Query psy15193
Match_columns 106
No_of_seqs 33 out of 35
Neff 2.6
Searched_HMMs 46136
Date Fri Aug 16 22:57:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15193.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15193hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13893 RRM_5: RNA recognitio 91.0 0.29 6.4E-06 28.7 2.8 23 21-43 34-56 (56)
2 PLN03134 glycine-rich RNA-bind 88.0 0.74 1.6E-05 33.1 3.6 29 20-48 88-116 (144)
3 PF03780 Asp23: Asp23 family; 81.7 5.6 0.00012 26.1 5.3 40 2-41 66-105 (108)
4 KOG4207|consensus 80.3 2.2 4.7E-05 35.3 3.5 34 21-54 68-101 (256)
5 KOG0125|consensus 78.2 1.9 4.1E-05 37.4 2.6 27 20-46 148-174 (376)
6 KOG0107|consensus 74.9 2.5 5.5E-05 33.8 2.4 27 22-48 61-87 (195)
7 TIGR01622 SF-CC1 splicing fact 72.6 5 0.00011 32.2 3.6 27 22-48 242-268 (457)
8 smart00361 RRM_1 RNA recogniti 67.6 5.9 0.00013 24.5 2.4 22 20-41 49-70 (70)
9 smart00362 RRM_2 RNA recogniti 66.4 6.9 0.00015 21.5 2.3 21 21-41 52-72 (72)
10 TIGR01661 ELAV_HUD_SF ELAV/HuD 65.2 6.7 0.00015 30.1 2.8 23 22-44 325-347 (352)
11 TIGR01649 hnRNP-L_PTB hnRNP-L/ 65.0 6.3 0.00014 32.9 2.8 28 21-48 326-353 (481)
12 TIGR01205 D_ala_D_alaTIGR D-al 63.3 27 0.00059 26.5 5.7 59 5-64 234-293 (315)
13 TIGR01661 ELAV_HUD_SF ELAV/HuD 59.0 9.1 0.0002 29.3 2.5 25 21-45 58-82 (352)
14 PF00076 RRM_1: RNA recognitio 58.7 14 0.00031 21.1 2.8 20 20-39 51-70 (70)
15 TIGR01628 PABP-1234 polyadenyl 58.5 9 0.0002 32.1 2.6 25 21-45 339-363 (562)
16 TIGR01648 hnRNP-R-Q heterogene 58.0 10 0.00022 33.9 3.0 24 22-45 283-306 (578)
17 KOG0145|consensus 57.5 9.9 0.00022 32.7 2.7 34 20-55 95-128 (360)
18 TIGR01142 purT phosphoribosylg 53.8 55 0.0012 25.6 6.1 57 6-64 223-280 (380)
19 TIGR01645 half-pint poly-U bin 52.0 14 0.00031 33.4 2.9 27 22-48 260-286 (612)
20 smart00360 RRM RNA recognition 51.5 15 0.00032 20.0 2.0 20 22-41 52-71 (71)
21 PF04420 CHD5: CHD5-like prote 51.2 16 0.00035 26.9 2.7 27 8-34 36-62 (161)
22 PRK14192 bifunctional 5,10-met 49.7 27 0.00059 28.1 3.9 35 2-42 66-101 (283)
23 KOG0110|consensus 48.9 13 0.00029 34.7 2.3 44 21-70 22-65 (725)
24 TIGR01649 hnRNP-L_PTB hnRNP-L/ 44.9 22 0.00047 29.8 2.8 28 22-49 148-177 (481)
25 PF11608 Limkain-b1: Limkain b 44.2 28 0.00062 24.9 2.9 38 2-48 42-79 (90)
26 PRK14629 hypothetical protein; 42.8 33 0.00071 24.3 3.1 37 7-43 5-45 (99)
27 PLN03213 repressor of silencin 42.5 26 0.00056 32.6 3.1 27 20-46 62-88 (759)
28 PF03880 DbpA: DbpA RNA bindin 42.4 18 0.00039 23.1 1.6 23 21-43 52-74 (74)
29 cd00590 RRM RRM (RNA recogniti 41.9 34 0.00074 18.7 2.5 22 21-42 53-74 (74)
30 TIGR01161 purK phosphoribosyla 41.1 1.1E+02 0.0024 24.1 6.0 62 5-67 214-277 (352)
31 TIGR01659 sex-lethal sex-letha 40.7 33 0.00072 28.3 3.2 29 20-48 247-277 (346)
32 PRK14626 hypothetical protein; 40.0 65 0.0014 23.0 4.2 32 15-46 15-50 (110)
33 PF10731 Anophelin: Thrombin i 38.0 22 0.00048 24.2 1.5 24 80-103 30-53 (65)
34 TIGR01642 U2AF_lg U2 snRNP aux 37.2 36 0.00079 27.7 2.9 27 21-47 350-376 (509)
35 TIGR01659 sex-lethal sex-letha 36.2 32 0.0007 28.3 2.5 26 20-45 161-186 (346)
36 PRK00153 hypothetical protein; 36.1 90 0.002 21.3 4.4 25 13-37 11-35 (104)
37 KOG0111|consensus 35.3 29 0.00063 29.3 2.1 38 21-62 65-102 (298)
38 PF08952 DUF1866: Domain of un 33.6 38 0.00083 25.7 2.4 20 23-42 84-103 (146)
39 KOG0117|consensus 33.6 34 0.00074 30.9 2.4 24 23-46 308-331 (506)
40 PF14436 EndoU_bacteria: Bacte 33.1 58 0.0013 22.4 3.1 40 5-44 69-117 (128)
41 PRK03762 hypothetical protein; 32.4 1.1E+02 0.0023 21.8 4.3 33 13-45 13-49 (103)
42 cd02641 R3H_Smubp-2_like R3H d 31.3 44 0.00096 21.2 2.0 16 4-19 20-35 (60)
43 PRK14624 hypothetical protein; 30.9 1.1E+02 0.0024 22.2 4.3 31 14-44 15-49 (115)
44 KOG0484|consensus 30.5 51 0.0011 24.9 2.5 15 4-18 39-53 (125)
45 PRK14285 chaperone protein Dna 30.4 70 0.0015 26.3 3.6 30 4-33 333-362 (365)
46 PRK14622 hypothetical protein; 30.3 1.2E+02 0.0026 21.3 4.3 32 14-45 10-45 (103)
47 PF00329 Complex1_30kDa: Respi 30.3 30 0.00065 23.2 1.2 55 36-94 43-101 (103)
48 PRK14627 hypothetical protein; 29.0 1.3E+02 0.0029 20.9 4.3 23 14-36 10-32 (100)
49 TIGR00103 DNA_YbaB_EbfC DNA-bi 29.0 1.3E+02 0.0029 20.8 4.3 29 15-43 15-47 (102)
50 PRK06019 phosphoribosylaminoim 28.0 2E+02 0.0043 23.1 5.7 62 5-67 216-279 (372)
51 PF04667 Endosulfine: cAMP-reg 27.7 45 0.00097 23.1 1.7 19 6-24 3-21 (86)
52 PRK14625 hypothetical protein; 27.6 1.4E+02 0.0031 21.4 4.3 31 14-44 11-45 (109)
53 cd02639 R3H_RRM R3H domain of 27.0 57 0.0012 21.1 2.0 16 4-19 20-35 (60)
54 PF11629 Mst1_SARAH: C termina 26.9 10 0.00022 24.5 -1.5 13 42-54 36-48 (49)
55 PRK14568 vanB D-alanine--D-lac 26.9 2.3E+02 0.0049 22.5 5.8 57 5-62 259-316 (343)
56 KOG0109|consensus 26.7 41 0.0009 29.1 1.7 24 21-44 125-148 (346)
57 smart00733 Mterf Mitochondrial 26.7 69 0.0015 15.5 2.0 24 5-29 6-29 (31)
58 PF10957 DUF2758: Protein of u 26.4 1.7E+02 0.0038 19.2 4.2 33 12-44 10-42 (60)
59 PF14259 RRM_6: RNA recognitio 26.2 1.4E+02 0.0031 17.4 3.7 19 21-39 52-70 (70)
60 TIGR01628 PABP-1234 polyadenyl 25.6 66 0.0014 27.0 2.7 30 21-50 55-84 (562)
61 PRK14189 bifunctional 5,10-met 25.1 1.1E+02 0.0023 25.2 3.7 68 3-85 66-134 (285)
62 KOG0138|consensus 24.9 38 0.00082 29.9 1.2 19 3-21 48-66 (432)
63 PRK14621 hypothetical protein; 24.7 1.6E+02 0.0036 21.0 4.2 34 13-46 12-49 (111)
64 TIGR01642 U2AF_lg U2 snRNP aux 24.6 75 0.0016 25.9 2.7 25 21-45 477-501 (509)
65 PRK09288 purT phosphoribosylgl 24.1 3.6E+02 0.0078 21.2 7.0 59 5-65 235-294 (395)
66 PRK14571 D-alanyl-alanine synt 22.9 2.6E+02 0.0057 21.4 5.3 52 6-59 216-268 (299)
67 PF11705 RNA_pol_3_Rpc31: DNA- 22.6 1.1E+02 0.0023 23.6 3.1 30 3-32 40-69 (233)
68 COG0724 RNA-binding proteins ( 22.6 1.3E+02 0.0028 20.1 3.2 31 20-50 169-201 (306)
69 KOG0108|consensus 21.3 62 0.0013 28.2 1.8 37 9-50 66-102 (435)
70 smart00340 HALZ homeobox assoc 21.2 90 0.002 19.9 2.1 18 9-26 16-33 (44)
71 PF10646 Germane: Sporulation 20.8 1.9E+02 0.0041 18.8 3.6 38 1-40 65-108 (117)
72 PRK14623 hypothetical protein; 20.8 2.5E+02 0.0055 20.0 4.5 33 15-47 11-47 (106)
73 PRK14569 D-alanyl-alanine synt 20.8 3.9E+02 0.0085 20.7 5.9 52 5-57 214-266 (296)
74 PLN02616 tetrahydrofolate dehy 20.6 1.4E+02 0.0031 25.7 3.7 59 3-76 137-196 (364)
No 1
>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=90.99 E-value=0.29 Score=28.74 Aligned_cols=23 Identities=43% Similarity=0.515 Sum_probs=20.7
Q ss_pred HHHHHHHhcCceeeeeEEEeeee
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLA 43 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiA 43 (106)
-++|++.|||..+.|-.|+|+.|
T Consensus 34 A~~a~~~l~~~~~~g~~l~V~~a 56 (56)
T PF13893_consen 34 AQKAIEQLNGRQFNGRPLKVSYA 56 (56)
T ss_dssp HHHHHHHHTTSEETTEEEEEEEE
T ss_pred HHHHHHHhCCCEECCcEEEEEEC
Confidence 36789999999999999999986
No 2
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=88.05 E-value=0.74 Score=33.12 Aligned_cols=29 Identities=14% Similarity=0.260 Sum_probs=25.4
Q ss_pred HHHHHHHHhcCceeeeeEEEeeeeccccc
Q psy15193 20 KYQKLKRKVNGTHVQGVKLKVSLARRQLK 48 (106)
Q Consensus 20 ~~qklk~emnGt~V~gIqLKVSiARRQP~ 48 (106)
-.++|+++|||..+.|..|+|+.|+..|.
T Consensus 88 ~A~~Al~~lng~~i~Gr~l~V~~a~~~~~ 116 (144)
T PLN03134 88 AATAAISEMDGKELNGRHIRVNPANDRPS 116 (144)
T ss_pred HHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence 45778899999999999999999987665
No 3
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=81.68 E-value=5.6 Score=26.15 Aligned_cols=40 Identities=23% Similarity=0.330 Sum_probs=36.2
Q ss_pred eEEeCCCCCCHHHHHHHHHHHHHHHHhcCceeeeeEEEee
Q psy15193 2 VYIHFPSNHTEEEITLQAKYQKLKRKVNGTHVQGVKLKVS 41 (106)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~qklk~emnGt~V~gIqLKVS 41 (106)
+-+.|+.|+.+-=..+|.+..+...+|-|-.|..|.+.|.
T Consensus 66 v~v~~g~~i~~v~~~iq~~V~~~v~~~tg~~v~~V~V~V~ 105 (108)
T PF03780_consen 66 VVVEYGVNIPEVAEEIQEKVKEAVEEMTGIEVSEVNVHVE 105 (108)
T ss_pred EEEECCccHHHHHHHHHHHHHHHHHHHHCCeeEEEEEEEE
Confidence 4567999999999999999999999999999999988774
No 4
>KOG4207|consensus
Probab=80.31 E-value=2.2 Score=35.29 Aligned_cols=34 Identities=18% Similarity=0.233 Sum_probs=30.0
Q ss_pred HHHHHHHhcCceeeeeEEEeeeeccccccccccc
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLARRQLKVAPIND 54 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiARRQP~ld~ind 54 (106)
-++|.+.|+|.+|.|=.|+|+|||=.+..+.+..
T Consensus 68 aedA~damDG~~ldgRelrVq~arygr~~d~~~s 101 (256)
T KOG4207|consen 68 AEDALDAMDGAVLDGRELRVQMARYGRPSDLPHS 101 (256)
T ss_pred HHHHHHhhcceeeccceeeehhhhcCCCcccccc
Confidence 4688999999999999999999999998776555
No 5
>KOG0125|consensus
Probab=78.19 E-value=1.9 Score=37.37 Aligned_cols=27 Identities=26% Similarity=0.438 Sum_probs=23.6
Q ss_pred HHHHHHHHhcCceeeeeEEEeeeeccc
Q psy15193 20 KYQKLKRKVNGTHVQGVKLKVSLARRQ 46 (106)
Q Consensus 20 ~~qklk~emnGt~V~gIqLKVSiARRQ 46 (106)
.-++|++||||++|+|=+|.|..|---
T Consensus 148 dadRARa~LHgt~VEGRkIEVn~ATar 174 (376)
T KOG0125|consen 148 DADRARAELHGTVVEGRKIEVNNATAR 174 (376)
T ss_pred hHHHHHHHhhcceeeceEEEEeccchh
Confidence 457899999999999999999998643
No 6
>KOG0107|consensus
Probab=74.93 E-value=2.5 Score=33.82 Aligned_cols=27 Identities=19% Similarity=0.457 Sum_probs=25.0
Q ss_pred HHHHHHhcCceeeeeEEEeeeeccccc
Q psy15193 22 QKLKRKVNGTHVQGVKLKVSLARRQLK 48 (106)
Q Consensus 22 qklk~emnGt~V~gIqLKVSiARRQP~ 48 (106)
+.|++.|||+.++|.+|+|-|.+-+|-
T Consensus 61 ~DAvr~LDG~~~cG~r~rVE~S~G~~r 87 (195)
T KOG0107|consen 61 EDAVRYLDGKDICGSRIRVELSTGRPR 87 (195)
T ss_pred HHHHhhcCCccccCceEEEEeecCCcc
Confidence 579999999999999999999988876
No 7
>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=72.59 E-value=5 Score=32.18 Aligned_cols=27 Identities=22% Similarity=0.299 Sum_probs=23.4
Q ss_pred HHHHHHhcCceeeeeEEEeeeeccccc
Q psy15193 22 QKLKRKVNGTHVQGVKLKVSLARRQLK 48 (106)
Q Consensus 22 qklk~emnGt~V~gIqLKVSiARRQP~ 48 (106)
++|+.+|||..+.|-.|+|++|...+.
T Consensus 242 ~~A~~~l~g~~i~g~~i~v~~a~~~~~ 268 (457)
T TIGR01622 242 KEALEVMNGFELAGRPIKVGYAQDSTY 268 (457)
T ss_pred HHHHHhcCCcEECCEEEEEEEccCCCc
Confidence 568889999999999999999995543
No 8
>smart00361 RRM_1 RNA recognition motif.
Probab=67.61 E-value=5.9 Score=24.50 Aligned_cols=22 Identities=18% Similarity=0.256 Sum_probs=18.8
Q ss_pred HHHHHHHHhcCceeeeeEEEee
Q psy15193 20 KYQKLKRKVNGTHVQGVKLKVS 41 (106)
Q Consensus 20 ~~qklk~emnGt~V~gIqLKVS 41 (106)
.-++|++.|||..+.|-.|+++
T Consensus 49 dA~~A~~~l~g~~~~gr~l~~~ 70 (70)
T smart00361 49 DAARAIVDLNGRYFDGRTVKAE 70 (70)
T ss_pred HHHHHHHHhCCCEECCEEEEeC
Confidence 3467899999999999999875
No 9
>smart00362 RRM_2 RNA recognition motif.
Probab=66.41 E-value=6.9 Score=21.52 Aligned_cols=21 Identities=33% Similarity=0.474 Sum_probs=17.1
Q ss_pred HHHHHHHhcCceeeeeEEEee
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVS 41 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVS 41 (106)
-+++.+.++|..+.|.+|+|+
T Consensus 52 a~~a~~~~~~~~~~~~~i~v~ 72 (72)
T smart00362 52 AEKAIEALNGTKLGGRPLRVE 72 (72)
T ss_pred HHHHHHHhCCcEECCEEEeeC
Confidence 355778899999999998874
No 10
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=65.18 E-value=6.7 Score=30.08 Aligned_cols=23 Identities=22% Similarity=0.190 Sum_probs=21.1
Q ss_pred HHHHHHhcCceeeeeEEEeeeec
Q psy15193 22 QKLKRKVNGTHVQGVKLKVSLAR 44 (106)
Q Consensus 22 qklk~emnGt~V~gIqLKVSiAR 44 (106)
++|+..|||..+.|-.|+|+++-
T Consensus 325 ~~Ai~~lnG~~~~gr~i~V~~~~ 347 (352)
T TIGR01661 325 AMAILSLNGYTLGNRVLQVSFKT 347 (352)
T ss_pred HHHHHHhCCCEECCeEEEEEEcc
Confidence 58999999999999999999874
No 11
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=64.95 E-value=6.3 Score=32.95 Aligned_cols=28 Identities=25% Similarity=0.275 Sum_probs=24.6
Q ss_pred HHHHHHHhcCceeeeeEEEeeeeccccc
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLARRQLK 48 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiARRQP~ 48 (106)
-++|+..|||..+.|-+|+|++|+.+..
T Consensus 326 A~~Ai~~lng~~l~g~~l~v~~s~~~~~ 353 (481)
T TIGR01649 326 AQLALTHLNGVKLFGKPLRVCPSKQQNV 353 (481)
T ss_pred HHHHHHHhCCCEECCceEEEEEcccccc
Confidence 4678999999999999999999988643
No 12
>TIGR01205 D_ala_D_alaTIGR D-alanine--D-alanine ligase. but a number of antibiotic resistance proteins score above the trusted cutoff of this model.
Probab=63.32 E-value=27 Score=26.51 Aligned_cols=59 Identities=17% Similarity=0.173 Sum_probs=43.0
Q ss_pred eCCCCCCHH-HHHHHHHHHHHHHHhcCceeeeeEEEeeeecccccccccccccCCccccce
Q psy15193 5 HFPSNHTEE-EITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWSAI 64 (106)
Q Consensus 5 ~~~~~~~~~-~~~~~~~~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA~s~s~Wssl 64 (106)
+.|..++++ ...+++--.++.+.|+..-+.+|++++. ...+|.+-+||...|-+.++.+
T Consensus 234 ~~p~~l~~~~~~~i~~~a~~~~~~lg~~G~~~vD~~~~-~~g~~~viEvN~~pg~~~~s~~ 293 (315)
T TIGR01205 234 VIPAPLDEELEEKIKELALKAYKALGCRGLARVDFFLD-EEGEIYLNEINTIPGMTAISLF 293 (315)
T ss_pred EeCCCCCHHHHHHHHHHHHHHHHHhCCCceEEEEEEEe-CCCCEEEEEeeCCCCCCCccHH
Confidence 467778754 4567777788899998776778888876 4447999999997666655443
No 13
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=58.98 E-value=9.1 Score=29.34 Aligned_cols=25 Identities=36% Similarity=0.438 Sum_probs=22.2
Q ss_pred HHHHHHHhcCceeeeeEEEeeeecc
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLARR 45 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiARR 45 (106)
-++|+.+|||..+.|-.|+|..|+.
T Consensus 58 A~~Ai~~l~g~~l~g~~i~v~~a~~ 82 (352)
T TIGR01661 58 AEKAVNSLNGLRLQNKTIKVSYARP 82 (352)
T ss_pred HHHHHhhcccEEECCeeEEEEeecc
Confidence 4678899999999999999999874
No 14
>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=58.71 E-value=14 Score=21.07 Aligned_cols=20 Identities=25% Similarity=0.526 Sum_probs=16.4
Q ss_pred HHHHHHHHhcCceeeeeEEE
Q psy15193 20 KYQKLKRKVNGTHVQGVKLK 39 (106)
Q Consensus 20 ~~qklk~emnGt~V~gIqLK 39 (106)
..++++++|||..+.|-.||
T Consensus 51 ~a~~a~~~l~g~~~~~~~ir 70 (70)
T PF00076_consen 51 DAEKALEELNGKKINGRKIR 70 (70)
T ss_dssp HHHHHHHHHTTEEETTEEEE
T ss_pred HHHHHHHHcCCCEECccCcC
Confidence 34678889999999998876
No 15
>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=58.49 E-value=9 Score=32.06 Aligned_cols=25 Identities=28% Similarity=0.418 Sum_probs=22.6
Q ss_pred HHHHHHHhcCceeeeeEEEeeeecc
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLARR 45 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiARR 45 (106)
-.+|+.+|||..+.|-.|+|.+|++
T Consensus 339 A~~A~~~~~g~~~~gk~l~V~~a~~ 363 (562)
T TIGR01628 339 ANRAVTEMHGRMLGGKPLYVALAQR 363 (562)
T ss_pred HHHHHHHhcCCeeCCceeEEEeccC
Confidence 3578899999999999999999986
No 16
>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=58.04 E-value=10 Score=33.89 Aligned_cols=24 Identities=29% Similarity=0.558 Sum_probs=21.9
Q ss_pred HHHHHHhcCceeeeeEEEeeeecc
Q psy15193 22 QKLKRKVNGTHVQGVKLKVSLARR 45 (106)
Q Consensus 22 qklk~emnGt~V~gIqLKVSiARR 45 (106)
++|+++|||+.+.|-.|+|++|+.
T Consensus 283 ~kAi~~lnG~~i~Gr~I~V~~Akp 306 (578)
T TIGR01648 283 VKAMDELNGKELEGSEIEVTLAKP 306 (578)
T ss_pred HHHHHHhCCCEECCEEEEEEEccC
Confidence 578899999999999999999964
No 17
>KOG0145|consensus
Probab=57.50 E-value=9.9 Score=32.65 Aligned_cols=34 Identities=35% Similarity=0.419 Sum_probs=28.7
Q ss_pred HHHHHHHHhcCceeeeeEEEeeeecccccccccccc
Q psy15193 20 KYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDA 55 (106)
Q Consensus 20 ~~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA 55 (106)
.-.||+.-+||...+.-.||||.|| |..+.|-+|
T Consensus 95 DAe~AintlNGLrLQ~KTIKVSyAR--PSs~~Ik~a 128 (360)
T KOG0145|consen 95 DAEKAINTLNGLRLQNKTIKVSYAR--PSSDSIKDA 128 (360)
T ss_pred HHHHHHhhhcceeeccceEEEEecc--CChhhhccc
Confidence 3478999999999999999999999 666666664
No 18
>TIGR01142 purT phosphoribosylglycinamide formyltransferase 2. This enzyme is an alternative to PurN (TIGR00639)
Probab=53.81 E-value=55 Score=25.60 Aligned_cols=57 Identities=16% Similarity=0.226 Sum_probs=42.2
Q ss_pred CCCCCCHHH-HHHHHHHHHHHHHhcCceeeeeEEEeeeecccccccccccccCCccccce
Q psy15193 6 FPSNHTEEE-ITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWSAI 64 (106)
Q Consensus 6 ~~~~~~~~~-~~~~~~~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA~s~s~Wssl 64 (106)
+|..++++. ..+++--.++.+.|++.-+-+|.+.+. ..+|.+-+||.-.+++.+..+
T Consensus 223 ~p~~l~~~~~~~i~~~a~~~~~~l~~~G~~~ie~~~~--~~~~~viEinpR~~~~~~~~~ 280 (380)
T TIGR01142 223 QPQEMSEKALEEAQRIAKRITDALGGYGLFGVELFVK--GDEVIFSEVSPRPHDTGMVTL 280 (380)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCCcceEEEEEEEE--CCcEEEEEeecCCCCCceEEe
Confidence 788888874 456666788999999877777777764 668999999986666533333
No 19
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=51.99 E-value=14 Score=33.38 Aligned_cols=27 Identities=15% Similarity=0.068 Sum_probs=24.8
Q ss_pred HHHHHHhcCceeeeeEEEeeeeccccc
Q psy15193 22 QKLKRKVNGTHVQGVKLKVSLARRQLK 48 (106)
Q Consensus 22 qklk~emnGt~V~gIqLKVSiARRQP~ 48 (106)
++|+.+|||..++|-.|+|..|+..|.
T Consensus 260 ~kAI~amNg~elgGr~LrV~kAi~pP~ 286 (612)
T TIGR01645 260 SEAIASMNLFDLGGQYLRVGKCVTPPD 286 (612)
T ss_pred HHHHHHhCCCeeCCeEEEEEecCCCcc
Confidence 589999999999999999999998774
No 20
>smart00360 RRM RNA recognition motif.
Probab=51.50 E-value=15 Score=19.97 Aligned_cols=20 Identities=35% Similarity=0.529 Sum_probs=16.4
Q ss_pred HHHHHHhcCceeeeeEEEee
Q psy15193 22 QKLKRKVNGTHVQGVKLKVS 41 (106)
Q Consensus 22 qklk~emnGt~V~gIqLKVS 41 (106)
+++++.|+|..+.|-+|+|+
T Consensus 52 ~~a~~~~~~~~~~~~~~~v~ 71 (71)
T smart00360 52 EKALEALNGKELDGRPLKVK 71 (71)
T ss_pred HHHHHHcCCCeeCCcEEEeC
Confidence 45688999999999888874
No 21
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=51.18 E-value=16 Score=26.95 Aligned_cols=27 Identities=30% Similarity=0.434 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCceee
Q psy15193 8 SNHTEEEITLQAKYQKLKRKVNGTHVQ 34 (106)
Q Consensus 8 ~~~~~~~~~~~~~~qklk~emnGt~V~ 34 (106)
+..++++..|+++++++++||++.--+
T Consensus 36 ~~~~~~~~~l~~Ei~~l~~E~~~iS~q 62 (161)
T PF04420_consen 36 SKSSKEQRQLRKEILQLKRELNAISAQ 62 (161)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHTTS-TT
T ss_pred ccccHHHHHHHHHHHHHHHHHHcCCcH
Confidence 556789999999999999999986443
No 22
>PRK14192 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=49.67 E-value=27 Score=28.05 Aligned_cols=35 Identities=20% Similarity=0.424 Sum_probs=26.3
Q ss_pred eEEeCCCCCCHHHHHHHHHHHHHHHHhcCc-eeeeeEEEeee
Q psy15193 2 VYIHFPSNHTEEEITLQAKYQKLKRKVNGT-HVQGVKLKVSL 42 (106)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~qklk~emnGt-~V~gIqLKVSi 42 (106)
.|++||.+.++|++ .++++++|.. .|.||-++.=+
T Consensus 66 ~~~~l~~~~~~~~l------~~~i~~Ln~d~~v~Gi~VqlPl 101 (283)
T PRK14192 66 LKVELPQETTTEQL------LAKIEELNANPDVHGILLQHPV 101 (283)
T ss_pred EEEECCCCCCHHHH------HHHHHHHhCCCCCCEEEEeCCC
Confidence 69999999997763 3566677776 68998887543
No 23
>KOG0110|consensus
Probab=48.89 E-value=13 Score=34.70 Aligned_cols=44 Identities=20% Similarity=0.329 Sum_probs=36.9
Q ss_pred HHHHHHHhcCceeeeeEEEeeeecccccccccccccCCccccceeeccCC
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWSAIACHQSL 70 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA~s~s~WsslA~~~Sq 70 (106)
-|+|++..|++-++-..|.|.+|+ ++.++.-..+||..|...+.
T Consensus 22 A~~Ai~~fn~s~i~ts~i~Ve~~~------~~gd~~kpr~wsk~a~~~~~ 65 (725)
T KOG0110|consen 22 AQKAIKYFNKSFINTSRITVEFCK------SFGDPNKPRPWSKYAKKSSE 65 (725)
T ss_pred HHHHHHHhhccccccceEEEEehh------hcCCcccCcchhhhhhhhhh
Confidence 489999999999999999999998 34566778999999865543
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=44.89 E-value=22 Score=29.80 Aligned_cols=28 Identities=25% Similarity=0.302 Sum_probs=23.4
Q ss_pred HHHHHHhcCceee--eeEEEeeeecccccc
Q psy15193 22 QKLKRKVNGTHVQ--GVKLKVSLARRQLKV 49 (106)
Q Consensus 22 qklk~emnGt~V~--gIqLKVSiARRQP~l 49 (106)
++|+..|||..+. ++.|+|..|+.+.+-
T Consensus 148 ~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~ 177 (481)
T TIGR01649 148 QHAKAALNGADIYNGCCTLKIEYAKPTRLN 177 (481)
T ss_pred HHHHHHhcCCcccCCceEEEEEEecCCCce
Confidence 6789999999995 379999999976653
No 25
>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=44.20 E-value=28 Score=24.95 Aligned_cols=38 Identities=21% Similarity=0.479 Sum_probs=23.2
Q ss_pred eEEeCCCCCCHHHHHHHHHHHHHHHHhcCceeeeeEEEeeeeccccc
Q psy15193 2 VYIHFPSNHTEEEITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLK 48 (106)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~qklk~emnGt~V~gIqLKVSiARRQP~ 48 (106)
.+|+|++. .--+.|.+.|+|-.|=|-+|.||.+.++--
T Consensus 42 AilrF~~~---------~~A~RA~KRmegEdVfG~kI~v~~~~~~r~ 79 (90)
T PF11608_consen 42 AILRFPNQ---------EFAERAQKRMEGEDVFGNKISVSFSPKNRE 79 (90)
T ss_dssp EEEEESSH---------HHHHHHHHHHTT--SSSS--EEESS--S--
T ss_pred EEEEeCCH---------HHHHHHHHhhcccccccceEEEEEcCCccc
Confidence 36778762 234578889999999999999999976644
No 26
>PRK14629 hypothetical protein; Provisional
Probab=42.80 E-value=33 Score=24.31 Aligned_cols=37 Identities=14% Similarity=0.297 Sum_probs=28.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcCceeeeeE----EEeeee
Q psy15193 7 PSNHTEEEITLQAKYQKLKRKVNGTHVQGVK----LKVSLA 43 (106)
Q Consensus 7 ~~~~~~~~~~~~~~~qklk~emnGt~V~gIq----LKVSiA 43 (106)
|.++-..-..+|+|.+++.++|...+|.|.- ++|.+-
T Consensus 5 ~~~~mkqaq~mQ~km~~~Q~eL~~~~veg~aggGlVkV~~n 45 (99)
T PRK14629 5 PLDFLKNMSSFKDNIDNIKKEISQIVVCGRAGSDVVVVEMN 45 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccEEEEEecCCEEEEEEE
Confidence 3344445567899999999999999998875 666663
No 27
>PLN03213 repressor of silencing 3; Provisional
Probab=42.48 E-value=26 Score=32.59 Aligned_cols=27 Identities=26% Similarity=0.358 Sum_probs=24.1
Q ss_pred HHHHHHHHhcCceeeeeEEEeeeeccc
Q psy15193 20 KYQKLKRKVNGTHVQGVKLKVSLARRQ 46 (106)
Q Consensus 20 ~~qklk~emnGt~V~gIqLKVSiARRQ 46 (106)
..++|+..|||+...|=+|||..||-.
T Consensus 62 EeeKAISaLNGAEWKGR~LKVNKAKP~ 88 (759)
T PLN03213 62 SLTKLFSTYNGCVWKGGRLRLEKAKEH 88 (759)
T ss_pred HHHHHHHHhcCCeecCceeEEeeccHH
Confidence 457999999999999999999999743
No 28
>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins [].; PDB: 2G0C_A 3MOJ_B.
Probab=42.42 E-value=18 Score=23.10 Aligned_cols=23 Identities=30% Similarity=0.527 Sum_probs=13.5
Q ss_pred HHHHHHHhcCceeeeeEEEeeee
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLA 43 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiA 43 (106)
-+++.+.|++..+.|-.|+|.+|
T Consensus 52 a~~v~~~l~~~~~~gk~v~ve~A 74 (74)
T PF03880_consen 52 AEKVLEALNGKKIKGKKVRVERA 74 (74)
T ss_dssp HHHHHHHHTT--SSS----EEE-
T ss_pred HHHHHHHhcCCCCCCeeEEEEEC
Confidence 35678899999999999999987
No 29
>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=41.88 E-value=34 Score=18.74 Aligned_cols=22 Identities=27% Similarity=0.443 Sum_probs=17.3
Q ss_pred HHHHHHHhcCceeeeeEEEeee
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSL 42 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSi 42 (106)
-+.++.+++|....|-.++|++
T Consensus 53 a~~a~~~~~~~~~~~~~~~v~~ 74 (74)
T cd00590 53 AEKALEALNGKELGGRPLRVEF 74 (74)
T ss_pred HHHHHHHhCCCeECCeEEEEeC
Confidence 3567788999999998888864
No 30
>TIGR01161 purK phosphoribosylaminoimidazole carboxylase, PurK protein. Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, N5-carboxyaminoimidazole ribonucleotide synthetase, which hydrolyzes ATP and converts AIR to N5-CAIR. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP.
Probab=41.13 E-value=1.1e+02 Score=24.06 Aligned_cols=62 Identities=11% Similarity=0.190 Sum_probs=40.8
Q ss_pred eCCCCCCHH-HHHHHHHHHHHHHHhcCceeeeeEEEeeeecccccccccccccCCc-cccceeec
Q psy15193 5 HFPSNHTEE-EITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAASST-TWSAIACH 67 (106)
Q Consensus 5 ~~~~~~~~~-~~~~~~~~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA~s~s-~WsslA~~ 67 (106)
.+|.+++++ ...+++--+++.+.|+..-+-+|.+.+. +.-+|.+-+||.--+++ .|+-.++.
T Consensus 214 ~~p~~~~~~~~~~~~~~a~~i~~~l~~~G~~~ve~~~~-~dg~~~v~EinpR~~~sg~~~~~~~~ 277 (352)
T TIGR01161 214 VAPAAVPDAIQARAEEIARRLMEELGYVGVLAVEMFVL-PDGRLLINELAPRVHNSGHYTLDGCS 277 (352)
T ss_pred ECCCCCCHHHHHHHHHHHHHHHHHcCceeEEEEEEEEe-CCCcEEEEEecCCCCCcCcCchhhcc
Confidence 468888765 4455666678888888765666666654 34469998899755433 45544443
No 31
>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=40.69 E-value=33 Score=28.26 Aligned_cols=29 Identities=28% Similarity=0.251 Sum_probs=23.7
Q ss_pred HHHHHHHHhcCceeee--eEEEeeeeccccc
Q psy15193 20 KYQKLKRKVNGTHVQG--VKLKVSLARRQLK 48 (106)
Q Consensus 20 ~~qklk~emnGt~V~g--IqLKVSiARRQP~ 48 (106)
.-++|+++|||..+.+ ..|+|.+|+.+..
T Consensus 247 ~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~ 277 (346)
T TIGR01659 247 EAQEAISALNNVIPEGGSQPLTVRLAEEHGK 277 (346)
T ss_pred HHHHHHHHhCCCccCCCceeEEEEECCcccc
Confidence 3468899999998876 7999999987644
No 32
>PRK14626 hypothetical protein; Provisional
Probab=39.96 E-value=65 Score=22.96 Aligned_cols=32 Identities=13% Similarity=0.100 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHhcCceeeeeE----EEeeeeccc
Q psy15193 15 ITLQAKYQKLKRKVNGTHVQGVK----LKVSLARRQ 46 (106)
Q Consensus 15 ~~~~~~~qklk~emnGt~V~gIq----LKVSiARRQ 46 (106)
+.+|++.+++..+|...+|.+-- ++|.+--.+
T Consensus 15 q~mQ~km~~~qeeL~~~~v~g~sggG~VkV~~nG~~ 50 (110)
T PRK14626 15 QSIKENVEKAKEELKKEEIVVEVGGGMVKVVSNGLG 50 (110)
T ss_pred HHHHHHHHHHHHHHhccEEEEEecCcEEEEEEECCc
Confidence 45789999999999999987754 666654443
No 33
>PF10731 Anophelin: Thrombin inhibitor from mosquito; InterPro: IPR018932 Members of this family are all inhibitors of thrombin, the peptidase that is at the end of the blood coagulation cascade and which creates the clot by cleaving fibrinogen. The interaction between thrombin and fibrinogen involves two different areas of contact - via the thrombin active site and via a second substrate-binding site known as an exosite. The inhibitor acts by blocking the exosite, rather than by interacting with the active site. The inhibitors are from mosquitoes that feed on human blood and which, by inhibiting thrombin, prevent the blood from clotting and keep it flowing.
Probab=37.97 E-value=22 Score=24.23 Aligned_cols=24 Identities=29% Similarity=0.371 Sum_probs=18.0
Q ss_pred eeeecccccCCCCCCCCCcccccc
Q psy15193 80 QVIYDDDIFGEEPPLEDPDSIAME 103 (106)
Q Consensus 80 lV~YddDlF~e~~~~~~~~~~~~~ 103 (106)
-=+||+|.|.++|-.+.-.|+.-+
T Consensus 30 eP~YDEdd~dde~l~phsss~~d~ 53 (65)
T PF10731_consen 30 EPSYDEDDDDDEPLKPHSSSITDD 53 (65)
T ss_pred CCCcCcccCcccccccCCCCCCcc
Confidence 347999999999887766666433
No 34
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=37.18 E-value=36 Score=27.67 Aligned_cols=27 Identities=22% Similarity=0.099 Sum_probs=23.2
Q ss_pred HHHHHHHhcCceeeeeEEEeeeecccc
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLARRQL 47 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiARRQP 47 (106)
-++|+..|||..+.|-.|+|..|+...
T Consensus 350 a~~A~~~l~g~~~~~~~l~v~~a~~~~ 376 (509)
T TIGR01642 350 TDVAIAALNGKDTGDNKLHVQRACVGA 376 (509)
T ss_pred HHHHHHHcCCCEECCeEEEEEECccCC
Confidence 357889999999999999999997544
No 35
>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=36.24 E-value=32 Score=28.33 Aligned_cols=26 Identities=38% Similarity=0.524 Sum_probs=22.6
Q ss_pred HHHHHHHHhcCceeeeeEEEeeeecc
Q psy15193 20 KYQKLKRKVNGTHVQGVKLKVSLARR 45 (106)
Q Consensus 20 ~~qklk~emnGt~V~gIqLKVSiARR 45 (106)
.-++|+++|||..+.+-.|+|+.|+.
T Consensus 161 ~A~~Ai~~LnG~~l~gr~i~V~~a~p 186 (346)
T TIGR01659 161 DSQRAIKNLNGITVRNKRLKVSYARP 186 (346)
T ss_pred HHHHHHHHcCCCccCCceeeeecccc
Confidence 34678889999999999999999974
No 36
>PRK00153 hypothetical protein; Validated
Probab=36.06 E-value=90 Score=21.34 Aligned_cols=25 Identities=24% Similarity=0.399 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHhcCceeeeeE
Q psy15193 13 EEITLQAKYQKLKRKVNGTHVQGVK 37 (106)
Q Consensus 13 ~~~~~~~~~qklk~emnGt~V~gIq 37 (106)
.-..+|++++++.++|...+|++--
T Consensus 11 qaq~~q~~~~~~q~~l~~~~~~~~s 35 (104)
T PRK00153 11 QAQQMQEKMQKMQEELAQMEVEGEA 35 (104)
T ss_pred HHHHHHHHHHHHHHHHhccEEEEEE
Confidence 3456899999999999999987653
No 37
>KOG0111|consensus
Probab=35.35 E-value=29 Score=29.26 Aligned_cols=38 Identities=16% Similarity=0.340 Sum_probs=28.7
Q ss_pred HHHHHHHhcCceeeeeEEEeeeecccccccccccccCCcccc
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWS 62 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA~s~s~Ws 62 (106)
-..|+.-||++...|-.|+|.+|+---.- .-++.-+|+
T Consensus 65 AaaAiDNMnesEL~GrtirVN~AkP~kik----egsqkPvWA 102 (298)
T KOG0111|consen 65 AAAAIDNMNESELFGRTIRVNLAKPEKIK----EGSQKPVWA 102 (298)
T ss_pred hHHHhhcCchhhhcceeEEEeecCCcccc----CCCCCCccc
Confidence 35689999999999999999999843322 335566665
No 38
>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function. ; PDB: 1UFW_A 2DNR_A.
Probab=33.62 E-value=38 Score=25.74 Aligned_cols=20 Identities=30% Similarity=0.473 Sum_probs=17.4
Q ss_pred HHHHHhcCceeeeeEEEeee
Q psy15193 23 KLKRKVNGTHVQGVKLKVSL 42 (106)
Q Consensus 23 klk~emnGt~V~gIqLKVSi 42 (106)
-+...|+|++|+|..|+|++
T Consensus 84 Laals~dg~~v~g~~l~i~L 103 (146)
T PF08952_consen 84 LAALSLDGIQVNGRTLKIRL 103 (146)
T ss_dssp HHHHHGCCSEETTEEEEEEE
T ss_pred HHHHccCCcEECCEEEEEEe
Confidence 34578999999999999987
No 39
>KOG0117|consensus
Probab=33.61 E-value=34 Score=30.90 Aligned_cols=24 Identities=29% Similarity=0.538 Sum_probs=21.7
Q ss_pred HHHHHhcCceeeeeEEEeeeeccc
Q psy15193 23 KLKRKVNGTHVQGVKLKVSLARRQ 46 (106)
Q Consensus 23 klk~emnGt~V~gIqLKVSiARRQ 46 (106)
||.++|||+.++|--|-|.||+-|
T Consensus 308 kAm~~~ngkeldG~~iEvtLAKP~ 331 (506)
T KOG0117|consen 308 KAMKETNGKELDGSPIEVTLAKPV 331 (506)
T ss_pred HHHHHhcCceecCceEEEEecCCh
Confidence 688999999999999999999743
No 40
>PF14436 EndoU_bacteria: Bacterial EndoU nuclease
Probab=33.10 E-value=58 Score=22.42 Aligned_cols=40 Identities=25% Similarity=0.355 Sum_probs=26.6
Q ss_pred eCCCCCCHHHHHHHHHHH--HH-------HHHhcCceeeeeEEEeeeec
Q psy15193 5 HFPSNHTEEEITLQAKYQ--KL-------KRKVNGTHVQGVKLKVSLAR 44 (106)
Q Consensus 5 ~~~~~~~~~~~~~~~~~q--kl-------k~emnGt~V~gIqLKVSiAR 44 (106)
=||.+.|+++++...+.. .. ....-|.+.+||+++|=+.+
T Consensus 69 ~FP~~ws~~~I~~~i~~a~~n~~~~~~~~~~~~~~~~~~Gv~i~v~~~~ 117 (128)
T PF14436_consen 69 FFPKNWSDEKILDEIQEAYKNKYSVPRRNGNCWVGGTSSGVKIEVYVDK 117 (128)
T ss_pred ECCccCCHHHHHHHHHHHHhCCCcceecCCCEEEEEecCCEEEEEEEeC
Confidence 499999999987655432 21 22344556778888876665
No 41
>PRK03762 hypothetical protein; Provisional
Probab=32.39 E-value=1.1e+02 Score=21.77 Aligned_cols=33 Identities=15% Similarity=0.139 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHhcCceeeeeE----EEeeeecc
Q psy15193 13 EEITLQAKYQKLKRKVNGTHVQGVK----LKVSLARR 45 (106)
Q Consensus 13 ~~~~~~~~~qklk~emnGt~V~gIq----LKVSiARR 45 (106)
--..+|+|.+++..++...+|.|.- ++|.+--.
T Consensus 13 qaqkmQ~km~~~Q~el~~~~v~g~sggGlVkV~~nG~ 49 (103)
T PRK03762 13 MLEQMQKKAKQLEEENANKEFTAKSGGGLVSVSANGK 49 (103)
T ss_pred HHHHHHHHHHHHHHHHhccEEEEEEcCceEEEEEEcC
Confidence 3456899999999999999998764 66655433
No 42
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=31.34 E-value=44 Score=21.20 Aligned_cols=16 Identities=19% Similarity=0.409 Sum_probs=12.9
Q ss_pred EeCCCCCCHHHHHHHH
Q psy15193 4 IHFPSNHTEEEITLQA 19 (106)
Q Consensus 4 ~~~~~~~~~~~~~~~~ 19 (106)
++||+++|..|..+=-
T Consensus 20 l~F~p~ls~~eR~~vH 35 (60)
T cd02641 20 LEFPPTLSSHDRLLVH 35 (60)
T ss_pred EECCCCCCHHHHHHHH
Confidence 7999999999876543
No 43
>PRK14624 hypothetical protein; Provisional
Probab=30.89 E-value=1.1e+02 Score=22.16 Aligned_cols=31 Identities=16% Similarity=0.305 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHhcCceeeeeE----EEeeeec
Q psy15193 14 EITLQAKYQKLKRKVNGTHVQGVK----LKVSLAR 44 (106)
Q Consensus 14 ~~~~~~~~qklk~emnGt~V~gIq----LKVSiAR 44 (106)
-+.+|+|.+++..+|...+|.|-- ++|.+--
T Consensus 15 Aq~mQ~km~~~QeeL~~~~v~g~sGgG~VkV~~nG 49 (115)
T PRK14624 15 MGNIREKMEEVKKRIASIRVVGDAGAGMVTVTATG 49 (115)
T ss_pred HHHHHHHHHHHHHHHhccEEEEEECCcEEEEEEEc
Confidence 356899999999999999998764 6665443
No 44
>KOG0484|consensus
Probab=30.49 E-value=51 Score=24.88 Aligned_cols=15 Identities=47% Similarity=0.751 Sum_probs=13.0
Q ss_pred EeCCCCCCHHHHHHH
Q psy15193 4 IHFPSNHTEEEITLQ 18 (106)
Q Consensus 4 ~~~~~~~~~~~~~~~ 18 (106)
-|||.-+|.||+.|.
T Consensus 39 THYPDIYTREEiA~k 53 (125)
T KOG0484|consen 39 THYPDIYTREEIALK 53 (125)
T ss_pred hcCCcchhHHHHHHh
Confidence 499999999998764
No 45
>PRK14285 chaperone protein DnaJ; Provisional
Probab=30.40 E-value=70 Score=26.33 Aligned_cols=30 Identities=20% Similarity=0.313 Sum_probs=24.9
Q ss_pred EeCCCCCCHHHHHHHHHHHHHHHHhcCcee
Q psy15193 4 IHFPSNHTEEEITLQAKYQKLKRKVNGTHV 33 (106)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~qklk~emnGt~V 33 (106)
+.||.+||+++..|-+++.++.+.++.-+.
T Consensus 333 v~~P~~l~~~q~~~l~~l~~~~~~~~~~~~ 362 (365)
T PRK14285 333 IKTPKNLNSNAIKLLENLSKELKDIDEITL 362 (365)
T ss_pred EECCCCCCHHHHHHHHHHHHHhccccceee
Confidence 568999999999999998888887766554
No 46
>PRK14622 hypothetical protein; Provisional
Probab=30.31 E-value=1.2e+02 Score=21.26 Aligned_cols=32 Identities=19% Similarity=0.266 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHhcCceeeeeE----EEeeeecc
Q psy15193 14 EITLQAKYQKLKRKVNGTHVQGVK----LKVSLARR 45 (106)
Q Consensus 14 ~~~~~~~~qklk~emnGt~V~gIq----LKVSiARR 45 (106)
-+.+|++.+++..+|....|.|-- ++|.+--.
T Consensus 10 aq~mQ~~m~~~q~el~~~~v~g~sggG~VkV~~nG~ 45 (103)
T PRK14622 10 AKKLEKAMADAKEKLAEIAVEAESGGGLVKVAMNGK 45 (103)
T ss_pred HHHHHHHHHHHHHHHhccEEEEEECCceEEEEEEcC
Confidence 355899999999999999998754 55555433
No 47
>PF00329 Complex1_30kDa: Respiratory-chain NADH dehydrogenase, 30 Kd subunit; InterPro: IPR001268 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. The 30 kDa subunit from NADH:ubiquinone oxidoreductase is found in both eukaryotes and prokaryotes. In mammals and in Neurospora crassa, it is nuclear-encoded as a precursor form with a transit peptide, while in Paramecium (protein P1), in the Dictyostelium discoideum (Slime mold) it is mitochondrial-encoded and it is chloroplast-encoded in various higher plants. It is also present in bacteria.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0055114 oxidation-reduction process; PDB: 2YBB_5 3IAS_E 2FUG_E 3I9V_5 3M9S_E 3IAM_5 3MCR_A.
Probab=30.29 E-value=30 Score=23.22 Aligned_cols=55 Identities=22% Similarity=0.407 Sum_probs=32.4
Q ss_pred eEEEeeeecccccccccccccCCccccceeec---c-CCCCCCCCCcceeeecccccCCCCCC
Q psy15193 36 VKLKVSLARRQLKVAPINDAASSTTWSAIACH---Q-SLKGNHKDKRHQVIYDDDIFGEEPPL 94 (106)
Q Consensus 36 IqLKVSiARRQP~ld~indA~s~s~WsslA~~---~-SqKGshkDkR~lV~YddDlF~e~~~~ 94 (106)
+.|+|.+.|..|.++.|.+.--++-|--.... + .-.| |.|.|.++.- +.|.. .||
T Consensus 43 ~~v~~~v~~~~~~ipSit~i~p~A~~~ERE~~DmfGI~f~G-hPd~rrlll~--~~~~~-~PL 101 (103)
T PF00329_consen 43 VRVKVKVPRENPEIPSITPIFPAADWYEREIYDMFGIRFEG-HPDLRRLLLP--EDWPG-HPL 101 (103)
T ss_dssp EEEEEEE-TTS-EEE--TTT-TTHHHHHHHHHHHCHHECCT--CCGS-SSSS--TTSSS--TT
T ss_pred EEEEEEeccCCCcccceeEEEcCceecCcHHHhhcCCEeCC-CCCCccccCC--CCCCC-CCC
Confidence 78999999999999988877777777654432 2 3455 8888877763 34555 555
No 48
>PRK14627 hypothetical protein; Provisional
Probab=29.02 E-value=1.3e+02 Score=20.90 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHhcCceeeee
Q psy15193 14 EITLQAKYQKLKRKVNGTHVQGV 36 (106)
Q Consensus 14 ~~~~~~~~qklk~emnGt~V~gI 36 (106)
-+.+|+|.+++..+|....|+|.
T Consensus 10 aq~mQ~km~~~Q~el~~~~veg~ 32 (100)
T PRK14627 10 AQQMQRQMQKVQEELAATIVEGT 32 (100)
T ss_pred HHHHHHHHHHHHHHHhccEEEEE
Confidence 34589999999999999999765
No 49
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=28.99 E-value=1.3e+02 Score=20.77 Aligned_cols=29 Identities=24% Similarity=0.416 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHhcCceeeeeE----EEeeee
Q psy15193 15 ITLQAKYQKLKRKVNGTHVQGVK----LKVSLA 43 (106)
Q Consensus 15 ~~~~~~~qklk~emnGt~V~gIq----LKVSiA 43 (106)
+.+|.+.+++.++|....|.|.- ++|.+-
T Consensus 15 q~mQ~k~~~~q~eL~~~~v~g~sggGlV~V~~~ 47 (102)
T TIGR00103 15 QQMQEKMKKLQEEIAQFEVTGKSGAGLVTVTIN 47 (102)
T ss_pred HHHHHHHHHHHHHHhccEEEEEECCCEEEEEEE
Confidence 45788999999999999998743 555543
No 50
>PRK06019 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed
Probab=28.03 E-value=2e+02 Score=23.12 Aligned_cols=62 Identities=19% Similarity=0.304 Sum_probs=41.3
Q ss_pred eCCCCCCHH-HHHHHHHHHHHHHHhcCceeeeeEEEeeeeccccccccccccc-CCccccceeec
Q psy15193 5 HFPSNHTEE-EITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAA-SSTTWSAIACH 67 (106)
Q Consensus 5 ~~~~~~~~~-~~~~~~~~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA~-s~s~WsslA~~ 67 (106)
.+|.+++++ +..+++--.++.+.|+..-|-+|.+.+. .-.+|.+.+||.-. ++.-|+..++.
T Consensus 216 ~~pa~~~~~~~~~~~~~a~~i~~~L~~~G~~~vEff~~-~dg~~~v~EinpR~~~sg~~t~~~~~ 279 (372)
T PRK06019 216 IAPARISAELQAQAEEIASRIAEELDYVGVLAVEFFVT-GDGELLVNEIAPRPHNSGHWTIEACS 279 (372)
T ss_pred ECCCCCCHHHHHHHHHHHHHHHHHcCccceeEEEEEEc-CCCeEEEEEecCCccCcccEEhhhcC
Confidence 478888764 3456666677888888866767777763 34569999999743 34567654443
No 51
>PF04667 Endosulfine: cAMP-regulated phosphoprotein/endosulfine conserved region; InterPro: IPR006760 This endosulphine family includes cAMP-regulated phosphoprotein 19 (ARPP-19), alpha endosulphine and protein Igo1. No function has yet been assigned to ARPP-19 []. Endosulphine is the endogenous ligand for the ATP-dependent potassium channels which occupy a key position in the control of insulin release from the pancreatic beta cell by coupling cell polarity to metabolism []. Igo1 is required for initiation of G0 program. In the absence of stimulatory signals, cells may enter into a reversible quiescence (or G0) state that is typically characterised by low metabolic activity, including low rates of protein synthesis and transcription. Igo proteins associate with the mRNA decapping activator Dhh1, sheltering newly expressed mRNAs from degradation via the 5'-3' mRNA decay pathway, and thereby enabling their proper translation during initiation of the G0 program [].
Probab=27.68 E-value=45 Score=23.05 Aligned_cols=19 Identities=53% Similarity=0.541 Sum_probs=15.1
Q ss_pred CCCCCCHHHHHHHHHHHHH
Q psy15193 6 FPSNHTEEEITLQAKYQKL 24 (106)
Q Consensus 6 ~~~~~~~~~~~~~~~~qkl 24 (106)
..+.++|||..|.+||=+|
T Consensus 3 ~~~~~~~eE~kl~~kYG~l 21 (86)
T PF04667_consen 3 DISSLSEEEAKLKAKYGKL 21 (86)
T ss_pred ccccccHHHHHHHHHcCCC
Confidence 3578899999999998544
No 52
>PRK14625 hypothetical protein; Provisional
Probab=27.57 E-value=1.4e+02 Score=21.39 Aligned_cols=31 Identities=23% Similarity=0.364 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHhcCceeeeeE----EEeeeec
Q psy15193 14 EITLQAKYQKLKRKVNGTHVQGVK----LKVSLAR 44 (106)
Q Consensus 14 ~~~~~~~~qklk~emnGt~V~gIq----LKVSiAR 44 (106)
-+.+|+|.+++.+++....|.|.- ++|.+--
T Consensus 11 aq~mQ~km~~~Q~el~~~~v~g~sggG~VkV~~~G 45 (109)
T PRK14625 11 AQAMQQKLADAQARLAETTVEGTSGGGMVTVTLMG 45 (109)
T ss_pred HHHHHHHHHHHHHHHhccEEEEEECCCeEEEEEec
Confidence 356899999999999999998854 5555533
No 53
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=26.96 E-value=57 Score=21.10 Aligned_cols=16 Identities=25% Similarity=0.424 Sum_probs=12.6
Q ss_pred EeCCCCCCHHHHHHHH
Q psy15193 4 IHFPSNHTEEEITLQA 19 (106)
Q Consensus 4 ~~~~~~~~~~~~~~~~ 19 (106)
|-||+++|.+|...--
T Consensus 20 L~Fp~~ls~~eRriih 35 (60)
T cd02639 20 LAFPSSLSPAERRIVH 35 (60)
T ss_pred EEcCCCCCHHHHHHHH
Confidence 5699999999976543
No 54
>PF11629 Mst1_SARAH: C terminal SARAH domain of Mst1; InterPro: IPR024205 The SARAH (Sav/Rassf/Hpo) domain is found at the C terminus in three classes of eukaryotic tumour suppressors that give the domain its name. In the Sav (Salvador) and Hpo (Hippo) families, the SARAH domain mediates signal transduction from Hpo via the Sav scaffolding protein to the downstream component Wts (Warts); the phosphorylation of Wts by Hpo triggers cell cycle arrest and apoptosis by down-regulating cyclin E, Diap 1 and other targets []. The SARAH domain is also involved in dimerisation, as in the human Hpo orthologue, Mst1, which homodimerises via its C-terminal SARAH domain. The SARAH domain is found associated with other domains, such as protein kinase domains, WW/rsp5/WWP domain (IPR001202 from INTERPRO), C1 domain (IPR002219 from INTERPRO), LIM domain (IPR001781 from INTERPRO), or the Ras-associating (RA) domain (IPR000159 from INTERPRO).; GO: 0004674 protein serine/threonine kinase activity; PDB: 2JO8_A.
Probab=26.91 E-value=10 Score=24.52 Aligned_cols=13 Identities=31% Similarity=0.332 Sum_probs=9.6
Q ss_pred eeccccccccccc
Q psy15193 42 LARRQLKVAPIND 54 (106)
Q Consensus 42 iARRQP~ld~ind 54 (106)
-|.|||+++.|.+
T Consensus 36 ~~KRqPIldAiea 48 (49)
T PF11629_consen 36 QAKRQPILDAIEA 48 (49)
T ss_dssp HHHHHHHHHHHTT
T ss_pred HHhhccHHHHHhc
Confidence 3679999987653
No 55
>PRK14568 vanB D-alanine--D-lactate ligase; Provisional
Probab=26.87 E-value=2.3e+02 Score=22.52 Aligned_cols=57 Identities=16% Similarity=0.236 Sum_probs=42.9
Q ss_pred eCCCCCCHHH-HHHHHHHHHHHHHhcCceeeeeEEEeeeecccccccccccccCCcccc
Q psy15193 5 HFPSNHTEEE-ITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWS 62 (106)
Q Consensus 5 ~~~~~~~~~~-~~~~~~~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA~s~s~Ws 62 (106)
.+|.+++++. ..+++--.++-+.++-.-+..|.+++. .-..|.+-+||--.|-+.+|
T Consensus 259 ~~Pa~l~~~~~~~i~~~a~~~~~~Lg~~G~~rvDf~l~-~~g~~~llEINt~Pg~t~~S 316 (343)
T PRK14568 259 IVPADISAEERSRVQETAKAIYRALGCRGLARVDMFLQ-EDGTVVLNEVNTLPGFTSYS 316 (343)
T ss_pred EeCCCCCHHHHHHHHHHHHHHHHHhCCCcEEEEEEEEe-CCCCEEEEEeeCCCCCCccC
Confidence 3688888763 457777888899999888888888876 34578888899866655544
No 56
>KOG0109|consensus
Probab=26.73 E-value=41 Score=29.06 Aligned_cols=24 Identities=25% Similarity=0.382 Sum_probs=20.2
Q ss_pred HHHHHHHhcCceeeeeEEEeeeec
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLAR 44 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiAR 44 (106)
-+.++++|||+.++|-.++|++.-
T Consensus 125 a~~air~l~~~~~~gk~m~vq~st 148 (346)
T KOG0109|consen 125 AVEAIRGLDNTEFQGKRMHVQLST 148 (346)
T ss_pred hHHHHhcccccccccceeeeeeec
Confidence 367899999999999888887763
No 57
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=26.69 E-value=69 Score=15.51 Aligned_cols=24 Identities=29% Similarity=0.357 Sum_probs=19.5
Q ss_pred eCCCCCCHHHHHHHHHHHHHHHHhc
Q psy15193 5 HFPSNHTEEEITLQAKYQKLKRKVN 29 (106)
Q Consensus 5 ~~~~~~~~~~~~~~~~~qklk~emn 29 (106)
-+|.-++..+..|+.+++-|+ +++
T Consensus 6 ~~P~il~~~~~~l~~~~~~l~-~~g 29 (31)
T smart00733 6 KFPQILGYSEKKLKPKVEFLK-ELG 29 (31)
T ss_pred hCcCcccccHHHhhHHHHHHH-HcC
Confidence 478888888889999999888 664
No 58
>PF10957 DUF2758: Protein of unknown function (DUF2758); InterPro: IPR020296 Cse60 is expressed during sporulation in Bacillus subtilis. Transcription commences around 2h after the start of sporulation and had an absolute requirement for the transcription factor sigmaE. Maximal expression of cse60 further depended on the DNA-binding protein SpoIIID. Cse60 is an acidic product of only 60 residues, whose function is not known [].
Probab=26.38 E-value=1.7e+02 Score=19.15 Aligned_cols=33 Identities=21% Similarity=0.324 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHhcCceeeeeEEEeeeec
Q psy15193 12 EEEITLQAKYQKLKRKVNGTHVQGVKLKVSLAR 44 (106)
Q Consensus 12 ~~~~~~~~~~qklk~emnGt~V~gIqLKVSiAR 44 (106)
+.|.-|+.+.-.-.+++.+..|-+|+..|+.+.
T Consensus 10 ~he~dLe~~vN~fL~~~~~~~viDIKy~va~~~ 42 (60)
T PF10957_consen 10 EHEKDLEDQVNDFLAKLDDDQVIDIKYQVAASC 42 (60)
T ss_pred hhHHHHHHHHHHHHHhCCCCcEEEEEEEEEEec
Confidence 345678888888889999999999999998874
No 59
>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=26.24 E-value=1.4e+02 Score=17.36 Aligned_cols=19 Identities=26% Similarity=0.496 Sum_probs=12.3
Q ss_pred HHHHHHHhcCceeeeeEEE
Q psy15193 21 YQKLKRKVNGTHVQGVKLK 39 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLK 39 (106)
.+++...++|..+.|-+|+
T Consensus 52 a~~al~~~~~~~~~g~~l~ 70 (70)
T PF14259_consen 52 AKRALELLNGKEIDGRKLR 70 (70)
T ss_dssp HHHHHHHHTTEEETTEEEE
T ss_pred HHHHHHHCCCcEECCEEcC
Confidence 3455566677777777664
No 60
>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=25.62 E-value=66 Score=27.02 Aligned_cols=30 Identities=10% Similarity=0.214 Sum_probs=25.6
Q ss_pred HHHHHHHhcCceeeeeEEEeeeeccccccc
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLARRQLKVA 50 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiARRQP~ld 50 (106)
-++|+.++|++.+.|-.|+|..+.|.|...
T Consensus 55 A~~Al~~ln~~~i~gk~i~i~~s~~~~~~~ 84 (562)
T TIGR01628 55 AERALETMNFKRLGGKPIRIMWSQRDPSLR 84 (562)
T ss_pred HHHHHHHhCCCEECCeeEEeeccccccccc
Confidence 357888999999999999999998887643
No 61
>PRK14189 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=25.11 E-value=1.1e+02 Score=25.19 Aligned_cols=68 Identities=19% Similarity=0.307 Sum_probs=44.4
Q ss_pred EEeCCCCCCHHHHHHHHHHHHHHHHhcC-ceeeeeEEEeeeecccccccccccccCCccccceeeccCCCCCCCCCccee
Q psy15193 3 YIHFPSNHTEEEITLQAKYQKLKRKVNG-THVQGVKLKVSLARRQLKVAPINDAASSTTWSAIACHQSLKGNHKDKRHQV 81 (106)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~qklk~emnG-t~V~gIqLKVSiARRQP~ld~indA~s~s~WsslA~~~SqKGshkDkR~lV 81 (106)
-+|||.+.|++|+ .++++++|. ..|+||=++--| =.-+ .....+.+|...+..-|=|....-.+
T Consensus 66 ~~~l~~~~~~~~l------~~~I~~lN~d~~V~GIlvq~Pl------p~~i---~~~~i~~~I~p~KDVDGl~~~n~g~l 130 (285)
T PRK14189 66 KDRYPADLSEAEL------LARIDELNRDPKIHGILVQLPL------PKHI---DSHKVIEAIAPEKDVDGFHVANAGAL 130 (285)
T ss_pred EEECCCCCCHHHH------HHHHHHHcCCCCCCeEEEeCCC------CCCC---CHHHHHhhcCcccCcccCChhhhhHh
Confidence 4799999998875 356777876 679999987444 2211 22346777777777777666555444
Q ss_pred eecc
Q psy15193 82 IYDD 85 (106)
Q Consensus 82 ~Ydd 85 (106)
.+++
T Consensus 131 ~~~~ 134 (285)
T PRK14189 131 MTGQ 134 (285)
T ss_pred hCCC
Confidence 4443
No 62
>KOG0138|consensus
Probab=24.94 E-value=38 Score=29.88 Aligned_cols=19 Identities=21% Similarity=0.434 Sum_probs=16.3
Q ss_pred EEeCCCCCCHHHHHHHHHH
Q psy15193 3 YIHFPSNHTEEEITLQAKY 21 (106)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~ 21 (106)
|+||-++|||||+.+..+.
T Consensus 48 ~~~l~dqLT~dE~air~~~ 66 (432)
T KOG0138|consen 48 PLVLEDQLTEDEIAIRDTF 66 (432)
T ss_pred hhhhhhhcCHHHHHHHHHH
Confidence 7899999999999876554
No 63
>PRK14621 hypothetical protein; Provisional
Probab=24.74 E-value=1.6e+02 Score=21.02 Aligned_cols=34 Identities=18% Similarity=0.254 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHhcCceeeeeE----EEeeeeccc
Q psy15193 13 EEITLQAKYQKLKRKVNGTHVQGVK----LKVSLARRQ 46 (106)
Q Consensus 13 ~~~~~~~~~qklk~emnGt~V~gIq----LKVSiARRQ 46 (106)
.-+.+|+|.+++.+++...+|.|.- ++|.+--.+
T Consensus 12 qaq~mQ~km~~~Q~eL~~~~v~g~sGgG~VkV~~~G~~ 49 (111)
T PRK14621 12 QIQQAGEKMQDVQKQLEKLVAHGEAGGGMVKASVNGKQ 49 (111)
T ss_pred HHHHHHHHHHHHHHHHHccEEEEEECCceEEEEEEcCc
Confidence 3456899999999999999998643 566554444
No 64
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=24.61 E-value=75 Score=25.88 Aligned_cols=25 Identities=12% Similarity=0.129 Sum_probs=21.7
Q ss_pred HHHHHHHhcCceeeeeEEEeeeecc
Q psy15193 21 YQKLKRKVNGTHVQGVKLKVSLARR 45 (106)
Q Consensus 21 ~qklk~emnGt~V~gIqLKVSiARR 45 (106)
-++|+.+|||..++|=.|.|++.-.
T Consensus 477 A~~A~~~lnGr~~~gr~v~~~~~~~ 501 (509)
T TIGR01642 477 AEKAMEGMNGRKFNDRVVVAAFYGE 501 (509)
T ss_pred HHHHHHHcCCCEECCeEEEEEEeCH
Confidence 3689999999999999999988644
No 65
>PRK09288 purT phosphoribosylglycinamide formyltransferase 2; Validated
Probab=24.05 E-value=3.6e+02 Score=21.22 Aligned_cols=59 Identities=15% Similarity=0.210 Sum_probs=41.2
Q ss_pred eCCCCCCHHHH-HHHHHHHHHHHHhcCceeeeeEEEeeeecccccccccccccCCcccccee
Q psy15193 5 HFPSNHTEEEI-TLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWSAIA 65 (106)
Q Consensus 5 ~~~~~~~~~~~-~~~~~~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA~s~s~WsslA 65 (106)
.+|.+++++.. .+++--.++.++|+..-+-+|.+.+. ...|.+-+||.-.+.+-+..+.
T Consensus 235 ~~p~~l~~~~~~~i~~~~~~~~~~L~~~G~~~ve~~~~--~~~~~viEinpR~~~~~~~~~~ 294 (395)
T PRK09288 235 WQPQPMSPAALEEAQEIAKKVTDALGGRGLFGVELFVK--GDEVYFSEVSPRPHDTGMVTLI 294 (395)
T ss_pred ECCCCCCHHHHHHHHHHHHHHHHHcCCeeEEEEEEEEe--CCeEEEEEecCCCCCCcceeee
Confidence 36888887643 35666778889998666666666664 5589999999876665444454
No 66
>PRK14571 D-alanyl-alanine synthetase A; Provisional
Probab=22.94 E-value=2.6e+02 Score=21.38 Aligned_cols=52 Identities=17% Similarity=0.073 Sum_probs=38.6
Q ss_pred CCCCCCHHH-HHHHHHHHHHHHHhcCceeeeeEEEeeeecccccccccccccCCc
Q psy15193 6 FPSNHTEEE-ITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAASST 59 (106)
Q Consensus 6 ~~~~~~~~~-~~~~~~~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA~s~s 59 (106)
+|..++++. ..++.--.++-+.++-.-+.+|.+++. ..+|.+-+||...|-+
T Consensus 216 ~p~~l~~~~~~~i~~~a~~~~~~lg~~g~~rvD~~~~--~~~~~viEiN~~Pg~~ 268 (299)
T PRK14571 216 LPAPLNPEEERLVKETALKAFVEAGCRGFGRVDGIFS--DGRFYFLEINTVPGLT 268 (299)
T ss_pred eCCCCCHHHHHHHHHHHHHHHHHhCCCceEEEEEEEE--CCcEEEEEeeCCCCCC
Confidence 588887764 446666777788888677888998875 5689999999855543
No 67
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=22.59 E-value=1.1e+02 Score=23.58 Aligned_cols=30 Identities=27% Similarity=0.309 Sum_probs=25.5
Q ss_pred EEeCCCCCCHHHHHHHHHHHHHHHHhcCce
Q psy15193 3 YIHFPSNHTEEEITLQAKYQKLKRKVNGTH 32 (106)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~qklk~emnGt~ 32 (106)
++..|..+|++|..+-+.|+.+...|+.+-
T Consensus 40 ~~P~~~~~t~~E~~~v~~~~~lr~~~~~sP 69 (233)
T PF11705_consen 40 NLPVPLPLTEEERYLVALKRELRERMRDSP 69 (233)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHhCC
Confidence 567788999999999999999999987653
No 68
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=22.56 E-value=1.3e+02 Score=20.15 Aligned_cols=31 Identities=26% Similarity=0.381 Sum_probs=25.5
Q ss_pred HHHHHHHHhcCceeeeeEEEeeeec--cccccc
Q psy15193 20 KYQKLKRKVNGTHVQGVKLKVSLAR--RQLKVA 50 (106)
Q Consensus 20 ~~qklk~emnGt~V~gIqLKVSiAR--RQP~ld 50 (106)
-.+.++..|||....|-.|+|..++ .++..+
T Consensus 169 ~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~ 201 (306)
T COG0724 169 SAEKAIEELNGKELEGRPLRVQKAQPASQPRSE 201 (306)
T ss_pred HHHHHHHHcCCCeECCceeEeeccccccccccc
Confidence 3567899999999999999999987 555544
No 69
>KOG0108|consensus
Probab=21.35 E-value=62 Score=28.20 Aligned_cols=37 Identities=30% Similarity=0.500 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCceeeeeEEEeeeeccccccc
Q psy15193 9 NHTEEEITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVA 50 (106)
Q Consensus 9 ~~~~~~~~~~~~~qklk~emnGt~V~gIqLKVSiARRQP~ld 50 (106)
.|+++|.+ +++++.|||..+.|-.|||..|-.-+.-+
T Consensus 66 ~~~~~~~~-----~~a~~~lNg~~~~gr~l~v~~~~~~~~~~ 102 (435)
T KOG0108|consen 66 EFTDEETA-----ERAIRNLNGAEFNGRKLRVNYASNRKNAE 102 (435)
T ss_pred ecCchhhH-----HHHHHhcCCcccCCceEEeecccccchhH
Confidence 45555544 57899999999999999999987666533
No 70
>smart00340 HALZ homeobox associated leucin zipper.
Probab=21.23 E-value=90 Score=19.91 Aligned_cols=18 Identities=39% Similarity=0.434 Sum_probs=15.8
Q ss_pred CCCHHHHHHHHHHHHHHH
Q psy15193 9 NHTEEEITLQAKYQKLKR 26 (106)
Q Consensus 9 ~~~~~~~~~~~~~qklk~ 26 (106)
.||||-..||...|.|++
T Consensus 16 ~LteeNrRL~ke~~eLra 33 (44)
T smart00340 16 SLTEENRRLQKEVQELRA 33 (44)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 589999999999998875
No 71
>PF10646 Germane: Sporulation and spore germination; InterPro: IPR019606 The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. It is also found in lipoprotein LpqB. The domain is present in a number of different bacterial species both alone and in association with other domains such as Gmad1 and Gmad2. It is predicted to have a novel alpha-beta fold.
Probab=20.80 E-value=1.9e+02 Score=18.84 Aligned_cols=38 Identities=21% Similarity=0.315 Sum_probs=20.1
Q ss_pred CeEEeCCCCCCH------HHHHHHHHHHHHHHHhcCceeeeeEEEe
Q psy15193 1 MVYIHFPSNHTE------EEITLQAKYQKLKRKVNGTHVQGVKLKV 40 (106)
Q Consensus 1 ~~~~~~~~~~~~------~~~~~~~~~qklk~emnGt~V~gIqLKV 40 (106)
.+|++|.+++.+ |..++++=-.=|..... .|+.|+|.|
T Consensus 65 ~~~Vd~s~~~~~~~~~~~~~~~~~~i~~Tl~~~~~--~v~~V~i~v 108 (117)
T PF10646_consen 65 TLTVDFSSEFLNFLGSSQEALLLAQIVNTLTEQFP--GVKKVQILV 108 (117)
T ss_pred EEEEECCHHHhhcCChHHHHHHHHHHHHHHHHhcC--CccEEEEEE
Confidence 368888886643 23333332223332443 377777765
No 72
>PRK14623 hypothetical protein; Provisional
Probab=20.76 E-value=2.5e+02 Score=19.99 Aligned_cols=33 Identities=18% Similarity=0.259 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHhcCceeeeeE----EEeeeecccc
Q psy15193 15 ITLQAKYQKLKRKVNGTHVQGVK----LKVSLARRQL 47 (106)
Q Consensus 15 ~~~~~~~qklk~emnGt~V~gIq----LKVSiARRQP 47 (106)
+.+|++.+++..+|....|+|.- ++|.+--++-
T Consensus 11 qkmQ~km~~~Qeel~~~~v~g~sggG~VkVt~~G~~~ 47 (106)
T PRK14623 11 KEAQQKVEATKKRLDTVLIDEQSSDGLLKVTVTANRE 47 (106)
T ss_pred HHHHHHHHHHHHHHhccEEEEEECCceEEEEEEcCcc
Confidence 56799999999999999997754 6666654443
No 73
>PRK14569 D-alanyl-alanine synthetase A; Provisional
Probab=20.75 E-value=3.9e+02 Score=20.73 Aligned_cols=52 Identities=17% Similarity=0.222 Sum_probs=38.1
Q ss_pred eCCCCCCHHH-HHHHHHHHHHHHHhcCceeeeeEEEeeeecccccccccccccC
Q psy15193 5 HFPSNHTEEE-ITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAAS 57 (106)
Q Consensus 5 ~~~~~~~~~~-~~~~~~~qklk~emnGt~V~gIqLKVSiARRQP~ld~indA~s 57 (106)
++|..+.++- ..+++--.++-+.|+..-+..|.+++. ...+|.+-+||.--|
T Consensus 214 ~~P~~l~~~~~~~i~~~a~~~~~~Lg~~G~~rvD~~~~-~~g~~~vlEIN~~Pg 266 (296)
T PRK14569 214 HSPSGLCEQKELEVRQLAKKAYDLLGCSGHARVDFIYD-DRGNFYIMEINSSPG 266 (296)
T ss_pred EeCCCCCHHHHHHHHHHHHHHHHHhCCceEEEEEEEEc-CCCCEEEEEeeCCCC
Confidence 5788776543 355666668888998888888888876 446799989997444
No 74
>PLN02616 tetrahydrofolate dehydrogenase/cyclohydrolase, putative
Probab=20.56 E-value=1.4e+02 Score=25.68 Aligned_cols=59 Identities=20% Similarity=0.407 Sum_probs=36.1
Q ss_pred EEeCCCCCCHHHHHHHHHHHHHHHHhcC-ceeeeeEEEeeeecccccccccccccCCccccceeeccCCCCCCCC
Q psy15193 3 YIHFPSNHTEEEITLQAKYQKLKRKVNG-THVQGVKLKVSLARRQLKVAPINDAASSTTWSAIACHQSLKGNHKD 76 (106)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~qklk~emnG-t~V~gIqLKVSiARRQP~ld~indA~s~s~WsslA~~~SqKGshkD 76 (106)
-+|||.+.||+|+. +++++||. ..|+||=++--|- .-+ .......+|.-.+..-|=|.-
T Consensus 137 ~~~lpe~~te~ell------~~I~~LN~D~~V~GIlVQlPLP------~~i---d~~~i~~aI~P~KDVDGl~p~ 196 (364)
T PLN02616 137 EVRLPEDSTEQEVL------KFISGFNNDPSVHGILVQLPLP------SHM---DEQNILNAVSIEKDVDGFHPL 196 (364)
T ss_pred EEECCCCCCHHHHH------HHHHHHcCCCCCCEEEEeCCCC------CCC---CHHHHHhccCcccCcccCChh
Confidence 36899999988754 45666665 7799999875442 111 123455566655555554443
Done!