Query 009879
Match_columns 523
No_of_seqs 154 out of 229
Neff 3.6
Searched_HMMs 46136
Date Thu Mar 28 18:25:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009879.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009879hhsearch_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 1.9E-50 4.2E-55 377.7 7.0 170 1-170 1-176 (176)
2 KOG1295 Nonsense-mediated deca 99.9 8.1E-28 1.7E-32 246.9 7.6 176 1-215 1-176 (376)
3 PF04059 RRM_2: RNA recognitio 98.0 3E-05 6.4E-10 68.0 8.2 87 7-96 1-87 (97)
4 PF00076 RRM_1: RNA recognitio 97.5 0.00031 6.6E-09 53.5 6.1 66 10-80 1-66 (70)
5 cd00590 RRM RRM (RNA recogniti 97.4 0.00079 1.7E-08 50.0 7.5 67 9-80 1-67 (74)
6 PF14259 RRM_6: RNA recognitio 97.2 0.0015 3.3E-08 50.8 7.4 65 10-79 1-65 (70)
7 smart00362 RRM_2 RNA recogniti 97.2 0.0023 5E-08 47.2 7.5 65 9-79 1-65 (72)
8 PLN03134 glycine-rich RNA-bind 96.4 0.017 3.6E-07 53.2 8.3 80 5-93 32-111 (144)
9 TIGR01659 sex-lethal sex-letha 96.0 0.033 7.2E-07 58.2 9.1 82 3-93 103-184 (346)
10 TIGR01642 U2AF_lg U2 snRNP aux 95.9 0.076 1.7E-06 56.2 11.7 85 6-99 294-378 (509)
11 smart00360 RRM RNA recognition 95.8 0.033 7.2E-07 40.7 6.2 64 12-79 1-64 (71)
12 TIGR01661 ELAV_HUD_SF ELAV/HuD 95.5 0.068 1.5E-06 53.6 9.0 79 6-93 2-80 (352)
13 TIGR01659 sex-lethal sex-letha 94.8 0.18 3.9E-06 52.9 9.8 82 6-94 192-273 (346)
14 TIGR01622 SF-CC1 splicing fact 94.6 0.16 3.5E-06 53.1 8.9 79 7-94 186-264 (457)
15 TIGR01661 ELAV_HUD_SF ELAV/HuD 93.9 0.25 5.5E-06 49.5 8.5 78 8-94 270-347 (352)
16 TIGR01628 PABP-1234 polyadenyl 93.6 0.2 4.4E-06 54.3 7.7 67 9-79 2-68 (562)
17 TIGR01648 hnRNP-R-Q heterogene 92.4 0.51 1.1E-05 53.0 8.7 72 8-94 234-305 (578)
18 COG0724 RNA-binding proteins ( 92.2 0.69 1.5E-05 41.7 7.8 72 7-82 115-186 (306)
19 PLN03120 nucleic acid binding 91.9 1.1 2.3E-05 46.1 9.6 75 7-94 4-78 (260)
20 TIGR01649 hnRNP-L_PTB hnRNP-L/ 91.7 0.97 2.1E-05 48.8 9.5 84 6-93 393-477 (481)
21 TIGR01622 SF-CC1 splicing fact 91.0 0.92 2E-05 47.6 8.3 71 5-80 87-157 (457)
22 TIGR01628 PABP-1234 polyadenyl 90.6 0.84 1.8E-05 49.6 7.9 70 7-81 178-247 (562)
23 TIGR01648 hnRNP-R-Q heterogene 90.4 0.9 2E-05 51.1 8.1 71 4-81 55-127 (578)
24 TIGR01645 half-pint poly-U bin 87.0 2.1 4.6E-05 48.6 8.2 73 5-81 105-177 (612)
25 PLN03121 nucleic acid binding 86.9 2.2 4.7E-05 43.6 7.4 69 6-82 4-72 (243)
26 TIGR01649 hnRNP-L_PTB hnRNP-L/ 86.7 4.7 0.0001 43.6 10.3 80 6-99 274-354 (481)
27 KOG0107 Alternative splicing f 85.9 4.4 9.5E-05 40.1 8.6 77 5-95 8-84 (195)
28 TIGR01645 half-pint poly-U bin 85.7 2.6 5.6E-05 47.9 7.9 69 7-79 204-272 (612)
29 TIGR01642 U2AF_lg U2 snRNP aux 85.6 2.3 5.1E-05 45.1 7.2 66 6-80 174-249 (509)
30 PF07576 BRAP2: BRCA1-associat 80.9 7.9 0.00017 35.0 7.6 72 4-79 9-80 (110)
31 KOG4206 Spliceosomal protein s 75.2 8.2 0.00018 39.1 6.6 71 5-81 7-80 (221)
32 KOG4660 Protein Mei2, essentia 74.9 3.6 7.9E-05 46.1 4.4 90 6-98 360-475 (549)
33 KOG0122 Translation initiation 73.3 10 0.00022 39.3 6.8 77 8-93 190-266 (270)
34 PF08777 RRM_3: RNA binding mo 68.5 13 0.00028 32.9 5.6 58 9-76 3-60 (105)
35 KOG0127 Nucleolar protein fibr 67.0 16 0.00034 41.6 7.1 69 5-78 115-183 (678)
36 KOG0114 Predicted RNA-binding 66.3 21 0.00046 33.1 6.6 70 4-80 15-84 (124)
37 PF13893 RRM_5: RNA recognitio 63.7 23 0.00051 26.6 5.5 48 34-93 9-56 (56)
38 KOG0145 RNA-binding protein EL 60.6 19 0.00042 37.8 5.9 72 6-81 40-111 (360)
39 KOG0108 mRNA cleavage and poly 60.6 24 0.00052 38.9 7.0 68 8-79 19-86 (435)
40 PLN03213 repressor of silencin 59.0 42 0.00092 38.1 8.5 69 4-80 7-77 (759)
41 KOG0127 Nucleolar protein fibr 58.4 22 0.00047 40.6 6.2 64 7-74 292-355 (678)
42 KOG0110 RNA-binding protein (R 55.0 4.2 9.2E-05 46.8 0.2 46 8-80 228-273 (725)
43 KOG4676 Splicing factor, argin 53.1 26 0.00056 38.6 5.6 89 9-100 9-108 (479)
44 KOG0129 Predicted RNA-binding 50.9 28 0.00061 39.2 5.6 65 6-74 258-327 (520)
45 smart00361 RRM_1 RNA recogniti 48.3 56 0.0012 26.0 5.6 27 54-80 38-64 (70)
46 PF04355 SmpA_OmlA: SmpA / Oml 47.2 36 0.00078 27.4 4.4 49 12-63 9-64 (71)
47 PF11608 Limkain-b1: Limkain b 38.7 89 0.0019 28.0 5.7 73 9-98 4-79 (90)
48 KOG0804 Cytoplasmic Zn-finger 36.8 86 0.0019 35.2 6.5 74 4-82 71-144 (493)
49 KOG4208 Nucleolar RNA-binding 35.2 82 0.0018 32.0 5.6 71 8-81 50-120 (214)
50 KOG0533 RRM motif-containing p 32.1 1.1E+02 0.0024 31.5 6.0 65 6-75 82-146 (243)
51 KOG1548 Transcription elongati 31.6 1.9E+02 0.0042 31.6 7.9 84 4-98 131-223 (382)
52 COG4499 Predicted membrane pro 31.5 9.5 0.00021 41.7 -1.6 68 15-82 134-215 (434)
53 PF14026 DUF4242: Protein of u 30.8 76 0.0017 26.8 4.0 60 10-77 3-70 (77)
54 KOG0117 Heterogeneous nuclear 29.3 60 0.0013 36.3 3.9 60 7-78 258-318 (506)
55 KOG1456 Heterogeneous nuclear 28.5 1.4E+02 0.0031 33.1 6.4 79 8-92 407-485 (494)
56 KOG4211 Splicing factor hnRNP- 25.8 2.1E+02 0.0046 32.4 7.3 59 7-74 10-70 (510)
57 PF00585 Thr_dehydrat_C: C-ter 25.8 1.7E+02 0.0038 25.2 5.4 57 22-85 25-85 (91)
58 COG4453 Uncharacterized protei 23.0 59 0.0013 29.2 2.0 25 112-136 59-83 (95)
59 PF07467 BLIP: Beta-lactamase 22.4 1.4E+02 0.003 29.9 4.5 45 16-62 116-172 (183)
60 KOG0105 Alternative splicing f 21.0 2.4E+02 0.0051 28.8 5.9 79 7-97 6-84 (241)
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=1.9e-50 Score=377.70 Aligned_cols=170 Identities=44% Similarity=0.798 Sum_probs=68.9
Q ss_pred CCCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEee--CCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009879 1 MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFR--PGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF 78 (523)
Q Consensus 1 mk~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFV--pGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF 78 (523)
||.+..++|||||||||+|||++||++|++++.+.++|.||. .|+.+.++++||||||+|++.++|..|++.|+||+|
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 899999999999999999999999999999777667777664 555556889999999999999999999999999999
Q ss_pred EeCCCCeeeeEEEeccCCCCCC-CCCCCCCCCccccCCHHHHHHHHHHcCCCCCC---CcHHHHhhhHHhhhcCCCCCCc
Q 009879 79 VNEKGAQFKAIVEYAPSQRVPK-PFSRKDSREGTIFKDPDYLEFLKVIAKPAENL---PSAEIQLERKEAELSGAPKETL 154 (523)
Q Consensus 79 vDsKGne~~A~VEfAPYQKvPk-~k~KkD~ReGTIEqDpeYkaFLEsL~~P~e~~---pSaE~~lE~~Eae~a~~~kek~ 154 (523)
+|++|++++|+|||||||++|. .+.|.|+++||||+|++|++|||+|++|.+.+ .+++..++..|.+...+.+..+
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 56789999999999999999999998776543 2344455554444333334455
Q ss_pred ccChhHHHHHHHHHHh
Q 009879 155 VVTPLMEYVRQKRAAE 170 (523)
Q Consensus 155 ~tTPLlEyLReKKAaK 170 (523)
++||||+|||+||++|
T Consensus 161 ~~TpLie~lk~kk~~k 176 (176)
T PF03467_consen 161 VTTPLIEYLKEKKANK 176 (176)
T ss_dssp ----------------
T ss_pred cchHHHHHHHHHhhcC
Confidence 6999999999999885
No 2
>KOG1295 consensus Nonsense-mediated decay protein Upf3 [RNA processing and modification]
Probab=99.94 E-value=8.1e-28 Score=246.89 Aligned_cols=176 Identities=34% Similarity=0.496 Sum_probs=142.7
Q ss_pred CCCCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009879 1 MKEPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 80 (523)
Q Consensus 1 mk~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD 80 (523)
|+.....+|||||||||.||+++|+++|+|. +..+.|.+|.+++.+..++.||||||+|++++++.+|.+.|+||+|+|
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 4455567899999999999999999999995 456999999999999999999999999999999999999999999999
Q ss_pred CCCCeeeeEEEeccCCCCCCCCCCCCCCCccccCCHHHHHHHHHHcCCCCCCCcHHHHhhhHHhhhcCCCCCCcccChhH
Q 009879 81 EKGAQFKAIVEYAPSQRVPKPFSRKDSREGTIFKDPDYLEFLKVIAKPAENLPSAEIQLERKEAELSGAPKETLVVTPLM 160 (523)
Q Consensus 81 sKGne~~A~VEfAPYQKvPk~k~KkD~ReGTIEqDpeYkaFLEsL~~P~e~~pSaE~~lE~~Eae~a~~~kek~~tTPLl 160 (523)
.+| |||++|++|++||+.++-+.+..++.....+..+.+.....++..++|||+
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 999999999999999999988777664443333333333446788899999
Q ss_pred HHHHHHHHHhhhchhhhhhccccccccccccCCCCCcccccCcccceeEeccccc
Q 009879 161 EYVRQKRAAESGAQESLAVGRVGRRSRAASASKTSSTTTKRGSEKKKYILKDSAK 215 (523)
Q Consensus 161 EyLReKKAaK~k~q~~~~~~k~~rr~~~~~~~~~~~~~~kr~~ek~~yv~rd~~k 215 (523)
.||+.. .+|.+..-.+..|+-.-....... .++++|++++++|
T Consensus 134 ~~~~~~-----~~q~irk~~r~~r~~r~ie~k~~r-------~~vkk~keke~~K 176 (376)
T KOG1295|consen 134 SFIKQA-----DKQRIRKLRREERRRREIEEKENR-------EEVKKDKEKESGK 176 (376)
T ss_pred Hhhhhh-----hHHHHHHhhccchHHHHHHhccch-------hhhhhhhhccccc
Confidence 999986 355565656555554444332221 7888999999876
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=3e-05 Score=68.00 Aligned_cols=87 Identities=26% Similarity=0.498 Sum_probs=71.1
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009879 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF 86 (523)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~ 86 (523)
|+-|.||++|..+|.+.+++.|+....+.||++| .|=+... ..-..-|+|+|.+++++..|.+.|+|+.|-.-. ..-
T Consensus 1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~Y-LPiDf~~-~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~-s~K 77 (97)
T PF04059_consen 1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFY-LPIDFKN-KCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFN-SKK 77 (97)
T ss_pred CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEE-eeeeccC-CCceEEEEEEcCCHHHHHHHHHHHcCCccccCC-CCc
Confidence 5679999999999999999999988888999765 4555543 345778999999999999999999999996433 344
Q ss_pred eeEEEeccCC
Q 009879 87 KAIVEYAPSQ 96 (523)
Q Consensus 87 ~A~VEfAPYQ 96 (523)
.+.|-||=.|
T Consensus 78 vc~i~yAriQ 87 (97)
T PF04059_consen 78 VCEISYARIQ 87 (97)
T ss_pred EEEEehhHhh
Confidence 6788887665
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=97.49 E-value=0.00031 Score=53.53 Aligned_cols=66 Identities=18% Similarity=0.296 Sum_probs=52.2
Q ss_pred EEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009879 10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 80 (523)
Q Consensus 10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD 80 (523)
|.|.+||+.+|++++.+.+... +.+....+... ........|||.|.+.+++....+.++|+.|-+
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 34544444332 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=97.42 E-value=0.00079 Score=49.97 Aligned_cols=67 Identities=22% Similarity=0.359 Sum_probs=53.3
Q ss_pred eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009879 9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 80 (523)
Q Consensus 9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD 80 (523)
.|+|+.||+.++++++++.+... +.+....+..-... .....|||.|.+.++...+.+.+++..|-+
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 47899999999999999999875 45666555532222 336689999999999999999999998643
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=97.23 E-value=0.0015 Score=50.85 Aligned_cols=65 Identities=29% Similarity=0.350 Sum_probs=50.5
Q ss_pred EEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009879 10 VVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 79 (523)
Q Consensus 10 VVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv 79 (523)
|.|++||++.|++++.+.+... +.+.-+.+...+. ......|||.|.+++++..+.+..++..|-
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 6899999999999999999886 3566666654432 234667999999999999999999877763
No 7
>smart00362 RRM_2 RNA recognition motif.
Probab=97.17 E-value=0.0023 Score=47.21 Aligned_cols=65 Identities=22% Similarity=0.319 Sum_probs=51.2
Q ss_pred eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009879 9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 79 (523)
Q Consensus 9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv 79 (523)
+|.|++||+.++++++.+.+... +.+.+..+.... .....-|||.|.+.++.....+.++++.|-
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 223457999999999999999999998873
No 8
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=96.36 E-value=0.017 Score=53.17 Aligned_cols=80 Identities=14% Similarity=0.070 Sum_probs=58.6
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009879 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA 84 (523)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn 84 (523)
...+||.|.+||+.+||+++++.+.+. +.|.....+.-..+. ..-.-|||.|.+.+++....+.++++.+.+.
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 346899999999999999999999874 345554444322221 1224699999999999999999999876432
Q ss_pred eeeeEEEec
Q 009879 85 QFKAIVEYA 93 (523)
Q Consensus 85 e~~A~VEfA 93 (523)
...|++|
T Consensus 105 --~l~V~~a 111 (144)
T PLN03134 105 --HIRVNPA 111 (144)
T ss_pred --EEEEEeC
Confidence 4556665
No 9
>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=95.95 E-value=0.033 Score=58.20 Aligned_cols=82 Identities=23% Similarity=0.297 Sum_probs=59.8
Q ss_pred CCCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009879 3 EPLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK 82 (523)
Q Consensus 3 ~p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK 82 (523)
.....++|.|.+||+.+||++|.+.+... +.|.....+.-+.+.+ ...-|||.|.+.+++...++.+++..+.+.
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 TNNSGTNLIVNYLPQDMTDRELYALFRTI--GPINTCRIMRDYKTGY--SFGYAFVDFGSEADSQRAIKNLNGITVRNK- 177 (346)
T ss_pred CCCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCCc--cCcEEEEEEccHHHHHHHHHHcCCCccCCc-
Confidence 35678999999999999999999999864 2454444332222111 123499999999999999999999888653
Q ss_pred CCeeeeEEEec
Q 009879 83 GAQFKAIVEYA 93 (523)
Q Consensus 83 Gne~~A~VEfA 93 (523)
+..|+||
T Consensus 178 ----~i~V~~a 184 (346)
T TIGR01659 178 ----RLKVSYA 184 (346)
T ss_pred ----eeeeecc
Confidence 4556665
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=95.92 E-value=0.076 Score=56.16 Aligned_cols=85 Identities=19% Similarity=0.176 Sum_probs=63.2
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009879 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ 85 (523)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne 85 (523)
+..+|.|.+||+.+|++++.+.|..+ +.|..+.++......+ ...-|||.|.+.+++..-++.++|..|.+.
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 35799999999999999999999874 3455555554322211 234599999999999999999999998544
Q ss_pred eeeEEEeccCCCCC
Q 009879 86 FKAIVEYAPSQRVP 99 (523)
Q Consensus 86 ~~A~VEfAPYQKvP 99 (523)
...|++|-+...+
T Consensus 366 -~l~v~~a~~~~~~ 378 (509)
T TIGR01642 366 -KLHVQRACVGANQ 378 (509)
T ss_pred -EEEEEECccCCCC
Confidence 3578888665443
No 11
>smart00360 RRM RNA recognition motif.
Probab=95.83 E-value=0.033 Score=40.72 Aligned_cols=64 Identities=22% Similarity=0.353 Sum_probs=47.9
Q ss_pred EecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009879 12 IRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 79 (523)
Q Consensus 12 IRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv 79 (523)
|++||+.++++++.+.+... +.+....+...... ......|||.|.+.+++..+.+.++++.|.
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 57899999999999988764 34555544433221 122358999999999999999999998884
No 12
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=95.51 E-value=0.068 Score=53.61 Aligned_cols=79 Identities=22% Similarity=0.339 Sum_probs=59.1
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009879 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ 85 (523)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne 85 (523)
+.+.|.|++||+.+||++|.+.+... |.|.-...+.-+... ..-.-|||.|.+.++...-++.++|..+.+.
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 46889999999999999999999874 355544444333221 1235699999999999999999999776533
Q ss_pred eeeEEEec
Q 009879 86 FKAIVEYA 93 (523)
Q Consensus 86 ~~A~VEfA 93 (523)
...|+||
T Consensus 74 -~i~v~~a 80 (352)
T TIGR01661 74 -TIKVSYA 80 (352)
T ss_pred -eEEEEee
Confidence 4667776
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=94.77 E-value=0.18 Score=52.87 Aligned_cols=82 Identities=17% Similarity=0.154 Sum_probs=59.0
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009879 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ 85 (523)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne 85 (523)
..++|.|.+||+.+||+++.+.+... +.|.....+.-+...++ -.-|||.|.+.+++..-++.+++..|... .
T Consensus 192 ~~~~lfV~nLp~~vtee~L~~~F~~f--G~V~~v~i~~d~~tg~~--kG~aFV~F~~~e~A~~Ai~~lng~~~~g~---~ 264 (346)
T TIGR01659 192 KDTNLYVTNLPRTITDDQLDTIFGKY--GQIVQKNILRDKLTGTP--RGVAFVRFNKREEAQEAISALNNVIPEGG---S 264 (346)
T ss_pred ccceeEEeCCCCcccHHHHHHHHHhc--CCEEEEEEeecCCCCcc--ceEEEEEECCHHHHHHHHHHhCCCccCCC---c
Confidence 46789999999999999999998764 24444333332222111 25799999999999999999999987442 3
Q ss_pred eeeEEEecc
Q 009879 86 FKAIVEYAP 94 (523)
Q Consensus 86 ~~A~VEfAP 94 (523)
.+..|.+|-
T Consensus 265 ~~l~V~~a~ 273 (346)
T TIGR01659 265 QPLTVRLAE 273 (346)
T ss_pred eeEEEEECC
Confidence 456666664
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=94.55 E-value=0.16 Score=53.13 Aligned_cols=79 Identities=14% Similarity=0.195 Sum_probs=58.3
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009879 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF 86 (523)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~ 86 (523)
..+|.|++||+.+||+++.+.+... +.|.+..++.-.... ..-.-|||.|.+.++...-++.++|..|.+ .
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 4789999999999999999988764 356655544322211 112359999999999999999999977633 2
Q ss_pred eeEEEecc
Q 009879 87 KAIVEYAP 94 (523)
Q Consensus 87 ~A~VEfAP 94 (523)
...|.||-
T Consensus 257 ~i~v~~a~ 264 (457)
T TIGR01622 257 PIKVGYAQ 264 (457)
T ss_pred EEEEEEcc
Confidence 56778765
No 15
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=93.90 E-value=0.25 Score=49.55 Aligned_cols=78 Identities=15% Similarity=0.126 Sum_probs=57.5
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009879 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK 87 (523)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~ 87 (523)
..|.|++||+..||+++++.+.+. |.|.....+....+. ..-.-|||.|.+.++...-++.++|..|-+ + .
T Consensus 270 ~~lfV~NL~~~~~e~~L~~~F~~f--G~v~~v~i~~d~~t~--~skG~aFV~F~~~~~A~~Ai~~lnG~~~~g-r----~ 340 (352)
T TIGR01661 270 YCIFVYNLSPDTDETVLWQLFGPF--GAVQNVKIIRDLTTN--QCKGYGFVSMTNYDEAAMAILSLNGYTLGN-R----V 340 (352)
T ss_pred cEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEeEcCCCC--CccceEEEEECCHHHHHHHHHHhCCCEECC-e----E
Confidence 369999999999999999999975 356665554332221 112348999999999999999999998733 2 4
Q ss_pred eEEEecc
Q 009879 88 AIVEYAP 94 (523)
Q Consensus 88 A~VEfAP 94 (523)
-.|.|+.
T Consensus 341 i~V~~~~ 347 (352)
T TIGR01661 341 LQVSFKT 347 (352)
T ss_pred EEEEEcc
Confidence 5666653
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=93.62 E-value=0.2 Score=54.25 Aligned_cols=67 Identities=16% Similarity=0.222 Sum_probs=51.3
Q ss_pred eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009879 9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 79 (523)
Q Consensus 9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv 79 (523)
-|.|.+||+++||+++.+.+... +.|.......-+.+.+ ...-|||.|.+.++.....+.+++..|.
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 37899999999999999999875 3465555544333222 2346999999999999999999988763
No 17
>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=92.37 E-value=0.51 Score=53.02 Aligned_cols=72 Identities=14% Similarity=0.135 Sum_probs=56.8
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009879 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK 87 (523)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~ 87 (523)
.+|.|++||..+||+++.+.+...-.+.|.-...+.| -|||.|.+.++...-++.+++..|.+ ..
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 5699999999999999999998753355654433322 59999999999999999999998844 25
Q ss_pred eEEEecc
Q 009879 88 AIVEYAP 94 (523)
Q Consensus 88 A~VEfAP 94 (523)
..|++|.
T Consensus 299 I~V~~Ak 305 (578)
T TIGR01648 299 IEVTLAK 305 (578)
T ss_pred EEEEEcc
Confidence 6788873
No 18
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=92.19 E-value=0.69 Score=41.70 Aligned_cols=72 Identities=18% Similarity=0.244 Sum_probs=54.8
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009879 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK 82 (523)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK 82 (523)
...|.|.+||+.+|++++.+.+.... .+.+....--+ .......-|||.|.+.+++....+.++|..|.+..
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 58999999999999999999998763 23333322111 12234567999999999999999999988887663
No 19
>PLN03120 nucleic acid binding protein; Provisional
Probab=91.89 E-value=1.1 Score=46.15 Aligned_cols=75 Identities=20% Similarity=0.318 Sum_probs=57.7
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009879 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF 86 (523)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~ 86 (523)
..+|-|.+||+..||+++.+.+..+ |+|.+.......- .-.-|||.|.+++++.... .++|..|.|.
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 4689999999999999999999764 5777766543221 1357999999999998888 4999988765
Q ss_pred eeEEEecc
Q 009879 87 KAIVEYAP 94 (523)
Q Consensus 87 ~A~VEfAP 94 (523)
...|+.+.
T Consensus 71 ~V~Vt~a~ 78 (260)
T PLN03120 71 SVTITPAE 78 (260)
T ss_pred eEEEEecc
Confidence 35666664
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=91.65 E-value=0.97 Score=48.80 Aligned_cols=84 Identities=21% Similarity=0.334 Sum_probs=62.4
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC-
Q 009879 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA- 84 (523)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn- 84 (523)
+..+|.|.+||+++||+++.+.+...-...+..+.+++.+-. ...-|+|.|.+.++...-...++++.+-+..|.
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 346799999999999999999998753213555555565532 134599999999999999999999998666542
Q ss_pred eeeeEEEec
Q 009879 85 QFKAIVEYA 93 (523)
Q Consensus 85 e~~A~VEfA 93 (523)
-+...|.||
T Consensus 469 ~~~lkv~fs 477 (481)
T TIGR01649 469 PYHLKVSFS 477 (481)
T ss_pred cceEEEEec
Confidence 345566766
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=90.96 E-value=0.92 Score=47.56 Aligned_cols=71 Identities=18% Similarity=0.243 Sum_probs=52.8
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009879 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 80 (523)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD 80 (523)
.+...|.|.+||+.+||+++.+.+... +.|.....+.-+.+. ..-.-|||.|.+.+++...+. ++|..|.+
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 346689999999999999999988874 356665555433222 123569999999999998886 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=90.61 E-value=0.84 Score=49.61 Aligned_cols=70 Identities=20% Similarity=0.248 Sum_probs=54.1
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009879 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 81 (523)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs 81 (523)
-+.|.|++||+.+||+++.+.+... +.|....+..... ...-..|||.|.+.++.....+.++|..|.+.
T Consensus 178 ~~~l~V~nl~~~~tee~L~~~F~~f--G~i~~~~i~~~~~---g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~ 247 (562)
T TIGR01628 178 FTNLYVKNLDPSVNEDKLRELFAKF--GEITSAAVMKDGS---GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLA 247 (562)
T ss_pred CCeEEEeCCCCcCCHHHHHHHHHhc--CCEEEEEEEECCC---CCcccEEEEEECCHHHHHHHHHHhCCcEeccc
Confidence 4679999999999999999998864 3466555543321 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=90.43 E-value=0.9 Score=51.11 Aligned_cols=71 Identities=20% Similarity=0.214 Sum_probs=53.5
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcce--eEEEEecCcccHHHHHHHhcCCeeEeC
Q 009879 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYS--RAYVELKKPAGVFEFAELLNGHVFVNE 81 (523)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~yS--RAYI~Fkn~Edl~~F~d~fdG~vFvDs 81 (523)
|...++|-|-+||+.+||+++.+.+... +.|.-...+.- .+ -.| -|||.|.+.+++..-++.++++.+.+.
T Consensus 55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~--G~I~~vrl~~D-~s----G~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~G 127 (578)
T TIGR01648 55 PGRGCEVFVGKIPRDLYEDELVPLFEKA--GPIYELRLMMD-FS----GQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPG 127 (578)
T ss_pred CCCCCEEEeCCCCCCCCHHHHHHHHHhh--CCEEEEEEEEC-CC----CCccceEEEEeCCHHHHHHHHHHcCCCeecCC
Confidence 4456999999999999999999998764 23433333222 11 123 499999999999999999999988643
No 24
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=87.03 E-value=2.1 Score=48.55 Aligned_cols=73 Identities=15% Similarity=0.153 Sum_probs=54.2
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009879 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 81 (523)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs 81 (523)
...++|.|.+||+.+||+++.+.+..+ |.|.-...+.-..+.+ ...-|||.|.+.++...-++.++|..|.+.
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 456799999999999999999999874 3454444332222222 234699999999999999999999887543
No 25
>PLN03121 nucleic acid binding protein; Provisional
Probab=86.92 E-value=2.2 Score=43.58 Aligned_cols=69 Identities=20% Similarity=0.307 Sum_probs=52.8
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009879 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK 82 (523)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK 82 (523)
...-|.|.+|+|..||+++.+-+.. .|+|...+-+.-.- .-.-|||.|++++++ +-+-.++|..|+|..
T Consensus 4 ~g~TV~V~NLS~~tTE~dLrefFS~--~G~I~~V~I~~D~e-----t~gfAfVtF~d~~aa-etAllLnGa~l~d~~ 72 (243)
T PLN03121 4 GGYTAEVTNLSPKATEKDVYDFFSH--CGAIEHVEIIRSGE-----YACTAYVTFKDAYAL-ETAVLLSGATIVDQR 72 (243)
T ss_pred CceEEEEecCCCCCCHHHHHHHHHh--cCCeEEEEEecCCC-----cceEEEEEECCHHHH-HHHHhcCCCeeCCce
Confidence 3467899999999999999998885 46777766443211 124799999999999 445589999998874
No 26
>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=86.66 E-value=4.7 Score=43.61 Aligned_cols=80 Identities=19% Similarity=0.150 Sum_probs=62.2
Q ss_pred CCceEEEecCCC-CCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009879 6 QRTKVVIRHLPP-SLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA 84 (523)
Q Consensus 6 ~r~KVVIRrLPP-~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn 84 (523)
+...|.|.+||+ .+|++++++.+..+ |.|....++..+ ..-|+|.|.+.++...-.+.++|+.|.+
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 456666555432 2469999999999999999999998843
Q ss_pred eeeeEEEeccCCCCC
Q 009879 85 QFKAIVEYAPSQRVP 99 (523)
Q Consensus 85 e~~A~VEfAPYQKvP 99 (523)
....|+++-.+.+.
T Consensus 341 -~~l~v~~s~~~~~~ 354 (481)
T TIGR01649 341 -KPLRVCPSKQQNVQ 354 (481)
T ss_pred -ceEEEEEccccccc
Confidence 25667777655543
No 27
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=85.93 E-value=4.4 Score=40.12 Aligned_cols=77 Identities=22% Similarity=0.288 Sum_probs=61.5
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCC
Q 009879 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGA 84 (523)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGn 84 (523)
.-.+||-|=+||+.-|+.||...+..+-.-.-.|..+.| +--|+|.|.++.|..+-...+||..|...
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 447999999999999999999988765322235765543 34589999999999999999999998876
Q ss_pred eeeeEEEeccC
Q 009879 85 QFKAIVEYAPS 95 (523)
Q Consensus 85 e~~A~VEfAPY 95 (523)
.+.||++--
T Consensus 76 --r~rVE~S~G 84 (195)
T KOG0107|consen 76 --RIRVELSTG 84 (195)
T ss_pred --eEEEEeecC
Confidence 578887643
No 28
>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=85.69 E-value=2.6 Score=47.92 Aligned_cols=69 Identities=12% Similarity=0.137 Sum_probs=53.8
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009879 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 79 (523)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv 79 (523)
..+|.|.+||+.++++++.+.+..+ +.|....+.......+ .---|||.|.+.++...-.+.++++.|-
T Consensus 204 ~~rLfVgnLp~~vteedLk~lFs~F--G~I~svrl~~D~~tgk--sKGfGFVeFe~~e~A~kAI~amNg~elg 272 (612)
T TIGR01645 204 FNRIYVASVHPDLSETDIKSVFEAF--GEIVKCQLARAPTGRG--HKGYGFIEYNNLQSQSEAIASMNLFDLG 272 (612)
T ss_pred cceEEeecCCCCCCHHHHHHHHhhc--CCeeEEEEEecCCCCC--cCCeEEEEECCHHHHHHHHHHhCCCeeC
Confidence 4689999999999999999999874 4566666655433221 1235999999999999999999998664
No 29
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=85.57 E-value=2.3 Score=45.13 Aligned_cols=66 Identities=15% Similarity=0.297 Sum_probs=46.3
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCC----------CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcC
Q 009879 6 QRTKVVIRHLPPSLSQNDLLALFRDHFN----------DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNG 75 (523)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~----------gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG 75 (523)
..-+|.|.+||+.+|++++.+.+...+. ..|....+ + +. -.-|||.|.+.+++...+ .++|
T Consensus 174 ~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~--~----~~--kg~afVeF~~~e~A~~Al-~l~g 244 (509)
T TIGR01642 174 QARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI--N----KE--KNFAFLEFRTVEEATFAM-ALDS 244 (509)
T ss_pred cccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE--C----CC--CCEEEEEeCCHHHHhhhh-cCCC
Confidence 3458999999999999999988876421 11111111 1 11 235999999999998887 5999
Q ss_pred CeeEe
Q 009879 76 HVFVN 80 (523)
Q Consensus 76 ~vFvD 80 (523)
..|.+
T Consensus 245 ~~~~g 249 (509)
T TIGR01642 245 IIYSN 249 (509)
T ss_pred eEeeC
Confidence 88865
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=80.89 E-value=7.9 Score=34.96 Aligned_cols=72 Identities=21% Similarity=0.376 Sum_probs=54.7
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009879 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 79 (523)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv 79 (523)
...++.|.|=..||.|+-..|+-.+...+...+..+..+.- ..++.| =+-|.|.+.++..+|...|+|..|-
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 34556777779999999999998888877666766555431 123333 3678999999999999999999994
No 31
>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]
Probab=75.17 E-value=8.2 Score=39.07 Aligned_cols=71 Identities=17% Similarity=0.211 Sum_probs=57.9
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccC---CCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009879 5 LQRTKVVIRHLPPSLSQNDLLALFRDHF---NDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 81 (523)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~---~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs 81 (523)
.+.-.++||+|+-.+..+++..+|..++ ..-++...|...+..- =|.+.|++.+..-.-...++|..|.|.
T Consensus 7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRG------QA~VvFk~~~~As~A~r~l~gfpFygK 80 (221)
T KOG4206|consen 7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRG------QAFVVFKETEAASAALRALQGFPFYGK 80 (221)
T ss_pred CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccC------ceEEEecChhHHHHHHHHhcCCcccCc
Confidence 3444999999999999999999888776 3345666676665543 599999999999888889999999986
No 32
>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=74.87 E-value=3.6 Score=46.13 Aligned_cols=90 Identities=23% Similarity=0.415 Sum_probs=64.3
Q ss_pred CCceEEEecCCCCCCHHHHHHHhccc--------------------------CCCceeEEEeeCCCCCCCCCcceeEEEE
Q 009879 6 QRTKVVIRHLPPSLSQNDLLALFRDH--------------------------FNDRYNWFCFRPGKSSYKHQRYSRAYVE 59 (523)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~eqL~p~--------------------------~~gkvdwfyFVpGK~S~Kp~~ySRAYI~ 59 (523)
.++-+-|+.+|-.+++..+..+++-. ..+.||+ -|.|=+...|-+ ---|.||
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 34555666666666666666665332 2345664 445666655433 4569999
Q ss_pred ecCcccHHHHHHHhcCCeeEeCCCCeeeeEEEeccCCCC
Q 009879 60 LKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYAPSQRV 98 (523)
Q Consensus 60 Fkn~Edl~~F~d~fdG~vFvDsKGne~~A~VEfAPYQKv 98 (523)
|.+++++..|.+.|+|..|..=. .+..|.+-||-+|..
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 99999999999999999987655 688999999999964
No 33
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=73.28 E-value=10 Score=39.26 Aligned_cols=77 Identities=19% Similarity=0.213 Sum_probs=56.5
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009879 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK 87 (523)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~ 87 (523)
.-|=|=+||-.|+|+++.+.+.+.- .|.-.|-+.-+..- -.-.-||++|.+.||....++.++||-+- ..+
T Consensus 190 ~tvRvtNLsed~~E~dL~eLf~~fg--~i~rvylardK~TG--~~kGFAFVtF~sRddA~rAI~~LnG~gyd-----~LI 260 (270)
T KOG0122|consen 190 ATVRVTNLSEDMREDDLEELFRPFG--PITRVYLARDKETG--LSKGFAFVTFESRDDAARAIADLNGYGYD-----NLI 260 (270)
T ss_pred ceeEEecCccccChhHHHHHhhccC--ccceeEEEEccccC--cccceEEEEEecHHHHHHHHHHccCcccc-----eEE
Confidence 4477889999999999999988753 34555554444332 12345999999999999999999998642 346
Q ss_pred eEEEec
Q 009879 88 AIVEYA 93 (523)
Q Consensus 88 A~VEfA 93 (523)
..||+|
T Consensus 261 LrvEws 266 (270)
T KOG0122|consen 261 LRVEWS 266 (270)
T ss_pred EEEEec
Confidence 677776
No 34
>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=68.46 E-value=13 Score=32.95 Aligned_cols=58 Identities=21% Similarity=0.288 Sum_probs=37.6
Q ss_pred eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCC
Q 009879 9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGH 76 (523)
Q Consensus 9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~ 76 (523)
=|-|.-|++.++.++|-+.|...- .|.|..|..|.. =|||.|.+++....+.+.+...
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g--~V~yVD~~~G~~--------~g~VRf~~~~~A~~a~~~~~~~ 60 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFG--EVAYVDFSRGDT--------EGYVRFKTPEAAQKALEKLKEA 60 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS----EEEEE--TT-S--------EEEEEESS---HHHHHHHHHHT
T ss_pred EEEEecCCCCcCHHHHHHHHHhcC--CcceEEecCCCC--------EEEEEECCcchHHHHHHHHHhc
Confidence 356777999999999999999843 799999999965 4899999999998888887654
No 35
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=66.99 E-value=16 Score=41.64 Aligned_cols=69 Identities=23% Similarity=0.345 Sum_probs=52.8
Q ss_pred CCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009879 5 LQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF 78 (523)
Q Consensus 5 ~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF 78 (523)
.+.-|||||+||-...+..+...++.. . + -|--++|-+.- .-.+.-|+|.|++..+...-++.|+|+.|
T Consensus 115 ~~k~rLIIRNLPf~~k~~dLk~vFs~~-G-~-V~Ei~IP~k~d--gklcGFaFV~fk~~~dA~~Al~~~N~~~i 183 (678)
T KOG0127|consen 115 LPKWRLIIRNLPFKCKKPDLKNVFSNF-G-K-VVEIVIPRKKD--GKLCGFAFVQFKEKKDAEKALEFFNGNKI 183 (678)
T ss_pred CccceEEeecCCcccCcHHHHHHHhhc-c-e-EEEEEcccCCC--CCccceEEEEEeeHHHHHHHHHhccCcee
Confidence 347799999999999999887766654 2 2 34456673332 34458999999999999999999999876
No 36
>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=66.30 E-value=21 Score=33.11 Aligned_cols=70 Identities=20% Similarity=0.252 Sum_probs=53.5
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009879 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 80 (523)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD 80 (523)
|...--|-||+||-.+|.|+..+.++-+- .|. .-.-|. .+.+-..||+.+.+..|...-.+.+.|+-+.+
T Consensus 15 pevnriLyirNLp~~ITseemydlFGkyg--~Ir--QIRiG~---~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ 84 (124)
T KOG0114|consen 15 PEVNRILYIRNLPFKITSEEMYDLFGKYG--TIR--QIRIGN---TKETRGTAFVVYEDIFDAKKACDHLSGYNVDN 84 (124)
T ss_pred hhhheeEEEecCCccccHHHHHHHhhccc--ceE--EEEecC---ccCcCceEEEEehHhhhHHHHHHHhcccccCC
Confidence 33445578999999999999999998652 332 223343 45577889999999999999999999997643
No 37
>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=63.69 E-value=23 Score=26.63 Aligned_cols=48 Identities=25% Similarity=0.215 Sum_probs=34.7
Q ss_pred CceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeeeeEEEec
Q 009879 34 DRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFKAIVEYA 93 (523)
Q Consensus 34 gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~A~VEfA 93 (523)
|.|.-..+.+.+ ...|||.|.+.++.....+.++|..|.+. +-.|+||
T Consensus 9 G~V~~i~~~~~~-------~~~a~V~f~~~~~A~~a~~~l~~~~~~g~-----~l~V~~a 56 (56)
T PF13893_consen 9 GEVKKIKIFKKK-------RGFAFVEFASVEDAQKAIEQLNGRQFNGR-----PLKVSYA 56 (56)
T ss_dssp S-EEEEEEETTS-------TTEEEEEESSHHHHHHHHHHHTTSEETTE-----EEEEEEE
T ss_pred ccEEEEEEEeCC-------CCEEEEEECCHHHHHHHHHHhCCCEECCc-----EEEEEEC
Confidence 345555554443 57899999999999999999999998332 4556664
No 38
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=60.64 E-value=19 Score=37.82 Aligned_cols=72 Identities=21% Similarity=0.320 Sum_probs=55.4
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009879 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 81 (523)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs 81 (523)
.++-|+|--||-+||+|||...+... ++|+..-.|.-|+.- ....--++++.+++|...-+..++|.-..+.
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 46889999999999999999988865 356665566666543 2234457888899999999999999876654
No 39
>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]
Probab=60.57 E-value=24 Score=38.85 Aligned_cols=68 Identities=19% Similarity=0.229 Sum_probs=50.3
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeE
Q 009879 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFV 79 (523)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFv 79 (523)
+.|.|+++|...+||++.+.+... +.|-.+.+|--..+-++. .-+|+.|.++++...-.+.++|+.|-
T Consensus 19 ~~v~vgnip~~~se~~l~~~~~~~--g~v~s~~~v~D~~tG~~~--G~~f~~~~~~~~~~~a~~~lNg~~~~ 86 (435)
T KOG0108|consen 19 SSVFVGNIPYEGSEEQLLSIFSGV--GPVLSFRLVYDRETGKPK--GFGFCEFTDEETAERAIRNLNGAEFN 86 (435)
T ss_pred cceEecCCCCcccHHHHHHHHhcc--CccceeeecccccCCCcC--ceeeEecCchhhHHHHHHhcCCcccC
Confidence 789999999999999999888754 234334444222222333 35788899999999999999998763
No 40
>PLN03213 repressor of silencing 3; Provisional
Probab=58.98 E-value=42 Score=38.10 Aligned_cols=69 Identities=19% Similarity=0.278 Sum_probs=55.9
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCc--ccHHHHHHHhcCCeeEe
Q 009879 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKP--AGVFEFAELLNGHVFVN 80 (523)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~--Edl~~F~d~fdG~vFvD 80 (523)
....++|-|-.|++..|++++...+.++ |.|.-.+++ .-+ . -.-|||.|.+. +.+...+..++|..|..
T Consensus 7 ~~~gMRIYVGNLSydVTEDDLravFSeF--GsVkdVEIp--RET-G---RGFAFVEMssdddaEeeKAISaLNGAEWKG 77 (759)
T PLN03213 7 GGGGVRLHVGGLGESVGRDDLLKIFSPM--GTVDAVEFV--RTK-G---RSFAYIDFSPSSTNSLTKLFSTYNGCVWKG 77 (759)
T ss_pred CCcceEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEe--ccc-C---CceEEEEecCCcHHHHHHHHHHhcCCeecC
Confidence 4567899999999999999999999986 567776765 111 1 57899999987 67999999999999843
No 41
>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]
Probab=58.36 E-value=22 Score=40.58 Aligned_cols=64 Identities=17% Similarity=0.266 Sum_probs=49.7
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhc
Q 009879 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLN 74 (523)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fd 74 (523)
..-|-||+||-.-|||++.+.|... |.|.|..-|--+.+ .+.-.+|++.|+++.+....+...+
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 3568899999999999999988864 35777666643332 3446799999999999988888773
No 42
>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=54.97 E-value=4.2 Score=46.81 Aligned_cols=46 Identities=33% Similarity=0.574 Sum_probs=40.2
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEe
Q 009879 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVN 80 (523)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvD 80 (523)
-.|.||+||.+-||++|+..+ ||+.|..++....-...+||++|.-
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 357899999999999998877 8999999999888888999988853
No 43
>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]
Probab=53.13 E-value=26 Score=38.61 Aligned_cols=89 Identities=25% Similarity=0.406 Sum_probs=57.2
Q ss_pred eEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcce-eEEEEecCcccHHHHHHHhcCCeeEeCC-----
Q 009879 9 KVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYS-RAYVELKKPAGVFEFAELLNGHVFVNEK----- 82 (523)
Q Consensus 9 KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~yS-RAYI~Fkn~Edl~~F~d~fdG~vFvDsK----- 82 (523)
-|-|=+|-|+.|.+++...++.+ |+|.-...+|---..+-++-+ .|||.|.+...+ ..++.+-..+|||.-
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 45678999999999998888754 455544444422222345555 599999987554 456777778888863
Q ss_pred -CCeee----eEEEeccCCCCCC
Q 009879 83 -GAQFK----AIVEYAPSQRVPK 100 (523)
Q Consensus 83 -Gne~~----A~VEfAPYQKvPk 100 (523)
++... |.++||+-.-||.
T Consensus 86 ~~~~~~p~r~af~~l~~~navpr 108 (479)
T KOG4676|consen 86 YGDEVIPDRFAFVELADQNAVPR 108 (479)
T ss_pred cCCCCCccHHHHHhcCccccccc
Confidence 22211 5666666666654
No 44
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=50.88 E-value=28 Score=39.18 Aligned_cols=65 Identities=18% Similarity=0.357 Sum_probs=48.8
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCC---C--CcceeEEEEecCcccHHHHHHHhc
Q 009879 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYK---H--QRYSRAYVELKKPAGVFEFAELLN 74 (523)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~K---p--~~ySRAYI~Fkn~Edl~~F~d~fd 74 (523)
--.||.|=-|||.|+|++++..+...-.-.||| ||+.-.+ + -.+.-+||.|.++..|..+.+..-
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----PGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS 327 (520)
T ss_pred cccceeecCCCccccHHHHHhhcccccceEeec----CCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence 346999999999999999999988754446788 5443321 2 234689999999999988877653
No 45
>smart00361 RRM_1 RNA recognition motif.
Probab=48.31 E-value=56 Score=26.03 Aligned_cols=27 Identities=19% Similarity=0.317 Sum_probs=24.1
Q ss_pred eeEEEEecCcccHHHHHHHhcCCeeEe
Q 009879 54 SRAYVELKKPAGVFEFAELLNGHVFVN 80 (523)
Q Consensus 54 SRAYI~Fkn~Edl~~F~d~fdG~vFvD 80 (523)
..+||.|.+.++.......++|..|-.
T Consensus 38 G~~fV~f~~~~dA~~A~~~l~g~~~~g 64 (70)
T smart00361 38 GNVYITFERSEDAARAIVDLNGRYFDG 64 (70)
T ss_pred EEEEEEECCHHHHHHHHHHhCCCEECC
Confidence 569999999999999999999987643
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=47.18 E-value=36 Score=27.35 Aligned_cols=49 Identities=10% Similarity=0.281 Sum_probs=30.0
Q ss_pred EecCCCCCCHHHHHHHhcccC-----CCceeEEE--eeCCCCCCCCCcceeEEEEecCc
Q 009879 12 IRHLPPSLSQNDLLALFRDHF-----NDRYNWFC--FRPGKSSYKHQRYSRAYVELKKP 63 (523)
Q Consensus 12 IRrLPP~LTEEeF~eqL~p~~-----~gkvdwfy--FVpGK~S~Kp~~ySRAYI~Fkn~ 63 (523)
|..|-|+||.++....|++.. ... .|.| .+... .......+..|.|.+-
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 4543 22221 1224577888888763
No 47
>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=38.65 E-value=89 Score=27.99 Aligned_cols=73 Identities=15% Similarity=0.211 Sum_probs=41.8
Q ss_pred eEEEecCCCCCCHHHHHH---HhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCe
Q 009879 9 KVVIRHLPPSLSQNDLLA---LFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQ 85 (523)
Q Consensus 9 KVVIRrLPP~LTEEeF~e---qL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne 85 (523)
=|+|.+||-+-.-...-. +|.....|+|-. +.| .+|+|.|.++|....-..+++|-. --|+
T Consensus 4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~---v~~---------~tAilrF~~~~~A~RA~KRmegEd---VfG~- 67 (90)
T PF11608_consen 4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLS---VSG---------GTAILRFPNQEFAERAQKRMEGED---VFGN- 67 (90)
T ss_dssp EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----T---------T-EEEEESSHHHHHHHHHHHTT-----SSSS-
T ss_pred EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEE---EeC---------CEEEEEeCCHHHHHHHHHhhcccc---cccc-
Confidence 478999999999877744 555555676632 222 689999999999999999998752 2222
Q ss_pred eeeEEEeccCCCC
Q 009879 86 FKAIVEYAPSQRV 98 (523)
Q Consensus 86 ~~A~VEfAPYQKv 98 (523)
.-.|-|.|-++.
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 345666665553
No 48
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=36.77 E-value=86 Score=35.18 Aligned_cols=74 Identities=19% Similarity=0.262 Sum_probs=57.3
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCC
Q 009879 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEK 82 (523)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsK 82 (523)
+.+.+=|.|=-.|-.||-.+|+.-+.+... .|..+.++.- .-|+.|+ +-|.|++.+++..|.+.|+|..|-+-.
T Consensus 71 ~~~~~mLcilaVP~~mt~~Dll~F~~~~~~-~I~~irivRd---~~pnrym-vLIkFr~q~da~~Fy~efNGk~Fn~le 144 (493)
T KOG0804|consen 71 ASSSTMLCILAVPAYMTSHDLLRFCASFIK-QISDIRIVRD---GMPNRYM-VLIKFRDQADADTFYEEFNGKQFNSLE 144 (493)
T ss_pred CCCCcEEEEEeccccccHHHHHHHHHHHhh-hhheeEEeec---CCCceEE-EEEEeccchhHHHHHHHcCCCcCCCCC
Confidence 334667788889999999999999986543 4666677761 1245555 679999999999999999999996543
No 49
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]
Probab=35.19 E-value=82 Score=32.03 Aligned_cols=71 Identities=20% Similarity=0.318 Sum_probs=50.1
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeC
Q 009879 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNE 81 (523)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDs 81 (523)
.=+.|++||-++-|.+.+.-+.+. .+.+.-+.--.-+-. -+.---|||.|.++|...--++.+++|.|..-
T Consensus 50 g~~~~~~~p~g~~e~~~~~~~~q~-~g~v~r~rlsRnkrT--GNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~ 120 (214)
T KOG4208|consen 50 GVVYVDHIPHGFFETEILNYFRQF-GGTVTRFRLSRNKRT--GNSKGYAFVEFESEEVAKIAAETMNNYLLMEH 120 (214)
T ss_pred cceeecccccchhHHHHhhhhhhc-CCeeEEEEeeccccc--CCcCceEEEEeccHHHHHHHHHHhhhhhhhhh
Confidence 346789999999998888777664 455654432111111 12334699999999999999999999998643
No 50
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=32.07 E-value=1.1e+02 Score=31.49 Aligned_cols=65 Identities=20% Similarity=0.180 Sum_probs=51.6
Q ss_pred CCceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcC
Q 009879 6 QRTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNG 75 (523)
Q Consensus 6 ~r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG 75 (523)
..+||.|=+||.+.+++++.+.+...-. + .=|..+|-.--..+.-|=|.|+..+|+...++.|+|
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--L---KRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNG 146 (243)
T ss_pred CcceeeeecCCcCcchHHHHHHHHHhcc--c---eEEeeccCCCCCCCccceeeecchHhHHHHHHHhcC
Confidence 3489999999999999999998887521 1 223445544445578999999999999999999999
No 51
>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]
Probab=31.63 E-value=1.9e+02 Score=31.61 Aligned_cols=84 Identities=21% Similarity=0.155 Sum_probs=59.3
Q ss_pred CCCCceEEEecCCCCCCHHHHHHHhcccC-------CCceeEEEee--CCCCCCCCCcceeEEEEecCcccHHHHHHHhc
Q 009879 4 PLQRTKVVIRHLPPSLSQNDLLALFRDHF-------NDRYNWFCFR--PGKSSYKHQRYSRAYVELKKPAGVFEFAELLN 74 (523)
Q Consensus 4 p~~r~KVVIRrLPP~LTEEeF~eqL~p~~-------~gkvdwfyFV--pGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fd 74 (523)
|..++.|-|-.||+.+|-+||.+.+.-.. .++.--.-|+ +|++.- =|-|.|-..|.|..-...+|
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 56788999999999999999999875432 1222223344 666543 23344445778888889999
Q ss_pred CCeeEeCCCCeeeeEEEeccCCCC
Q 009879 75 GHVFVNEKGAQFKAIVEYAPSQRV 98 (523)
Q Consensus 75 G~vFvDsKGne~~A~VEfAPYQKv 98 (523)
+..|. | ..-.||.|-||..
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 99988 2 3578999999964
No 52
>COG4499 Predicted membrane protein [Function unknown]
Probab=31.50 E-value=9.5 Score=41.67 Aligned_cols=68 Identities=19% Similarity=0.458 Sum_probs=54.8
Q ss_pred CCC-CCCHHHHHHHhccc----CCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHH-h--------cCCeeEe
Q 009879 15 LPP-SLSQNDLLALFRDH----FNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAEL-L--------NGHVFVN 80 (523)
Q Consensus 15 LPP-~LTEEeF~eqL~p~----~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~-f--------dG~vFvD 80 (523)
||| -|||+.||..+... +.+++.+-.|+.|+.+.+-.-++-+-|.+.+.++|.+|++. + ..+.||-
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 69999999998764 36777777889999998888899999999999999999998 2 3556665
Q ss_pred CC
Q 009879 81 EK 82 (523)
Q Consensus 81 sK 82 (523)
.+
T Consensus 214 K~ 215 (434)
T COG4499 214 KK 215 (434)
T ss_pred cc
Confidence 54
No 53
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=30.75 E-value=76 Score=26.80 Aligned_cols=60 Identities=18% Similarity=0.265 Sum_probs=37.6
Q ss_pred EEEecCCCCCCHHHHHHHhcccC----C-CceeEEEe-eCCCCCCCCCcceeEEEEe--cCcccHHHHHHHhcCCe
Q 009879 10 VVIRHLPPSLSQNDLLALFRDHF----N-DRYNWFCF-RPGKSSYKHQRYSRAYVEL--KKPAGVFEFAELLNGHV 77 (523)
Q Consensus 10 VVIRrLPP~LTEEeF~eqL~p~~----~-gkvdwfyF-VpGK~S~Kp~~ySRAYI~F--kn~Edl~~F~d~fdG~v 77 (523)
+|.|.||..||.+++.+.-.... . ..|.|..+ |--+- -++|=.+ .|.|.|.+-.+.- |..
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 25788753 32111 1444444 5778888777765 443
No 54
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=29.32 E-value=60 Score=36.35 Aligned_cols=60 Identities=22% Similarity=0.330 Sum_probs=45.3
Q ss_pred CceE-EEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCee
Q 009879 7 RTKV-VIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVF 78 (523)
Q Consensus 7 r~KV-VIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vF 78 (523)
.+|| -||+||-+.|||.+.+.+... +.|+-.- |+. --|+|||.+.++.+.-++..+|+..
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 4554 599999999999998888764 3443221 121 1689999999999999999999864
No 55
>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]
Probab=28.55 E-value=1.4e+02 Score=33.08 Aligned_cols=79 Identities=15% Similarity=0.158 Sum_probs=52.5
Q ss_pred ceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCeee
Q 009879 8 TKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQFK 87 (523)
Q Consensus 8 ~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~~ 87 (523)
.-|.-=+-|+.||||+|+.++...-...+.. .-+++| ..+.|---|.|.+.++..+-...++-+..... +..++
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----SERSSSGLLEFENKSDAVEALMKLNHYPIEGP-NGSFP 480 (494)
T ss_pred ceeEEecCCCccCHHHHHHHhhhcCCCcceE-Eeeccc----ccccccceeeeehHHHHHHHHHHhccccccCC-CCCCC
Confidence 3455678899999999999987643221222 223555 33456678999999999999888886665444 44555
Q ss_pred eEEEe
Q 009879 88 AIVEY 92 (523)
Q Consensus 88 A~VEf 92 (523)
-+|.+
T Consensus 481 filKl 485 (494)
T KOG1456|consen 481 FILKL 485 (494)
T ss_pred eeeee
Confidence 54443
No 56
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=25.84 E-value=2.1e+02 Score=32.43 Aligned_cols=59 Identities=24% Similarity=0.309 Sum_probs=43.8
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEee--CCCCCCCCCcceeEEEEecCcccHHHHHHHhc
Q 009879 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFR--PGKSSYKHQRYSRAYVELKKPAGVFEFAELLN 74 (523)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFV--pGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fd 74 (523)
.+-|=+|=||.+-|++++++-|..+ .|..+.|. .|+.+ -=|||.|.+.|++..-.++=+
T Consensus 10 ~~~vr~rGLPwsat~~ei~~Ff~~~---~I~~~~~~r~~Gr~s------GeA~Ve~~seedv~~AlkkdR 70 (510)
T KOG4211|consen 10 AFEVRLRGLPWSATEKEILDFFSNC---GIENLEIPRRNGRPS------GEAYVEFTSEEDVEKALKKDR 70 (510)
T ss_pred ceEEEecCCCccccHHHHHHHHhcC---ceeEEEEeccCCCcC------cceEEEeechHHHHHHHHhhH
Confidence 3445688999999999999999876 35555553 24443 359999999999987766543
No 57
>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=25.78 E-value=1.7e+02 Score=25.15 Aligned_cols=57 Identities=18% Similarity=0.284 Sum_probs=38.3
Q ss_pred HHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEec--CcccHHHHHHHhc--CCeeEeCCCCe
Q 009879 22 NDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELK--KPAGVFEFAELLN--GHVFVNEKGAQ 85 (523)
Q Consensus 22 EeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fk--n~Edl~~F~d~fd--G~vFvDsKGne 85 (523)
-.|+..|.+.|+ |.-|.|.-. ....+++.+-|. +.+++..|.+.++ |+.|.|-.+|+
T Consensus 25 ~~F~~~l~~~~n--ITeF~YR~~-----~~~~a~vlvgi~v~~~~~~~~l~~~L~~~gy~~~dls~ne 85 (91)
T PF00585_consen 25 KRFLDALGPRNN--ITEFHYRYS-----GDDFARVLVGIEVPDAEDLEELIERLKALGYPYEDLSDNE 85 (91)
T ss_dssp HHHHHCCSSSE---EEEEEEE-T-----TTSCSEEEEEEE-SSTHHHHHHHHHHTSSS-EEECTTT-H
T ss_pred HHHHHHhCCCce--EEEEEEcCC-----CCCeeeEEEEEEeCCHHHHHHHHHHHHHcCCCeEECCCCH
Confidence 367888887764 888888622 125778887775 4577788888887 66888887764
No 58
>COG4453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.05 E-value=59 Score=29.24 Aligned_cols=25 Identities=28% Similarity=0.604 Sum_probs=19.7
Q ss_pred ccCCHHHHHHHHHHcCCCCCCCcHH
Q 009879 112 IFKDPDYLEFLKVIAKPAENLPSAE 136 (523)
Q Consensus 112 IEqDpeYkaFLEsL~~P~e~~pSaE 136 (523)
+-.+..|..||+.|.+|.++.|..+
T Consensus 59 ~L~e~~~~~fl~~LD~P~~pn~~L~ 83 (95)
T COG4453 59 ILDEEDYRRFLAALDNPPSPNPKLK 83 (95)
T ss_pred hCCHHHHHHHHHHhcCCCCCCHHHH
Confidence 3468899999999999987655443
No 59
>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=22.42 E-value=1.4e+02 Score=29.85 Aligned_cols=45 Identities=16% Similarity=0.290 Sum_probs=24.4
Q ss_pred CCCCCHHHHHHHhcccCCCceeEEEeeCCCCCC------------CCCcceeEEEEecC
Q 009879 16 PPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSY------------KHQRYSRAYVELKK 62 (523)
Q Consensus 16 PP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~------------Kp~~ySRAYI~Fkn 62 (523)
--+||++|||..|.-.-+ .+|..+.|+=.+. -..-+.-|||+|.+
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 347899999998865322 2444444543332 12345579999975
No 60
>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]
Probab=21.03 E-value=2.4e+02 Score=28.82 Aligned_cols=79 Identities=18% Similarity=0.222 Sum_probs=55.1
Q ss_pred CceEEEecCCCCCCHHHHHHHhcccCCCceeEEEeeCCCCCCCCCcceeEEEEecCcccHHHHHHHhcCCeeEeCCCCee
Q 009879 7 RTKVVIRHLPPSLSQNDLLALFRDHFNDRYNWFCFRPGKSSYKHQRYSRAYVELKKPAGVFEFAELLNGHVFVNEKGAQF 86 (523)
Q Consensus 7 r~KVVIRrLPP~LTEEeF~eqL~p~~~gkvdwfyFVpGK~S~Kp~~ySRAYI~Fkn~Edl~~F~d~fdG~vFvDsKGne~ 86 (523)
...+-|=+|||.+-|.++...+--+ +.| .++.=|. .+-.+.-|++.|.++-|..+-+-.-|||-|- -+
T Consensus 6 ~~~iyvGNLP~diRekeieDlFyKy--g~i---~~ieLK~--r~g~ppfafVeFEd~RDAeDAiygRdGYdyd-----g~ 73 (241)
T KOG0105|consen 6 SRRIYVGNLPGDIREKEIEDLFYKY--GRI---REIELKN--RPGPPPFAFVEFEDPRDAEDAIYGRDGYDYD-----GC 73 (241)
T ss_pred cceEEecCCCcchhhccHHHHHhhh--cce---EEEEecc--CCCCCCeeEEEecCccchhhhhhcccccccC-----cc
Confidence 3567889999999999987766543 223 2222222 2334667999999999988888887887653 35
Q ss_pred eeEEEeccCCC
Q 009879 87 KAIVEYAPSQR 97 (523)
Q Consensus 87 ~A~VEfAPYQK 97 (523)
...|||+---+
T Consensus 74 rLRVEfprggr 84 (241)
T KOG0105|consen 74 RLRVEFPRGGR 84 (241)
T ss_pred eEEEEeccCCC
Confidence 78899876554
Done!