Query 010224
Match_columns 514
No_of_seqs 156 out of 229
Neff 3.7
Searched_HMMs 46136
Date Thu Mar 28 22:30:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010224.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010224hhsearch_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 7.2E-51 1.6E-55 380.3 7.6 170 1-170 1-176 (176)
2 KOG1295 Nonsense-mediated deca 99.9 8.4E-28 1.8E-32 246.5 6.7 139 1-166 1-139 (376)
3 PF04059 RRM_2: RNA recognitio 98.0 3.5E-05 7.6E-10 67.4 8.7 87 7-96 1-87 (97)
4 PF00076 RRM_1: RNA recognitio 97.6 0.00023 4.9E-09 54.2 6.9 66 10-80 1-66 (70)
5 cd00590 RRM RRM (RNA recogniti 97.5 0.00056 1.2E-08 50.8 7.9 67 9-80 1-67 (74)
6 PF14259 RRM_6: RNA recognitio 97.4 0.001 2.3E-08 51.7 8.1 65 10-79 1-65 (70)
7 smart00362 RRM_2 RNA recogniti 97.3 0.0018 3.9E-08 47.8 7.8 65 9-79 1-65 (72)
8 PLN03134 glycine-rich RNA-bind 96.3 0.026 5.7E-07 51.8 9.2 80 5-93 32-111 (144)
9 smart00360 RRM RNA recognition 96.2 0.023 4.9E-07 41.6 6.6 64 12-79 1-64 (71)
10 TIGR01642 U2AF_lg U2 snRNP aux 96.2 0.056 1.2E-06 57.1 12.0 85 6-99 294-378 (509)
11 TIGR01659 sex-lethal sex-letha 95.9 0.034 7.4E-07 58.1 8.7 82 3-93 103-184 (346)
12 TIGR01661 ELAV_HUD_SF ELAV/HuD 95.8 0.054 1.2E-06 54.3 9.5 79 6-93 2-80 (352)
13 TIGR01659 sex-lethal sex-letha 95.0 0.14 3.1E-06 53.5 9.9 82 6-94 192-273 (346)
14 TIGR01622 SF-CC1 splicing fact 94.9 0.14 3E-06 53.5 9.4 79 7-94 186-264 (457)
15 TIGR01661 ELAV_HUD_SF ELAV/HuD 94.6 0.18 3.8E-06 50.7 8.9 79 7-94 269-347 (352)
16 TIGR01628 PABP-1234 polyadenyl 94.2 0.15 3.4E-06 55.1 8.2 67 9-79 2-68 (562)
17 TIGR01649 hnRNP-L_PTB hnRNP-L/ 93.2 0.53 1.1E-05 50.7 9.9 84 6-93 393-477 (481)
18 TIGR01648 hnRNP-R-Q heterogene 93.1 0.38 8.3E-06 53.9 9.0 72 8-94 234-305 (578)
19 COG0724 RNA-binding proteins ( 93.1 0.52 1.1E-05 42.5 8.2 72 7-82 115-186 (306)
20 PLN03120 nucleic acid binding 92.3 0.57 1.2E-05 48.0 8.2 75 7-94 4-78 (260)
21 TIGR01622 SF-CC1 splicing fact 91.5 0.85 1.8E-05 47.8 8.8 71 5-80 87-157 (457)
22 TIGR01628 PABP-1234 polyadenyl 91.5 0.7 1.5E-05 50.2 8.4 71 6-81 177-247 (562)
23 TIGR01648 hnRNP-R-Q heterogene 91.3 0.78 1.7E-05 51.5 8.6 73 4-81 55-127 (578)
24 TIGR01649 hnRNP-L_PTB hnRNP-L/ 88.9 3.2 6.9E-05 44.8 10.6 79 6-98 274-353 (481)
25 TIGR01645 half-pint poly-U bin 88.5 1.8 3.9E-05 49.0 8.7 73 5-81 105-177 (612)
26 PLN03121 nucleic acid binding 88.5 2.1 4.7E-05 43.6 8.4 69 6-82 4-72 (243)
27 KOG0107 Alternative splicing f 87.4 3 6.4E-05 41.2 8.3 77 5-95 8-84 (195)
28 TIGR01642 U2AF_lg U2 snRNP aux 86.6 2.2 4.7E-05 45.3 7.6 65 7-80 175-249 (509)
29 TIGR01645 half-pint poly-U bin 85.6 3.1 6.8E-05 47.2 8.5 79 7-94 204-282 (612)
30 PF07576 BRAP2: BRCA1-associat 82.7 7.2 0.00016 35.2 7.9 87 5-95 10-100 (110)
31 PF08777 RRM_3: RNA binding mo 78.1 6.3 0.00014 34.9 6.0 59 8-76 2-60 (105)
32 KOG4660 Protein Mei2, essentia 76.5 3.5 7.5E-05 46.2 4.8 90 6-98 360-475 (549)
33 KOG0122 Translation initiation 74.9 18 0.00039 37.5 8.9 77 8-93 190-266 (270)
34 KOG0114 Predicted RNA-binding 72.2 9.1 0.0002 35.3 5.5 70 4-80 15-84 (124)
35 KOG0127 Nucleolar protein fibr 71.4 12 0.00026 42.4 7.3 69 6-79 116-184 (678)
36 PF13893 RRM_5: RNA recognitio 69.9 23 0.0005 26.6 6.6 48 34-93 9-56 (56)
37 KOG4206 Spliceosomal protein s 67.9 15 0.00033 37.2 6.6 70 6-81 8-80 (221)
38 PLN03213 repressor of silencin 66.0 28 0.0006 39.4 8.6 69 4-80 7-77 (759)
39 KOG0108 mRNA cleavage and poly 65.4 19 0.00042 39.5 7.3 68 8-79 19-86 (435)
40 KOG0145 RNA-binding protein EL 60.7 24 0.00051 37.1 6.5 72 6-81 40-111 (360)
41 KOG0127 Nucleolar protein fibr 58.5 25 0.00055 40.0 6.8 65 6-74 291-355 (678)
42 KOG0110 RNA-binding protein (R 56.8 4.5 9.7E-05 46.5 0.7 46 8-80 228-273 (725)
43 KOG4676 Splicing factor, argin 56.1 27 0.00059 38.4 6.3 89 9-100 9-108 (479)
44 KOG0129 Predicted RNA-binding 55.5 23 0.0005 39.8 5.8 64 6-73 258-326 (520)
45 smart00361 RRM_1 RNA recogniti 52.9 56 0.0012 26.0 6.3 27 54-80 38-64 (70)
46 PF04355 SmpA_OmlA: SmpA / Oml 48.9 33 0.0007 27.6 4.4 51 12-63 9-64 (71)
47 KOG0804 Cytoplasmic Zn-finger 42.9 65 0.0014 36.0 6.7 74 4-82 71-144 (493)
48 KOG0144 RNA-binding protein CU 40.5 42 0.00091 37.3 4.8 82 7-97 124-207 (510)
49 KOG4208 Nucleolar RNA-binding 40.3 71 0.0015 32.4 6.0 71 8-81 50-120 (214)
50 KOG0533 RRM motif-containing p 39.6 81 0.0018 32.3 6.5 65 6-75 82-146 (243)
51 PF11608 Limkain-b1: Limkain b 36.8 1.2E+02 0.0025 27.2 6.1 73 9-98 4-79 (90)
52 COG4499 Predicted membrane pro 36.2 8.6 0.00019 41.9 -1.0 68 15-82 134-215 (434)
53 KOG1295 Nonsense-mediated deca 33.9 3 6.4E-05 44.9 -4.8 119 6-124 70-206 (376)
54 KOG0117 Heterogeneous nuclear 32.1 71 0.0015 35.7 5.0 60 7-78 258-318 (506)
55 PF14026 DUF4242: Protein of u 31.4 72 0.0016 26.9 3.9 60 10-77 3-70 (77)
56 KOG1456 Heterogeneous nuclear 30.1 1.4E+02 0.0031 33.0 6.7 79 8-92 407-485 (494)
57 PF02426 MIase: Muconolactone 24.0 2.6E+02 0.0056 24.8 6.1 60 14-79 10-77 (91)
58 KOG1548 Transcription elongati 23.8 2.5E+02 0.0054 30.8 7.1 84 4-98 131-223 (382)
59 KOG4211 Splicing factor hnRNP- 22.6 2.8E+02 0.0061 31.5 7.4 60 6-74 9-70 (510)
60 PF07467 BLIP: Beta-lactamase 21.8 1.2E+02 0.0027 30.1 4.1 45 16-62 116-172 (183)
61 KOG0145 RNA-binding protein EL 21.7 1.8E+02 0.0038 31.0 5.4 81 7-94 127-207 (360)
62 COG4453 Uncharacterized protei 21.2 66 0.0014 28.8 2.0 24 112-135 59-82 (95)
63 KOG4212 RNA-binding protein hn 21.0 1.5E+02 0.0033 33.3 5.0 63 6-78 535-598 (608)
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=7.2e-51 Score=380.26 Aligned_cols=170 Identities=46% Similarity=0.779 Sum_probs=68.8
Q ss_pred CCCCCCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEee--cCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCee
Q 010224 1 MKGPLDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFR--QGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVF 78 (514)
Q Consensus 1 mk~p~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFV--pGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vF 78 (514)
||.+..++|||||||||+|||++||++|++++.+.++|.||. .|+.+.++++||||||+|.+.++|..|.+.|+||+|
T Consensus 1 ~~~~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F 80 (176)
T PF03467_consen 1 MKKEKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVF 80 (176)
T ss_dssp --------EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEE
T ss_pred CCCcccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEE
Confidence 899999999999999999999999999999777677786664 455556889999999999999999999999999999
Q ss_pred EeCCCCeeeeeEEeccCCCCCC-CCCCCCCCCCccCCcHHHHHHHHHhcCCCCCC---CchHHHhhHHHHHHhhhccccc
Q 010224 79 VNEKGVQFKTIVEYAPSQRVPK-QWSKKDGREGTLLKDPEYLEFLEFISKPVENL---PSAEIQLERREAERAGAAKEAL 154 (514)
Q Consensus 79 vDsKGne~~AiVEfAPYQKvPk-~k~KkD~ReGTIEqDpeYlaFLEsL~~P~e~~---pSaE~~le~~Eae~a~~~kek~ 154 (514)
+|++|++++|+|||||||++|. .+.|.|+++||||+||+|++|||+|++|.+.+ +|++..++..|.+.....+..+
T Consensus 81 ~D~kg~~~~~~VE~Apyqk~p~~~k~k~d~r~GTIe~D~~y~~Fle~L~~~~~~~~~~~s~~~~l~k~e~~~~~~~~~~~ 160 (176)
T PF03467_consen 81 VDSKGNEYPAVVEFAPYQKVPKPSKKKKDPREGTIEQDPEYQAFLESLEEPEEKPSQDISAEKSLEKKEKEEKAKEKAEK 160 (176)
T ss_dssp E-TTS-EEEEEEEE-SS---------------------------------------------------------------
T ss_pred ECCCCCCcceeEEEcchhcccccccccccccCCCccCCHHHHHHHHHHhccccccccCcchhhhhhhhhhhhhccccccc
Confidence 9999999999999999999998 56789999999999999999999998776552 2445556554444333334456
Q ss_pred ccChhHHHHHHHHHHh
Q 010224 155 IVTPLMDFVRQKRAAK 170 (514)
Q Consensus 155 ~tTPLLEYLreKKaaK 170 (514)
++||||+||++||++|
T Consensus 161 ~~TpLie~lk~kk~~k 176 (176)
T PF03467_consen 161 VTTPLIEYLKEKKANK 176 (176)
T ss_dssp ----------------
T ss_pred cchHHHHHHHHHhhcC
Confidence 6999999999999986
No 2
>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]
Probab=99.94 E-value=8.4e-28 Score=246.46 Aligned_cols=139 Identities=37% Similarity=0.557 Sum_probs=120.2
Q ss_pred CCCCCCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEe
Q 010224 1 MKGPLDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVN 80 (514)
Q Consensus 1 mk~p~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvD 80 (514)
|+.....+|||||||||.||+++|+++|+|+ +..+.|.+|.+++.+..++.||||||+|++++++.+|.++|+||+|+|
T Consensus 1 ~~~~~~~~Kvv~rrlpp~l~~~~~~eqi~p~-~~~v~~~~F~~a~~s~~~~~ysrayinFk~~~dv~ef~~~f~g~ifld 79 (376)
T KOG1295|consen 1 GKKKEAKVKVVVRRLPPKLTEEQLLEQINPF-PEHVNWEFFAKADESLRNHKYSRAYINFKNPEDVEEFRRRFDGYIFLD 79 (376)
T ss_pred CcccccceeeeeecCCCcccHHHHhhhcCCC-ccccchheeccccccchhhhhhhhhhccccHHHHHHHHhhCCceEEec
Confidence 4556677999999999999999999999995 456899999999999999999999999999999999999999999999
Q ss_pred CCCCeeeeeEEeccCCCCCCCCCCCCCCCCccCCcHHHHHHHHHhcCCCCCCCchHHHhhHHHHHHhhhcccccccChhH
Q 010224 81 EKGVQFKTIVEYAPSQRVPKQWSKKDGREGTLLKDPEYLEFLEFISKPVENLPSAEIQLERREAERAGAAKEALIVTPLM 160 (514)
Q Consensus 81 sKGne~~AiVEfAPYQKvPk~k~KkD~ReGTIEqDpeYlaFLEsL~~P~e~~pSaE~~le~~Eae~a~~~kek~~tTPLL 160 (514)
.+| |||++|++|++||+.++.+.+..+++....+.-+.+.....++..++|||+
T Consensus 80 ~Kg--------------------------gti~d~~~yre~~~~~~~~ke~~~s~~~et~~g~~e~d~~~~~fk~~t~~~ 133 (376)
T KOG1295|consen 80 NKG--------------------------GTIDDDPAYREFLKNYALAKEDKASKLKETLLGEIEGDTKSLAFKKVTPLL 133 (376)
T ss_pred CCC--------------------------CCccccHHHHHHHhhccccccCccccchhhhhchhcccccchhhhccchHH
Confidence 999 999999999999999999998877764443333333323336678899999
Q ss_pred HHHHHH
Q 010224 161 DFVRQK 166 (514)
Q Consensus 161 EYLreK 166 (514)
.||++.
T Consensus 134 ~~~~~~ 139 (376)
T KOG1295|consen 134 SFIKQA 139 (376)
T ss_pred Hhhhhh
Confidence 999986
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=97.98 E-value=3.5e-05 Score=67.42 Aligned_cols=87 Identities=28% Similarity=0.490 Sum_probs=71.1
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCee
Q 010224 7 RTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQF 86 (514)
Q Consensus 7 ~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne~ 86 (514)
++-|.||++|..+|++.+++.|.....+.+|.+ |.|=+...+ .-..-|+|+|.+++++..|.+.|+|+.|..-+ ..-
T Consensus 1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~-YLPiDf~~~-~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~-s~K 77 (97)
T PF04059_consen 1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFF-YLPIDFKNK-CNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFN-SKK 77 (97)
T ss_pred CeeEEEecCCCCCCHHHHHHHHHHhccCcceEE-EeeeeccCC-CceEEEEEEcCCHHHHHHHHHHHcCCccccCC-CCc
Confidence 467999999999999999999999888889874 556665443 34688999999999999999999999996443 335
Q ss_pred eeeEEeccCC
Q 010224 87 KTIVEYAPSQ 96 (514)
Q Consensus 87 ~AiVEfAPYQ 96 (514)
.+.|-||=.|
T Consensus 78 vc~i~yAriQ 87 (97)
T PF04059_consen 78 VCEISYARIQ 87 (97)
T ss_pred EEEEehhHhh
Confidence 7788887665
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=97.61 E-value=0.00023 Score=54.21 Aligned_cols=66 Identities=23% Similarity=0.376 Sum_probs=52.3
Q ss_pred EEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEe
Q 010224 10 VVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVN 80 (514)
Q Consensus 10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvD 80 (514)
|.|.+||+.+|++++.+.+... +.+....+..- ........|||.|.+.+++....+.++|+.|-+
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 6899999999999999999984 33443333332 234456789999999999999999999988754
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=97.53 E-value=0.00056 Score=50.78 Aligned_cols=67 Identities=27% Similarity=0.414 Sum_probs=53.5
Q ss_pred eEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEe
Q 010224 9 KVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVN 80 (514)
Q Consensus 9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvD 80 (514)
.|+|+.||+.++++++++.+... +.+....+..-... .....|||.|.+.+++..+.+.+++..|-+
T Consensus 1 ~i~i~~l~~~~~~~~i~~~~~~~--g~i~~~~~~~~~~~---~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~ 67 (74)
T cd00590 1 TLFVGNLPPDVTEEDLRELFSKF--GKVESVRIVRDKDT---KSKGFAFVEFEDEEDAEKALEALNGKELGG 67 (74)
T ss_pred CEEEeCCCCccCHHHHHHHHHhc--CCEEEEEEeeCCCC---CcceEEEEEECCHHHHHHHHHHhCCCeECC
Confidence 47899999999999999999885 45666555543222 335789999999999999999999998643
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=97.39 E-value=0.001 Score=51.68 Aligned_cols=65 Identities=28% Similarity=0.389 Sum_probs=51.0
Q ss_pred EEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeE
Q 010224 10 VVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFV 79 (514)
Q Consensus 10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFv 79 (514)
|+|++||++.|++++.+.+... +.|....+...+- ......|||.|.+++++..+.+..++..|.
T Consensus 1 v~i~nlp~~~~~~~l~~~f~~~--g~v~~v~~~~~~~---~~~~~~a~v~f~~~~~a~~al~~~~~~~~~ 65 (70)
T PF14259_consen 1 VYISNLPPSTTEEDLRNFFSRF--GPVEKVRLIKNKD---GQSRGFAFVEFSSEEDAKRALELLNGKEID 65 (70)
T ss_dssp EEEESSTTT--HHHHHHHCTTS--SBEEEEEEEESTT---SSEEEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred CEEeCCCCCCCHHHHHHHHHhc--CCcceEEEEeeec---cccCCEEEEEeCCHHHHHHHHHHCCCcEEC
Confidence 6899999999999999999986 3566666665432 244677999999999999999999877773
No 7
>smart00362 RRM_2 RNA recognition motif.
Probab=97.27 E-value=0.0018 Score=47.77 Aligned_cols=65 Identities=26% Similarity=0.383 Sum_probs=51.3
Q ss_pred eEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeE
Q 010224 9 KVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFV 79 (514)
Q Consensus 9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFv 79 (514)
+|+|++||+.++++++.+.+..+ +.+.+..+.... .....-|||.|.+.++.....+.++++.|-
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 48999999999999999999864 345555555443 223467999999999999999999998883
No 8
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=96.30 E-value=0.026 Score=51.84 Aligned_cols=80 Identities=13% Similarity=0.124 Sum_probs=58.9
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCC
Q 010224 5 LDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGV 84 (514)
Q Consensus 5 ~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGn 84 (514)
...+||.|.+||+.+||+++++.+..+ +.|.....+.-..+. ..-.-|||.|.+.+++....+.++++.+.+.
T Consensus 32 ~~~~~lfVgnL~~~~te~~L~~~F~~~--G~I~~v~i~~d~~tg--~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr--- 104 (144)
T PLN03134 32 LMSTKLFIGGLSWGTDDASLRDAFAHF--GDVVDAKVIVDRETG--RSRGFGFVNFNDEGAATAAISEMDGKELNGR--- 104 (144)
T ss_pred CCCCEEEEeCCCCCCCHHHHHHHHhcC--CCeEEEEEEecCCCC--CcceEEEEEECCHHHHHHHHHHcCCCEECCE---
Confidence 356899999999999999999999975 345544443322221 1225699999999999999999999876432
Q ss_pred eeeeeEEec
Q 010224 85 QFKTIVEYA 93 (514)
Q Consensus 85 e~~AiVEfA 93 (514)
...|++|
T Consensus 105 --~l~V~~a 111 (144)
T PLN03134 105 --HIRVNPA 111 (144)
T ss_pred --EEEEEeC
Confidence 4566665
No 9
>smart00360 RRM RNA recognition motif.
Probab=96.17 E-value=0.023 Score=41.56 Aligned_cols=64 Identities=28% Similarity=0.422 Sum_probs=48.1
Q ss_pred EecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeE
Q 010224 12 VRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFV 79 (514)
Q Consensus 12 IRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFv 79 (514)
|++||+.++++++.+.+... +.+....+...... ......|||.|.+.+++..+.+.++++.|.
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 57899999999999988864 34555444433221 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=96.15 E-value=0.056 Score=57.14 Aligned_cols=85 Identities=16% Similarity=0.186 Sum_probs=63.8
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCe
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQ 85 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne 85 (514)
...+|.|.+||+.+|++++.+.+..+ |.|..+.++......+ ...-|||.|.+.+++..-++.++|..|.+.
T Consensus 294 ~~~~l~v~nlp~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~g~--~~g~afv~f~~~~~a~~A~~~l~g~~~~~~---- 365 (509)
T TIGR01642 294 SKDRIYIGNLPLYLGEDQIKELLESF--GDLKAFNLIKDIATGL--SKGYAFCEYKDPSVTDVAIAALNGKDTGDN---- 365 (509)
T ss_pred CCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEecCCCCC--cCeEEEEEECCHHHHHHHHHHcCCCEECCe----
Confidence 45799999999999999999999875 3455555554332211 235699999999999999999999998544
Q ss_pred eeeeEEeccCCCCC
Q 010224 86 FKTIVEYAPSQRVP 99 (514)
Q Consensus 86 ~~AiVEfAPYQKvP 99 (514)
...|++|-+...+
T Consensus 366 -~l~v~~a~~~~~~ 378 (509)
T TIGR01642 366 -KLHVQRACVGANQ 378 (509)
T ss_pred -EEEEEECccCCCC
Confidence 4678888665543
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=95.86 E-value=0.034 Score=58.07 Aligned_cols=82 Identities=21% Similarity=0.215 Sum_probs=59.9
Q ss_pred CCCCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCC
Q 010224 3 GPLDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEK 82 (514)
Q Consensus 3 ~p~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsK 82 (514)
.....++|.|.+||+.+||+++.+.+..+- .|.....+.-..+.+ ...-|||.|.+.+++...++.+++..+.+.
T Consensus 103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G--~V~~v~i~~d~~tg~--srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr- 177 (346)
T TIGR01659 103 TNNSGTNLIVNYLPQDMTDRELYALFRTIG--PINTCRIMRDYKTGY--SFGYAFVDFGSEADSQRAIKNLNGITVRNK- 177 (346)
T ss_pred CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC--CEEEEEEEecCCCCc--cCcEEEEEEccHHHHHHHHHHcCCCccCCc-
Confidence 355789999999999999999999998753 354433332222111 124599999999999999999999888653
Q ss_pred CCeeeeeEEec
Q 010224 83 GVQFKTIVEYA 93 (514)
Q Consensus 83 Gne~~AiVEfA 93 (514)
+..|+||
T Consensus 178 ----~i~V~~a 184 (346)
T TIGR01659 178 ----RLKVSYA 184 (346)
T ss_pred ----eeeeecc
Confidence 4556665
No 12
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=95.79 E-value=0.054 Score=54.28 Aligned_cols=79 Identities=24% Similarity=0.404 Sum_probs=59.4
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCe
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQ 85 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne 85 (514)
+.+.|.|++||+.+||++|.+.+..+ |.|.....+.-+.+. ....-|||.|.+.++...-++.++|..+.+.
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--GEIESCKLVRDKVTG--QSLGYGFVNYVRPEDAEKAVNSLNGLRLQNK---- 73 (352)
T ss_pred CCcEEEEeCCCCCCCHHHHHHHHHcc--CCEEEEEEEEcCCCC--ccceEEEEEECcHHHHHHHHhhcccEEECCe----
Confidence 46889999999999999999999885 345444444333221 1236799999999999999999999876533
Q ss_pred eeeeEEec
Q 010224 86 FKTIVEYA 93 (514)
Q Consensus 86 ~~AiVEfA 93 (514)
...|+||
T Consensus 74 -~i~v~~a 80 (352)
T TIGR01661 74 -TIKVSYA 80 (352)
T ss_pred -eEEEEee
Confidence 5667776
No 13
>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=95.02 E-value=0.14 Score=53.53 Aligned_cols=82 Identities=20% Similarity=0.161 Sum_probs=58.9
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCe
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQ 85 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne 85 (514)
..++|.|.+||+.+||+++.+.+..+- .|.....+.-+..-++ -.-|||.|.+.+++..-++.+++..|.+. .
T Consensus 192 ~~~~lfV~nLp~~vtee~L~~~F~~fG--~V~~v~i~~d~~tg~~--kG~aFV~F~~~e~A~~Ai~~lng~~~~g~---~ 264 (346)
T TIGR01659 192 KDTNLYVTNLPRTITDDQLDTIFGKYG--QIVQKNILRDKLTGTP--RGVAFVRFNKREEAQEAISALNNVIPEGG---S 264 (346)
T ss_pred ccceeEEeCCCCcccHHHHHHHHHhcC--CEEEEEEeecCCCCcc--ceEEEEEECCHHHHHHHHHHhCCCccCCC---c
Confidence 467899999999999999999997652 3443333332222111 25799999999999999999999987542 2
Q ss_pred eeeeEEecc
Q 010224 86 FKTIVEYAP 94 (514)
Q Consensus 86 ~~AiVEfAP 94 (514)
.+..|.+|-
T Consensus 265 ~~l~V~~a~ 273 (346)
T TIGR01659 265 QPLTVRLAE 273 (346)
T ss_pred eeEEEEECC
Confidence 455666654
No 14
>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=94.86 E-value=0.14 Score=53.52 Aligned_cols=79 Identities=23% Similarity=0.277 Sum_probs=58.5
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCee
Q 010224 7 RTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQF 86 (514)
Q Consensus 7 ~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne~ 86 (514)
..+|.|++||+.+||+++.+.+..+ +.|.+..++.-.... ..-.-|||.|.+.+++..-++.++|..+.+ .
T Consensus 186 ~~~l~v~nl~~~~te~~l~~~f~~~--G~i~~v~~~~d~~~g--~~~g~afV~f~~~e~A~~A~~~l~g~~i~g-----~ 256 (457)
T TIGR01622 186 FLKLYVGNLHFNITEQELRQIFEPF--GDIEDVQLHRDPETG--RSKGFGFIQFHDAEEAKEALEVMNGFELAG-----R 256 (457)
T ss_pred CCEEEEcCCCCCCCHHHHHHHHHhc--CCeEEEEEEEcCCCC--ccceEEEEEECCHHHHHHHHHhcCCcEECC-----E
Confidence 4789999999999999999988865 345555444322211 112459999999999999999999977632 3
Q ss_pred eeeEEecc
Q 010224 87 KTIVEYAP 94 (514)
Q Consensus 87 ~AiVEfAP 94 (514)
...|.||-
T Consensus 257 ~i~v~~a~ 264 (457)
T TIGR01622 257 PIKVGYAQ 264 (457)
T ss_pred EEEEEEcc
Confidence 56788765
No 15
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=94.59 E-value=0.18 Score=50.66 Aligned_cols=79 Identities=15% Similarity=0.140 Sum_probs=58.2
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCee
Q 010224 7 RTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQF 86 (514)
Q Consensus 7 ~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne~ 86 (514)
+..|.|++||+..+|+++++.+.+. |.|.....+.-..+. ..-.-|||.|.+.++...-++.++|..|-+ -
T Consensus 269 ~~~lfV~NL~~~~~e~~L~~~F~~f--G~v~~v~i~~d~~t~--~skG~aFV~F~~~~~A~~Ai~~lnG~~~~g-----r 339 (352)
T TIGR01661 269 GYCIFVYNLSPDTDETVLWQLFGPF--GAVQNVKIIRDLTTN--QCKGYGFVSMTNYDEAAMAILSLNGYTLGN-----R 339 (352)
T ss_pred CcEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEeEcCCCC--CccceEEEEECCHHHHHHHHHHhCCCEECC-----e
Confidence 3469999999999999999999975 356665554332221 112458999999999999999999998833 2
Q ss_pred eeeEEecc
Q 010224 87 KTIVEYAP 94 (514)
Q Consensus 87 ~AiVEfAP 94 (514)
.-.|.|+.
T Consensus 340 ~i~V~~~~ 347 (352)
T TIGR01661 340 VLQVSFKT 347 (352)
T ss_pred EEEEEEcc
Confidence 55666654
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=94.22 E-value=0.15 Score=55.11 Aligned_cols=67 Identities=19% Similarity=0.276 Sum_probs=51.7
Q ss_pred eEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeE
Q 010224 9 KVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFV 79 (514)
Q Consensus 9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFv 79 (514)
-|.|.+||+++||+++++.+..+ |.|.....+.-+.+.+ ...-|||.|.+.+++....+.+++..|.
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--GPVLSVRVCRDSVTRR--SLGYGYVNFQNPADAERALETMNFKRLG 68 (562)
T ss_pred eEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCCC--cceEEEEEECCHHHHHHHHHHhCCCEEC
Confidence 37899999999999999999876 3465555544433322 2356999999999999999999988764
No 17
>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=93.15 E-value=0.53 Score=50.72 Aligned_cols=84 Identities=14% Similarity=0.228 Sum_probs=62.9
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCC-
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGV- 84 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGn- 84 (514)
+..+|.|.+||+.+||+++.+.+...-...+....+++.+-. ...-|+|.|.+.++...-...++++.+.+..|.
T Consensus 393 ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~----~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~ 468 (481)
T TIGR01649 393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNE----RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSA 468 (481)
T ss_pred CCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCC----cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCc
Confidence 346799999999999999999998753223555556665532 134699999999999999999999998766544
Q ss_pred eeeeeEEec
Q 010224 85 QFKTIVEYA 93 (514)
Q Consensus 85 e~~AiVEfA 93 (514)
-+...|-||
T Consensus 469 ~~~lkv~fs 477 (481)
T TIGR01649 469 PYHLKVSFS 477 (481)
T ss_pred cceEEEEec
Confidence 245566666
No 18
>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=93.14 E-value=0.38 Score=53.90 Aligned_cols=72 Identities=21% Similarity=0.245 Sum_probs=57.3
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCeee
Q 010224 8 TKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQFK 87 (514)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne~~ 87 (514)
.+|.|++||..+||+++.+.+...-++.|.-...+.| -|||.|.+.+++..-++.+++..|.+ ..
T Consensus 234 k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rg----------fAFVeF~s~e~A~kAi~~lnG~~i~G-----r~ 298 (578)
T TIGR01648 234 KILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD----------YAFVHFEDREDAVKAMDELNGKELEG-----SE 298 (578)
T ss_pred cEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecC----------eEEEEeCCHHHHHHHHHHhCCCEECC-----EE
Confidence 5699999999999999999998763455654433322 59999999999999999999998844 36
Q ss_pred eeEEecc
Q 010224 88 TIVEYAP 94 (514)
Q Consensus 88 AiVEfAP 94 (514)
..|++|.
T Consensus 299 I~V~~Ak 305 (578)
T TIGR01648 299 IEVTLAK 305 (578)
T ss_pred EEEEEcc
Confidence 6788773
No 19
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=93.06 E-value=0.52 Score=42.45 Aligned_cols=72 Identities=19% Similarity=0.252 Sum_probs=54.9
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCC
Q 010224 7 RTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEK 82 (514)
Q Consensus 7 ~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsK 82 (514)
...|.|.+||+.+||+++.+.+..... +.+...+--+ .......-|||.|.+.+++....+.++|..|.+..
T Consensus 115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~--~~~~~~~~d~--~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~ 186 (306)
T COG0724 115 NNTLFVGNLPYDVTEEDLRELFKKFGP--VKRVRLVRDR--ETGKSRGFAFVEFESEESAEKAIEELNGKELEGRP 186 (306)
T ss_pred CceEEEeCCCCCCCHHHHHHHHHhcCc--eeEEEeeecc--ccCccCceEEEEecCHHHHHHHHHHcCCCeECCce
Confidence 589999999999999999999987643 3332222111 12234578999999999999999999998887763
No 20
>PLN03120 nucleic acid binding protein; Provisional
Probab=92.28 E-value=0.57 Score=47.96 Aligned_cols=75 Identities=20% Similarity=0.306 Sum_probs=57.8
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCee
Q 010224 7 RTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQF 86 (514)
Q Consensus 7 ~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne~ 86 (514)
..+|-|.+||+..||+++.+.+..+ |.|.........- .-.-|||.|.+++++.... .++|..|.|.
T Consensus 4 ~rtVfVgNLs~~tTE~dLrefFS~~--G~I~~V~I~~d~~-----~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr----- 70 (260)
T PLN03120 4 VRTVKVSNVSLKATERDIKEFFSFS--GDIEYVEMQSENE-----RSQIAYVTFKDPQGAETAL-LLSGATIVDQ----- 70 (260)
T ss_pred CCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeecCC-----CCCEEEEEeCcHHHHHHHH-HhcCCeeCCc-----
Confidence 4689999999999999999999864 6677766543221 2358999999999998888 4999988765
Q ss_pred eeeEEecc
Q 010224 87 KTIVEYAP 94 (514)
Q Consensus 87 ~AiVEfAP 94 (514)
...|+.+.
T Consensus 71 ~V~Vt~a~ 78 (260)
T PLN03120 71 SVTITPAE 78 (260)
T ss_pred eEEEEecc
Confidence 45666664
No 21
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=91.55 E-value=0.85 Score=47.77 Aligned_cols=71 Identities=21% Similarity=0.303 Sum_probs=52.9
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEe
Q 010224 5 LDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVN 80 (514)
Q Consensus 5 ~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvD 80 (514)
.+...|.|.+||+.+||+++.+.+... +.|.....+.-+.+. ..-.-|||.|.+.+++...+. ++|..|.+
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--GKVRDVQCIKDRNSR--RSKGVAYVEFYDVESVIKALA-LTGQMLLG 157 (457)
T ss_pred cCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEeecCCCC--CcceEEEEEECCHHHHHHHHH-hCCCEECC
Confidence 346689999999999999999988875 356655555433222 123679999999999999886 78877753
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=91.54 E-value=0.7 Score=50.17 Aligned_cols=71 Identities=23% Similarity=0.303 Sum_probs=54.8
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeC
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNE 81 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDs 81 (514)
..+.|.|++||+.+||+++.+.+..+ +.|....+..... ...-..|||.|.+.+++....+.++|..|.+.
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 34679999999999999999999875 3455555544321 12245799999999999999999999988643
No 23
>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=91.29 E-value=0.78 Score=51.53 Aligned_cols=73 Identities=16% Similarity=0.200 Sum_probs=53.8
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeC
Q 010224 4 PLDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNE 81 (514)
Q Consensus 4 p~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDs 81 (514)
|...++|-|-+||+.+||+++.+.+... +.|.-...+.- .+. . .-.-|||.|.+.+++..-++.++++.+.+.
T Consensus 55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~--G~I~~vrl~~D-~sG-~-sRGfaFV~F~~~e~A~~Ai~~lng~~i~~G 127 (578)
T TIGR01648 55 PGRGCEVFVGKIPRDLYEDELVPLFEKA--GPIYELRLMMD-FSG-Q-NRGYAFVTFCGKEEAKEAVKLLNNYEIRPG 127 (578)
T ss_pred CCCCCEEEeCCCCCCCCHHHHHHHHHhh--CCEEEEEEEEC-CCC-C-ccceEEEEeCCHHHHHHHHHHcCCCeecCC
Confidence 4457999999999999999999999875 23433333222 111 1 113499999999999999999999988643
No 24
>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=88.87 E-value=3.2 Score=44.84 Aligned_cols=79 Identities=16% Similarity=0.129 Sum_probs=62.4
Q ss_pred CCceEEEecCCC-CCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCC
Q 010224 6 DRTKVVVRNLPP-AITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGV 84 (514)
Q Consensus 6 ~~~KVVIRrLPP-~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGn 84 (514)
+...|.|.+||+ .+|++++++.+..+ |.|....++..+ ..-|+|.|.+.+++..-++.++|+.|.+
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 69999999999975 456666665432 2569999999999999999999998843
Q ss_pred eeeeeEEeccCCCC
Q 010224 85 QFKTIVEYAPSQRV 98 (514)
Q Consensus 85 e~~AiVEfAPYQKv 98 (514)
....|+++-.+.+
T Consensus 341 -~~l~v~~s~~~~~ 353 (481)
T TIGR01649 341 -KPLRVCPSKQQNV 353 (481)
T ss_pred -ceEEEEEcccccc
Confidence 2566777755554
No 25
>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=88.51 E-value=1.8 Score=49.03 Aligned_cols=73 Identities=15% Similarity=0.211 Sum_probs=54.5
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeC
Q 010224 5 LDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNE 81 (514)
Q Consensus 5 ~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDs 81 (514)
...++|.|.+||+.+||+++.+.+..+ |.|.-...+.-..+.+ ...-|||.|.+.++...-++.++|..|.+.
T Consensus 105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~f--G~I~sV~I~~D~~Tgk--skGfAFVeF~s~e~A~~Ai~~lnG~~i~GR 177 (612)
T TIGR01645 105 AIMCRVYVGSISFELREDTIRRAFDPF--GPIKSINMSWDPATGK--HKGFAFVEYEVPEAAQLALEQMNGQMLGGR 177 (612)
T ss_pred cCCCEEEEcCCCCCCCHHHHHHHHHcc--CCEEEEEEeecCCCCC--cCCeEEEEeCcHHHHHHHHHhcCCeEEecc
Confidence 456899999999999999999999874 3454433332222222 235699999999999999999999887543
No 26
>PLN03121 nucleic acid binding protein; Provisional
Probab=88.47 E-value=2.1 Score=43.56 Aligned_cols=69 Identities=22% Similarity=0.327 Sum_probs=53.2
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCC
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEK 82 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsK 82 (514)
.+.-|.|.+|+|..||+++.+.++. .|+|...+-+.-. ..-.-|||.|++++++ +-+-.++|..|.|..
T Consensus 4 ~g~TV~V~NLS~~tTE~dLrefFS~--~G~I~~V~I~~D~-----et~gfAfVtF~d~~aa-etAllLnGa~l~d~~ 72 (243)
T PLN03121 4 GGYTAEVTNLSPKATEKDVYDFFSH--CGAIEHVEIIRSG-----EYACTAYVTFKDAYAL-ETAVLLSGATIVDQR 72 (243)
T ss_pred CceEEEEecCCCCCCHHHHHHHHHh--cCCeEEEEEecCC-----CcceEEEEEECCHHHH-HHHHhcCCCeeCCce
Confidence 4577899999999999999998885 5677776544321 1124799999999999 445589999998873
No 27
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=87.39 E-value=3 Score=41.18 Aligned_cols=77 Identities=22% Similarity=0.308 Sum_probs=62.3
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCC
Q 010224 5 LDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGV 84 (514)
Q Consensus 5 ~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGn 84 (514)
.-.+||-|=+||+..|+.|+...+..+-+-.-.|..+.| +.-|+|.|.++.|+.+-...+||..|...
T Consensus 8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP---------PGfAFVEFed~RDA~DAvr~LDG~~~cG~--- 75 (195)
T KOG0107|consen 8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP---------PGFAFVEFEDPRDAEDAVRYLDGKDICGS--- 75 (195)
T ss_pred CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC---------CCceEEeccCcccHHHHHhhcCCccccCc---
Confidence 457999999999999999999998876433345766544 34589999999999999999999998875
Q ss_pred eeeeeEEeccC
Q 010224 85 QFKTIVEYAPS 95 (514)
Q Consensus 85 e~~AiVEfAPY 95 (514)
.+.||++-=
T Consensus 76 --r~rVE~S~G 84 (195)
T KOG0107|consen 76 --RIRVELSTG 84 (195)
T ss_pred --eEEEEeecC
Confidence 678887643
No 28
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=86.56 E-value=2.2 Score=45.31 Aligned_cols=65 Identities=17% Similarity=0.307 Sum_probs=46.1
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCc----------ceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCC
Q 010224 7 RTKVVVRNLPPAITQPAFTEQIDGAFGG----------RYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGH 76 (514)
Q Consensus 7 ~~KVVIRrLPP~LTEEeF~eqL~p~~~g----------kvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~ 76 (514)
..+|.|.+||+.+||+++.+.+...+.. .|....+ + +. -.-|||.|.+.+++...+ .++|.
T Consensus 175 ~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~--~----~~--kg~afVeF~~~e~A~~Al-~l~g~ 245 (509)
T TIGR01642 175 ARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI--N----KE--KNFAFLEFRTVEEATFAM-ALDSI 245 (509)
T ss_pred ccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE--C----CC--CCEEEEEeCCHHHHhhhh-cCCCe
Confidence 4589999999999999998888764310 1111111 1 11 235999999999999887 49998
Q ss_pred eeEe
Q 010224 77 VFVN 80 (514)
Q Consensus 77 vFvD 80 (514)
.|.+
T Consensus 246 ~~~g 249 (509)
T TIGR01642 246 IYSN 249 (509)
T ss_pred EeeC
Confidence 8865
No 29
>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=85.61 E-value=3.1 Score=47.22 Aligned_cols=79 Identities=9% Similarity=0.106 Sum_probs=58.7
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCee
Q 010224 7 RTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQF 86 (514)
Q Consensus 7 ~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne~ 86 (514)
..+|.|.+||+.++++++.+.+..+ |.|....++......+ .-.-|||.|.+.+++..-++.++++.|-+ .
T Consensus 204 ~~rLfVgnLp~~vteedLk~lFs~F--G~I~svrl~~D~~tgk--sKGfGFVeFe~~e~A~kAI~amNg~elgG---r-- 274 (612)
T TIGR01645 204 FNRIYVASVHPDLSETDIKSVFEAF--GEIVKCQLARAPTGRG--HKGYGFIEYNNLQSQSEAIASMNLFDLGG---Q-- 274 (612)
T ss_pred cceEEeecCCCCCCHHHHHHHHhhc--CCeeEEEEEecCCCCC--cCCeEEEEECCHHHHHHHHHHhCCCeeCC---e--
Confidence 4689999999999999999999875 4566666655443221 12459999999999999999999996642 2
Q ss_pred eeeEEecc
Q 010224 87 KTIVEYAP 94 (514)
Q Consensus 87 ~AiVEfAP 94 (514)
.-.|.+|.
T Consensus 275 ~LrV~kAi 282 (612)
T TIGR01645 275 YLRVGKCV 282 (612)
T ss_pred EEEEEecC
Confidence 34455554
No 30
>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=82.66 E-value=7.2 Score=35.18 Aligned_cols=87 Identities=23% Similarity=0.343 Sum_probs=60.9
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCC-
Q 010224 5 LDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKG- 83 (514)
Q Consensus 5 ~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKG- 83 (514)
..++.|.|=..||.|+-..|+-.+...+...+..+..+.-. .++.| =+-|.|.+.++..+|...|+|..|--=..
T Consensus 10 ~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~---~pnry-mVLikF~~~~~Ad~Fy~~fNGk~FnslEpE 85 (110)
T PF07576_consen 10 ERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG---TPNRY-MVLIKFRDQESADEFYEEFNGKPFNSLEPE 85 (110)
T ss_pred CCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC---CCceE-EEEEEECCHHHHHHHHHHhCCCccCCCCCc
Confidence 45567777799999999999988887776667665554311 23333 36789999999999999999999943222
Q ss_pred ---CeeeeeEEeccC
Q 010224 84 ---VQFKTIVEYAPS 95 (514)
Q Consensus 84 ---ne~~AiVEfAPY 95 (514)
..|...|||--.
T Consensus 86 ~ChvvfV~~Ve~~~~ 100 (110)
T PF07576_consen 86 TCHVVFVKSVEFTSS 100 (110)
T ss_pred eeEEEEEEEEEEEcc
Confidence 123445665444
No 31
>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=78.06 E-value=6.3 Score=34.86 Aligned_cols=59 Identities=20% Similarity=0.301 Sum_probs=37.8
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCC
Q 010224 8 TKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGH 76 (514)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~ 76 (514)
+=|-|..|++.++-++|.+.|..+- .|.|..|..|.. -|||.|.+++....+.+.+...
T Consensus 2 ~il~~~g~~~~~~re~iK~~f~~~g--~V~yVD~~~G~~--------~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 2 CILKFSGLGEPTSREDIKEAFSQFG--EVAYVDFSRGDT--------EGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp -EEEEEE--SS--HHHHHHHT-SS----EEEEE--TT-S--------EEEEEESS---HHHHHHHHHHT
T ss_pred eEEEEecCCCCcCHHHHHHHHHhcC--CcceEEecCCCC--------EEEEEECCcchHHHHHHHHHhc
Confidence 3466777999999999999999853 799999999976 4899999999988888877654
No 32
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=76.53 E-value=3.5 Score=46.19 Aligned_cols=90 Identities=23% Similarity=0.409 Sum_probs=66.4
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccc--------------------------CCcceeEEEeecCCCCCCCCcceEEEEE
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGA--------------------------FGGRYNWVSFRQGKTSQKHQSCARAYLD 59 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~--------------------------~~gkvdwfyFVpGk~S~Kp~~ySRAYI~ 59 (514)
.++-+-|+.+|-.+++..+..+++-. ..+.||+ -|.|=+...|-+ -.-|.||
T Consensus 360 ~Rtt~~i~ni~n~~~~~dl~~Ildge~~rtt~~iknipNK~T~~ml~~~d~~~~gtYDF-lYLPiDF~nkcN-vGYAFIN 437 (549)
T KOG4660|consen 360 RRTTVMIKNIPNKYGQLDLLRILDGECPRTTLMIKNIPNKYTSKMLLAADEKNKGTYDF-LYLPIDFKNKCN-VGYAFIN 437 (549)
T ss_pred chhhhhhhccccchhHHHHHHHHhCcCchhhhHhhccCchhhHHhhhhhhccccCccce-EEeccccccccc-cceeEEe
Confidence 45556677777777777776666542 1334554 556766665443 3669999
Q ss_pred cCChhhHHHHHHHhCCCeeEeCCCCeeeeeEEeccCCCC
Q 010224 60 FKKPEDVLEFAEFFNGHVFVNEKGVQFKTIVEYAPSQRV 98 (514)
Q Consensus 60 Fkn~Edl~~F~~~fdG~vFvDsKGne~~AiVEfAPYQKv 98 (514)
|.+++++..|.+.|+|..|..=. .+..|.+-||-+|..
T Consensus 438 m~sp~ai~~F~kAFnGk~W~~Fn-S~Kia~itYArIQGk 475 (549)
T KOG4660|consen 438 MTSPEAIIRFYKAFNGKKWEKFN-SEKIASITYARIQGK 475 (549)
T ss_pred ecCHHHHHHHHHHHcCCchhhhc-ceeeeeeehhhhhch
Confidence 99999999999999999997665 778999999999875
No 33
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=74.93 E-value=18 Score=37.48 Aligned_cols=77 Identities=19% Similarity=0.194 Sum_probs=57.2
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCeee
Q 010224 8 TKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQFK 87 (514)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne~~ 87 (514)
.-|=|=+||-.|+|+++.+.+.+.-. |.-.|-+.-+.+-. .-.-||++|.+.||....++.++||-+. ..+
T Consensus 190 ~tvRvtNLsed~~E~dL~eLf~~fg~--i~rvylardK~TG~--~kGFAFVtF~sRddA~rAI~~LnG~gyd-----~LI 260 (270)
T KOG0122|consen 190 ATVRVTNLSEDMREDDLEELFRPFGP--ITRVYLARDKETGL--SKGFAFVTFESRDDAARAIADLNGYGYD-----NLI 260 (270)
T ss_pred ceeEEecCccccChhHHHHHhhccCc--cceeEEEEccccCc--ccceEEEEEecHHHHHHHHHHccCcccc-----eEE
Confidence 34778899999999999999988633 44445544443321 2356999999999999999999998653 256
Q ss_pred eeEEec
Q 010224 88 TIVEYA 93 (514)
Q Consensus 88 AiVEfA 93 (514)
..||+|
T Consensus 261 LrvEws 266 (270)
T KOG0122|consen 261 LRVEWS 266 (270)
T ss_pred EEEEec
Confidence 778876
No 34
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=72.18 E-value=9.1 Score=35.32 Aligned_cols=70 Identities=19% Similarity=0.224 Sum_probs=53.4
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEe
Q 010224 4 PLDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVN 80 (514)
Q Consensus 4 p~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvD 80 (514)
|-..--|-||+||-.+|-|+..+.++.+- .|.- -.=|. ...+-..||+.+.+..|...-.+.+.|+-+.+
T Consensus 15 pevnriLyirNLp~~ITseemydlFGkyg--~IrQ--IRiG~---~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ 84 (124)
T KOG0114|consen 15 PEVNRILYIRNLPFKITSEEMYDLFGKYG--TIRQ--IRIGN---TKETRGTAFVVYEDIFDAKKACDHLSGYNVDN 84 (124)
T ss_pred hhhheeEEEecCCccccHHHHHHHhhccc--ceEE--EEecC---ccCcCceEEEEehHhhhHHHHHHHhcccccCC
Confidence 33445678999999999999999998763 2322 22233 34567889999999999999999999997754
No 35
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=71.43 E-value=12 Score=42.44 Aligned_cols=69 Identities=25% Similarity=0.433 Sum_probs=53.8
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeE
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFV 79 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFv 79 (514)
+.-+||||+||-...+..+...++.+ |. -|--++|-+. ..-.+.-|+|.|++..+...-++.|+|+.|-
T Consensus 116 ~k~rLIIRNLPf~~k~~dLk~vFs~~--G~-V~Ei~IP~k~--dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~ 184 (678)
T KOG0127|consen 116 PKWRLIIRNLPFKCKKPDLKNVFSNF--GK-VVEIVIPRKK--DGKLCGFAFVQFKEKKDAEKALEFFNGNKID 184 (678)
T ss_pred ccceEEeecCCcccCcHHHHHHHhhc--ce-EEEEEcccCC--CCCccceEEEEEeeHHHHHHHHHhccCceec
Confidence 47799999999999999887777764 22 2555777322 2345699999999999999999999998763
No 36
>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=69.93 E-value=23 Score=26.59 Aligned_cols=48 Identities=27% Similarity=0.350 Sum_probs=34.9
Q ss_pred cceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCeeeeeEEec
Q 010224 34 GRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQFKTIVEYA 93 (514)
Q Consensus 34 gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne~~AiVEfA 93 (514)
|.|.-..+.+.+ ...|||.|.+.++.....+.++|..|.+ . +-.|+||
T Consensus 9 G~V~~i~~~~~~-------~~~a~V~f~~~~~A~~a~~~l~~~~~~g---~--~l~V~~a 56 (56)
T PF13893_consen 9 GEVKKIKIFKKK-------RGFAFVEFASVEDAQKAIEQLNGRQFNG---R--PLKVSYA 56 (56)
T ss_dssp S-EEEEEEETTS-------TTEEEEEESSHHHHHHHHHHHTTSEETT---E--EEEEEEE
T ss_pred ccEEEEEEEeCC-------CCEEEEEECCHHHHHHHHHHhCCCEECC---c--EEEEEEC
Confidence 345544554444 4789999999999999999999999833 2 4566664
No 37
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=67.88 E-value=15 Score=37.17 Aligned_cols=70 Identities=19% Similarity=0.299 Sum_probs=56.6
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccC---CcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeC
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAF---GGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNE 81 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~---~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDs 81 (514)
+.-.++||+|+-.+..+++..+|-.++ ..-++...|-.++.. .=|.+.|++.+..-.-...++|..|.|.
T Consensus 8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmR------GQA~VvFk~~~~As~A~r~l~gfpFygK 80 (221)
T KOG4206|consen 8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMR------GQAFVVFKETEAASAALRALQGFPFYGK 80 (221)
T ss_pred CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCcc------CceEEEecChhHHHHHHHHhcCCcccCc
Confidence 334999999999999999999888765 223556666555553 4699999999999888889999999986
No 38
>PLN03213 repressor of silencing 3; Provisional
Probab=65.99 E-value=28 Score=39.42 Aligned_cols=69 Identities=19% Similarity=0.289 Sum_probs=56.6
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCCh--hhHHHHHHHhCCCeeEe
Q 010224 4 PLDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKP--EDVLEFAEFFNGHVFVN 80 (514)
Q Consensus 4 p~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~--Edl~~F~~~fdG~vFvD 80 (514)
.....+|-|-.|++..|++++...+..+ |.|.-.+++. -+ . -.-|||.|.+. +.+...+..++|..|..
T Consensus 7 ~~~gMRIYVGNLSydVTEDDLravFSeF--GsVkdVEIpR--ET-G---RGFAFVEMssdddaEeeKAISaLNGAEWKG 77 (759)
T PLN03213 7 GGGGVRLHVGGLGESVGRDDLLKIFSPM--GTVDAVEFVR--TK-G---RSFAYIDFSPSSTNSLTKLFSTYNGCVWKG 77 (759)
T ss_pred CCcceEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEec--cc-C---CceEEEEecCCcHHHHHHHHHHhcCCeecC
Confidence 4467899999999999999999999987 5677767761 11 1 57899999987 67999999999999954
No 39
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=65.38 E-value=19 Score=39.54 Aligned_cols=68 Identities=16% Similarity=0.181 Sum_probs=51.4
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeE
Q 010224 8 TKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFV 79 (514)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFv 79 (514)
+.|.|+++|+.++||++.+.+...- .|-.+.+|--..+-++. .-+|+.|.++++...-.+.++|+.|-
T Consensus 19 ~~v~vgnip~~~se~~l~~~~~~~g--~v~s~~~v~D~~tG~~~--G~~f~~~~~~~~~~~a~~~lNg~~~~ 86 (435)
T KOG0108|consen 19 SSVFVGNIPYEGSEEQLLSIFSGVG--PVLSFRLVYDRETGKPK--GFGFCEFTDEETAERAIRNLNGAEFN 86 (435)
T ss_pred cceEecCCCCcccHHHHHHHHhccC--ccceeeecccccCCCcC--ceeeEecCchhhHHHHHHhcCCcccC
Confidence 7899999999999999999888643 23344444333333333 55888999999999999999999873
No 40
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=60.66 E-value=24 Score=37.14 Aligned_cols=72 Identities=21% Similarity=0.376 Sum_probs=55.6
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeC
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNE 81 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDs 81 (514)
.++-|+|--||-+||+|||...+... +.|+..-.|.-|+.- ....--++++.+++|...-+..++|.-..+.
T Consensus 40 skTNLIvNYLPQ~MTqdE~rSLF~Si--GeiEScKLvRDKitG--qSLGYGFVNYv~p~DAe~AintlNGLrLQ~K 111 (360)
T KOG0145|consen 40 SKTNLIVNYLPQNMTQDELRSLFGSI--GEIESCKLVRDKITG--QSLGYGFVNYVRPKDAEKAINTLNGLRLQNK 111 (360)
T ss_pred ccceeeeeecccccCHHHHHHHhhcc--cceeeeeeeeccccc--cccccceeeecChHHHHHHHhhhcceeeccc
Confidence 46789999999999999999988875 345655566666532 2334457888999999999999999877654
No 41
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=58.54 E-value=25 Score=40.00 Aligned_cols=65 Identities=23% Similarity=0.316 Sum_probs=50.1
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhC
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFN 74 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fd 74 (514)
.+.-|-||+||-.-|||++.+.+... |.|.|..-|--+.+ ...-.+|++.|+++.+....+...+
T Consensus 291 ~~~tVFvRNL~fD~tEEel~~~fskF--G~v~ya~iV~~k~T--~~skGtAFv~Fkt~~~~~~ci~~As 355 (678)
T KOG0127|consen 291 EGKTVFVRNLPFDTTEEELKEHFSKF--GEVKYAIIVKDKDT--GHSKGTAFVKFKTQIAAQNCIEAAS 355 (678)
T ss_pred ccceEEEecCCccccHHHHHHHHHhh--ccceeEEEEeccCC--CCcccceEEEeccHHHHHHHHHhcC
Confidence 34568899999999999999988875 34666555543332 2445899999999999999888873
No 42
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=56.80 E-value=4.5 Score=46.55 Aligned_cols=46 Identities=28% Similarity=0.481 Sum_probs=39.0
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEe
Q 010224 8 TKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVN 80 (514)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvD 80 (514)
-.|.||+||.+-||++|+..+ ||+.|..++....-...+||++|.-
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 357899999999999998776 8888888888888888888888754
No 43
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=56.09 E-value=27 Score=38.37 Aligned_cols=89 Identities=21% Similarity=0.365 Sum_probs=57.1
Q ss_pred eEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcce-EEEEEcCChhhHHHHHHHhCCCeeEeCC-----
Q 010224 9 KVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCA-RAYLDFKKPEDVLEFAEFFNGHVFVNEK----- 82 (514)
Q Consensus 9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~yS-RAYI~Fkn~Edl~~F~~~fdG~vFvDsK----- 82 (514)
-|-|=+|-|+.|.+++...++.+ |+|.-...+|---..+-++-+ .|||.|.+...+ ..++.+-..+|+|.-
T Consensus 9 vIqvanispsat~dqm~tlFg~l--GkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv-~vaQhLtntvfvdraliv~p 85 (479)
T KOG4676|consen 9 VIQVANISPSATKDQMQTLFGNL--GKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSV-TVAQHLTNTVFVDRALIVRP 85 (479)
T ss_pred eeeecccCchhhHHHHHHHHhhc--cccccccccCCCCCccCcceeeeEEEeccCCcce-eHHhhhccceeeeeeEEEEe
Confidence 45678999999999999888854 455544444422222334444 499999986543 455666667777753
Q ss_pred -CCeee----eeEEeccCCCCCC
Q 010224 83 -GVQFK----TIVEYAPSQRVPK 100 (514)
Q Consensus 83 -Gne~~----AiVEfAPYQKvPk 100 (514)
++..+ |.++||+-.-||.
T Consensus 86 ~~~~~~p~r~af~~l~~~navpr 108 (479)
T KOG4676|consen 86 YGDEVIPDRFAFVELADQNAVPR 108 (479)
T ss_pred cCCCCCccHHHHHhcCccccccc
Confidence 33221 6777777766665
No 44
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=55.48 E-value=23 Score=39.75 Aligned_cols=64 Identities=22% Similarity=0.307 Sum_probs=49.0
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCC---CC--cceEEEEEcCChhhHHHHHHHh
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQK---HQ--SCARAYLDFKKPEDVLEFAEFF 73 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~K---p~--~ySRAYI~Fkn~Edl~~F~~~f 73 (514)
--.||.|=-|||.|+|++++..+.....-.||| ||+.-.+ ++ .+.-+||.|.++..|..+....
T Consensus 258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdW----P~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC 326 (520)
T KOG0129|consen 258 YSRKVFVGGLPWDITEAQINASFGQFGSVKVDW----PGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC 326 (520)
T ss_pred cccceeecCCCccccHHHHHhhcccccceEeec----CCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence 346999999999999999999998765556888 5443321 22 3479999999998888877664
No 45
>smart00361 RRM_1 RNA recognition motif.
Probab=52.89 E-value=56 Score=26.01 Aligned_cols=27 Identities=26% Similarity=0.461 Sum_probs=24.3
Q ss_pred eEEEEEcCChhhHHHHHHHhCCCeeEe
Q 010224 54 ARAYLDFKKPEDVLEFAEFFNGHVFVN 80 (514)
Q Consensus 54 SRAYI~Fkn~Edl~~F~~~fdG~vFvD 80 (514)
..+||.|.+.+++......++|..|..
T Consensus 38 G~~fV~f~~~~dA~~A~~~l~g~~~~g 64 (70)
T smart00361 38 GNVYITFERSEDAARAIVDLNGRYFDG 64 (70)
T ss_pred EEEEEEECCHHHHHHHHHHhCCCEECC
Confidence 679999999999999999999987753
No 46
>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=48.93 E-value=33 Score=27.56 Aligned_cols=51 Identities=8% Similarity=0.190 Sum_probs=30.3
Q ss_pred EecCCCCCCHHHHHHHhcccC-----CcceeEEEeecCCCCCCCCcceEEEEEcCCh
Q 010224 12 VRNLPPAITQPAFTEQIDGAF-----GGRYNWVSFRQGKTSQKHQSCARAYLDFKKP 63 (514)
Q Consensus 12 IRrLPP~LTEEeF~eqL~p~~-----~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~ 63 (514)
|..|-|+||.++....|+... ... .|.|...=..........+..|.|.+-
T Consensus 9 ~~~i~~GmTk~qV~~lLG~P~~~~~~~~~-~W~Y~~~~~~~~~~~~~~~l~V~Fd~~ 64 (71)
T PF04355_consen 9 LAQIKPGMTKDQVRALLGSPSLRDPFDPN-RWYYVYSKRRGNGANEQRQLKVYFDDD 64 (71)
T ss_dssp HTTT-TTSBHHHHHHHHTS-SEE-CTTSS-EEEEEEEETTCSSSSCEEEEEEEECTT
T ss_pred HHhhcCCCCHHHHHHhcCCCCccccccCC-EEEEEEEEecCCCccEEEEEEEEEcCC
Confidence 457889999999999999643 222 454322111111224578888888763
No 47
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=42.85 E-value=65 Score=36.02 Aligned_cols=74 Identities=15% Similarity=0.199 Sum_probs=57.6
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCC
Q 010224 4 PLDRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEK 82 (514)
Q Consensus 4 p~~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsK 82 (514)
+.+.+=|.|=-.|..||-.+|+.-+.+... .|..+.+|. -.-|+.|+ +-|.|++.+++..|.+.|+|..|-+-.
T Consensus 71 ~~~~~mLcilaVP~~mt~~Dll~F~~~~~~-~I~~irivR---d~~pnrym-vLIkFr~q~da~~Fy~efNGk~Fn~le 144 (493)
T KOG0804|consen 71 ASSSTMLCILAVPAYMTSHDLLRFCASFIK-QISDIRIVR---DGMPNRYM-VLIKFRDQADADTFYEEFNGKQFNSLE 144 (493)
T ss_pred CCCCcEEEEEeccccccHHHHHHHHHHHhh-hhheeEEee---cCCCceEE-EEEEeccchhHHHHHHHcCCCcCCCCC
Confidence 334667788889999999999999986544 466677877 12345554 679999999999999999999996543
No 48
>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]
Probab=40.46 E-value=42 Score=37.35 Aligned_cols=82 Identities=20% Similarity=0.268 Sum_probs=63.3
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceE--EEEEcCChhhHHHHHHHhCCCeeEeCCCC
Q 010224 7 RTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCAR--AYLDFKKPEDVLEFAEFFNGHVFVNEKGV 84 (514)
Q Consensus 7 ~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySR--AYI~Fkn~Edl~~F~~~fdG~vFvDsKGn 84 (514)
..||-|+-|+-.-||.|..+.+..+ |.|...|-..|... -|| |++.|.+.|....-++.++|.--+ +|.
T Consensus 124 e~KLFvg~lsK~~te~evr~iFs~f--G~Ied~~ilrd~~~-----~sRGcaFV~fstke~A~~Aika~ng~~tm--eGc 194 (510)
T KOG0144|consen 124 ERKLFVGMLSKQCTENEVREIFSRF--GHIEDCYILRDPDG-----LSRGCAFVKFSTKEMAVAAIKALNGTQTM--EGC 194 (510)
T ss_pred chhhhhhhccccccHHHHHHHHHhh--Cccchhhheecccc-----cccceeEEEEehHHHHHHHHHhhccceee--ccC
Confidence 4699999999999999999999976 33555455455443 366 889999999999999999986433 466
Q ss_pred eeeeeEEeccCCC
Q 010224 85 QFKTIVEYAPSQR 97 (514)
Q Consensus 85 e~~AiVEfAPYQK 97 (514)
..+-+|.||==||
T Consensus 195 s~PLVVkFADtqk 207 (510)
T KOG0144|consen 195 SQPLVVKFADTQK 207 (510)
T ss_pred CCceEEEecccCC
Confidence 6788999986544
No 49
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]
Probab=40.33 E-value=71 Score=32.40 Aligned_cols=71 Identities=18% Similarity=0.250 Sum_probs=50.0
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeC
Q 010224 8 TKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNE 81 (514)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDs 81 (514)
.=+.|++||-++-|.+.+.-+... .+.+.-+.--.-+- --+.-.-|||-|.++|...--++.+++|.|..-
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 346788999999988887776654 35554433312111 123345699999999999999999999998643
No 50
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=39.62 E-value=81 Score=32.34 Aligned_cols=65 Identities=22% Similarity=0.227 Sum_probs=52.5
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCC
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNG 75 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG 75 (514)
..+||.|=+||.+.+++++.+.+...-. ..=|..+|-.--..+.-|=|.|...+|+...++.|+|
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-----LKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNG 146 (243)
T ss_pred CcceeeeecCCcCcchHHHHHHHHHhcc-----ceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcC
Confidence 3489999999999999999999887521 1233556654445679999999999999999999999
No 51
>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=36.78 E-value=1.2e+02 Score=27.17 Aligned_cols=73 Identities=25% Similarity=0.342 Sum_probs=42.3
Q ss_pred eEEEecCCCCCCHHHHHH---HhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCe
Q 010224 9 KVVVRNLPPAITQPAFTE---QIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQ 85 (514)
Q Consensus 9 KVVIRrLPP~LTEEeF~e---qL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne 85 (514)
=|+|.+||-+-.-...-. +|+....|+|- .|.| .+|+|.|.+.|....-..+++|- |--|+
T Consensus 4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl---~v~~---------~tAilrF~~~~~A~RA~KRmegE---dVfG~- 67 (90)
T PF11608_consen 4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVL---SVSG---------GTAILRFPNQEFAERAQKRMEGE---DVFGN- 67 (90)
T ss_dssp EEEEES--TTS-HHHHHHHHHHHHHTTT--EE---E--T---------T-EEEEESSHHHHHHHHHHHTT-----SSSS-
T ss_pred EEEEecCCCCCCHHHHHHHHHHHhhccCCEEE---EEeC---------CEEEEEeCCHHHHHHHHHhhccc---ccccc-
Confidence 478999999999887754 44444566653 2232 78999999999999999999875 23344
Q ss_pred eeeeEEeccCCCC
Q 010224 86 FKTIVEYAPSQRV 98 (514)
Q Consensus 86 ~~AiVEfAPYQKv 98 (514)
.-.|-|.|-++.
T Consensus 68 -kI~v~~~~~~r~ 79 (90)
T PF11608_consen 68 -KISVSFSPKNRE 79 (90)
T ss_dssp ---EEESS--S--
T ss_pred -eEEEEEcCCccc
Confidence 456777766654
No 52
>COG4499 Predicted membrane protein [Function unknown]
Probab=36.17 E-value=8.6 Score=41.92 Aligned_cols=68 Identities=26% Similarity=0.502 Sum_probs=55.1
Q ss_pred CCC-CCCHHHHHHHhccc----CCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHH---------hCCCeeEe
Q 010224 15 LPP-AITQPAFTEQIDGA----FGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEF---------FNGHVFVN 80 (514)
Q Consensus 15 LPP-~LTEEeF~eqL~p~----~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~---------fdG~vFvD 80 (514)
||| -|||+.||..+... +.+++-+-.||.|+.+.+-.-++-+-|.+.+.++|.+|++. =..+.||-
T Consensus 134 lpPye~tee~f~~~ykA~~~~~fn~k~~Fe~l~~g~lt~k~t~f~ksil~a~Tld~l~e~i~e~~~kE~e~~~kn~a~Vp 213 (434)
T COG4499 134 LPPYEMTEERFLKEYKALAIYAFNGKFSFESLVNGNLTLKGTPFEKSILDAETLDDLAEFIDEEYQKETEKINKNYAFVP 213 (434)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHcCCccHHHHhcchhhhcCCHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHhcceeecc
Confidence 455 69999999998874 46666666789999998888889999999999999999988 34566665
Q ss_pred CC
Q 010224 81 EK 82 (514)
Q Consensus 81 sK 82 (514)
.+
T Consensus 214 K~ 215 (434)
T COG4499 214 KK 215 (434)
T ss_pred cc
Confidence 54
No 53
>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]
Probab=33.89 E-value=3 Score=44.90 Aligned_cols=119 Identities=11% Similarity=-0.064 Sum_probs=77.2
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccC------C---c--ceeEEEeecCCCCC---CCCcceEEEEEcCChhhHHHHHH
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAF------G---G--RYNWVSFRQGKTSQ---KHQSCARAYLDFKKPEDVLEFAE 71 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~------~---g--kvdwfyFVpGk~S~---Kp~~ySRAYI~Fkn~Edl~~F~~ 71 (514)
.++..+|+.+++++|-+++.+.+..+- + . ...-..+.-|+... +..+++++||.|.....|.....
T Consensus 70 ~~f~g~ifld~Kggti~d~~~yre~~~~~~~~ke~~~s~~~et~~g~~e~d~~~~~fk~~t~~~~~~~~~~~q~irk~~r 149 (376)
T KOG1295|consen 70 RRFDGYIFLDNKGGTIDDDPAYREFLKNYALAKEDKASKLKETLLGEIEGDTKSLAFKKVTPLLSFIKQADKQRIRKLRR 149 (376)
T ss_pred hhCCceEEecCCCCCccccHHHHHHHhhccccccCccccchhhhhchhcccccchhhhccchHHHhhhhhhHHHHHHhhc
Confidence 568899999999999777766654321 1 0 11123677888876 56899999999997778888888
Q ss_pred HhCCCeeEeCCCC-eeeeeEEeccCCC--CCCCCCCCCCCCCccC-CcHHHHHHHHH
Q 010224 72 FFNGHVFVNEKGV-QFKTIVEYAPSQR--VPKQWSKKDGREGTLL-KDPEYLEFLEF 124 (514)
Q Consensus 72 ~fdG~vFvDsKGn-e~~AiVEfAPYQK--vPk~k~KkD~ReGTIE-qDpeYlaFLEs 124 (514)
.-+-..|+|.+.+ ....-----|+.| .-....+.|..+++|+ .|..+.-|...
T Consensus 150 ~~r~~r~ie~k~~r~~vkk~keke~~Krk~td~~kK~~k~e~~~e~ed~~dk~~~~~ 206 (376)
T KOG1295|consen 150 EERRRREIEEKENREEVKKDKEKESGKRKDTDKQKKIDKDEPRIEKEDENDKPFEKG 206 (376)
T ss_pred cchHHHHHHhccchhhhhhhhhccccccchHHHHHHHhhhcCcccccccccCcccch
Confidence 8888899999877 2222212223333 1111123366888998 66666655443
No 54
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=32.06 E-value=71 Score=35.71 Aligned_cols=60 Identities=27% Similarity=0.398 Sum_probs=45.0
Q ss_pred CceE-EEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCee
Q 010224 7 RTKV-VVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVF 78 (514)
Q Consensus 7 ~~KV-VIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vF 78 (514)
.+|| -||+||-+.|||.+.+.+... +.|+-.- |+. --|+|||.+-++++.-++.++|+..
T Consensus 258 ~VKvLYVRNL~~~tTeE~lk~~F~~~--G~veRVk--------k~r--DYaFVHf~eR~davkAm~~~ngkel 318 (506)
T KOG0117|consen 258 KVKVLYVRNLMESTTEETLKKLFNEF--GKVERVK--------KPR--DYAFVHFAEREDAVKAMKETNGKEL 318 (506)
T ss_pred heeeeeeeccchhhhHHHHHHHHHhc--cceEEee--------ccc--ceeEEeecchHHHHHHHHHhcCcee
Confidence 3454 599999999999998887764 3333211 221 2689999999999999999999875
No 55
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=31.43 E-value=72 Score=26.88 Aligned_cols=60 Identities=20% Similarity=0.308 Sum_probs=37.9
Q ss_pred EEEecCCCCCCHHHHHHHhcccC----C-cceeEE-EeecCCCCCCCCcceEEEEEc--CChhhHHHHHHHhCCCe
Q 010224 10 VVVRNLPPAITQPAFTEQIDGAF----G-GRYNWV-SFRQGKTSQKHQSCARAYLDF--KKPEDVLEFAEFFNGHV 77 (514)
Q Consensus 10 VVIRrLPP~LTEEeF~eqL~p~~----~-gkvdwf-yFVpGk~S~Kp~~ySRAYI~F--kn~Edl~~F~~~fdG~v 77 (514)
+|.|.||..||.+++.+.-.... . ..|.|. +||--+- -++|=.| .|.|.|.+-.+.- |..
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 MVERDFPGGITAEDLAAAHAKSCAVQAEMPGVQWLRSYVSEDD-------GKIFCLYEAPDEEAVREHARRA-GLP 70 (77)
T ss_pred EEEEeCCCCCCHHHHHHHHHHhHHHHhhcCCeEEEEEEEecCC-------CeEEEEEECCCHHHHHHHHHHc-CCC
Confidence 68999999999999877654322 1 246675 3333111 1444444 6788888877765 543
No 56
>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]
Probab=30.06 E-value=1.4e+02 Score=32.96 Aligned_cols=79 Identities=15% Similarity=0.117 Sum_probs=53.1
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCeee
Q 010224 8 TKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQFK 87 (514)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne~~ 87 (514)
.-|.-=+-|+.||||+|++++...-..-+.. .-++++ ..+.|---|.|.+.++..+-...++-+......|. ++
T Consensus 407 ~vLHffNaP~~vtEe~l~~i~nek~v~~~sv-kvFp~k----serSssGllEfe~~s~Aveal~~~NH~pi~~p~gs-~P 480 (494)
T KOG1456|consen 407 NVLHFFNAPLGVTEEQLIGICNEKDVPPTSV-KVFPLK----SERSSSGLLEFENKSDAVEALMKLNHYPIEGPNGS-FP 480 (494)
T ss_pred ceeEEecCCCccCHHHHHHHhhhcCCCcceE-Eeeccc----ccccccceeeeehHHHHHHHHHHhccccccCCCCC-CC
Confidence 3455678899999999999988643221222 223554 34456678999999999999999886665555443 55
Q ss_pred eeEEe
Q 010224 88 TIVEY 92 (514)
Q Consensus 88 AiVEf 92 (514)
-+|.+
T Consensus 481 filKl 485 (494)
T KOG1456|consen 481 FILKL 485 (494)
T ss_pred eeeee
Confidence 44443
No 57
>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=24.04 E-value=2.6e+02 Score=24.76 Aligned_cols=60 Identities=12% Similarity=0.236 Sum_probs=40.1
Q ss_pred cCCCCCCHHHHHHHhcccC--------CcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeE
Q 010224 14 NLPPAITQPAFTEQIDGAF--------GGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFV 79 (514)
Q Consensus 14 rLPP~LTEEeF~eqL~p~~--------~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFv 79 (514)
++|+.|+.++|.+...... .|++--++-++|.+.. -+-+...+.+.|.+....+-=+.|.
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 NVPPDMPPEEVDRLKAREKARAQELQRQGKWRHLWRVVGRYAN------VSIFDVEDNDELHELLSSLPLFPYM 77 (91)
T ss_pred eCCCCCCHHHHHHHHHHHHHHHHHHHHCCeeeEEEEecCCcce------EEEEECCCHHHHHHHHHhCCCccce
Confidence 5799999999988876543 5666655667887643 2334445667777766665555554
No 58
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=23.82 E-value=2.5e+02 Score=30.76 Aligned_cols=84 Identities=30% Similarity=0.243 Sum_probs=58.2
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccC-------CcceeEEEee--cCCCCCCCCcceEEEEEcCChhhHHHHHHHhC
Q 010224 4 PLDRTKVVVRNLPPAITQPAFTEQIDGAF-------GGRYNWVSFR--QGKTSQKHQSCARAYLDFKKPEDVLEFAEFFN 74 (514)
Q Consensus 4 p~~~~KVVIRrLPP~LTEEeF~eqL~p~~-------~gkvdwfyFV--pGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fd 74 (514)
|..++.|-|-.||+.+|-+||.+.+.-.. .++.--.-|+ +|++.- =|-|.|-..|.|..-...||
T Consensus 131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKG------DaLc~y~K~ESVeLA~~ilD 204 (382)
T KOG1548|consen 131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKG------DALCCYIKRESVELAIKILD 204 (382)
T ss_pred cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccC------ceEEEeecccHHHHHHHHhC
Confidence 56788999999999999999999887532 1222222343 455532 23334444677777788899
Q ss_pred CCeeEeCCCCeeeeeEEeccCCCC
Q 010224 75 GHVFVNEKGVQFKTIVEYAPSQRV 98 (514)
Q Consensus 75 G~vFvDsKGne~~AiVEfAPYQKv 98 (514)
+..|. | ....||.|-||..
T Consensus 205 e~~~r---g--~~~rVerAkfq~K 223 (382)
T KOG1548|consen 205 EDELR---G--KKLRVERAKFQMK 223 (382)
T ss_pred ccccc---C--cEEEEehhhhhhc
Confidence 99888 3 3678999999874
No 59
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=22.56 E-value=2.8e+02 Score=31.46 Aligned_cols=60 Identities=22% Similarity=0.272 Sum_probs=44.2
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeec--CCCCCCCCcceEEEEEcCChhhHHHHHHHhC
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQ--GKTSQKHQSCARAYLDFKKPEDVLEFAEFFN 74 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVp--Gk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fd 74 (514)
..+-|=+|=||.+-|++++++-++.+- |..+.|.. |+.+ .=|||-|.+.||+..-.++=+
T Consensus 9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~---I~~~~~~r~~Gr~s------GeA~Ve~~seedv~~AlkkdR 70 (510)
T KOG4211|consen 9 TAFEVRLRGLPWSATEKEILDFFSNCG---IENLEIPRRNGRPS------GEAYVEFTSEEDVEKALKKDR 70 (510)
T ss_pred cceEEEecCCCccccHHHHHHHHhcCc---eeEEEEeccCCCcC------cceEEEeechHHHHHHHHhhH
Confidence 345566889999999999999998763 44455532 4443 469999999999987776533
No 60
>PF07467 BLIP: Beta-lactamase inhibitor (BLIP); InterPro: IPR009099 The beta-lactamase-inhibitor protein (BLIP) is produced by Streptomyces species. BLIP acts as a potent inhibitor of beta-lactamases such as TEM-1, which is the most widespread resistance enzyme to penicillin antibiotics. BLIP binds competitively to TEM-1 and makes direct contacts with TEM-1 active site residues. BLIP is able to inhibit a variety of class A beta-lactamases, possibly through flexibility of its two domains. The two tandemly repeated domains of BLIP have an alpha(2)-beta(4) structure, the beta-hairpin loop from domain 1 inserting into the active site of beta-lactamase []. BLIP shows no sequence similarity with BLIP-II, even though both bind to and inhibit TEM-1 [].; PDB: 3GMY_B 3GMX_B 3C4O_B 1XXM_C 1S0W_D 3N4I_B 3C7U_B 2G2W_B 3C7V_D 3E2K_C ....
Probab=21.77 E-value=1.2e+02 Score=30.07 Aligned_cols=45 Identities=16% Similarity=0.245 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHhcccCCcceeEEEeecCCCCC------------CCCcceEEEEEcCC
Q 010224 16 PPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQ------------KHQSCARAYLDFKK 62 (514)
Q Consensus 16 PP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~------------Kp~~ySRAYI~Fkn 62 (514)
--+||++|||..|...-+ .+|..+.|+-.+. -..-+.-||++|.+
T Consensus 116 ~~GMT~aQv~A~v~~~sC--~~~~e~YP~~Ps~~G~~~~~~C~s~~~~~~~~a~f~fTD 172 (183)
T PF07467_consen 116 TTGMTEAQVWAAVGGDSC--TDWWEEYPNYPSTAGWEESYQCTSATGEFYPSAYFHFTD 172 (183)
T ss_dssp -TT-BHHHHHHHS-GGGE--EEEEEE-TTTTS-TT-EEEEEEESSSSSTSSEEEEEEET
T ss_pred hccccHHHHHHHcCCcch--hhhHhhCCCCCCCCCceEEEEecccccccCCceEEEEec
Confidence 347899999999875322 2344444443332 12234568999975
No 61
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=21.73 E-value=1.8e+02 Score=30.98 Aligned_cols=81 Identities=19% Similarity=0.191 Sum_probs=55.2
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCcceeEEEeecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCeeEeCCCCee
Q 010224 7 RTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSFRQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVFVNEKGVQF 86 (514)
Q Consensus 7 ~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vFvDsKGne~ 86 (514)
.--|-|--||-+||+.|+...++++- .|--.+-..-... -..-.-.+|.|...+...+-+..++|.. .-|...
T Consensus 127 ~aNLYvSGlPktMtqkelE~iFs~fG--rIItSRiL~dqvt--g~srGVgFiRFDKr~EAe~AIk~lNG~~---P~g~te 199 (360)
T KOG0145|consen 127 DANLYVSGLPKTMTQKELEQIFSPFG--RIITSRILVDQVT--GLSRGVGFIRFDKRIEAEEAIKGLNGQK---PSGCTE 199 (360)
T ss_pred ccceEEecCCccchHHHHHHHHHHhh--hhhhhhhhhhccc--ceecceeEEEecchhHHHHHHHhccCCC---CCCCCC
Confidence 34567888999999999999988753 1111111110010 1122458999999999999999999986 567767
Q ss_pred eeeEEecc
Q 010224 87 KTIVEYAP 94 (514)
Q Consensus 87 ~AiVEfAP 94 (514)
+-+|.||-
T Consensus 200 pItVKFan 207 (360)
T KOG0145|consen 200 PITVKFAN 207 (360)
T ss_pred CeEEEecC
Confidence 77888874
No 62
>COG4453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.15 E-value=66 Score=28.85 Aligned_cols=24 Identities=25% Similarity=0.551 Sum_probs=19.4
Q ss_pred cCCcHHHHHHHHHhcCCCCCCCch
Q 010224 112 LLKDPEYLEFLEFISKPVENLPSA 135 (514)
Q Consensus 112 IEqDpeYlaFLEsL~~P~e~~pSa 135 (514)
+-.+..|..||+.|.+|.++.|..
T Consensus 59 ~L~e~~~~~fl~~LD~P~~pn~~L 82 (95)
T COG4453 59 ILDEEDYRRFLAALDNPPSPNPKL 82 (95)
T ss_pred hCCHHHHHHHHHHhcCCCCCCHHH
Confidence 357899999999999998765543
No 63
>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]
Probab=20.98 E-value=1.5e+02 Score=33.35 Aligned_cols=63 Identities=22% Similarity=0.451 Sum_probs=45.4
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCcceeEEEe-ecCCCCCCCCcceEEEEEcCChhhHHHHHHHhCCCee
Q 010224 6 DRTKVVVRNLPPAITQPAFTEQIDGAFGGRYNWVSF-RQGKTSQKHQSCARAYLDFKKPEDVLEFAEFFNGHVF 78 (514)
Q Consensus 6 ~~~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyF-VpGk~S~Kp~~ySRAYI~Fkn~Edl~~F~~~fdG~vF 78 (514)
.-+.++||+||-+.|++-+.+-+..+ +.+.|... -+|+ |+--|.|.++++...-...++|...
T Consensus 535 Ka~qIiirNlP~dfTWqmlrDKfre~--G~v~yadime~Gk--------skGVVrF~s~edAEra~a~Mngs~l 598 (608)
T KOG4212|consen 535 KACQIIIRNLPFDFTWQMLRDKFREI--GHVLYADIMENGK--------SKGVVRFFSPEDAERACALMNGSRL 598 (608)
T ss_pred cccEEEEecCCccccHHHHHHHHHhc--cceehhhhhccCC--------ccceEEecCHHHHHHHHHHhccCcc
Confidence 34679999999999999888877754 23332211 1333 4448999999999999888887653
Done!