0 172 1-174 1-176 (176)
2 KOG1295 Nonsense-mediated deca 99.9 1.8E-27 3.9E-32 244.6 7.8 176 1-219 1-176 (376)
3 PF04059 RRM_2: RNA recognitio 97.9 5.7E-05 1.2E-09 66.3 8.2 87 7-100 1-87 (97)
4 PF00076 RRM_1: RNA recognitio 97.2 0.00086 1.9E-08 51.2 6.0 66 10-84 1-66 (70)
5 cd00590 RRM RRM (RNA recogniti 97.1 0.0028 6.1E-08 47.1 7.2 67 9-84 1-67 (74)
6 PF14259 RRM_6: RNA recognitio 97.0 0.0028 6.1E-08 49.4 7.1 65 10-83 1-65 (70)
7 smart00362 RRM_2 RNA recogniti 96.7 0.0094 2E-07 44.0 7.1 65 9-83 1-65 (72)
8 PLN03134 glycine-rich RNA-bind 96.0 0.033 7.2E-07 51.3 8.3 80 5-97 32-111 (144)
9 smart00360 RRM RNA recognition 95.7 0.036 7.8E-07 40.6 5.9 64 12-83 1-64 (71)
10 TIGR01642 U2AF_lg U2 snRNP aux 95.6 0.11 2.4E-06 55.1 11.4 85 6-103 294-378 (509)
11 TIGR01659 sex-lethal sex-letha 95.4 0.064 1.4E-06 56.2 8.8 82 3-97 103-184 (346)
12 TIGR01661 ELAV_HUD_SF ELAV/HuD 95.4 0.068 1.5E-06 53.7 8.7 79 6-97 2-80 (352)
13 TIGR01661 ELAV_HUD_SF ELAV/HuD 94.2 0.2 4.2E-06 50.5 8.4 78 8-98 270-347 (352)
14 TIGR01659 sex-lethal sex-letha 94.1 0.28 6.1E-06 51.5 9.4 82 6-98 192-273 (346)
15 TIGR01622 SF-CC1 splicing fact 93.5 0.34 7.4E-06 50.8 8.9 79 7-98 186-264 (457)
16 TIGR01628 PABP-1234 polyadenyl 91.7 0.52 1.1E-05 51.3 7.6 67 9-83 2-68 (562)
17 COG0724 RNA-binding proteins ( 90.8 1 2.3E-05 40.6 7.5 72 7-86 115-186 (306)
18 PLN03120 nucleic acid binding 90.8 0.76 1.6E-05 47.2 7.3 75 7-98 4-78 (260)
19 TIGR01648 hnRNP-R-Q heterogene 90.5 0.8 1.7E-05 51.6 7.8 71 4-85 55-127 (578)
20 TIGR01649 hnRNP-L_PTB hnRNP-L/ 90.2 1.5 3.2E-05 47.5 9.3 84 6-97 393-477 (481)
21 TIGR01648 hnRNP-R-Q heterogene 90.0 1.2 2.7E-05 50.1 8.7 72 8-98 234-305 (578)
22 TIGR01628 PABP-1234 polyadenyl 89.8 0.91 2E-05 49.4 7.4 71 6-85 177-247 (562)
23 TIGR01622 SF-CC1 splicing fact 88.1 2 4.3E-05 45.2 8.2 71 5-84 87-157 (457)
24 PLN03121 nucleic acid binding 84.9 2.9 6.3E-05 42.7 7.2 69 6-86 4-72 (243)
25 TIGR01642 U2AF_lg U2 snRNP aux 83.9 2.6 5.6E-05 44.9 6.7 75 6-84 174-249 (509)
26 KOG0107 Alternative splicing f 82.8 5.7 0.00012 39.4 7.9 77 5-99 8-84 (195)
27 TIGR01645 half-pint poly-U bin 82.6 3.8 8.3E-05 46.7 7.7 69 7-83 204-272 (612)
28 PF08777 RRM_3: RNA binding mo 82.6 3.5 7.5E-05 36.6 5.9 59 8-80 2-60 (105)
29 TIGR01649 hnRNP-L_PTB hnRNP-L/ 82.3 9.1 0.0002 41.6 10.1 80 6-103 274-354 (481)
30 TIGR01645 half-pint poly-U bin 80.8 5.2 0.00011 45.6 7.9 73 5-85 105-177 (612)
31 PF07576 BRAP2: BRCA1-associat 79.6 8 0.00017 35.0 7.2 88 4-99 9-100 (110)
32 KOG4206 Spliceosomal protein s 70.2 11 0.00024 38.2 6.2 71 5-85 7-80 (221)
33 KOG4660 Protein Mei2, essentia 69.8 5.7 0.00012 44.7 4.4 90 6-102 360-475 (549)
34 KOG4676 Splicing factor, argin 65.6 8.3 0.00018 42.3 4.5 71 9-86 9-80 (479)
35 KOG0122 Translation initiation 63.7 22 0.00048 36.9 6.9 77 8-97 190-266 (270)
36 KOG0145 RNA-binding protein EL 59.0 22 0.00047 37.5 6.0 73 5-85 39-111 (360)
37 KOG0127 Nucleolar protein fibr 58.8 27 0.0006 39.9 7.1 69 5-82 115-183 (678)
38 KOG0127 Nucleolar protein fibr 58.7 20 0.00043 40.9 6.0 64 7-78 292-355 (678)
39 PLN03213 repressor of silencin 57.4 43 0.00092 38.1 8.2 69 4-84 7-77 (759)
40 KOG0114 Predicted RNA-binding 54.2 26 0.00056 32.6 5.0 70 4-84 15-84 (124)
41 PF13893 RRM_5: RNA recognitio 54.1 24 0.00053 26.6 4.2 36 57-97 21-56 (56)
42 KOG0108 mRNA cleavage and poly 51.7 35 0.00075 37.7 6.4 68 8-83 19-86 (435)
43 KOG0129 Predicted RNA-binding 51.5 26 0.00057 39.4 5.5 68 6-78 258-327 (520)
44 KOG1295 Nonsense-mediated deca 46.8 3 6.5E-05 45.0 -2.4 123 6-129 70-207 (376)
45 KOG0110 RNA-binding protein (R 46.1 7.3 0.00016 45.0 0.3 46 8-84 228-273 (725)
46 PF00585 Thr_dehydrat_C: C-ter 40.0 69 0.0015 27.7 5.2 57 22-89 25-85 (91)
47 COG4499 Predicted membrane pro 37.6 8 0.00017 42.3 -1.0 58 15-76 134-196 (434)
48 PF04355 SmpA_OmlA: SmpA / Oml 36.1 67 0.0014 25.8 4.3 51 12-67 9-64 (71)
49 KOG4208 Nucleolar RNA-binding 35.8 74 0.0016 32.4 5.4 71 8-85 50-120 (214)
50 KOG0144 RNA-binding protein CU 35.0 47 0.001 37.1 4.2 82 7-101 124-207 (510)
51 KOG0804 Cytoplasmic Zn-finger 34.5 97 0.0021 34.8 6.5 74 4-86 71-144 (493)
52 KOG1548 Transcription elongati 33.1 1.5E+02 0.0033 32.3 7.5 84 4-102 131-223 (382)
53 smart00361 RRM_1 RNA recogniti 29.6 52 0.0011 26.2 2.7 27 58-84 38-64 (70)
54 KOG0110 RNA-binding protein (R 27.2 1.2E+02 0.0025 35.8 5.7 81 5-104 383-463 (725)
55 PF14026 DUF4242: Protein of u 25.2 1E+02 0.0022 26.1 3.8 63 10-81 3-70 (77)
56 KOG0117 Heterogeneous nuclear 23.4 1.1E+02 0.0024 34.5 4.5 60 7-82 258-318 (506)
57 KOG1456 Heterogeneous nuclear 23.1 1.9E+02 0.0041 32.2 6.1 78 8-95 407-484 (494)
58 COG4453 Uncharacterized protei 22.2 62 0.0013 29.1 2.0 24 117-140 60-83 (95)
59 PF02426 MIase: Muconolactone 21.5 2.5E+02 0.0053 25.0 5.5 60 14-83 10-77 (91)
60 PF11608 Limkain-b1: Limkain b 20.3 1.7E+02 0.0037 26.3 4.3 73 9-102 4-79 (90)
61 KOG0533 RRM motif-containing p 20.0 2.4E+02 0.0053 29.1 6.0 65 6-79 82-146 (243)
No 1
>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.
Probab=100.00 E-value=3.2e-50 Score=376.89 Aligned_cols=172 Identities=44% Similarity=0.778 Sum_probs=70.9
Q ss_pred CCCCCCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCC
Q 009733 1 MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGH 80 (527)
Q Consensus 1 ~k~p~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~ 80 (527)
||.+..++|||||||||+|||++||++|++++.+.++|.|| +|+++ ..++++++||||||+|++.++|..|.+.|+||
T Consensus 1 ~~~~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~-~g~~~-~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~ 78 (176)
T PF03467_consen 1 MKKEKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYF-QGKYG-KKSFKPPTYSRAYINFKNPEDLLEFRDRFDGH 78 (176)
T ss_dssp --------EEEEEEE-TTS-HHHHCCCCSS--SSE---EEE-EEEES--SSSTTS--EEEEEEESSCHHHHHHHHHCTTE
T ss_pred CCCcccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEE-ecCCC-CccCCCCcceEEEEEeCCHHHHHHHHHhcCCc
Confidence 89999999999999999999999999999977777778766 57666 33489999999999999999999999999999
Q ss_pred eeEcCCCCeeeeEEEeccCCCCCC-CCCCCCCCCCcccCCHHHHHHHHHHcCCCCCC---CcHHHHhhhHHhhhcCCCCC
Q 009733 81 VFVNEKGAQFKAIVEYAPSQRVPK-PFSRKDSREGTIFKDPDYLEFLKVIAKPAENL---PSAEIQLERKEAELSGAPKE 156 (527)
Q Consensus 81 vFvDsKGne~~A~VEfAPYQKvPk-~k~KkD~ReGTIEqDpeYkaFLEsL~~P~e~~---pSaEi~lE~~EaE~a~a~ke 156 (527)
+|+|++|++++|+|||||||++|. .+.|.|+++||||+|++|++|||+|++|.+.+ .|++..++..|.+...+.+.
T Consensus 79 ~F~D~kg~~~~~~VE~Apyqk~p~~~k~k~d~r~GTIe~D~~y~~Fle~L~~~~~~~~~~~s~~~~l~k~e~~~~~~~~~ 158 (176)
T PF03467_consen 79 VFVDSKGNEYPAVVEFAPYQKVPKPSKKKKDPREGTIEQDPEYQAFLESLEEPEEKPSQDISAEKSLEKKEKEEKAKEKA 158 (176)
T ss_dssp EEE-TTS-EEEEEEEE-SS-------------------------------------------------------------
T ss_pred EEECCCCCCcceeEEEcchhcccccccccccccCCCccCCHHHHHHHHHHhccccccccCcchhhhhhhhhhhhhccccc
Confidence 999999999999999999999998 56789999999999999999999998776542 23444555544443333334
Q ss_pred CcccCchHHHHHHHHHHh
Q 009733 157 TLVVTPLMEYVRQKRAAE 174 (527)
Q Consensus 157 k~~tTPLlEyLReKKAaK 174 (527)
.+++||||+||++||++|
T Consensus 159 ~~~~TpLie~lk~kk~~k 176 (176)
T PF03467_consen 159 EKVTTPLIEYLKEKKANK 176 (176)
T ss_dssp ------------------
T ss_pred cccchHHHHHHHHHhhcC
Confidence 556999999999999885
No 2
>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]
Probab=99.94 E-value=1.8e-27 Score=244.63 Aligned_cols=176 Identities=35% Similarity=0.510 Sum_probs=148.8
Q ss_pred CCCCCCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCC
Q 009733 1 MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGH 80 (527)
Q Consensus 1 ~k~p~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~ 80 (527)
|+.....+|||||||||.||+++|+++|+| +...+.|.+|.++..+ +.++.||||||+|++++++.+|.+.|+||
T Consensus 1 ~~~~~~~~Kvv~rrlpp~l~~~~~~eqi~p-~~~~v~~~~F~~a~~s----~~~~~ysrayinFk~~~dv~ef~~~f~g~ 75 (376)
T KOG1295|consen 1 GKKKEAKVKVVVRRLPPKLTEEQLLEQINP-FPEHVNWEFFAKADES----LRNHKYSRAYINFKNPEDVEEFRRRFDGY 75 (376)
T ss_pred CcccccceeeeeecCCCcccHHHHhhhcCC-Cccccchheecccccc----chhhhhhhhhhccccHHHHHHHHhhCCce
Confidence 445566789999999999999999999999 4557999999999988 88999999999999999999999999999
Q ss_pred eeEcCCCCeeeeEEEeccCCCCCCCCCCCCCCCCcccCCHHHHHHHHHHcCCCCCCCcHHHHhhhHHhhhcCCCCCCccc
Q 009733 81 VFVNEKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVV 160 (527)
Q Consensus 81 vFvDsKGne~~A~VEfAPYQKvPk~k~KkD~ReGTIEqDpeYkaFLEsL~~P~e~~pSaEi~lE~~EaE~a~a~kek~~t 160 (527)
+|+|.+| |||++|++|++||+.++.+.+..+++....+..+.|......+..++
T Consensus 76 ifld~Kg--------------------------gti~d~~~yre~~~~~~~~ke~~~s~~~et~~g~~e~d~~~~~fk~~ 129 (376)
T KOG1295|consen 76 IFLDNKG--------------------------GTIDDDPAYREFLKNYALAKEDKASKLKETLLGEIEGDTKSLAFKKV 129 (376)
T ss_pred EEecCCC--------------------------CCccccHHHHHHHhhccccccCccccchhhhhchhcccccchhhhcc
Confidence 9999999 99999999999999999998887776555444444444444677889
Q ss_pred CchHHHHHHHHHHhhhhhhhhhhccccccccccccCCCCCcccccCcccceeEeccccc
Q 009733 161 TPLMEYVRQKRAAESGAQESLAVGRVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAK 219 (527)
Q Consensus 161 TPLlEyLReKKAaK~k~Q~~~~~~k~~rr~~~~~~~~~~~~~~kr~~~k~~yv~rd~~k 219 (527)
|||+.||+.. .+|.++...+..|+.+........ .++++|++++++|
T Consensus 130 t~~~~~~~~~-----~~q~irk~~r~~r~~r~ie~k~~r-------~~vkk~keke~~K 176 (376)
T KOG1295|consen 130 TPLLSFIKQA-----DKQRIRKLRREERRRREIEEKENR-------EEVKKDKEKESGK 176 (376)
T ss_pred chHHHhhhhh-----hHHHHHHhhccchHHHHHHhccch-------hhhhhhhhccccc
Confidence 9999999986 467788888888877776554332 7889999999876
No 3
>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2. It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).
Probab=97.88 E-value=5.7e-05 Score=66.31 Aligned_cols=87 Identities=26% Similarity=0.522 Sum_probs=70.4
Q ss_pred CceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcCC
Q 009733 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK 86 (527)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDsK 86 (527)
||-|.||++|..+|.+.+++.|+....+.||++|- |=+.. ...-..-|+|+|.+++.+..|.+.|+|+.|-.-.
T Consensus 1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YL-PiDf~-----~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~ 74 (97)
T PF04059_consen 1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYL-PIDFK-----NKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFN 74 (97)
T ss_pred CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEe-eeecc-----CCCceEEEEEEcCCHHHHHHHHHHHcCCccccCC
Confidence 56799999999999999999999888888987665 43332 2345778999999999999999999999996433
Q ss_pred CCeeeeEEEeccCC
Q 009733 87 GAQFKAIVEYAPSQ 100 (527)
Q Consensus 87 Gne~~A~VEfAPYQ 100 (527)
..-.+.|-||=.|
T Consensus 75 -s~Kvc~i~yAriQ 87 (97)
T PF04059_consen 75 -SKKVCEISYARIQ 87 (97)
T ss_pred -CCcEEEEehhHhh
Confidence 3446788888665
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=97.24 E-value=0.00086 Score=51.16 Aligned_cols=66 Identities=18% Similarity=0.296 Sum_probs=51.6
Q ss_pred EEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 10 VVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
|.|.+||+++|++++.+.+... +.+....+..- ........|||.|.+.+++....+.++|+.|-+
T Consensus 1 l~v~nlp~~~t~~~l~~~f~~~--g~i~~~~~~~~-------~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~ 66 (70)
T PF00076_consen 1 LYVGNLPPDVTEEELRDFFSQF--GKIESIKVMRN-------SSGKSKGYAFVEFESEEDAEKALEELNGKKING 66 (70)
T ss_dssp EEEESETTTSSHHHHHHHHHTT--STEEEEEEEEE-------TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred cEEcCCCCcCCHHHHHHHHHHh--hhccccccccc-------ccccccceEEEEEcCHHHHHHHHHHcCCCEECc
Confidence 6899999999999999999884 34544444331 123446689999999999999999999988754
No 5
>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=97.07 E-value=0.0028 Score=47.11 Aligned_cols=67 Identities=22% Similarity=0.352 Sum_probs=52.7
Q ss_pred eEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 9 KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
.|+|+.||+.++++++++.+... +.+....+..-.. . .....|||.|.+.++...+.+.+++..|-+
T Consensus 1 ~i~i~~l~~~~~~~~i~~~~~~~--g~i~~~~~~~~~~------~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~ 67 (74)
T cd00590 1 TLFVGNLPPDVTEEDLRELFSKF--GKVESVRIVRDKD------T-KSKGFAFVEFEDEEDAEKALEALNGKELGG 67 (74)
T ss_pred CEEEeCCCCccCHHHHHHHHHhc--CCEEEEEEeeCCC------C-CcceEEEEEECCHHHHHHHHHHhCCCeECC
Confidence 47899999999999999999875 4566655543211 1 336689999999999999999999988643
No 6
>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=97.02 E-value=0.0028 Score=49.43 Aligned_cols=65 Identities=29% Similarity=0.333 Sum_probs=49.9
Q ss_pred EEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeE
Q 009733 10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 83 (527)
Q Consensus 10 VVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFv 83 (527)
|.|++||++.|++++.+.+... +.|....+...+ . ......|||.|.+.+++..+.+..++..|.
T Consensus 1 v~i~nlp~~~~~~~l~~~f~~~--g~v~~v~~~~~~------~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~ 65 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNFFSRF--GPVEKVRLIKNK------D-GQSRGFAFVEFSSEEDAKRALELLNGKEID 65 (70)
T ss_dssp EEEESSTTT--HHHHHHHCTTS--SBEEEEEEEEST------T-SSEEEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred CEEeCCCCCCCHHHHHHHHHhc--CCcceEEEEeee------c-cccCCEEEEEeCCHHHHHHHHHHCCCcEEC
Confidence 6899999999999999999886 356666665321 1 234667999999999999999999877763
No 7
>smart00362 RRM_2 RNA recognition motif.
Probab=96.66 E-value=0.0094 Score=44.03 Aligned_cols=65 Identities=22% Similarity=0.319 Sum_probs=50.2
Q ss_pred eEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeE
Q 009733 9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 83 (527)
Q Consensus 9 KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFv 83 (527)
+|.|++||+.++++++.+.+... +.+.+..+...+ .....-|||.|.+.+......+.++++.|-
T Consensus 1 ~v~i~~l~~~~~~~~l~~~~~~~--g~v~~~~~~~~~--------~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~ 65 (72)
T smart00362 1 TLFVGNLPPDVTEEDLKELFSKF--GPIESVKIPKDT--------GKSKGFAFVEFESEEDAEKAIEALNGTKLG 65 (72)
T ss_pred CEEEcCCCCcCCHHHHHHHHHhc--CCEEEEEEecCC--------CCCCceEEEEeCCHHHHHHHHHHhCCcEEC
Confidence 48999999999999999988764 345555554322 112357999999999999999999998873
No 8
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=95.99 E-value=0.033 Score=51.32 Aligned_cols=80 Identities=14% Similarity=0.081 Sum_probs=58.5
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
...+||.|.+||+.+||+++++.+.++ +.|.....+.-+.. ...-.-|||.|.+.+++....+.++++.+.+
T Consensus 32 ~~~~~lfVgnL~~~~te~~L~~~F~~~--G~I~~v~i~~d~~t------g~~kGfaFV~F~~~e~A~~Al~~lng~~i~G 103 (144)
T PLN03134 32 LMSTKLFIGGLSWGTDDASLRDAFAHF--GDVVDAKVIVDRET------GRSRGFGFVNFNDEGAATAAISEMDGKELNG 103 (144)
T ss_pred CCCCEEEEeCCCCCCCHHHHHHHHhcC--CCeEEEEEEecCCC------CCcceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence 356899999999999999999999875 34555444422211 1123469999999999999999999987643
Q ss_pred CCCCeeeeEEEec
Q 009733 85 EKGAQFKAIVEYA 97 (527)
Q Consensus 85 sKGne~~A~VEfA 97 (527)
. ...|++|
T Consensus 104 r-----~l~V~~a 111 (144)
T PLN03134 104 R-----HIRVNPA 111 (144)
T ss_pred E-----EEEEEeC
Confidence 2 4556665
No 9
>smart00360 RRM RNA recognition motif.
Probab=95.67 E-value=0.036 Score=40.64 Aligned_cols=64 Identities=22% Similarity=0.353 Sum_probs=47.6
Q ss_pred EecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeE
Q 009733 12 IRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 83 (527)
Q Consensus 12 IRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFv 83 (527)
|+.||+.++++++.+.+... +.+....+...... ......|||.|.+.+++..+.+.++++.|.
T Consensus 1 i~~l~~~~~~~~l~~~f~~~--g~v~~~~i~~~~~~------~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~ 64 (71)
T smart00360 1 VGNLPPDVTEEELRELFSKF--GKIESVRLVRDKDT------GKSKGFAFVEFESEEDAEKALEALNGKELD 64 (71)
T ss_pred CCCCCcccCHHHHHHHHHhh--CCEeEEEEEeCCCC------CCCCceEEEEeCCHHHHHHHHHHcCCCeeC
Confidence 57899999999999988754 34555544432211 122358999999999999999999998884
No 10
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=95.60 E-value=0.11 Score=55.06 Aligned_cols=85 Identities=19% Similarity=0.189 Sum_probs=63.1
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcC
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 85 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDs 85 (527)
+..+|.|.+||+.+|++++.+.|..+ +.|..+.++..... .....-|||.|.+.+++..-++.++|..|.+.
T Consensus 294 ~~~~l~v~nlp~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~------g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~ 365 (509)
T TIGR01642 294 SKDRIYIGNLPLYLGEDQIKELLESF--GDLKAFNLIKDIAT------GLSKGYAFCEYKDPSVTDVAIAALNGKDTGDN 365 (509)
T ss_pred CCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEecCCC------CCcCeEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence 45799999999999999999988874 34555555533221 11234699999999999999999999998544
Q ss_pred CCCeeeeEEEeccCCCCC
Q 009733 86 KGAQFKAIVEYAPSQRVP 103 (527)
Q Consensus 86 KGne~~A~VEfAPYQKvP 103 (527)
...|++|-+...+
T Consensus 366 -----~l~v~~a~~~~~~ 378 (509)
T TIGR01642 366 -----KLHVQRACVGANQ 378 (509)
T ss_pred -----EEEEEECccCCCC
Confidence 3578888665543
No 11
>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=95.43 E-value=0.064 Score=56.25 Aligned_cols=82 Identities=23% Similarity=0.310 Sum_probs=59.6
Q ss_pred CCCCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCee
Q 009733 3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF 82 (527)
Q Consensus 3 ~p~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vF 82 (527)
.....++|.|.+||+.+||+++.+.+..+ +.|.....+.-+.. -....-|||.|.+.+++...++.+++..+
T Consensus 103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~--G~V~~v~i~~d~~t------g~srGyaFVeF~~~e~A~~Ai~~LnG~~l 174 (346)
T TIGR01659 103 TNNSGTNLIVNYLPQDMTDRELYALFRTI--GPINTCRIMRDYKT------GYSFGYAFVDFGSEADSQRAIKNLNGITV 174 (346)
T ss_pred CCCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCC------CccCcEEEEEEccHHHHHHHHHHcCCCcc
Confidence 35678999999999999999999999864 33544444321111 11123499999999999999999999988
Q ss_pred EcCCCCeeeeEEEec
Q 009733 83 VNEKGAQFKAIVEYA 97 (527)
Q Consensus 83 vDsKGne~~A~VEfA 97 (527)
.+. ...|+||
T Consensus 175 ~gr-----~i~V~~a 184 (346)
T TIGR01659 175 RNK-----RLKVSYA 184 (346)
T ss_pred CCc-----eeeeecc
Confidence 653 3556665
No 12
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=95.41 E-value=0.068 Score=53.70 Aligned_cols=79 Identities=22% Similarity=0.350 Sum_probs=59.0
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcC
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 85 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDs 85 (527)
+.+.|.|++||+.+||++|.+.+..+ |.|.....+.-+.. ...-.-|||.|.+.++...-++.++|..+.+.
T Consensus 2 ~~~~l~V~nLp~~~~e~~l~~~F~~~--G~i~~v~i~~d~~~------g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~ 73 (352)
T TIGR01661 2 SKTNLIVNYLPQTMTQEEIRSLFTSI--GEIESCKLVRDKVT------GQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNK 73 (352)
T ss_pred CCcEEEEeCCCCCCCHHHHHHHHHcc--CCEEEEEEEEcCCC------CccceEEEEEECcHHHHHHHHhhcccEEECCe
Confidence 46889999999999999999998874 35544444432221 11235699999999999999999999876533
Q ss_pred CCCeeeeEEEec
Q 009733 86 KGAQFKAIVEYA 97 (527)
Q Consensus 86 KGne~~A~VEfA 97 (527)
...|+||
T Consensus 74 -----~i~v~~a 80 (352)
T TIGR01661 74 -----TIKVSYA 80 (352)
T ss_pred -----eEEEEee
Confidence 4667776
No 13
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=94.22 E-value=0.2 Score=50.46 Aligned_cols=78 Identities=15% Similarity=0.112 Sum_probs=57.3
Q ss_pred ceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcCCC
Q 009733 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG 87 (527)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG 87 (527)
..|.|++||+..+|+++++.+.+. |.|.....+....+ ...-.-|||.|.+.++...-++.++|..|-+
T Consensus 270 ~~lfV~NL~~~~~e~~L~~~F~~f--G~v~~v~i~~d~~t------~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~g--- 338 (352)
T TIGR01661 270 YCIFVYNLSPDTDETVLWQLFGPF--GAVQNVKIIRDLTT------NQCKGYGFVSMTNYDEAAMAILSLNGYTLGN--- 338 (352)
T ss_pred cEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEeEcCCC------CCccceEEEEECCHHHHHHHHHHhCCCEECC---
Confidence 369999999999999999999875 45666555432211 1113358999999999999999999998733
Q ss_pred CeeeeEEEecc
Q 009733 88 AQFKAIVEYAP 98 (527)
Q Consensus 88 ne~~A~VEfAP 98 (527)
..-.|.|+.
T Consensus 339 --r~i~V~~~~ 347 (352)
T TIGR01661 339 --RVLQVSFKT 347 (352)
T ss_pred --eEEEEEEcc
Confidence 245566653
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=94.06 E-value=0.28 Score=51.50 Aligned_cols=82 Identities=17% Similarity=0.170 Sum_probs=58.8
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcC
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 85 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDs 85 (527)
..++|.|.+||+.+||+++.+.+..+ +.|.....+.-+.. ...-.-|||.|.+.+++..-++.+++..|..
T Consensus 192 ~~~~lfV~nLp~~vtee~L~~~F~~f--G~V~~v~i~~d~~t------g~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g- 262 (346)
T TIGR01659 192 KDTNLYVTNLPRTITDDQLDTIFGKY--GQIVQKNILRDKLT------GTPRGVAFVRFNKREEAQEAISALNNVIPEG- 262 (346)
T ss_pred ccceeEEeCCCCcccHHHHHHHHHhc--CCEEEEEEeecCCC------CccceEEEEEECCHHHHHHHHHHhCCCccCC-
Confidence 46789999999999999999988764 23444333322211 1112579999999999999999999998744
Q ss_pred CCCeeeeEEEecc
Q 009733 86 KGAQFKAIVEYAP 98 (527)
Q Consensus 86 KGne~~A~VEfAP 98 (527)
...+..|.+|-
T Consensus 263 --~~~~l~V~~a~ 273 (346)
T TIGR01659 263 --GSQPLTVRLAE 273 (346)
T ss_pred --CceeEEEEECC
Confidence 23456666664
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=93.50 E-value=0.34 Score=50.84 Aligned_cols=79 Identities=14% Similarity=0.206 Sum_probs=58.0
Q ss_pred CceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcCC
Q 009733 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK 86 (527)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDsK 86 (527)
..+|.|++||+.+||+++.+.+..+ +.|.+..++.-... ...-.-|||.|.+.++...-.+.++|..|.+
T Consensus 186 ~~~l~v~nl~~~~te~~l~~~f~~~--G~i~~v~~~~d~~~------g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g-- 255 (457)
T TIGR01622 186 FLKLYVGNLHFNITEQELRQIFEPF--GDIEDVQLHRDPET------GRSKGFGFIQFHDAEEAKEALEVMNGFELAG-- 255 (457)
T ss_pred CCEEEEcCCCCCCCHHHHHHHHHhc--CCeEEEEEEEcCCC------CccceEEEEEECCHHHHHHHHHhcCCcEECC--
Confidence 4789999999999999999988764 34655554422111 1112359999999999999999999977633
Q ss_pred CCeeeeEEEecc
Q 009733 87 GAQFKAIVEYAP 98 (527)
Q Consensus 87 Gne~~A~VEfAP 98 (527)
....|.||-
T Consensus 256 ---~~i~v~~a~ 264 (457)
T TIGR01622 256 ---RPIKVGYAQ 264 (457)
T ss_pred ---EEEEEEEcc
Confidence 346778865
No 16
>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=91.67 E-value=0.52 Score=51.26 Aligned_cols=67 Identities=16% Similarity=0.228 Sum_probs=50.9
Q ss_pred eEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeE
Q 009733 9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 83 (527)
Q Consensus 9 KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFv 83 (527)
-|.|.+||+++||+++.+.+..+ +.|.......-+.. .....-|||.|.+.++.....+.+++..|.
T Consensus 2 sl~VgnLp~~vte~~L~~~F~~~--G~v~~v~v~~d~~t------~~s~G~afV~F~~~~~A~~Al~~ln~~~i~ 68 (562)
T TIGR01628 2 SLYVGDLDPDVTEAKLYDLFKPF--GPVLSVRVCRDSVT------RRSLGYGYVNFQNPADAERALETMNFKRLG 68 (562)
T ss_pred eEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCC------CCcceEEEEEECCHHHHHHHHHHhCCCEEC
Confidence 37899999999999999998865 34655555433322 112356999999999999999999988763
No 17
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=90.81 E-value=1 Score=40.65 Aligned_cols=72 Identities=18% Similarity=0.244 Sum_probs=54.6
Q ss_pred CceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcCC
Q 009733 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK 86 (527)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDsK 86 (527)
...|.|.+||+.+||+++.+.+.... .+.+...+--+ .......-|||.|.+.+++....+.++|..|.+..
T Consensus 115 ~~~l~v~nL~~~~~~~~l~~~F~~~g--~~~~~~~~~d~------~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~ 186 (306)
T COG0724 115 NNTLFVGNLPYDVTEEDLRELFKKFG--PVKRVRLVRDR------ETGKSRGFAFVEFESEESAEKAIEELNGKELEGRP 186 (306)
T ss_pred CceEEEeCCCCCCCHHHHHHHHHhcC--ceeEEEeeecc------ccCccCceEEEEecCHHHHHHHHHHcCCCeECCce
Confidence 58999999999999999999998753 23333322111 12333567999999999999999999988887764
No 18
>PLN03120 nucleic acid binding protein; Provisional
Probab=90.76 E-value=0.76 Score=47.23 Aligned_cols=75 Identities=20% Similarity=0.318 Sum_probs=57.6
Q ss_pred CceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcCC
Q 009733 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK 86 (527)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDsK 86 (527)
..+|-|.+||+..||+++.+.+..+ |.|.+......+. .-.-|||.|.+++++.... .++|..|.|..
T Consensus 4 ~rtVfVgNLs~~tTE~dLrefFS~~--G~I~~V~I~~d~~---------~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~ 71 (260)
T PLN03120 4 VRTVKVSNVSLKATERDIKEFFSFS--GDIEYVEMQSENE---------RSQIAYVTFKDPQGAETAL-LLSGATIVDQS 71 (260)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeecCC---------CCCEEEEEeCcHHHHHHHH-HhcCCeeCCce
Confidence 4689999999999999999999764 6777766643211 1347999999999998888 49999887653
Q ss_pred CCeeeeEEEecc
Q 009733 87 GAQFKAIVEYAP 98 (527)
Q Consensus 87 Gne~~A~VEfAP 98 (527)
..|+.+.
T Consensus 72 -----V~Vt~a~ 78 (260)
T PLN03120 72 -----VTITPAE 78 (260)
T ss_pred -----EEEEecc
Confidence 5666665
No 19
>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=90.49 E-value=0.8 Score=51.57 Aligned_cols=71 Identities=18% Similarity=0.205 Sum_probs=53.5
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcce--eEEEEccCcccHHHHHHHhCCCe
Q 009733 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYS--RAYVELKKPAGVFEFAELLNGHV 81 (527)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~S--RAYI~Fkn~Edl~~F~d~fdG~v 81 (527)
+...++|-|-+||+.+||+++.+.+... +.|.....+.- . .-.| -|||.|.+.+++..-++.++++.
T Consensus 55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~--G~I~~vrl~~D-~--------sG~sRGfaFV~F~~~e~A~~Ai~~lng~~ 123 (578)
T TIGR01648 55 PGRGCEVFVGKIPRDLYEDELVPLFEKA--GPIYELRLMMD-F--------SGQNRGYAFVTFCGKEEAKEAVKLLNNYE 123 (578)
T ss_pred CCCCCEEEeCCCCCCCCHHHHHHHHHhh--CCEEEEEEEEC-C--------CCCccceEEEEeCCHHHHHHHHHHcCCCe
Confidence 4457999999999999999999988764 33433333321 1 1133 49999999999999999999998
Q ss_pred eEcC
Q 009733 82 FVNE 85 (527)
Q Consensus 82 FvDs 85 (527)
+.+.
T Consensus 124 i~~G 127 (578)
T TIGR01648 124 IRPG 127 (578)
T ss_pred ecCC
Confidence 8643
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=90.23 E-value=1.5 Score=47.52 Aligned_cols=84 Identities=23% Similarity=0.339 Sum_probs=61.9
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcC
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 85 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDs 85 (527)
+..+|.|.+||+++||+++.+.+...-...+....+.+.+-. ...-|+|.|.+.++...-...++++.+.+.
T Consensus 393 ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~--------~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~ 464 (481)
T TIGR01649 393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNE--------RSKMGLLEWESVEDAVEALIALNHHQLNEP 464 (481)
T ss_pred CCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCC--------cceeEEEEcCCHHHHHHHHHHhcCCccCCC
Confidence 446799999999999999999888752213555555554321 123599999999999999999999998766
Q ss_pred CC-CeeeeEEEec
Q 009733 86 KG-AQFKAIVEYA 97 (527)
Q Consensus 86 KG-ne~~A~VEfA 97 (527)
.| .-+...|.||
T Consensus 465 ~~~~~~~lkv~fs 477 (481)
T TIGR01649 465 NGSAPYHLKVSFS 477 (481)
T ss_pred CCCccceEEEEec
Confidence 54 2345667776
No 21
>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=89.96 E-value=1.2 Score=50.12 Aligned_cols=72 Identities=14% Similarity=0.137 Sum_probs=55.5
Q ss_pred ceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcCCC
Q 009733 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG 87 (527)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG 87 (527)
.+|.|++||..+||+++.+.+...-.+.|.....+. --|||.|.+.++...-++.+++..|.+
T Consensus 234 k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------------gfAFVeF~s~e~A~kAi~~lnG~~i~G--- 296 (578)
T TIGR01648 234 KILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------------DYAFVHFEDREDAVKAMDELNGKELEG--- 296 (578)
T ss_pred cEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------------CeEEEEeCCHHHHHHHHHHhCCCEECC---
Confidence 569999999999999999999875334454332211 159999999999999999999998844
Q ss_pred CeeeeEEEecc
Q 009733 88 AQFKAIVEYAP 98 (527)
Q Consensus 88 ne~~A~VEfAP 98 (527)
....|++|.
T Consensus 297 --r~I~V~~Ak 305 (578)
T TIGR01648 297 --SEIEVTLAK 305 (578)
T ss_pred --EEEEEEEcc
Confidence 356788873
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=89.83 E-value=0.91 Score=49.42 Aligned_cols=71 Identities=20% Similarity=0.251 Sum_probs=54.2
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcC
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 85 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDs 85 (527)
..+.|.|++||+.+||+++.+.+..+ +.|....+..... ...-..|||.|.+.++.....+.++|..|.+.
T Consensus 177 ~~~~l~V~nl~~~~tee~L~~~F~~f--G~i~~~~i~~~~~-------g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~ 247 (562)
T TIGR01628 177 KFTNLYVKNLDPSVNEDKLRELFAKF--GEITSAAVMKDGS-------GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLA 247 (562)
T ss_pred CCCeEEEeCCCCcCCHHHHHHHHHhc--CCEEEEEEEECCC-------CCcccEEEEEECCHHHHHHHHHHhCCcEeccc
Confidence 34679999999999999999988864 3465555543221 12245799999999999999999999988643
No 23
>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=88.09 E-value=2 Score=45.24 Aligned_cols=71 Identities=18% Similarity=0.254 Sum_probs=52.5
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
.+...|.|.+||+.+||+++.+.+... +.|.....+.-+.. ...-.-|||.|.+.+++...+. ++|..|.+
T Consensus 87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~--G~v~~v~i~~d~~~------~~skg~afVeF~~~e~A~~Al~-l~g~~~~g 157 (457)
T TIGR01622 87 RDDRTVFVLQLALKARERDLYEFFSKV--GKVRDVQCIKDRNS------RRSKGVAYVEFYDVESVIKALA-LTGQMLLG 157 (457)
T ss_pred cCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEeecCCC------CCcceEEEEEECCHHHHHHHHH-hCCCEECC
Confidence 346689999999999999999988774 35666565532222 1223569999999999998886 78877753
No 24
>PLN03121 nucleic acid binding protein; Provisional
Probab=84.91 E-value=2.9 Score=42.75 Aligned_cols=69 Identities=20% Similarity=0.307 Sum_probs=53.2
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcC
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 85 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDs 85 (527)
.+.-|.|.+|+|..||+++.+-+.. .|+|...+-+.-.-. -.-|||.|++++++ +-+-.++|..|.|.
T Consensus 4 ~g~TV~V~NLS~~tTE~dLrefFS~--~G~I~~V~I~~D~et---------~gfAfVtF~d~~aa-etAllLnGa~l~d~ 71 (243)
T PLN03121 4 GGYTAEVTNLSPKATEKDVYDFFSH--CGAIEHVEIIRSGEY---------ACTAYVTFKDAYAL-ETAVLLSGATIVDQ 71 (243)
T ss_pred CceEEEEecCCCCCCHHHHHHHHHh--cCCeEEEEEecCCCc---------ceEEEEEECCHHHH-HHHHhcCCCeeCCc
Confidence 4567899999999999999988875 467777665532111 14799999999998 55558999999887
Q ss_pred C
Q 009733 86 K 86 (527)
Q Consensus 86 K 86 (527)
.
T Consensus 72 ~ 72 (243)
T PLN03121 72 R 72 (243)
T ss_pred e
Confidence 4
No 25
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=83.86 E-value=2.6 Score=44.90 Aligned_cols=75 Identities=17% Similarity=0.276 Sum_probs=46.3
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCC-CCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGK-SSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK-~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
...+|.|.+||+.+||+++.+.|...+.. +....-.+|. +......+. -.-|||.|.+.+++...+ .++|..|.+
T Consensus 174 ~~r~lyVgnLp~~~t~~~l~~~F~~~~~~-~~~~~~~~~~~v~~~~~~~~--kg~afVeF~~~e~A~~Al-~l~g~~~~g 249 (509)
T TIGR01642 174 QARRLYVGGIPPEFVEEAVVDFFNDLMIA-TGYHKAEDGKHVSSVNINKE--KNFAFLEFRTVEEATFAM-ALDSIIYSN 249 (509)
T ss_pred cccEEEEeCCCCCCCHHHHHHHHHHHHHh-cCCCCCCCCCceEEEEECCC--CCEEEEEeCCHHHHhhhh-cCCCeEeeC
Confidence 34589999999999999998888764310 0000000010 000000011 235999999999998877 599988865
No 26
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=82.81 E-value=5.7 Score=39.39 Aligned_cols=77 Identities=22% Similarity=0.288 Sum_probs=61.2
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
.-.+||-|=+||+..|+.|+...+..+-.-.-.|..+.| +--|+|.|.++.|..+-...+||..|..
T Consensus 8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-------------PGfAFVEFed~RDA~DAvr~LDG~~~cG 74 (195)
T KOG0107|consen 8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-------------PGFAFVEFEDPRDAEDAVRYLDGKDICG 74 (195)
T ss_pred CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-------------CCceEEeccCcccHHHHHhhcCCccccC
Confidence 457999999999999999999888765322235655543 4558999999999999999999999887
Q ss_pred CCCCeeeeEEEeccC
Q 009733 85 EKGAQFKAIVEYAPS 99 (527)
Q Consensus 85 sKGne~~A~VEfAPY 99 (527)
. .+.||++-=
T Consensus 75 ~-----r~rVE~S~G 84 (195)
T KOG0107|consen 75 S-----RIRVELSTG 84 (195)
T ss_pred c-----eEEEEeecC
Confidence 6 478887643
No 27
>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=82.64 E-value=3.8 Score=46.66 Aligned_cols=69 Identities=12% Similarity=0.149 Sum_probs=53.6
Q ss_pred CceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeE
Q 009733 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 83 (527)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFv 83 (527)
..+|.|.+||+.++++++.+.+..+ |.|....++..... ...---|||.|.+.++...-.+.+++..|-
T Consensus 204 ~~rLfVgnLp~~vteedLk~lFs~F--G~I~svrl~~D~~t------gksKGfGFVeFe~~e~A~kAI~amNg~elg 272 (612)
T TIGR01645 204 FNRIYVASVHPDLSETDIKSVFEAF--GEIVKCQLARAPTG------RGHKGYGFIEYNNLQSQSEAIASMNLFDLG 272 (612)
T ss_pred cceEEeecCCCCCCHHHHHHHHhhc--CCeeEEEEEecCCC------CCcCCeEEEEECCHHHHHHHHHHhCCCeeC
Confidence 4689999999999999999999874 45666666543322 111235999999999999999999998764
No 28
>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=82.59 E-value=3.5 Score=36.59 Aligned_cols=59 Identities=20% Similarity=0.309 Sum_probs=38.1
Q ss_pred ceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCC
Q 009733 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGH 80 (527)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~ 80 (527)
+=|-|.-|++.++.++|-+.|..+ +.|.|..|..|... |||.|.+++....+.+.+...
T Consensus 2 ~il~~~g~~~~~~re~iK~~f~~~--g~V~yVD~~~G~~~------------g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 2 CILKFSGLGEPTSREDIKEAFSQF--GEVAYVDFSRGDTE------------GYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp -EEEEEE--SS--HHHHHHHT-SS----EEEEE--TT-SE------------EEEEESS---HHHHHHHHHHT
T ss_pred eEEEEecCCCCcCHHHHHHHHHhc--CCcceEEecCCCCE------------EEEEECCcchHHHHHHHHHhc
Confidence 346677799999999999999975 37999999999766 999999999998888887654
No 29
>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=82.34 E-value=9.1 Score=41.57 Aligned_cols=80 Identities=19% Similarity=0.150 Sum_probs=61.5
Q ss_pred CCceEEEecCCC-CCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 6 QRTKVVIRHLPP-SLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 6 ~r~KVVIRrLPP-~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
+...|.|.+||+ .+|++++++.+..+ |.|....++..+ ..-|+|.|.+.++...-++.++|+.|.+
T Consensus 274 ~~~~l~v~nL~~~~vt~~~L~~lF~~y--G~V~~vki~~~~-----------~g~afV~f~~~~~A~~Ai~~lng~~l~g 340 (481)
T TIGR01649 274 PGSVLMVSGLHQEKVNCDRLFNLFCVY--GNVERVKFMKNK-----------KETALIEMADPYQAQLALTHLNGVKLFG 340 (481)
T ss_pred CCCEEEEeCCCCCCCCHHHHHHHHHhc--CCeEEEEEEeCC-----------CCEEEEEECCHHHHHHHHHHhCCCEECC
Confidence 567999999999 69999999999875 456655554321 2469999999999999999999998843
Q ss_pred CCCCeeeeEEEeccCCCCC
Q 009733 85 EKGAQFKAIVEYAPSQRVP 103 (527)
Q Consensus 85 sKGne~~A~VEfAPYQKvP 103 (527)
....|+|+-.+.+.
T Consensus 341 -----~~l~v~~s~~~~~~ 354 (481)
T TIGR01649 341 -----KPLRVCPSKQQNVQ 354 (481)
T ss_pred -----ceEEEEEccccccc
Confidence 24567777665543
No 30
>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=80.83 E-value=5.2 Score=45.62 Aligned_cols=73 Identities=14% Similarity=0.157 Sum_probs=54.2
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
...++|.|.+||+.+||+++.+.+..+ |.|.....+.-+.. .....-|||.|.+.++...-++.++|..|.+
T Consensus 105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~f--G~I~sV~I~~D~~T------gkskGfAFVeF~s~e~A~~Ai~~lnG~~i~G 176 (612)
T TIGR01645 105 AIMCRVYVGSISFELREDTIRRAFDPF--GPIKSINMSWDPAT------GKHKGFAFVEYEVPEAAQLALEQMNGQMLGG 176 (612)
T ss_pred cCCCEEEEcCCCCCCCHHHHHHHHHcc--CCEEEEEEeecCCC------CCcCCeEEEEeCcHHHHHHHHHhcCCeEEec
Confidence 456899999999999999999999874 34544444321111 1123469999999999999999999988754
Q ss_pred C
Q 009733 85 E 85 (527)
Q Consensus 85 s 85 (527)
.
T Consensus 177 R 177 (612)
T TIGR01645 177 R 177 (612)
T ss_pred c
Confidence 3
No 31
>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []. These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.
Probab=79.62 E-value=8 Score=34.98 Aligned_cols=88 Identities=22% Similarity=0.364 Sum_probs=62.1
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeE
Q 009733 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 83 (527)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFv 83 (527)
...++.|.|=..||.|+-..|+-.+...+.+.+.....+.- ..++.| =+-|.|.+.++..+|...|+|..|-
T Consensus 9 ~~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird-------~~pnry-mVLikF~~~~~Ad~Fy~~fNGk~Fn 80 (110)
T PF07576_consen 9 DERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRD-------GTPNRY-MVLIKFRDQESADEFYEEFNGKPFN 80 (110)
T ss_pred CCCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeC-------CCCceE-EEEEEECCHHHHHHHHHHhCCCccC
Confidence 34567777889999999999998888877766766665531 223333 3678999999999999999999994
Q ss_pred cCCC----CeeeeEEEeccC
Q 009733 84 NEKG----AQFKAIVEYAPS 99 (527)
Q Consensus 84 DsKG----ne~~A~VEfAPY 99 (527)
-=.- ..|...|||--.
T Consensus 81 slEpE~ChvvfV~~Ve~~~~ 100 (110)
T PF07576_consen 81 SLEPETCHVVFVKSVEFTSS 100 (110)
T ss_pred CCCCceeEEEEEEEEEEEcc
Confidence 3222 223445666544
No 32
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=70.16 E-value=11 Score=38.21 Aligned_cols=71 Identities=17% Similarity=0.232 Sum_probs=57.4
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhccccC--C-CceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCe
Q 009733 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFN--D-RYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHV 81 (527)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~e~L~p~~~--g-kvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~v 81 (527)
.+.-.++||+|+-.+.-+++..+|..++. | -++...|...+.+ .=|.+.|++.+..-.-...++|..
T Consensus 7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmR----------GQA~VvFk~~~~As~A~r~l~gfp 76 (221)
T KOG4206|consen 7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMR----------GQAFVVFKETEAASAALRALQGFP 76 (221)
T ss_pred CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCcc----------CceEEEecChhHHHHHHHHhcCCc
Confidence 34449999999999999999998887762 3 3566666555554 349999999999998888999999
Q ss_pred eEcC
Q 009733 82 FVNE 85 (527)
Q Consensus 82 FvDs 85 (527)
|.|.
T Consensus 77 FygK 80 (221)
T KOG4206|consen 77 FYGK 80 (221)
T ss_pred ccCc
Confidence 9986
No 33
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=69.76 E-value=5.7 Score=44.70 Aligned_cols=90 Identities=22% Similarity=0.416 Sum_probs=63.1
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccc--------------------------cCCCceeEEeeCCCCCCccCCCCCccee
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDH--------------------------FNDRYNWFCFRPGKSSFFYSYKHQRYSR 59 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~--------------------------~~gkvdw~yFVpGK~S~k~p~K~~~~SR 59 (527)
.++-+-|+.+|-.+++..+..+++-. ..+.||+.|- |=+.. ...----
T Consensus 360 ~Rtt~~i~ni~n~~~~~dl~~Ildge~~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYL-PiDF~-----nkcNvGY 433 (549)
T KOG4660|consen 360 RRTTVMIKNIPNKYGQLDLLRILDGECPRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYL-PIDFK-----NKCNVGY 433 (549)
T ss_pred chhhhhhhccccchhHHHHHHHHhCcCchhhhHhhccCchhhHHhhhhhhccccCccceEEe-ccccc-----cccccce
Confidence 34555666666666666666666332 2345655443 44433 1222456
Q ss_pred EEEEccCcccHHHHHHHhCCCeeEcCCCCeeeeEEEeccCCCC
Q 009733 60 AYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRV 102 (527)
Q Consensus 60 AYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A~VEfAPYQKv 102 (527)
|.|+|.+++++..|.+.|+|..|..=. .+..|.+-||-+|..
T Consensus 434 AFINm~sp~ai~~F~kAFnGk~W~~Fn-S~Kia~itYArIQGk 475 (549)
T KOG4660|consen 434 AFINMTSPEAIIRFYKAFNGKKWEKFN-SEKIASITYARIQGK 475 (549)
T ss_pred eEEeecCHHHHHHHHHHHcCCchhhhc-ceeeeeeehhhhhch
Confidence 999999999999999999999987665 688999999999874
No 34
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=65.64 E-value=8.3 Score=42.26 Aligned_cols=71 Identities=21% Similarity=0.366 Sum_probs=50.0
Q ss_pred eEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCccee-EEEEccCcccHHHHHHHhCCCeeEcCC
Q 009733 9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSR-AYVELKKPAGVFEFAELLNGHVFVNEK 86 (527)
Q Consensus 9 KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SR-AYI~Fkn~Edl~~F~d~fdG~vFvDsK 86 (527)
-|-|=+|-|+.|.+++...++.+ |+|.-...+|--. +.+-++-+| |||.|.+... ...++.+-..+|+|.-
T Consensus 9 vIqvanispsat~dqm~tlFg~l--GkI~elrlyp~~~----d~~~pv~sRtcyVkf~d~~s-v~vaQhLtntvfvdra 80 (479)
T KOG4676|consen 9 VIQVANISPSATKDQMQTLFGNL--GKIPELRLYPNVD----DSKIPVISRTCYVKFLDSQS-VTVAQHLTNTVFVDRA 80 (479)
T ss_pred eeeecccCchhhHHHHHHHHhhc--cccccccccCCCC----CccCcceeeeEEEeccCCcc-eeHHhhhccceeeeee
Confidence 45678999999999998888754 4565554444211 145667775 9999999644 4567778888888863
No 35
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=63.73 E-value=22 Score=36.91 Aligned_cols=77 Identities=19% Similarity=0.224 Sum_probs=56.4
Q ss_pred ceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcCCC
Q 009733 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG 87 (527)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG 87 (527)
.-|=|=+||-.|+|+++.+.+.+.- .|.-.|.+.-+.. --.-.-||++|.+.|+....++.++||-+-
T Consensus 190 ~tvRvtNLsed~~E~dL~eLf~~fg--~i~rvylardK~T------G~~kGFAFVtF~sRddA~rAI~~LnG~gyd---- 257 (270)
T KOG0122|consen 190 ATVRVTNLSEDMREDDLEELFRPFG--PITRVYLARDKET------GLSKGFAFVTFESRDDAARAIADLNGYGYD---- 257 (270)
T ss_pred ceeEEecCccccChhHHHHHhhccC--ccceeEEEEcccc------CcccceEEEEEecHHHHHHHHHHccCcccc----
Confidence 3477889999999999999888753 3555555543333 112346999999999999999999998642
Q ss_pred CeeeeEEEec
Q 009733 88 AQFKAIVEYA 97 (527)
Q Consensus 88 ne~~A~VEfA 97 (527)
..+..||+|
T Consensus 258 -~LILrvEws 266 (270)
T KOG0122|consen 258 -NLILRVEWS 266 (270)
T ss_pred -eEEEEEEec
Confidence 346677776
No 36
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=59.05 E-value=22 Score=37.48 Aligned_cols=73 Identities=21% Similarity=0.315 Sum_probs=56.1
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
..++-|+|--||-+||+|||...++.. +.|+.--.|.-|+. -....--++++.+++|...-+..++|.-..+
T Consensus 39 ~skTNLIvNYLPQ~MTqdE~rSLF~Si--GeiEScKLvRDKit------GqSLGYGFVNYv~p~DAe~AintlNGLrLQ~ 110 (360)
T KOG0145|consen 39 ESKTNLIVNYLPQNMTQDELRSLFGSI--GEIESCKLVRDKIT------GQSLGYGFVNYVRPKDAEKAINTLNGLRLQN 110 (360)
T ss_pred cccceeeeeecccccCHHHHHHHhhcc--cceeeeeeeecccc------ccccccceeeecChHHHHHHHhhhcceeecc
Confidence 357889999999999999999988865 34666666655544 2234456788889999999999999987765
Q ss_pred C
Q 009733 85 E 85 (527)
Q Consensus 85 s 85 (527)
.
T Consensus 111 K 111 (360)
T KOG0145|consen 111 K 111 (360)
T ss_pred c
Confidence 4
No 37
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=58.76 E-value=27 Score=39.85 Aligned_cols=69 Identities=23% Similarity=0.333 Sum_probs=53.5
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCee
Q 009733 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF 82 (527)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vF 82 (527)
.+.-|||||+||=...+..+...++.+ |+ .|--++|-+ ...-.+.-|+|.|++..+...-++.|+|+.|
T Consensus 115 ~~k~rLIIRNLPf~~k~~dLk~vFs~~--G~-V~Ei~IP~k------~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i 183 (678)
T KOG0127|consen 115 LPKWRLIIRNLPFKCKKPDLKNVFSNF--GK-VVEIVIPRK------KDGKLCGFAFVQFKEKKDAEKALEFFNGNKI 183 (678)
T ss_pred CccceEEeecCCcccCcHHHHHHHhhc--ce-EEEEEcccC------CCCCccceEEEEEeeHHHHHHHHHhccCcee
Confidence 347899999999999999877666654 22 366777733 2344458999999999999999999999876
No 38
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=58.69 E-value=20 Score=40.90 Aligned_cols=64 Identities=17% Similarity=0.266 Sum_probs=49.9
Q ss_pred CceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhC
Q 009733 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLN 78 (527)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fd 78 (527)
..-|-||+||-.-|||++.+.|... |.|.|..-|--+.+ ...-.+|++.|+++.+....+...+
T Consensus 292 ~~tVFvRNL~fD~tEEel~~~fskF--G~v~ya~iV~~k~T------~~skGtAFv~Fkt~~~~~~ci~~As 355 (678)
T KOG0127|consen 292 GKTVFVRNLPFDTTEEELKEHFSKF--GEVKYAIIVKDKDT------GHSKGTAFVKFKTQIAAQNCIEAAS 355 (678)
T ss_pred cceEEEecCCccccHHHHHHHHHhh--ccceeEEEEeccCC------CCcccceEEEeccHHHHHHHHHhcC
Confidence 4568899999999999999888764 35677666643333 4456799999999999998888774
No 39
>PLN03213 repressor of silencing 3; Provisional
Probab=57.40 E-value=43 Score=38.12 Aligned_cols=69 Identities=19% Similarity=0.264 Sum_probs=56.4
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCc--ccHHHHHHHhCCCe
Q 009733 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKP--AGVFEFAELLNGHV 81 (527)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~--Edl~~F~d~fdG~v 81 (527)
....++|-|-.|++..|++++...+.++ |.|....++ .-. . -.-|||.|.+. +.+...+..++|..
T Consensus 7 ~~~gMRIYVGNLSydVTEDDLravFSeF--GsVkdVEIp--RET----G----RGFAFVEMssdddaEeeKAISaLNGAE 74 (759)
T PLN03213 7 GGGGVRLHVGGLGESVGRDDLLKIFSPM--GTVDAVEFV--RTK----G----RSFAYIDFSPSSTNSLTKLFSTYNGCV 74 (759)
T ss_pred CCcceEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEe--ccc----C----CceEEEEecCCcHHHHHHHHHHhcCCe
Confidence 4567899999999999999999999986 567777776 111 1 57899999987 67999999999999
Q ss_pred eEc
Q 009733 82 FVN 84 (527)
Q Consensus 82 FvD 84 (527)
|..
T Consensus 75 WKG 77 (759)
T PLN03213 75 WKG 77 (759)
T ss_pred ecC
Confidence 844
No 40
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=54.15 E-value=26 Score=32.56 Aligned_cols=70 Identities=20% Similarity=0.242 Sum_probs=52.7
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeE
Q 009733 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 83 (527)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFv 83 (527)
|...--|-||+||-.+|-|+..+.++-+- .|- .-.-| ....+-.-||+.+.+..|...-.+.+.|+-+.
T Consensus 15 pevnriLyirNLp~~ITseemydlFGkyg--~Ir--QIRiG-------~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~ 83 (124)
T KOG0114|consen 15 PEVNRILYIRNLPFKITSEEMYDLFGKYG--TIR--QIRIG-------NTKETRGTAFVVYEDIFDAKKACDHLSGYNVD 83 (124)
T ss_pred hhhheeEEEecCCccccHHHHHHHhhccc--ceE--EEEec-------CccCcCceEEEEehHhhhHHHHHHHhcccccC
Confidence 33445578999999999999999998652 222 12223 34456678999999999999999999999764
Q ss_pred c
Q 009733 84 N 84 (527)
Q Consensus 84 D 84 (527)
+
T Consensus 84 ~ 84 (124)
T KOG0114|consen 84 N 84 (124)
T ss_pred C
Confidence 4
No 41
>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=54.10 E-value=24 Score=26.56 Aligned_cols=36 Identities=31% Similarity=0.339 Sum_probs=29.4
Q ss_pred ceeEEEEccCcccHHHHHHHhCCCeeEcCCCCeeeeEEEec
Q 009733 57 YSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYA 97 (527)
Q Consensus 57 ~SRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A~VEfA 97 (527)
...|||.|.+.++.....+.++|..|.+. +-.|+||
T Consensus 21 ~~~a~V~f~~~~~A~~a~~~l~~~~~~g~-----~l~V~~a 56 (56)
T PF13893_consen 21 RGFAFVEFASVEDAQKAIEQLNGRQFNGR-----PLKVSYA 56 (56)
T ss_dssp TTEEEEEESSHHHHHHHHHHHTTSEETTE-----EEEEEEE
T ss_pred CCEEEEEECCHHHHHHHHHHhCCCEECCc-----EEEEEEC
Confidence 47899999999999999999999998332 4556664
No 42
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=51.72 E-value=35 Score=37.71 Aligned_cols=68 Identities=19% Similarity=0.212 Sum_probs=50.5
Q ss_pred ceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeE
Q 009733 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 83 (527)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFv 83 (527)
+.|.|+++|+..+||++.+.+... +.|-.+.+|--..+ -++ ..-+|+.|.++++...-.+.++|+.|-
T Consensus 19 ~~v~vgnip~~~se~~l~~~~~~~--g~v~s~~~v~D~~t----G~~--~G~~f~~~~~~~~~~~a~~~lNg~~~~ 86 (435)
T KOG0108|consen 19 SSVFVGNIPYEGSEEQLLSIFSGV--GPVLSFRLVYDRET----GKP--KGFGFCEFTDEETAERAIRNLNGAEFN 86 (435)
T ss_pred cceEecCCCCcccHHHHHHHHhcc--CccceeeecccccC----CCc--CceeeEecCchhhHHHHHHhcCCcccC
Confidence 789999999999999999888754 23444455421111 122 346889999999999999999998773
No 43
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=51.52 E-value=26 Score=39.41 Aligned_cols=68 Identities=18% Similarity=0.281 Sum_probs=48.9
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCC--cceeEEEEccCcccHHHHHHHhC
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQ--RYSRAYVELKKPAGVFEFAELLN 78 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~--~~SRAYI~Fkn~Edl~~F~d~fd 78 (527)
--.||.|=-|||.++|++++..+...-.-.||| ||+.-... .-++ .+.-+||.|.++..|..+....-
T Consensus 258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdW----P~k~~~~~-~~ppkGs~~YvflvFe~E~sV~~Ll~aC~ 327 (520)
T KOG0129|consen 258 YSRKVFVGGLPWDITEAQINASFGQFGSVKVDW----PGKANSRG-RAPPKGSYGYVFLVFEDERSVQSLLSACS 327 (520)
T ss_pred cccceeecCCCccccHHHHHhhcccccceEeec----CCCccccc-cCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence 346999999999999999999988754445788 54333111 1111 24689999999999988877653
No 44
>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]
Probab=46.81 E-value=3 Score=44.99 Aligned_cols=123 Identities=12% Similarity=-0.049 Sum_probs=80.1
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccc------C-----CCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHH
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDHF------N-----DRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFA 74 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~~------~-----gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~ 74 (527)
.++..+|+.+++++|-++|.+.+...- + -...-..+.-|+..... ++..+++++||.+.....|....
T Consensus 70 ~~f~g~ifld~Kggti~d~~~yre~~~~~~~~ke~~~s~~~et~~g~~e~d~~~~~-fk~~t~~~~~~~~~~~q~irk~~ 148 (376)
T KOG1295|consen 70 RRFDGYIFLDNKGGTIDDDPAYREFLKNYALAKEDKASKLKETLLGEIEGDTKSLA-FKKVTPLLSFIKQADKQRIRKLR 148 (376)
T ss_pred hhCCceEEecCCCCCccccHHHHHHHhhccccccCccccchhhhhchhcccccchh-hhccchHHHhhhhhhHHHHHHhh
Confidence 568899999999999777766553210 0 12233466778877444 88999999999999667777777
Q ss_pred HHhCCCeeEcCCCCe-eeeEEEeccCCC--CCCCCCCCCCCCCccc-CCHHHHHHHHHH
Q 009733 75 ELLNGHVFVNEKGAQ-FKAIVEYAPSQR--VPKPFSRKDSREGTIF-KDPDYLEFLKVI 129 (527)
Q Consensus 75 d~fdG~vFvDsKGne-~~A~VEfAPYQK--vPk~k~KkD~ReGTIE-qDpeYkaFLEsL 129 (527)
..-+-..|+|.+.+. ....----|+-| .-...++.|..+++|+ .|..+.-|....
T Consensus 149 r~~r~~r~ie~k~~r~~vkk~keke~~Krk~td~~kK~~k~e~~~e~ed~~dk~~~~~~ 207 (376)
T KOG1295|consen 149 REERRRREIEEKENREEVKKDKEKESGKRKDTDKQKKIDKDEPRIEKEDENDKPFEKGK 207 (376)
T ss_pred ccchHHHHHHhccchhhhhhhhhccccccchHHHHHHHhhhcCcccccccccCcccchh
Confidence 777778888888763 222111223322 1111234567899999 777776665543
No 45
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=46.11 E-value=7.3 Score=45.04 Aligned_cols=46 Identities=33% Similarity=0.574 Sum_probs=37.5
Q ss_pred ceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
-.|.||+||.+-||++|+..+ ||+.|..++....-...+||++|.-
T Consensus 228 grlf~RNLpyt~~eed~~~lf-------------------------------a~v~~~~~~~avka~~~~D~k~fqg 273 (725)
T KOG0110|consen 228 GRLFVRNLPYTSTEEDLLKLF-------------------------------AFVTFMFPEHAVKAYSELDGKVFQG 273 (725)
T ss_pred hhhhhccCCccccHHHHHHhh-------------------------------HHHhhhhhHHHHhhhhhcccccccc
Confidence 357899999999999998766 7777888888887778888888753
No 46
>PF00585 Thr_dehydrat_C: C-terminal regulatory domain of Threonine dehydratase; InterPro: IPR001721 Threonine dehydratases including Serine/threonine dehydratase (see IPR001926 from INTERPRO) contain a common C-terminal region that may have a regulatory role. Some members contain two copies of this region [].; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process; PDB: 1TDJ_A 3IAU_A.
Probab=40.00 E-value=69 Score=27.67 Aligned_cols=57 Identities=18% Similarity=0.282 Sum_probs=38.9
Q ss_pred HHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEcc--CcccHHHHHHHhC--CCeeEcCCCCe
Q 009733 22 NDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELK--KPAGVFEFAELLN--GHVFVNEKGAQ 89 (527)
Q Consensus 22 EeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fk--n~Edl~~F~d~fd--G~vFvDsKGne 89 (527)
..|++.|.+.|+ |+-|.|.- .....+++.+-|. +.+++..|.+.++ |+.|.|-.+|+
T Consensus 25 ~~F~~~l~~~~n--ITeF~YR~---------~~~~~a~vlvgi~v~~~~~~~~l~~~L~~~gy~~~dls~ne 85 (91)
T PF00585_consen 25 KRFLDALGPRNN--ITEFHYRY---------SGDDFARVLVGIEVPDAEDLEELIERLKALGYPYEDLSDNE 85 (91)
T ss_dssp HHHHHCCSSSE---EEEEEEE----------TTTSCSEEEEEEE-SSTHHHHHHHHHHTSSS-EEECTTT-H
T ss_pred HHHHHHhCCCce--EEEEEEcC---------CCCCeeeEEEEEEeCCHHHHHHHHHHHHHcCCCeEECCCCH
Confidence 368888887764 88888862 2225788887775 4577788888887 66888887754
No 47
>COG4499 Predicted membrane protein [Function unknown]
Probab=37.62 E-value=8 Score=42.27 Aligned_cols=58 Identities=17% Similarity=0.462 Sum_probs=49.9
Q ss_pred CCC-CCCHHHHHHHhccc----cCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHH
Q 009733 15 LPP-SLSQNDLLALFRDH----FNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAEL 76 (527)
Q Consensus 15 LPP-~LTEEeF~e~L~p~----~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~ 76 (527)
||| -|||+.||..+... +.+++.+-.|+.|+.. .+...++-+-|.+.+.++|.+|++.
T Consensus 134 lpPye~tee~f~~~ykA~~~~~fn~k~~Fe~l~~g~lt----~k~t~f~ksil~a~Tld~l~e~i~e 196 (434)
T COG4499 134 LPPYEMTEERFLKEYKALAIYAFNGKFSFESLVNGNLT----LKGTPFEKSILDAETLDDLAEFIDE 196 (434)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHcCCccHHHHhcchhh----hcCCHHHHHHhhhhhHHHHHHHHHH
Confidence 444 69999999988764 3677878889999998 7888899999999999999999998
No 48
>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=36.14 E-value=67 Score=25.84 Aligned_cols=51 Identities=10% Similarity=0.293 Sum_probs=30.3
Q ss_pred EecCCCCCCHHHHHHHhcccc-----CCCceeEEeeCCCCCCccCCCCCcceeEEEEccCc
Q 009733 12 IRHLPPSLSQNDLLALFRDHF-----NDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKP 67 (527)
Q Consensus 12 IRrLPP~LTEEeF~e~L~p~~-----~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~ 67 (527)
|..|-|+||.++....|++.. ... .|.|...=... .......+..|.|.+.
T Consensus 9 ~~~i~~GmTk~qV~~lLG~P~~~~~~~~~-~W~Y~~~~~~~----~~~~~~~~l~V~Fd~~ 64 (71)
T PF04355_consen 9 LAQIKPGMTKDQVRALLGSPSLRDPFDPN-RWYYVYSKRRG----NGANEQRQLKVYFDDD 64 (71)
T ss_dssp HTTT-TTSBHHHHHHHHTS-SEE-CTTSS-EEEEEEEETTC----SSSSCEEEEEEEECTT
T ss_pred HHhhcCCCCHHHHHHhcCCCCccccccCC-EEEEEEEEecC----CCccEEEEEEEEEcCC
Confidence 457889999999999998643 222 45433211111 2234577888888764
No 49
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]
Probab=35.77 E-value=74 Score=32.36 Aligned_cols=71 Identities=20% Similarity=0.311 Sum_probs=49.7
Q ss_pred ceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcC
Q 009733 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 85 (527)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDs 85 (527)
.=+.|++||-++-|.+.+.-+.+. .+.+..+.--.-+- --+.---|||-|.++|...--++.+++|.|..-
T Consensus 50 g~~~~~~~p~g~~e~~~~~~~~q~-~g~v~r~rlsRnkr------TGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~ 120 (214)
T KOG4208|consen 50 GVVYVDHIPHGFFETEILNYFRQF-GGTVTRFRLSRNKR------TGNSKGYAFVEFESEEVAKIAAETMNNYLLMEH 120 (214)
T ss_pred cceeecccccchhHHHHhhhhhhc-CCeeEEEEeecccc------cCCcCceEEEEeccHHHHHHHHHHhhhhhhhhh
Confidence 346788999999998887776654 35555444422111 112233599999999999999999999998643
No 50
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=34.99 E-value=47 Score=37.09 Aligned_cols=82 Identities=18% Similarity=0.292 Sum_probs=63.7
Q ss_pred CceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCccee--EEEEccCcccHHHHHHHhCCCeeEc
Q 009733 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSR--AYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SR--AYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
..||-|+-|+-.-||.|..+.+..+ |.|...|-..|.+. -|| |++.|.+.|....-++.++|.-=+
T Consensus 124 e~KLFvg~lsK~~te~evr~iFs~f--G~Ied~~ilrd~~~---------~sRGcaFV~fstke~A~~Aika~ng~~tm- 191 (510)
T KOG0144|consen 124 ERKLFVGMLSKQCTENEVREIFSRF--GHIEDCYILRDPDG---------LSRGCAFVKFSTKEMAVAAIKALNGTQTM- 191 (510)
T ss_pred chhhhhhhccccccHHHHHHHHHhh--Cccchhhheecccc---------cccceeEEEEehHHHHHHHHHhhccceee-
Confidence 4699999999999999999999875 34555555555443 555 889999999999999999986422
Q ss_pred CCCCeeeeEEEeccCCC
Q 009733 85 EKGAQFKAIVEYAPSQR 101 (527)
Q Consensus 85 sKGne~~A~VEfAPYQK 101 (527)
+|-..+-+|.||-=||
T Consensus 192 -eGcs~PLVVkFADtqk 207 (510)
T KOG0144|consen 192 -EGCSQPLVVKFADTQK 207 (510)
T ss_pred -ccCCCceEEEecccCC
Confidence 5666788999997554
No 51
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=34.53 E-value=97 Score=34.81 Aligned_cols=74 Identities=19% Similarity=0.262 Sum_probs=57.7
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeE
Q 009733 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 83 (527)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFv 83 (527)
+.+.+=|.|=-.|..||--+|+.-+++... .|..+.+|.- .-++.|+ +-|.|++.+++..|.+.|+|..|-
T Consensus 71 ~~~~~mLcilaVP~~mt~~Dll~F~~~~~~-~I~~irivRd-------~~pnrym-vLIkFr~q~da~~Fy~efNGk~Fn 141 (493)
T KOG0804|consen 71 ASSSTMLCILAVPAYMTSHDLLRFCASFIK-QISDIRIVRD-------GMPNRYM-VLIKFRDQADADTFYEEFNGKQFN 141 (493)
T ss_pred CCCCcEEEEEeccccccHHHHHHHHHHHhh-hhheeEEeec-------CCCceEE-EEEEeccchhHHHHHHHcCCCcCC
Confidence 344667888889999999999999986543 4777788761 2244454 679999999999999999999996
Q ss_pred cCC
Q 009733 84 NEK 86 (527)
Q Consensus 84 DsK 86 (527)
+-.
T Consensus 142 ~le 144 (493)
T KOG0804|consen 142 SLE 144 (493)
T ss_pred CCC
Confidence 543
No 52
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=33.07 E-value=1.5e+02 Score=32.35 Aligned_cols=84 Identities=21% Similarity=0.150 Sum_probs=59.0
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccc-------CCCceeEEee--CCCCCCccCCCCCcceeEEEEccCcccHHHHH
Q 009733 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHF-------NDRYNWFCFR--PGKSSFFYSYKHQRYSRAYVELKKPAGVFEFA 74 (527)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~e~L~p~~-------~gkvdw~yFV--pGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~ 74 (527)
+..++.|-|-.||+.+|-+||.+.+.-.. .++.-..-|+ +|++.- =|-|.|-..|.|.--.
T Consensus 131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKG----------DaLc~y~K~ESVeLA~ 200 (382)
T KOG1548|consen 131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKG----------DALCCYIKRESVELAI 200 (382)
T ss_pred cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccC----------ceEEEeecccHHHHHH
Confidence 56778999999999999999999885432 2333334454 566541 1334444567777778
Q ss_pred HHhCCCeeEcCCCCeeeeEEEeccCCCC
Q 009733 75 ELLNGHVFVNEKGAQFKAIVEYAPSQRV 102 (527)
Q Consensus 75 d~fdG~vFvDsKGne~~A~VEfAPYQKv 102 (527)
..+|+..|. | ....||.|-||..
T Consensus 201 ~ilDe~~~r---g--~~~rVerAkfq~K 223 (382)
T KOG1548|consen 201 KILDEDELR---G--KKLRVERAKFQMK 223 (382)
T ss_pred HHhCccccc---C--cEEEEehhhhhhc
Confidence 889999887 2 3568999999974
No 53
>smart00361 RRM_1 RNA recognition motif.
Probab=29.64 E-value=52 Score=26.24 Aligned_cols=27 Identities=19% Similarity=0.317 Sum_probs=24.1
Q ss_pred eeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 58 SRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 58 SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
..+||.|.+.++.......++|..|..
T Consensus 38 G~~fV~f~~~~dA~~A~~~l~g~~~~g 64 (70)
T smart00361 38 GNVYITFERSEDAARAIVDLNGRYFDG 64 (70)
T ss_pred EEEEEEECCHHHHHHHHHHhCCCEECC
Confidence 569999999999999999999987743
No 54
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=27.18 E-value=1.2e+02 Score=35.80 Aligned_cols=81 Identities=17% Similarity=0.187 Sum_probs=58.7
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEc
Q 009733 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 84 (527)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvD 84 (527)
...+.++|++||..-..++|-+.+..+. .|.-.-+ |+.---||+.|.++.+..+-...+...-|.+
T Consensus 383 rs~~vil~kNlpa~t~~~elt~~F~~fG--~i~rvll------------p~~G~~aiv~fl~p~eAr~Afrklaysr~k~ 448 (725)
T KOG0110|consen 383 RSDTVILVKNLPAGTLSEELTEAFLRFG--EIGRVLL------------PPGGTGAIVEFLNPLEARKAFRKLAYSRFKS 448 (725)
T ss_pred hhcceeeeccCccccccHHHHHHhhccc--ccceeec------------CcccceeeeeecCccchHHHHHHhchhhhcc
Confidence 4567899999999999999998887753 2222122 2223458999999988887777787777766
Q ss_pred CCCCeeeeEEEeccCCCCCC
Q 009733 85 EKGAQFKAIVEYAPSQRVPK 104 (527)
Q Consensus 85 sKGne~~A~VEfAPYQKvPk 104 (527)
. +.-+|.||+..++.
T Consensus 449 ~-----plyle~aP~dvf~~ 463 (725)
T KOG0110|consen 449 A-----PLYLEWAPEDVFTE 463 (725)
T ss_pred C-----ccccccChhhhccC
Confidence 6 34578888887763
No 55
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=25.16 E-value=1e+02 Score=26.07 Aligned_cols=63 Identities=19% Similarity=0.199 Sum_probs=38.1
Q ss_pred EEEecCCCCCCHHHHHHHhcccc----C-CCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCe
Q 009733 10 VVIRHLPPSLSQNDLLALFRDHF----N-DRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHV 81 (527)
Q Consensus 10 VVIRrLPP~LTEEeF~e~L~p~~----~-gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~v 81 (527)
+|.|.||..||.+++.+.-.... . ..|.|..+.-.. ...-.-|-..=.|.|.|.+-.+.- |..
T Consensus 3 mver~~p~~it~e~l~~~~~~~~~~~~~~~~V~w~~s~v~~--------d~~k~~Cly~Ap~~eaV~~~~~~a-G~p 70 (77)
T PF14026_consen 3 MVERDFPGGITAEDLAAAHAKSCAVQAEMPGVQWLRSYVSE--------DDGKIFCLYEAPDEEAVREHARRA-GLP 70 (77)
T ss_pred EEEEeCCCCCCHHHHHHHHHHhHHHHhhcCCeEEEEEEEec--------CCCeEEEEEECCCHHHHHHHHHHc-CCC
Confidence 68999999999999877653322 1 257777443110 111122334446888888877765 443
No 56
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=23.44 E-value=1.1e+02 Score=34.47 Aligned_cols=60 Identities=23% Similarity=0.365 Sum_probs=44.4
Q ss_pred CceE-EEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCee
Q 009733 7 RTKV-VIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF 82 (527)
Q Consensus 7 r~KV-VIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vF 82 (527)
.+|| -||+||-+.|||.+.+.+... +.|+- -+.+. --|+|||.+-++...-++..+|+..
T Consensus 258 ~VKvLYVRNL~~~tTeE~lk~~F~~~--G~veR-------------Vkk~r-DYaFVHf~eR~davkAm~~~ngkel 318 (506)
T KOG0117|consen 258 KVKVLYVRNLMESTTEETLKKLFNEF--GKVER-------------VKKPR-DYAFVHFAEREDAVKAMKETNGKEL 318 (506)
T ss_pred heeeeeeeccchhhhHHHHHHHHHhc--cceEE-------------eeccc-ceeEEeecchHHHHHHHHHhcCcee
Confidence 4454 599999999999998887764 33321 11111 1689999999999999999999864
No 57
>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]
Probab=23.05 E-value=1.9e+02 Score=32.16 Aligned_cols=78 Identities=18% Similarity=0.229 Sum_probs=52.3
Q ss_pred ceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcCCC
Q 009733 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKG 87 (527)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDsKG 87 (527)
.-|.-=+-|+.||||+|+.++...-...+...-| ++ |..+.|---|.|.+.++..+-...++-+......|
T Consensus 407 ~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvF-p~--------kserSssGllEfe~~s~Aveal~~~NH~pi~~p~g 477 (494)
T KOG1456|consen 407 NVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVF-PL--------KSERSSSGLLEFENKSDAVEALMKLNHYPIEGPNG 477 (494)
T ss_pred ceeEEecCCCccCHHHHHHHhhhcCCCcceEEee-cc--------cccccccceeeeehHHHHHHHHHHhccccccCCCC
Confidence 3455678899999999999987653222323233 43 34445667899999999999988888666554444
Q ss_pred CeeeeEEE
Q 009733 88 AQFKAIVE 95 (527)
Q Consensus 88 ne~~A~VE 95 (527)
.++-+|.
T Consensus 478 -s~PfilK 484 (494)
T KOG1456|consen 478 -SFPFILK 484 (494)
T ss_pred -CCCeeee
Confidence 5554443
No 58
>COG4453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.16 E-value=62 Score=29.11 Aligned_cols=24 Identities=25% Similarity=0.574 Sum_probs=19.4
Q ss_pred cCCHHHHHHHHHHcCCCCCCCcHH
Q 009733 117 FKDPDYLEFLKVIAKPAENLPSAE 140 (527)
Q Consensus 117 EqDpeYkaFLEsL~~P~e~~pSaE 140 (527)
-.+.+|..||+.|.+|.++.|..+
T Consensus 60 L~e~~~~~fl~~LD~P~~pn~~L~ 83 (95)
T COG4453 60 LDEEDYRRFLAALDNPPSPNPKLK 83 (95)
T ss_pred CCHHHHHHHHHHhcCCCCCCHHHH
Confidence 368999999999999987655443
No 59
>PF02426 MIase: Muconolactone delta-isomerase; InterPro: IPR003464 This small enzyme forms a homodecameric complex, that catalyses the third step in the catabolism of catechol to succinate- and acetyl-coa in the beta-ketoadipate pathway (5.3.3.4 from EC). The protein has a ferredoxin-like fold according to SCOP.; GO: 0006725 cellular aromatic compound metabolic process
Probab=21.51 E-value=2.5e+02 Score=24.96 Aligned_cols=60 Identities=10% Similarity=0.226 Sum_probs=37.6
Q ss_pred cCCCCCCHHHHHHHhcccc--------CCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeE
Q 009733 14 HLPPSLSQNDLLALFRDHF--------NDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 83 (527)
Q Consensus 14 rLPP~LTEEeF~e~L~p~~--------~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFv 83 (527)
++|+.|+.++|.+...... .|++--++-++|.+. .-+-+...+.+.|.+....+-=+.|.
T Consensus 10 ~~P~~~~~~~~~~~~a~E~~~a~eLq~~G~~~~lWr~~G~~~----------n~~Ifdv~d~~eLh~lL~sLPL~p~m 77 (91)
T PF02426_consen 10 NVPPDMPPEEVDRLKAREKARAQELQRQGKWRHLWRVVGRYA----------NVSIFDVEDNDELHELLSSLPLFPYM 77 (91)
T ss_pred eCCCCCCHHHHHHHHHHHHHHHHHHHHCCeeeEEEEecCCcc----------eEEEEECCCHHHHHHHHHhCCCccce
Confidence 5799999999988775543 477666666788765 11334445556666555554444443
No 60
>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=20.32 E-value=1.7e+02 Score=26.29 Aligned_cols=73 Identities=14% Similarity=0.160 Sum_probs=40.8
Q ss_pred eEEEecCCCCCCHHHHHH---HhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCCCeeEcC
Q 009733 9 KVVIRHLPPSLSQNDLLA---LFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 85 (527)
Q Consensus 9 KVVIRrLPP~LTEEeF~e---~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG~vFvDs 85 (527)
=|+|.+||-+-.-...-. +|.....|+|-. | .-.+|+|.|.+.|....-..+++|-. -
T Consensus 4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~---v-------------~~~tAilrF~~~~~A~RA~KRmegEd---V 64 (90)
T PF11608_consen 4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLS---V-------------SGGTAILRFPNQEFAERAQKRMEGED---V 64 (90)
T ss_dssp EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------------TT-EEEEESSHHHHHHHHHHHTT-----S
T ss_pred EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEE---E-------------eCCEEEEEeCCHHHHHHHHHhhcccc---c
Confidence 478999999998877754 444444555421 1 14689999999999999999998752 2
Q ss_pred CCCeeeeEEEeccCCCC
Q 009733 86 KGAQFKAIVEYAPSQRV 102 (527)
Q Consensus 86 KGne~~A~VEfAPYQKv 102 (527)
-|+ .-.|-|.|-++.
T Consensus 65 fG~--kI~v~~~~~~r~ 79 (90)
T PF11608_consen 65 FGN--KISVSFSPKNRE 79 (90)
T ss_dssp SSS----EEESS--S--
T ss_pred ccc--eEEEEEcCCccc
Confidence 232 245667766553
No 61
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=20.02 E-value=2.4e+02 Score=29.06 Aligned_cols=65 Identities=20% Similarity=0.190 Sum_probs=50.0
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccccCCCceeEEeeCCCCCCccCCCCCcceeEEEEccCcccHHHHHHHhCC
Q 009733 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSFFYSYKHQRYSRAYVELKKPAGVFEFAELLNG 79 (527)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~e~L~p~~~gkvdw~yFVpGK~S~k~p~K~~~~SRAYI~Fkn~Edl~~F~d~fdG 79 (527)
-.+||.|=+||.+.+++++.+.+...-. ..-|..+|- .--..+.-|=|.|+..+|+...++.|+|
T Consensus 82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~-----~~r~~vhy~----~~G~s~Gta~v~~~r~~DA~~avk~~~g 146 (243)
T KOG0533|consen 82 RSTKVNVSNLPYGVIDADLKELFAEFGE-----LKRVAVHYD----RAGRSLGTADVSFNRRDDAERAVKKYNG 146 (243)
T ss_pred CcceeeeecCCcCcchHHHHHHHHHhcc-----ceEEeeccC----CCCCCCccceeeecchHhHHHHHHHhcC
Confidence 3489999999999999999998876521 112234444 2234468899999999999999999999
Done!