Query psy14680
Match_columns 78
No_of_seqs 116 out of 1046
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 17:58:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14680.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14680hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2191|consensus 99.7 2E-16 4.3E-21 114.4 7.0 66 6-71 31-96 (402)
2 cd02396 PCBP_like_KH K homolog 99.6 1.6E-16 3.5E-21 90.5 4.2 56 15-72 1-56 (65)
3 PF13014 KH_3: KH domain 99.5 2.3E-14 5E-19 75.7 5.2 43 24-68 1-43 (43)
4 cd02394 vigilin_like_KH K homo 99.5 3.1E-14 6.7E-19 79.8 2.6 52 16-72 2-53 (62)
5 cd00105 KH-I K homology RNA-bi 99.4 1.8E-13 4E-18 76.3 4.7 53 16-71 2-54 (64)
6 PF00013 KH_1: KH domain syndr 99.4 8.2E-14 1.8E-18 77.6 1.3 51 15-71 1-51 (60)
7 KOG2190|consensus 99.4 7.1E-13 1.5E-17 99.9 5.8 58 13-72 137-194 (485)
8 KOG1676|consensus 99.4 6.2E-13 1.4E-17 101.4 5.3 58 13-72 229-286 (600)
9 cd02393 PNPase_KH Polynucleoti 99.4 2E-12 4.3E-17 73.1 5.7 46 15-69 3-48 (61)
10 KOG2191|consensus 99.2 1.3E-11 2.8E-16 89.7 5.0 59 14-72 132-190 (402)
11 KOG2193|consensus 99.2 6.3E-12 1.4E-16 93.8 1.7 61 10-72 407-467 (584)
12 smart00322 KH K homology RNA-b 99.2 8.5E-11 1.8E-15 64.7 5.1 54 13-71 2-55 (69)
13 KOG1676|consensus 99.1 5.9E-11 1.3E-15 90.7 5.3 62 10-72 135-196 (600)
14 KOG2192|consensus 99.1 7.1E-11 1.5E-15 84.4 4.7 61 11-74 312-372 (390)
15 KOG2193|consensus 99.0 2.1E-10 4.5E-15 85.8 3.5 63 10-74 195-257 (584)
16 cd02395 SF1_like-KH Splicing f 98.9 4.8E-09 1E-13 66.6 6.3 38 17-54 3-46 (120)
17 KOG2190|consensus 98.8 1.7E-08 3.7E-13 76.4 6.4 56 11-69 40-95 (485)
18 KOG2192|consensus 98.8 1.6E-08 3.5E-13 72.5 5.4 54 11-69 45-98 (390)
19 TIGR03665 arCOG04150 arCOG0415 98.6 2.1E-08 4.6E-13 66.7 1.5 34 18-51 2-35 (172)
20 PRK13763 putative RNA-processi 98.5 8.1E-08 1.8E-12 64.3 2.9 46 14-67 3-48 (180)
21 KOG1588|consensus 98.4 5.2E-07 1.1E-11 63.7 5.4 46 10-55 88-139 (259)
22 KOG0336|consensus 98.4 2.5E-07 5.5E-12 69.8 3.0 57 7-69 40-96 (629)
23 PRK13763 putative RNA-processi 98.3 2.6E-07 5.7E-12 61.9 2.3 40 23-72 104-143 (180)
24 TIGR03665 arCOG04150 arCOG0415 98.3 3E-07 6.4E-12 61.2 1.8 40 23-72 98-137 (172)
25 KOG0119|consensus 98.2 1.7E-06 3.8E-11 65.7 4.7 42 13-54 137-184 (554)
26 cd02134 NusA_KH NusA_K homolog 98.2 4.7E-06 1E-10 46.9 4.5 37 13-49 24-60 (61)
27 TIGR02696 pppGpp_PNP guanosine 98.1 7.2E-06 1.6E-10 64.7 5.6 42 12-53 576-617 (719)
28 TIGR03591 polynuc_phos polyrib 98.0 2.9E-06 6.3E-11 66.5 2.5 41 13-53 550-590 (684)
29 COG5176 MSL5 Splicing factor ( 98.0 1.7E-05 3.6E-10 55.2 4.8 43 11-53 145-193 (269)
30 PRK00468 hypothetical protein; 97.7 5.6E-05 1.2E-09 44.5 3.6 34 10-43 26-59 (75)
31 PRK02821 hypothetical protein; 97.6 9.7E-05 2.1E-09 43.7 3.4 36 10-45 27-62 (77)
32 PRK01064 hypothetical protein; 97.5 0.00021 4.6E-09 42.3 4.2 34 10-43 26-59 (78)
33 COG1837 Predicted RNA-binding 97.4 0.00022 4.9E-09 42.1 3.7 33 10-42 26-58 (76)
34 KOG2113|consensus 97.4 0.00017 3.7E-09 52.8 3.3 56 11-72 23-78 (394)
35 KOG2279|consensus 97.4 0.00017 3.6E-09 55.7 3.4 59 11-73 65-123 (608)
36 COG1185 Pnp Polyribonucleotide 97.2 0.00023 4.9E-09 56.1 2.8 40 14-53 552-591 (692)
37 PRK12704 phosphodiesterase; Pr 97.2 0.00059 1.3E-08 52.3 4.7 39 13-51 209-248 (520)
38 PRK08406 transcription elongat 97.1 0.00062 1.3E-08 44.1 3.7 39 14-52 32-70 (140)
39 TIGR03319 YmdA_YtgF conserved 97.1 0.00068 1.5E-08 51.9 4.3 40 12-51 202-242 (514)
40 KOG2814|consensus 97.1 0.00027 5.8E-09 51.7 1.9 51 13-68 56-106 (345)
41 PLN00207 polyribonucleotide nu 97.1 0.00022 4.7E-09 57.7 1.5 42 12-53 683-725 (891)
42 COG1094 Predicted RNA-binding 97.0 0.00097 2.1E-08 45.6 3.9 39 24-72 112-150 (194)
43 PRK00106 hypothetical protein; 97.0 0.0012 2.5E-08 51.0 4.5 40 12-51 223-263 (535)
44 cd02409 KH-II KH-II (K homolo 96.9 0.0023 5E-08 35.0 4.3 35 13-47 24-58 (68)
45 PRK08406 transcription elongat 96.9 0.00093 2E-08 43.3 2.9 40 11-50 96-135 (140)
46 PRK11824 polynucleotide phosph 96.7 0.0005 1.1E-08 54.2 0.3 40 14-53 554-593 (693)
47 cd02414 jag_KH jag_K homology 96.5 0.0034 7.3E-08 36.5 3.0 35 14-48 24-58 (77)
48 PF13083 KH_4: KH domain; PDB: 96.5 0.00077 1.7E-08 38.7 0.2 35 11-45 26-60 (73)
49 PF13184 KH_5: NusA-like KH do 96.5 0.0018 4E-08 37.3 1.7 38 16-53 5-48 (69)
50 PRK04163 exosome complex RNA-b 96.4 0.0021 4.5E-08 44.7 2.1 37 16-52 147-183 (235)
51 TIGR01952 nusA_arch NusA famil 96.4 0.004 8.6E-08 40.6 3.1 38 15-52 34-71 (141)
52 PRK12705 hypothetical protein; 96.3 0.0035 7.6E-08 48.1 3.1 41 12-52 196-237 (508)
53 KOG4369|consensus 96.3 0.0014 2.9E-08 55.0 0.7 58 12-72 1338-1396(2131)
54 COG1094 Predicted RNA-binding 96.2 0.014 3E-07 40.0 5.0 54 13-74 7-61 (194)
55 PF07650 KH_2: KH domain syndr 96.2 0.0017 3.8E-08 37.4 0.5 35 14-48 25-59 (78)
56 PRK12328 nusA transcription el 95.9 0.014 2.9E-07 43.5 4.3 43 12-54 306-348 (374)
57 TIGR01953 NusA transcription t 95.8 0.01 2.2E-07 43.5 3.3 40 12-51 299-338 (341)
58 TIGR01952 nusA_arch NusA famil 95.8 0.0072 1.6E-07 39.4 2.2 39 12-50 98-136 (141)
59 PRK13764 ATPase; Provisional 95.8 0.0085 1.8E-07 46.9 2.8 43 12-54 479-521 (602)
60 cd02413 40S_S3_KH K homology R 95.7 0.014 2.9E-07 34.6 3.1 36 14-49 30-65 (81)
61 COG1855 ATPase (PilT family) [ 95.6 0.011 2.4E-07 45.7 2.9 40 15-54 487-526 (604)
62 COG0195 NusA Transcription elo 95.5 0.012 2.7E-07 40.0 2.6 38 15-52 143-180 (190)
63 PRK12327 nusA transcription el 95.2 0.024 5.2E-07 42.0 3.4 43 11-53 300-342 (362)
64 PRK09202 nusA transcription el 95.2 0.018 4E-07 43.9 2.9 40 13-52 301-340 (470)
65 KOG2279|consensus 95.1 0.0081 1.8E-07 46.7 0.8 57 11-70 137-193 (608)
66 PRK06418 transcription elongat 94.9 0.044 9.4E-07 36.7 3.6 38 15-53 62-99 (166)
67 KOG2208|consensus 94.7 0.018 3.8E-07 46.1 1.7 61 11-76 344-404 (753)
68 cd02412 30S_S3_KH K homology R 94.7 0.029 6.2E-07 34.7 2.3 30 15-44 62-91 (109)
69 cd02411 archeal_30S_S3_KH K ho 94.7 0.039 8.5E-07 32.6 2.8 28 16-43 40-67 (85)
70 PRK12329 nusA transcription el 94.4 0.036 7.9E-07 42.1 2.8 41 12-52 333-373 (449)
71 COG1097 RRP4 RNA-binding prote 94.4 0.06 1.3E-06 38.0 3.6 37 17-53 149-185 (239)
72 COG0092 RpsC Ribosomal protein 94.0 0.059 1.3E-06 37.9 2.8 30 13-42 50-79 (233)
73 cd02410 archeal_CPSF_KH The ar 93.9 0.11 2.5E-06 34.1 4.0 37 17-53 79-115 (145)
74 KOG2113|consensus 93.8 0.078 1.7E-06 39.1 3.4 56 11-72 112-167 (394)
75 COG0195 NusA Transcription elo 93.4 0.096 2.1E-06 35.7 3.1 37 17-53 79-115 (190)
76 TIGR00436 era GTP-binding prot 93.0 0.18 3.9E-06 35.0 4.1 30 14-43 221-251 (270)
77 PRK15494 era GTPase Era; Provi 92.2 0.26 5.7E-06 35.6 4.1 29 14-42 273-302 (339)
78 PRK00089 era GTPase Era; Revie 91.8 0.33 7.2E-06 33.8 4.2 29 14-42 226-255 (292)
79 COG1159 Era GTPase [General fu 90.4 0.45 9.7E-06 34.6 3.8 31 13-43 228-259 (298)
80 TIGR01008 rpsC_E_A ribosomal p 89.5 0.42 9.2E-06 32.7 3.0 30 14-43 38-67 (195)
81 PRK04191 rps3p 30S ribosomal p 89.5 0.42 9.2E-06 32.8 3.0 29 16-44 42-70 (207)
82 KOG3273|consensus 89.1 0.093 2E-06 36.6 -0.5 30 22-51 177-206 (252)
83 CHL00048 rps3 ribosomal protei 89.0 0.47 1E-05 32.8 2.9 29 15-43 67-95 (214)
84 PRK12327 nusA transcription el 88.5 0.5 1.1E-05 35.1 2.9 31 23-53 245-276 (362)
85 KOG1423|consensus 88.4 0.71 1.5E-05 34.3 3.6 32 13-44 327-359 (379)
86 PTZ00084 40S ribosomal protein 88.4 0.52 1.1E-05 32.8 2.8 29 15-43 45-73 (220)
87 KOG2208|consensus 88.4 0.4 8.7E-06 38.6 2.5 42 10-51 705-746 (753)
88 TIGR01953 NusA transcription t 87.9 0.61 1.3E-05 34.3 3.1 31 23-53 243-274 (341)
89 TIGR03675 arCOG00543 arCOG0054 86.9 1 2.2E-05 35.5 4.0 38 16-53 95-132 (630)
90 COG1847 Jag Predicted RNA-bind 86.3 0.55 1.2E-05 32.6 2.0 37 12-48 89-125 (208)
91 PRK12329 nusA transcription el 86.1 0.59 1.3E-05 35.7 2.2 31 23-53 277-308 (449)
92 PRK12328 nusA transcription el 84.9 0.62 1.3E-05 34.8 1.8 31 23-53 251-282 (374)
93 PRK09202 nusA transcription el 83.8 0.84 1.8E-05 35.0 2.1 31 23-53 245-276 (470)
94 TIGR01009 rpsC_bact ribosomal 83.5 1.2 2.7E-05 30.6 2.7 28 16-43 64-91 (211)
95 COG1782 Predicted metal-depend 82.1 1.9 4.1E-05 34.0 3.5 38 16-53 101-138 (637)
96 KOG1067|consensus 78.3 1.4 3E-05 35.2 1.7 40 11-50 594-633 (760)
97 PRK00310 rpsC 30S ribosomal pr 76.9 2.4 5.1E-05 29.6 2.4 29 15-43 63-91 (232)
98 KOG2874|consensus 76.4 2 4.3E-05 31.5 1.9 25 26-50 161-185 (356)
99 PF14611 SLS: Mitochondrial in 74.2 14 0.00029 24.7 5.5 49 15-71 27-75 (210)
100 KOG4369|consensus 73.6 1.6 3.5E-05 37.6 1.0 55 14-71 781-835 (2131)
101 COG5166 Uncharacterized conser 58.3 7.2 0.00016 30.9 1.8 38 14-51 449-486 (657)
102 cd07557 trimeric_dUTPase Trime 38.1 44 0.00095 19.1 2.7 26 14-39 26-51 (92)
103 COG1117 PstB ABC-type phosphat 31.9 32 0.0007 24.5 1.6 27 13-39 23-49 (253)
104 cd08072 MPN_archaeal Mov34/MPN 30.4 30 0.00064 21.3 1.1 14 20-33 17-30 (117)
105 cd03710 BipA_TypA_C BipA_TypA_ 29.5 20 0.00044 20.3 0.2 18 13-30 3-20 (79)
106 PF14597 Lactamase_B_5: Metall 27.3 95 0.0021 21.5 3.2 27 27-53 58-87 (199)
107 cd08073 MPN_NLPC_P60 Mpr1p, Pa 25.9 48 0.001 20.1 1.5 14 20-33 14-27 (108)
108 PF04025 DUF370: Domain of unk 24.8 1.5E+02 0.0033 17.2 3.7 46 17-68 7-55 (73)
109 PF01245 Ribosomal_L19: Riboso 24.8 1.2E+02 0.0027 18.8 3.2 33 4-36 15-54 (113)
110 COG3840 ThiQ ABC-type thiamine 24.3 1.1E+02 0.0023 21.6 3.0 34 5-38 7-40 (231)
111 PF04879 Molybdop_Fe4S4: Molyb 24.3 1.2E+02 0.0025 15.7 3.1 26 43-75 13-38 (55)
112 COG1702 PhoH Phosphate starvat 24.2 1.2E+02 0.0027 22.6 3.6 42 19-70 20-61 (348)
113 PHA02099 hypothetical protein 23.3 28 0.0006 20.4 0.1 38 16-53 3-52 (84)
114 PF02196 RBD: Raf-like Ras-bin 22.6 1.6E+02 0.0034 16.5 3.3 26 15-40 2-27 (71)
115 cd03709 lepA_C lepA_C: This fa 22.3 26 0.00056 19.9 -0.2 18 13-30 3-20 (80)
116 TIGR03021 pilP_fam type IV pil 20.7 60 0.0013 20.4 1.2 43 25-68 71-113 (119)
117 PHA01707 dut 2'-deoxyuridine 5 20.3 1.2E+02 0.0026 19.7 2.6 25 13-37 66-90 (158)
118 PRK00416 dcd deoxycytidine tri 20.1 1.3E+02 0.0028 19.8 2.8 23 14-36 83-105 (177)
No 1
>KOG2191|consensus
Probab=99.66 E-value=2e-16 Score=114.39 Aligned_cols=66 Identities=47% Similarity=0.752 Sum_probs=60.2
Q ss_pred CcccCCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680 6 PFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG 71 (78)
Q Consensus 6 ~~~~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~ 71 (78)
++.-.++...++++||+..+|.||||||++|.+|+++|||+|++++..||+||++||+|.|+|+-+
T Consensus 31 ~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~e 96 (402)
T KOG2191|consen 31 TNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVE 96 (402)
T ss_pred ccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHH
Confidence 443345569999999999999999999999999999999999999999999999999999999854
No 2
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.65 E-value=1.6e-16 Score=90.47 Aligned_cols=56 Identities=41% Similarity=0.662 Sum_probs=50.8
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
+++|+||.+.+|.||||+|++|++|+++|||+|++.+..+ ++..+|.|+|.|++++
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~ 56 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSA 56 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHH
Confidence 3789999999999999999999999999999999997653 5789999999999764
No 3
>PF13014 KH_3: KH domain
Probab=99.53 E-value=2.3e-14 Score=75.73 Aligned_cols=43 Identities=35% Similarity=0.548 Sum_probs=39.1
Q ss_pred ceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEec
Q psy14680 24 AAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLS 68 (78)
Q Consensus 24 ~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G 68 (78)
++|+||||+|++|++|+++|||+|+|++ +..++..+|.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~--~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP--ENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC--ccCCCCCceEEEEEC
Confidence 5899999999999999999999999998 335788999999997
No 4
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.46 E-value=3.1e-14 Score=79.85 Aligned_cols=52 Identities=25% Similarity=0.345 Sum_probs=47.0
Q ss_pred EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
.++.||.+++|.|||++|++|++|+++|||+|++++.. ..++.|+|+|++++
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-----~~~~~v~I~G~~~~ 53 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-----SKSDTITITGPKEN 53 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-----CCCCEEEEEcCHHH
Confidence 57899999999999999999999999999999999754 57899999999653
No 5
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.44 E-value=1.8e-13 Score=76.28 Aligned_cols=53 Identities=38% Similarity=0.613 Sum_probs=47.7
Q ss_pred EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG 71 (78)
Q Consensus 16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~ 71 (78)
.++.||..++|.|||++|++|++|+++|||+|.|++..+ +..++.|.|.|+++
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~ 54 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPE 54 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHH
Confidence 689999999999999999999999999999999997542 56899999999854
No 6
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.40 E-value=8.2e-14 Score=77.64 Aligned_cols=51 Identities=33% Similarity=0.497 Sum_probs=45.3
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG 71 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~ 71 (78)
+.+|.||.+++|+|||++|++|++|+++|||+|+++++ + .+..|+|+|+++
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~-----~-~~~~v~I~G~~~ 51 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD-----D-ERDIVTISGSPE 51 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST-----T-EEEEEEEEESHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC-----C-CcEEEEEEeCHH
Confidence 57899999999999999999999999999999999854 2 455999999654
No 7
>KOG2190|consensus
Probab=99.38 E-value=7.1e-13 Score=99.87 Aligned_cols=58 Identities=33% Similarity=0.578 Sum_probs=54.4
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
..+++|+||.+++|.||||+|+.||+|+++|||+|+|..+ ++|..++|.|+|.|.|+.
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~a 194 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDA 194 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHH
Confidence 4789999999999999999999999999999999999986 589999999999999864
No 8
>KOG1676|consensus
Probab=99.37 E-value=6.2e-13 Score=101.36 Aligned_cols=58 Identities=31% Similarity=0.497 Sum_probs=53.3
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
..++++.||.+.||.||||+|++||+|+.+||+||+|.++.+ +.+.||.+.|.|+++.
T Consensus 229 ~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~--p~speR~~~IiG~~d~ 286 (600)
T KOG1676|consen 229 SATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD--PSSPERPAQIIGTVDQ 286 (600)
T ss_pred cceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC--CCCccceeeeecCHHH
Confidence 458999999999999999999999999999999999999775 5789999999999763
No 9
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.36 E-value=2e-12 Score=73.12 Aligned_cols=46 Identities=28% Similarity=0.481 Sum_probs=41.9
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR 69 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~ 69 (78)
...+.||.+++|+||||+|++|++|+++|||+|.|++ ++.|.|+|+
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---------~g~v~I~G~ 48 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---------DGTVYIAAS 48 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---------CCEEEEEeC
Confidence 5678999999999999999999999999999999984 346999996
No 10
>KOG2191|consensus
Probab=99.23 E-value=1.3e-11 Score=89.68 Aligned_cols=59 Identities=39% Similarity=0.485 Sum_probs=53.3
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
.++++++|++.+|.||||+|.+||.+++++||.|+|++.....-+..||++++.|.|++
T Consensus 132 kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~ 190 (402)
T KOG2191|consen 132 KQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQ 190 (402)
T ss_pred ceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHH
Confidence 56999999999999999999999999999999999996544456789999999999864
No 11
>KOG2193|consensus
Probab=99.19 E-value=6.3e-12 Score=93.77 Aligned_cols=61 Identities=28% Similarity=0.475 Sum_probs=55.7
Q ss_pred CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
.++...++|+||...||+|||++|.+||+|.+.+||.|+|.+++ .+...+|+|+|+|.|+.
T Consensus 407 ~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE--~pdvseRMViItGppea 467 (584)
T KOG2193|consen 407 NPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE--IPDVSERMVIITGPPEA 467 (584)
T ss_pred CcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC--CCCcceeEEEecCChHH
Confidence 35678899999999999999999999999999999999999875 57789999999999863
No 12
>smart00322 KH K homology RNA-binding domain.
Probab=99.16 E-value=8.5e-11 Score=64.74 Aligned_cols=54 Identities=33% Similarity=0.582 Sum_probs=47.2
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG 71 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~ 71 (78)
....++.||...+|.+||++|++|++|++.|||+|.+.... .....+.|.|.++
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-----~~~~~v~i~g~~~ 55 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-----SEERVVEITGPPE 55 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-----CCccEEEEEcCHH
Confidence 35789999999999999999999999999999999998543 2678899999853
No 13
>KOG1676|consensus
Probab=99.15 E-value=5.9e-11 Score=90.72 Aligned_cols=62 Identities=31% Similarity=0.439 Sum_probs=55.9
Q ss_pred CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
+...++.++.||++.+|+||||+|++||+|+++|||++++.++++..++ .++.+.|+|+|+.
T Consensus 135 ~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ 196 (600)
T KOG1676|consen 135 GSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDK 196 (600)
T ss_pred CccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHH
Confidence 4567899999999999999999999999999999999999998865444 8899999999975
No 14
>KOG2192|consensus
Probab=99.13 E-value=7.1e-11 Score=84.37 Aligned_cols=61 Identities=23% Similarity=0.406 Sum_probs=54.4
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCCCC
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFEP 74 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~~~ 74 (78)
....+..+.||.+.-|.||||+|.+|++|++++||.|.+..+ ..|+.||+++|+|+-++-+
T Consensus 312 GPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep---leGsedrIitItGTqdQIq 372 (390)
T KOG2192|consen 312 GPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITITGTQDQIQ 372 (390)
T ss_pred CceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc---CCCCCceEEEEeccHHHHh
Confidence 446788999999999999999999999999999999999854 4689999999999976544
No 15
>KOG2193|consensus
Probab=99.02 E-value=2.1e-10 Score=85.78 Aligned_cols=63 Identities=30% Similarity=0.378 Sum_probs=57.1
Q ss_pred CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCCCC
Q psy14680 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFEP 74 (78)
Q Consensus 10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~~~ 74 (78)
..-..++|++||..++|+||||.|++||.|.+.|.|+|.|.+... .|..||.++|.|+|+..+
T Consensus 195 q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken--~Gaaek~itvh~tpEg~s 257 (584)
T KOG2193|consen 195 QLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN--AGAAEKIITVHSTPEGTS 257 (584)
T ss_pred cccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc--CCcccCceEEecCccchH
Confidence 345688999999999999999999999999999999999998763 699999999999998754
No 16
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.91 E-value=4.8e-09 Score=66.56 Aligned_cols=38 Identities=34% Similarity=0.652 Sum_probs=33.3
Q ss_pred EEEecC------CceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680 17 KILVPS------YAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54 (78)
Q Consensus 17 ~l~vP~------~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~ 54 (78)
+++||. .++|.|||++|++||+|+++|||+|.|..++.
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs 46 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGS 46 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcc
Confidence 455655 78999999999999999999999999998754
No 17
>KOG2190|consensus
Probab=98.78 E-value=1.7e-08 Score=76.41 Aligned_cols=56 Identities=27% Similarity=0.453 Sum_probs=50.3
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR 69 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~ 69 (78)
+...++|++++...+|.||||+|..||+||++|.++|.|... .++..||+++|+|.
T Consensus 40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~---~~~c~eRIiti~g~ 95 (485)
T KOG2190|consen 40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES---LPGCPERIITITGN 95 (485)
T ss_pred CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC---CCCCCcceEEEecc
Confidence 444558999999999999999999999999999999999854 47899999999994
No 18
>KOG2192|consensus
Probab=98.76 E-value=1.6e-08 Score=72.46 Aligned_cols=54 Identities=26% Similarity=0.434 Sum_probs=48.8
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR 69 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~ 69 (78)
...+.+++++.+..+|+||||+|+|||.|+.+.+|.|+|++. +.++|+++|+.+
T Consensus 45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-----~~peri~tisad 98 (390)
T KOG2192|consen 45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-----SGPERILTISAD 98 (390)
T ss_pred hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-----CCCceeEEEecc
Confidence 456899999999999999999999999999999999999964 468999999764
No 19
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.57 E-value=2.1e-08 Score=66.68 Aligned_cols=34 Identities=38% Similarity=0.723 Sum_probs=32.5
Q ss_pred EEecCCceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680 18 ILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51 (78)
Q Consensus 18 l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~ 51 (78)
+.||.+.+|.|||++|++|+.|+++|||+|++.+
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~ 35 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS 35 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc
Confidence 5789999999999999999999999999999995
No 20
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.50 E-value=8.1e-08 Score=64.34 Aligned_cols=46 Identities=26% Similarity=0.423 Sum_probs=40.2
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEe
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLL 67 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~ 67 (78)
....+.||.+.+|.|||++|++|+.|+++|||+|++..+ +..|.|.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------~g~V~I~ 48 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--------TGEVIIE 48 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--------CCeEEEE
Confidence 467899999999999999999999999999999999853 2456675
No 21
>KOG1588|consensus
Probab=98.42 E-value=5.2e-07 Score=63.72 Aligned_cols=46 Identities=26% Similarity=0.462 Sum_probs=41.0
Q ss_pred CCCeeEEEEEecC------CceeeEEecCCchHHHHHHHhCCeEEEecCCCC
Q psy14680 10 ADGVCQIKILVPS------YAAGAIIGKGGETIAQIQKDTGSKIKMSKANDF 55 (78)
Q Consensus 10 ~~~~~~~~l~vP~------~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~ 55 (78)
.....+.+++||. ++||.|+|..|.++|+|+++|||+|-|.-.++.
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSm 139 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSM 139 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcc
Confidence 4567889999987 599999999999999999999999999987753
No 22
>KOG0336|consensus
Probab=98.37 E-value=2.5e-07 Score=69.83 Aligned_cols=57 Identities=25% Similarity=0.443 Sum_probs=49.9
Q ss_pred cccCCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc
Q psy14680 7 FIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR 69 (78)
Q Consensus 7 ~~~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~ 69 (78)
...|.+.+++.+.|-+.+||.+||++|++||.||..|+++|+|.+.. .+-.|+|.|.
T Consensus 40 ~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~------~e~kv~ifg~ 96 (629)
T KOG0336|consen 40 AAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD------LEVKVTIFGI 96 (629)
T ss_pred cccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC------ceeEEEEech
Confidence 34567889999999999999999999999999999999999999754 5777888774
No 23
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.34 E-value=2.6e-07 Score=61.89 Aligned_cols=40 Identities=33% Similarity=0.458 Sum_probs=34.3
Q ss_pred CceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 23 YAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 23 ~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
...|+|||++|++++.|+..|||+|+|.. +.+.|.|+|+.
T Consensus 104 r~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~~ 143 (180)
T PRK13763 104 RIKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPEQ 143 (180)
T ss_pred HHhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHHH
Confidence 46899999999999999999999999973 23888897753
No 24
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.30 E-value=3e-07 Score=61.20 Aligned_cols=40 Identities=33% Similarity=0.430 Sum_probs=35.2
Q ss_pred CceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 23 YAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 23 ~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
..+|+|||++|++++.|+..|||+|.|.. +.|.|.|+|++
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~ 137 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQ 137 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHH
Confidence 36899999999999999999999999972 56999998754
No 25
>KOG0119|consensus
Probab=98.23 E-value=1.7e-06 Score=65.70 Aligned_cols=42 Identities=29% Similarity=0.499 Sum_probs=38.1
Q ss_pred eeEEEEEecC------CceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680 13 VCQIKILVPS------YAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54 (78)
Q Consensus 13 ~~~~~l~vP~------~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~ 54 (78)
.++-+++||. ++||+|||.+|.|.|+|+++|||||.|.-.+.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgS 184 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGS 184 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecccc
Confidence 7888999986 79999999999999999999999999987553
No 26
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=98.16 E-value=4.7e-06 Score=46.89 Aligned_cols=37 Identities=32% Similarity=0.540 Sum_probs=34.5
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEE
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKM 49 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i 49 (78)
.....+.||.+..|..|||+|.+|+.+++.+|.+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4688999999999999999999999999999998876
No 27
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.08 E-value=7.2e-06 Score=64.74 Aligned_cols=42 Identities=31% Similarity=0.527 Sum_probs=37.6
Q ss_pred CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
-.....+.||.+.+|.|||+||.+||.|+++||++|.|.+++
T Consensus 576 aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G 617 (719)
T TIGR02696 576 APRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDDG 617 (719)
T ss_pred CCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecCc
Confidence 345678899999999999999999999999999999998543
No 28
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.03 E-value=2.9e-06 Score=66.48 Aligned_cols=41 Identities=27% Similarity=0.427 Sum_probs=37.2
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
....++.||.+.+|.|||+||++||.|+++|||+|.|.+++
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG 590 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDG 590 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecCe
Confidence 45678899999999999999999999999999999998644
No 29
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.95 E-value=1.7e-05 Score=55.24 Aligned_cols=43 Identities=28% Similarity=0.441 Sum_probs=38.0
Q ss_pred CCeeEEEEEecC------CceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 11 DGVCQIKILVPS------YAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 11 ~~~~~~~l~vP~------~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
+...+-+++||. .+||+|||..|.++|+|+..|+|+|.|...+
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 456778888885 7899999999999999999999999998665
No 30
>PRK00468 hypothetical protein; Provisional
Probab=97.70 E-value=5.6e-05 Score=44.46 Aligned_cols=34 Identities=21% Similarity=0.337 Sum_probs=30.2
Q ss_pred CCCeeEEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDT 43 (78)
Q Consensus 10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T 43 (78)
++....+++.+..+-+|.||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 4566889999999999999999999999999754
No 31
>PRK02821 hypothetical protein; Provisional
Probab=97.57 E-value=9.7e-05 Score=43.71 Aligned_cols=36 Identities=19% Similarity=0.350 Sum_probs=30.9
Q ss_pred CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCC
Q psy14680 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGS 45 (78)
Q Consensus 10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga 45 (78)
+.....+++.+..+-+|.||||+|.+|+.||.--.+
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 345578999999999999999999999999986544
No 32
>PRK01064 hypothetical protein; Provisional
Probab=97.50 E-value=0.00021 Score=42.31 Aligned_cols=34 Identities=29% Similarity=0.336 Sum_probs=30.2
Q ss_pred CCCeeEEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDT 43 (78)
Q Consensus 10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T 43 (78)
+...+.+++.+...-.|.+|||+|.+|+.||.-.
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 4667889999999999999999999999999753
No 33
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=97.43 E-value=0.00022 Score=42.11 Aligned_cols=33 Identities=30% Similarity=0.457 Sum_probs=29.9
Q ss_pred CCCeeEEEEEecCCceeeEEecCCchHHHHHHH
Q psy14680 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKD 42 (78)
Q Consensus 10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~ 42 (78)
++....+++.+..+-+|.||||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 466788999999999999999999999999964
No 34
>KOG2113|consensus
Probab=97.39 E-value=0.00017 Score=52.75 Aligned_cols=56 Identities=20% Similarity=0.208 Sum_probs=47.2
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
+..++..+.||..+++.|.|++|..||.|+.+|.++|.-+..++ |-++.++|.++.
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e------ePiF~vTg~~ed 78 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE------EPIFPVTGRHED 78 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC------CCcceeccCchh
Confidence 47788999999999999999999999999999999999987653 455666766653
No 35
>KOG2279|consensus
Probab=97.38 E-value=0.00017 Score=55.72 Aligned_cols=59 Identities=31% Similarity=0.437 Sum_probs=47.9
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCCC
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFE 73 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~~ 73 (78)
...+.++++||...|-+|+||+|++|++|+..|++||.+..+. -..++...+.|.|...
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed----~g~e~~~~~~~~p~~v 123 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED----VGDERVLLISGFPVQV 123 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc----CCcccchhhccCCCCC
Confidence 3568899999999999999999999999999999999998653 2355666666555543
No 36
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.24 E-value=0.00023 Score=56.07 Aligned_cols=40 Identities=30% Similarity=0.444 Sum_probs=36.3
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
-...+.|+.+.++.+||++|.+|++|.++||++|+|.+++
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~IdieddG 591 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDG 591 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCCC
Confidence 4567889999999999999999999999999999999554
No 37
>PRK12704 phosphodiesterase; Provisional
Probab=97.20 E-value=0.00059 Score=52.27 Aligned_cols=39 Identities=23% Similarity=0.409 Sum_probs=33.4
Q ss_pred eeEEEEEecC-CceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680 13 VCQIKILVPS-YAAGAIIGKGGETIAQIQKDTGSKIKMSK 51 (78)
Q Consensus 13 ~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~ 51 (78)
...-.+.+|+ ++-|.||||.|.||+.++.-||+-|.|++
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd 248 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD 248 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC
Confidence 4455667888 55599999999999999999999999984
No 38
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.15 E-value=0.00062 Score=44.14 Aligned_cols=39 Identities=28% Similarity=0.505 Sum_probs=35.8
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA 52 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~ 52 (78)
..+.++|+...+|+.||++|++|+.|++..|-+|.|-.-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~ 70 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY 70 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc
Confidence 467788899999999999999999999999999999874
No 39
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.13 E-value=0.00068 Score=51.88 Aligned_cols=40 Identities=23% Similarity=0.392 Sum_probs=34.0
Q ss_pred CeeEEEEEecC-CceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680 12 GVCQIKILVPS-YAAGAIIGKGGETIAQIQKDTGSKIKMSK 51 (78)
Q Consensus 12 ~~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~ 51 (78)
....-.+.+|+ ++-|.||||.|.||+.++..||+-|.|++
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd 242 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD 242 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC
Confidence 34555678888 45599999999999999999999999985
No 40
>KOG2814|consensus
Probab=97.12 E-value=0.00027 Score=51.70 Aligned_cols=51 Identities=25% Similarity=0.346 Sum_probs=41.9
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEec
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLS 68 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G 68 (78)
.....+.++....|.|||++|.+.++|+++|+|+|.++++. ...-.++|.|
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~-----~n~~~i~i~~ 106 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN-----TNKEEIKIIG 106 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC-----CCcceEEEee
Confidence 35667889999999999999999999999999999999765 2344455544
No 41
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.11 E-value=0.00022 Score=57.69 Aligned_cols=42 Identities=24% Similarity=0.346 Sum_probs=37.2
Q ss_pred CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCe-EEEecCC
Q psy14680 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSK-IKMSKAN 53 (78)
Q Consensus 12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~-I~i~~~~ 53 (78)
-.....+.||.+++|.|||.||.+|+.|.++||++ |.+.+++
T Consensus 683 aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg 725 (891)
T PLN00207 683 APLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDDG 725 (891)
T ss_pred CCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCCe
Confidence 34577889999999999999999999999999999 9888543
No 42
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.02 E-value=0.00097 Score=45.58 Aligned_cols=39 Identities=28% Similarity=0.324 Sum_probs=33.7
Q ss_pred ceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 24 AAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 24 ~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
..|+|||++|.+-+.|+.-|+|.|.|.. ..|.|.|.+.+
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~ 150 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQ 150 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhh
Confidence 4699999999999999999999999983 33888888765
No 43
>PRK00106 hypothetical protein; Provisional
Probab=97.00 E-value=0.0012 Score=51.01 Aligned_cols=40 Identities=23% Similarity=0.415 Sum_probs=34.2
Q ss_pred CeeEEEEEecC-CceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680 12 GVCQIKILVPS-YAAGAIIGKGGETIAQIQKDTGSKIKMSK 51 (78)
Q Consensus 12 ~~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~ 51 (78)
....-.+.+|+ ++-|.||||.|.||+.++.-||+-|.|++
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 263 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD 263 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC
Confidence 34556678888 55599999999999999999999999985
No 44
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=96.93 E-value=0.0023 Score=34.97 Aligned_cols=35 Identities=31% Similarity=0.404 Sum_probs=28.3
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeE
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKI 47 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I 47 (78)
...+.+.+.....|.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35556666666789999999999999999988554
No 45
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=96.91 E-value=0.00093 Score=43.32 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=35.2
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEe
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMS 50 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~ 50 (78)
++...+.+.|+....|..|||+|.|++.+++-++-++.|.
T Consensus 96 ~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 96 NGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred CCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 3346777889999999999999999999999999988775
No 46
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.67 E-value=0.0005 Score=54.18 Aligned_cols=40 Identities=33% Similarity=0.544 Sum_probs=34.8
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
....+.||.+.++.+||.||.+||.|.++||++|.+.+++
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~G 593 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDG 593 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCCc
Confidence 4456677999999999999999999999999999987544
No 47
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=96.49 E-value=0.0034 Score=36.48 Aligned_cols=35 Identities=20% Similarity=0.335 Sum_probs=28.1
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEE
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK 48 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~ 48 (78)
..+.+.|.....|.+|||.|.++..||--++.-++
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 34667777888999999999999999987665444
No 48
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=96.48 E-value=0.00077 Score=38.66 Aligned_cols=35 Identities=26% Similarity=0.340 Sum_probs=29.4
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCC
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGS 45 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga 45 (78)
.....+.+.+..+..|.+|||+|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 45567778889999999999999999999976644
No 49
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=96.47 E-value=0.0018 Score=37.34 Aligned_cols=38 Identities=37% Similarity=0.507 Sum_probs=29.5
Q ss_pred EEEEecCCc-----eeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680 16 IKILVPSYA-----AGAIIGKGGETIAQIQKDT-GSKIKMSKAN 53 (78)
Q Consensus 16 ~~l~vP~~~-----vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~ 53 (78)
.++.|-... +|..||++|.+|+.|.++. |-+|.|-...
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s 48 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYS 48 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcC
Confidence 456666666 8999999999999999999 9999998643
No 50
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.43 E-value=0.0021 Score=44.67 Aligned_cols=37 Identities=22% Similarity=0.403 Sum_probs=33.7
Q ss_pred EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA 52 (78)
Q Consensus 16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~ 52 (78)
+.+.||...++.+||++|.+|+.|.+.|+++|.|-.+
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N 183 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN 183 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC
Confidence 5578899999999999999999999999999999754
No 51
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=96.38 E-value=0.004 Score=40.57 Aligned_cols=38 Identities=29% Similarity=0.532 Sum_probs=34.9
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA 52 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~ 52 (78)
.+-++|....+|+.||++|++|+.|++..|-+|.|-.-
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey 71 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY 71 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc
Confidence 66778899999999999999999999999999999874
No 52
>PRK12705 hypothetical protein; Provisional
Probab=96.35 E-value=0.0035 Score=48.13 Aligned_cols=41 Identities=27% Similarity=0.438 Sum_probs=33.8
Q ss_pred CeeEEEEEecCCce-eeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680 12 GVCQIKILVPSYAA-GAIIGKGGETIAQIQKDTGSKIKMSKA 52 (78)
Q Consensus 12 ~~~~~~l~vP~~~v-G~IIGk~G~~Ik~i~~~Tga~I~i~~~ 52 (78)
....-.+.+|++-+ |.||||.|.||+.++..||+-|.|++.
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt 237 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT 237 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence 34455567787554 999999999999999999999999853
No 53
>KOG4369|consensus
Probab=96.31 E-value=0.0014 Score=55.00 Aligned_cols=58 Identities=26% Similarity=0.247 Sum_probs=49.5
Q ss_pred CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEec-CCCCCCCCceeEEEEeccCCC
Q psy14680 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK-ANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~-~~~~~~g~~er~v~I~G~p~~ 72 (78)
+...-++-+|.....+|||++|.||..++.-||+.|.|.+ .+ .+..||.+.+.|.|+.
T Consensus 1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~---~Nqaers~~~kg~p~~ 1396 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP---DNQAERSKAPKGRPPS 1396 (2131)
T ss_pred cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC---ccchhhhcccCCCChh
Confidence 3445567889999999999999999999999999999987 43 3568999999999874
No 54
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.18 E-value=0.014 Score=40.00 Aligned_cols=54 Identities=22% Similarity=0.383 Sum_probs=44.4
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEecc-CCCCC
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSR-PGFEP 74 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~-p~~~~ 74 (78)
.....+.||...+|.+||+.|+.-+.|.+.+++++.++. .++.|.|..+ +..||
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--------~~~~V~i~~~~~t~Dp 61 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--------KTGSVTIRTTRKTEDP 61 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--------CCCeEEEEecCCCCCh
Confidence 345668999999999999999999999999999999983 4667787766 33444
No 55
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=96.17 E-value=0.0017 Score=37.44 Aligned_cols=35 Identities=29% Similarity=0.528 Sum_probs=29.3
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEE
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK 48 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~ 48 (78)
..+.+.+..+..|.+||++|++|++|++..+-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 45677889999999999999999999887765553
No 56
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.91 E-value=0.014 Score=43.51 Aligned_cols=43 Identities=21% Similarity=0.199 Sum_probs=38.6
Q ss_pred CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54 (78)
Q Consensus 12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~ 54 (78)
......+.||.+..++.|||+|.|++-..+-||.+|.|-.-++
T Consensus 306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 3457889999999999999999999999999999999987553
No 57
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.82 E-value=0.01 Score=43.51 Aligned_cols=40 Identities=28% Similarity=0.417 Sum_probs=36.8
Q ss_pred CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51 (78)
Q Consensus 12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~ 51 (78)
......+.||.+..++.|||+|.|++-..+-||.+|.|-.
T Consensus 299 ~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 299 DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 3467889999999999999999999999999999999975
No 58
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=95.81 E-value=0.0072 Score=39.36 Aligned_cols=39 Identities=23% Similarity=0.314 Sum_probs=34.7
Q ss_pred CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEe
Q psy14680 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMS 50 (78)
Q Consensus 12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~ 50 (78)
+.....+.||.+..++.|||+|.|++...+-++-++.|.
T Consensus 98 ~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 98 GKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 456678899999999999999999999999999888775
No 59
>PRK13764 ATPase; Provisional
Probab=95.75 E-value=0.0085 Score=46.90 Aligned_cols=43 Identities=28% Similarity=0.485 Sum_probs=38.1
Q ss_pred CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54 (78)
Q Consensus 12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~ 54 (78)
......++||...++.+|||+|.+|++|++..|..|.|.+..+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 3445678999999999999999999999999999999988654
No 60
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=95.73 E-value=0.014 Score=34.61 Aligned_cols=36 Identities=11% Similarity=0.345 Sum_probs=28.8
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEE
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKM 49 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i 49 (78)
..+++.|-...-|.+||++|++|++|++.-.....+
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 347788888899999999999999998876544444
No 61
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=95.61 E-value=0.011 Score=45.65 Aligned_cols=40 Identities=33% Similarity=0.539 Sum_probs=36.0
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCC
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~ 54 (78)
...+.||...++.+|||+|.+|++|++..|-+|.|...++
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 4567899999999999999999999999999999987653
No 62
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=95.50 E-value=0.012 Score=40.00 Aligned_cols=38 Identities=26% Similarity=0.410 Sum_probs=35.5
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA 52 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~ 52 (78)
...+.||.+..+..|||+|.|++-..+-||-++.|...
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 77888999999999999999999999999999999753
No 63
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.20 E-value=0.024 Score=41.95 Aligned_cols=43 Identities=26% Similarity=0.417 Sum_probs=38.5
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
+......+.||.+..++-|||+|.|++--.+-||.+|.|-...
T Consensus 300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 3446788999999999999999999999999999999998754
No 64
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.19 E-value=0.018 Score=43.86 Aligned_cols=40 Identities=28% Similarity=0.372 Sum_probs=37.0
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA 52 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~ 52 (78)
...+.+.||....+.-|||+|.|++-..+-||.+|.|-..
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 3588899999999999999999999999999999999864
No 65
>KOG2279|consensus
Probab=95.10 E-value=0.0081 Score=46.69 Aligned_cols=57 Identities=30% Similarity=0.431 Sum_probs=46.6
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccC
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRP 70 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p 70 (78)
+..+...+-+|...+++|+||+|.++..|+..++|+|.+..++. ..-.|...|.+.-
T Consensus 137 ~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr---~g~~~~~~i~~qq 193 (608)
T KOG2279|consen 137 NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR---LGLSRLIKISGQQ 193 (608)
T ss_pred CCcccccccchhhhcccccccchhhhcchhcccccccccccccc---cccccceeccccc
Confidence 44567778899999999999999999999999999999998763 3456666666543
No 66
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=94.85 E-value=0.044 Score=36.68 Aligned_cols=38 Identities=26% Similarity=0.462 Sum_probs=32.4
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
.+-++|.... |.-|||+|.+++.+++..|-+|.|-...
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s 99 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKT 99 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcC
Confidence 4456666666 9999999999999999999999998754
No 67
>KOG2208|consensus
Probab=94.69 E-value=0.018 Score=46.14 Aligned_cols=61 Identities=18% Similarity=0.230 Sum_probs=52.2
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCCCCCC
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGFEPST 76 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~~~~~ 76 (78)
.+...+.+.+-......++||+|.++.+|++++.|.|.+...+ ..+..+.++|.-.++++.
T Consensus 344 ~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~-----~~~~~v~~~~~~~~~~ka 404 (753)
T KOG2208|consen 344 ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQG-----SNNKKVVITGVSANDEKA 404 (753)
T ss_pred ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccccc-----CCCCCeEEeccccchhHH
Confidence 3447788888999999999999999999999999999999743 578889999988777654
No 68
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=94.67 E-value=0.029 Score=34.72 Aligned_cols=30 Identities=27% Similarity=0.556 Sum_probs=24.9
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHhC
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTG 44 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tg 44 (78)
.+++.|-...-|.|||++|++|++|++.-.
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 466777778899999999999999887643
No 69
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=94.66 E-value=0.039 Score=32.58 Aligned_cols=28 Identities=25% Similarity=0.512 Sum_probs=22.5
Q ss_pred EEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680 16 IKILVPSYAAGAIIGKGGETIAQIQKDT 43 (78)
Q Consensus 16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~T 43 (78)
+++.|-...-|.+||++|++|++|++.-
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 5555555888999999999999887753
No 70
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.43 E-value=0.036 Score=42.14 Aligned_cols=41 Identities=27% Similarity=0.371 Sum_probs=36.9
Q ss_pred CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecC
Q psy14680 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKA 52 (78)
Q Consensus 12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~ 52 (78)
......+.||.+..++-|||+|.|++--.+-||.+|.|...
T Consensus 333 ~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~ 373 (449)
T PRK12329 333 EGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS 373 (449)
T ss_pred CCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence 34567899999999999999999999999999999999753
No 71
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=94.36 E-value=0.06 Score=37.96 Aligned_cols=37 Identities=22% Similarity=0.460 Sum_probs=33.8
Q ss_pred EEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 17 ~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
=+.||...|-++||++|+.++-|.+.|+|.|.|-.++
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG 185 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG 185 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC
Confidence 3678999999999999999999999999999998765
No 72
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=93.95 E-value=0.059 Score=37.87 Aligned_cols=30 Identities=23% Similarity=0.480 Sum_probs=25.0
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHHHHH
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQIQKD 42 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~ 42 (78)
...+++.|-...-|.||||+|++|.+|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 346778888899999999999999887654
No 73
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=93.92 E-value=0.11 Score=34.05 Aligned_cols=37 Identities=30% Similarity=0.618 Sum_probs=32.2
Q ss_pred EEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 17 ~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
++.|=...-|++|||+|.++++|..+||-+-.|-+..
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp 115 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP 115 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence 4566678889999999999999999999999887643
No 74
>KOG2113|consensus
Probab=93.82 E-value=0.078 Score=39.14 Aligned_cols=56 Identities=23% Similarity=0.277 Sum_probs=48.5
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCCC
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPGF 72 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~~ 72 (78)
+........+|...+|++.|..|.+|+.+++.+...|.-.-+ ..+-++.++|.|.+
T Consensus 112 s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~------~~~~Vf~Vtg~~~n 167 (394)
T KOG2113|consen 112 SGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR------CGEPVFCVTGAPKN 167 (394)
T ss_pred cCCCceeeeccceeeeeccccccCccchheecccceEeeecc------CCCceEEEecCCcc
Confidence 566778889999999999999999999999999999988743 36778889998776
No 75
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=93.44 E-value=0.096 Score=35.67 Aligned_cols=37 Identities=27% Similarity=0.425 Sum_probs=31.3
Q ss_pred EEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 17 ~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
-+.+-.+.+|+.||++|++|+.|.++-|-+|.|-.-.
T Consensus 79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s 115 (190)
T COG0195 79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS 115 (190)
T ss_pred EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC
Confidence 3444557889999999999999999999999998644
No 76
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=93.03 E-value=0.18 Score=35.00 Aligned_cols=30 Identities=30% Similarity=0.295 Sum_probs=23.1
Q ss_pred eEEEEEecC-CceeeEEecCCchHHHHHHHh
Q psy14680 14 CQIKILVPS-YAAGAIIGKGGETIAQIQKDT 43 (78)
Q Consensus 14 ~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~T 43 (78)
+...++|.. ++-+.|||++|+.||+|...+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 556667764 566999999999999876543
No 77
>PRK15494 era GTPase Era; Provisional
Probab=92.15 E-value=0.26 Score=35.63 Aligned_cols=29 Identities=28% Similarity=0.361 Sum_probs=22.5
Q ss_pred eEEEEEecC-CceeeEEecCCchHHHHHHH
Q psy14680 14 CQIKILVPS-YAAGAIIGKGGETIAQIQKD 42 (78)
Q Consensus 14 ~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~ 42 (78)
+...++|.. ++-+.|||++|+.||+|...
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 556677765 56699999999999987543
No 78
>PRK00089 era GTPase Era; Reviewed
Probab=91.78 E-value=0.33 Score=33.80 Aligned_cols=29 Identities=34% Similarity=0.575 Sum_probs=21.8
Q ss_pred eEEEEEecC-CceeeEEecCCchHHHHHHH
Q psy14680 14 CQIKILVPS-YAAGAIIGKGGETIAQIQKD 42 (78)
Q Consensus 14 ~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~ 42 (78)
+...++|.. ++-+.|||++|+.||+|...
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 455566654 56699999999999987644
No 79
>COG1159 Era GTPase [General function prediction only]
Probab=90.36 E-value=0.45 Score=34.59 Aligned_cols=31 Identities=32% Similarity=0.435 Sum_probs=22.8
Q ss_pred eeEEEEEecC-CceeeEEecCCchHHHHHHHh
Q psy14680 13 VCQIKILVPS-YAAGAIIGKGGETIAQIQKDT 43 (78)
Q Consensus 13 ~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~T 43 (78)
.+...++|+. ++=|.||||+|+.||+|-..+
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 3455567765 556999999999999876543
No 80
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=89.52 E-value=0.42 Score=32.66 Aligned_cols=30 Identities=23% Similarity=0.522 Sum_probs=24.6
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDT 43 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T 43 (78)
..+++.|-...-|.+||++|.+|++|++.-
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 346777888888999999999999877653
No 81
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=89.45 E-value=0.42 Score=32.77 Aligned_cols=29 Identities=24% Similarity=0.499 Sum_probs=22.9
Q ss_pred EEEEecCCceeeEEecCCchHHHHHHHhC
Q psy14680 16 IKILVPSYAAGAIIGKGGETIAQIQKDTG 44 (78)
Q Consensus 16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tg 44 (78)
+++.|-...-|.+||++|++|++|++.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 45555558889999999999999877653
No 82
>KOG3273|consensus
Probab=89.11 E-value=0.093 Score=36.61 Aligned_cols=30 Identities=40% Similarity=0.548 Sum_probs=27.3
Q ss_pred CCceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680 22 SYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51 (78)
Q Consensus 22 ~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~ 51 (78)
+..+|+|+||+|.+--.|+..|.++|.+..
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad 206 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD 206 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC
Confidence 467899999999999999999999999974
No 83
>CHL00048 rps3 ribosomal protein S3
Probab=89.04 E-value=0.47 Score=32.77 Aligned_cols=29 Identities=17% Similarity=0.306 Sum_probs=23.6
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDT 43 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T 43 (78)
.+++.|-...-|.|||++|.+|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 45666667788999999999999988754
No 84
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=88.46 E-value=0.5 Score=35.06 Aligned_cols=31 Identities=29% Similarity=0.472 Sum_probs=27.7
Q ss_pred CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680 23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN 53 (78)
Q Consensus 23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~ 53 (78)
+-+|+.||++|++|+.|.++. |-+|.|-.-.
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s 276 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS 276 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcC
Confidence 568999999999999999888 9999998743
No 85
>KOG1423|consensus
Probab=88.41 E-value=0.71 Score=34.32 Aligned_cols=32 Identities=31% Similarity=0.589 Sum_probs=26.2
Q ss_pred eeEEEEEecC-CceeeEEecCCchHHHHHHHhC
Q psy14680 13 VCQIKILVPS-YAAGAIIGKGGETIAQIQKDTG 44 (78)
Q Consensus 13 ~~~~~l~vP~-~~vG~IIGk~G~~Ik~i~~~Tg 44 (78)
.++.++.+|. +..-.||||||..|++|-++.+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 5788899987 4557899999999999877643
No 86
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=88.39 E-value=0.52 Score=32.84 Aligned_cols=29 Identities=14% Similarity=0.354 Sum_probs=23.8
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDT 43 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T 43 (78)
.+++.|-...-|.|||++|..|++|++.-
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 46677777888999999999999877654
No 87
>KOG2208|consensus
Probab=88.37 E-value=0.4 Score=38.61 Aligned_cols=42 Identities=21% Similarity=0.368 Sum_probs=38.9
Q ss_pred CCCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51 (78)
Q Consensus 10 ~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~ 51 (78)
....++..+.+|.++...+||++|++.+++.+++++.+.+..
T Consensus 705 ~~~~~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 705 AKNLVTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred cccceeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 466788999999999999999999999999999999999986
No 88
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=87.90 E-value=0.61 Score=34.29 Aligned_cols=31 Identities=32% Similarity=0.513 Sum_probs=27.7
Q ss_pred CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680 23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN 53 (78)
Q Consensus 23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~ 53 (78)
+-+|+.||++|++|+.|.++- |-+|.|-.-.
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s 274 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS 274 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcC
Confidence 567999999999999999998 9999998743
No 89
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=86.88 E-value=1 Score=35.54 Aligned_cols=38 Identities=29% Similarity=0.539 Sum_probs=32.9
Q ss_pred EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
=+++|=+..-|.+|||+|.++++|-++||-+-.|-+..
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 35667778889999999999999999999999987643
No 90
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=86.30 E-value=0.55 Score=32.55 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=29.0
Q ss_pred CeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEE
Q psy14680 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK 48 (78)
Q Consensus 12 ~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~ 48 (78)
....+.+-+-.+..|.+||+.|.++..||--+.+-+.
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 4456667777777999999999999999977655443
No 91
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=86.07 E-value=0.59 Score=35.74 Aligned_cols=31 Identities=29% Similarity=0.463 Sum_probs=27.7
Q ss_pred CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680 23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN 53 (78)
Q Consensus 23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~ 53 (78)
+-+|+.||++|++|+.|.++- |-+|.|-.-.
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys 308 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS 308 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC
Confidence 567999999999999999998 9999998743
No 92
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=84.92 E-value=0.62 Score=34.83 Aligned_cols=31 Identities=26% Similarity=0.401 Sum_probs=27.6
Q ss_pred CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680 23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN 53 (78)
Q Consensus 23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~ 53 (78)
+-+|+.||++|++|+.|.++- |-+|.|-.-.
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s 282 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS 282 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC
Confidence 567999999999999999988 9999998743
No 93
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=83.81 E-value=0.84 Score=34.96 Aligned_cols=31 Identities=29% Similarity=0.429 Sum_probs=27.5
Q ss_pred CceeeEEecCCchHHHHHHHh-CCeEEEecCC
Q psy14680 23 YAAGAIIGKGGETIAQIQKDT-GSKIKMSKAN 53 (78)
Q Consensus 23 ~~vG~IIGk~G~~Ik~i~~~T-ga~I~i~~~~ 53 (78)
+-+|+.||++|++|+.|.++- |-+|.|-.-.
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s 276 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWS 276 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcC
Confidence 567999999999999999988 9999998743
No 94
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=83.46 E-value=1.2 Score=30.61 Aligned_cols=28 Identities=32% Similarity=0.646 Sum_probs=23.1
Q ss_pred EEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680 16 IKILVPSYAAGAIIGKGGETIAQIQKDT 43 (78)
Q Consensus 16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~T 43 (78)
+++.|-...-|.|||++|.++++|++.-
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 6677777778999999999999987543
No 95
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=82.13 E-value=1.9 Score=34.01 Aligned_cols=38 Identities=29% Similarity=0.548 Sum_probs=32.5
Q ss_pred EEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCC
Q psy14680 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 16 ~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
=+++|=+..-|++|||+|++.+.|-++||-.-.|-+..
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P 138 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP 138 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence 35677788889999999999999999999988877643
No 96
>KOG1067|consensus
Probab=78.25 E-value=1.4 Score=35.15 Aligned_cols=40 Identities=20% Similarity=0.277 Sum_probs=34.6
Q ss_pred CCeeEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEe
Q psy14680 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMS 50 (78)
Q Consensus 11 ~~~~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~ 50 (78)
.......+.++.+..-.+||.+|-..|+|+.+||+.-+++
T Consensus 594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD 633 (760)
T KOG1067|consen 594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD 633 (760)
T ss_pred cCceeeEEeecchhhheeecCccceeeeEeeeccceeeec
Confidence 3456788899999999999999999999999999666664
No 97
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=76.91 E-value=2.4 Score=29.64 Aligned_cols=29 Identities=24% Similarity=0.605 Sum_probs=22.7
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHh
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDT 43 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~T 43 (78)
.+++.|-...-|.|||++|.+|++|++.-
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 35556666778999999999999887654
No 98
>KOG2874|consensus
Probab=76.43 E-value=2 Score=31.51 Aligned_cols=25 Identities=24% Similarity=0.349 Sum_probs=23.4
Q ss_pred eeEEecCCchHHHHHHHhCCeEEEe
Q psy14680 26 GAIIGKGGETIAQIQKDTGSKIKMS 50 (78)
Q Consensus 26 G~IIGk~G~~Ik~i~~~Tga~I~i~ 50 (78)
-++||..|+++|.|+--|.|.|-|.
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq 185 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ 185 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee
Confidence 3689999999999999999999997
No 99
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=74.24 E-value=14 Score=24.71 Aligned_cols=49 Identities=10% Similarity=0.221 Sum_probs=39.5
Q ss_pred EEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG 71 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~ 71 (78)
.+.+.++....-++...+|..+++|....||+|.+.. .+..+.|+|+..
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--------~~~~i~I~g~k~ 75 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--------SENRIRITGTKS 75 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec--------CCcEEEEEccHH
Confidence 4455556888889999999999999888899999985 355789998754
No 100
>KOG4369|consensus
Probab=73.56 E-value=1.6 Score=37.64 Aligned_cols=55 Identities=15% Similarity=0.051 Sum_probs=47.4
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccCC
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRPG 71 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p~ 71 (78)
-.++...+..++.+||++.+.+|+-++.-+++++.|....| .+.|+.++|.+.-+
T Consensus 781 aniehrdkkgf~plImaatagh~tvV~~llk~ha~veaQsd---rtkdt~lSlacsgg 835 (2131)
T KOG4369|consen 781 ANIEHRDKKGFVPLIMAATAGHITVVQDLLKAHADVEAQSD---RTKDTMLSLACSGG 835 (2131)
T ss_pred ccccccccccchhhhhhcccCchHHHHHHHhhhhhhhhhcc---cccCceEEEecCCC
Confidence 35677889999999999999999999999999999987654 56899999987643
No 101
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=58.34 E-value=7.2 Score=30.89 Aligned_cols=38 Identities=21% Similarity=0.336 Sum_probs=33.5
Q ss_pred eEEEEEecCCceeeEEecCCchHHHHHHHhCCeEEEec
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~ 51 (78)
-.+.++||...+-.|||-||..|.+....-+.-|+..-
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n 486 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKN 486 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhh
Confidence 35678999999999999999999999888888888764
No 102
>cd07557 trimeric_dUTPase Trimeric dUTP diphosphatases. Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface.
Probab=38.10 E-value=44 Score=19.07 Aligned_cols=26 Identities=15% Similarity=0.124 Sum_probs=20.7
Q ss_pred eEEEEEecCCceeeEEecCCchHHHH
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETIAQI 39 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~Ik~i 39 (78)
..+++.+|...+|.|.+|.+-..+-|
T Consensus 26 t~~~i~~p~~~~~~i~~RSs~~~~Gi 51 (92)
T cd07557 26 TGEAIELPEGYVGLVFPRSSLARKGI 51 (92)
T ss_pred EeEEEEcCCCeEEEEEcCchhhcCCE
Confidence 45677899999999999998655444
No 103
>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=31.95 E-value=32 Score=24.55 Aligned_cols=27 Identities=22% Similarity=0.389 Sum_probs=22.0
Q ss_pred eeEEEEEecCCceeeEEecCCchHHHH
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIAQI 39 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik~i 39 (78)
...+.+-||...|=++||+.|+=-.-+
T Consensus 23 L~~i~l~i~~~~VTAlIGPSGcGKST~ 49 (253)
T COG1117 23 LKDINLDIPKNKVTALIGPSGCGKSTL 49 (253)
T ss_pred hccCceeccCCceEEEECCCCcCHHHH
Confidence 456788999999999999999865443
No 104
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=30.40 E-value=30 Score=21.32 Aligned_cols=14 Identities=36% Similarity=0.479 Sum_probs=12.6
Q ss_pred ecCCceeeEEecCC
Q psy14680 20 VPSYAAGAIIGKGG 33 (78)
Q Consensus 20 vP~~~vG~IIGk~G 33 (78)
-|.+.+|+++|+.+
T Consensus 17 ~P~E~CGlL~G~~~ 30 (117)
T cd08072 17 HPNEFAALLRGKDG 30 (117)
T ss_pred CCceEEEEEEeecc
Confidence 48899999999987
No 105
>cd03710 BipA_TypA_C BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secreti
Probab=29.53 E-value=20 Score=20.27 Aligned_cols=18 Identities=33% Similarity=0.508 Sum_probs=14.3
Q ss_pred eeEEEEEecCCceeeEEe
Q psy14680 13 VCQIKILVPSYAAGAIIG 30 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIG 30 (78)
-..+++.+|.+++|.|++
T Consensus 3 i~~v~I~~P~~~~g~V~~ 20 (79)
T cd03710 3 IEELTIDVPEEYSGAVIE 20 (79)
T ss_pred EEEEEEEeCchhhHHHHH
Confidence 356889999999987654
No 106
>PF14597 Lactamase_B_5: Metallo-beta-lactamase superfamily; PDB: 2P97_B.
Probab=27.32 E-value=95 Score=21.47 Aligned_cols=27 Identities=22% Similarity=0.281 Sum_probs=16.3
Q ss_pred eEEecCCchH---HHHHHHhCCeEEEecCC
Q psy14680 27 AIIGKGGETI---AQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 27 ~IIGk~G~~I---k~i~~~Tga~I~i~~~~ 53 (78)
.|+=-++..+ ++++++|+|+|.++...
T Consensus 58 ~IvLTn~dHvR~A~~ya~~~~a~i~~p~~d 87 (199)
T PF14597_consen 58 WIVLTNRDHVRAAEDYAEQTGAKIYGPAAD 87 (199)
T ss_dssp EEE-SSGGG-TTHHHHHHHS--EEEEEGGG
T ss_pred EEEEeCChhHhHHHHHHHHhCCeeeccHHH
Confidence 3444444444 67999999999999853
No 107
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=25.95 E-value=48 Score=20.11 Aligned_cols=14 Identities=36% Similarity=0.617 Sum_probs=12.2
Q ss_pred ecCCceeeEEecCC
Q psy14680 20 VPSYAAGAIIGKGG 33 (78)
Q Consensus 20 vP~~~vG~IIGk~G 33 (78)
-|.+.+|+|+|+++
T Consensus 14 ~P~E~CGll~g~~~ 27 (108)
T cd08073 14 YPREACGLVVRKGR 27 (108)
T ss_pred CCCcceEEEEecCC
Confidence 58999999999884
No 108
>PF04025 DUF370: Domain of unknown function (DUF370); InterPro: IPR007169 This is a bacterial family of unknown function.
Probab=24.84 E-value=1.5e+02 Score=17.17 Aligned_cols=46 Identities=11% Similarity=0.097 Sum_probs=33.4
Q ss_pred EEEecCCceeeEEecCCchHHHHHHHhC---CeEEEecCCCCCCCCceeEEEEec
Q psy14680 17 KILVPSYAAGAIIGKGGETIAQIQKDTG---SKIKMSKANDFYPVYQVITLFLLS 68 (78)
Q Consensus 17 ~l~vP~~~vG~IIGk~G~~Ik~i~~~Tg---a~I~i~~~~~~~~g~~er~v~I~G 68 (78)
-.+|+.+.+=+|+-..-+.+|+|.++.. --|... .|...|.+.|+-
T Consensus 7 gn~V~~~rIiAIv~~~Sap~Krl~~~ak~~~~lIdaT------~Grktrsviitd 55 (73)
T PF04025_consen 7 GNFVNADRIIAIVSPDSAPIKRLIQEAKEEGKLIDAT------YGRKTRSVIITD 55 (73)
T ss_pred CcEEEcceEEEEECCcchhHHHHHHHHHHcCcEEEee------CCCceeEEEEEc
Confidence 3577888888999999999999887763 334443 356777777763
No 109
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=24.82 E-value=1.2e+02 Score=18.83 Aligned_cols=33 Identities=12% Similarity=0.281 Sum_probs=24.4
Q ss_pred CCCcccCCCeeEEEEEecC-------CceeeEEecCCchH
Q psy14680 4 KSPFIRADGVCQIKILVPS-------YAAGAIIGKGGETI 36 (78)
Q Consensus 4 ~~~~~~~~~~~~~~l~vP~-------~~vG~IIGk~G~~I 36 (78)
+.+.......+.+.+.++. .+.|.+|++.+.-+
T Consensus 15 ~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~ 54 (113)
T PF01245_consen 15 DIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGL 54 (113)
T ss_dssp SSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSST
T ss_pred CCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCC
Confidence 3344455677888888883 68899999999743
No 110
>COG3840 ThiQ ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]
Probab=24.34 E-value=1.1e+02 Score=21.60 Aligned_cols=34 Identities=21% Similarity=0.236 Sum_probs=27.9
Q ss_pred CCcccCCCeeEEEEEecCCceeeEEecCCchHHH
Q psy14680 5 SPFIRADGVCQIKILVPSYAAGAIIGKGGETIAQ 38 (78)
Q Consensus 5 ~~~~~~~~~~~~~l~vP~~~vG~IIGk~G~~Ik~ 38 (78)
-.|..+...+.+.+.||...+=+|+|..|+--.-
T Consensus 7 V~~~y~~~~~~fdl~v~~ge~vAi~GpSGaGKST 40 (231)
T COG3840 7 VRFSYGHLPMRFDLTVPAGEIVAILGPSGAGKST 40 (231)
T ss_pred eEEeeCcceEEEEEeecCCcEEEEECCCCccHHH
Confidence 3566677788899999999999999999975544
No 111
>PF04879 Molybdop_Fe4S4: Molybdopterin oxidoreductase Fe4S4 domain; InterPro: IPR006963 The molybdopterin oxidoreductase Fe4S4 domain is found in a number of reductase/dehydrogenase families, which include the periplasmic nitrate reductase precursor and the formate dehydrogenase alpha chain [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2VPZ_A 2VPY_A 2VPW_A 2VPX_A 2NYA_A 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 ....
Probab=24.33 E-value=1.2e+02 Score=15.70 Aligned_cols=26 Identities=12% Similarity=0.093 Sum_probs=16.6
Q ss_pred hCCeEEEecCCCCCCCCceeEEEEeccCCCCCC
Q psy14680 43 TGSKIKMSKANDFYPVYQVITLFLLSRPGFEPS 75 (78)
Q Consensus 43 Tga~I~i~~~~~~~~g~~er~v~I~G~p~~~~~ 75 (78)
.||.|.+.-. ..+++.|.|.++...+
T Consensus 13 ~gC~i~~~v~-------~g~i~~v~g~~~~p~~ 38 (55)
T PF04879_consen 13 SGCGIDVYVK-------DGKIVKVEGDPDHPIN 38 (55)
T ss_dssp T--EEEEEEE-------TTEEEEEEE-TTSTTT
T ss_pred CCCcEEEEEe-------cCceEEEECCCCCCCC
Confidence 4777777742 5788999999877544
No 112
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=24.19 E-value=1.2e+02 Score=22.64 Aligned_cols=42 Identities=12% Similarity=0.150 Sum_probs=33.0
Q ss_pred EecCCceeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEeccC
Q psy14680 19 LVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLSRP 70 (78)
Q Consensus 19 ~vP~~~vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G~p 70 (78)
+-+...+-.+.|..+.+++.|++..|+.|.... +.+.|+|++
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----------~~~~i~g~~ 61 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVARG----------EAVRIIGAR 61 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeCC----------ceEEEEech
Confidence 334677889999999999999999998887652 236677764
No 113
>PHA02099 hypothetical protein
Probab=23.34 E-value=28 Score=20.42 Aligned_cols=38 Identities=26% Similarity=0.450 Sum_probs=27.8
Q ss_pred EEEEecCCceeeE------------EecCCchHHHHHHHhCCeEEEecCC
Q psy14680 16 IKILVPSYAAGAI------------IGKGGETIAQIQKDTGSKIKMSKAN 53 (78)
Q Consensus 16 ~~l~vP~~~vG~I------------IGk~G~~Ik~i~~~Tga~I~i~~~~ 53 (78)
+++.|.++..|-| .|.||+...-||..+|+-|.+..++
T Consensus 3 fkiiv~s~~~gpid~yi~~lkn~~rv~pg~~emhilr~~~g~diifha~g 52 (84)
T PHA02099 3 FKIIVKSSAKGPVDQYIANLKNAGRVGPGESEMHILRNFEGVDIVFHAEG 52 (84)
T ss_pred eEEEEecccCCCHHHHHHhhhccCccCCCCcEEEEEeecCCccEEEEcCC
Confidence 4555655555532 6888888888999999999888654
No 114
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=22.55 E-value=1.6e+02 Score=16.51 Aligned_cols=26 Identities=15% Similarity=0.198 Sum_probs=21.9
Q ss_pred EEEEEecCCceeeEEecCCchHHHHH
Q psy14680 15 QIKILVPSYAAGAIIGKGGETIAQIQ 40 (78)
Q Consensus 15 ~~~l~vP~~~vG~IIGk~G~~Ik~i~ 40 (78)
..++.+|+.+.-.|.=|-|.++++.-
T Consensus 2 ~~~v~LP~~q~t~V~vrpg~ti~d~L 27 (71)
T PF02196_consen 2 TCRVHLPNGQRTVVQVRPGMTIRDAL 27 (71)
T ss_dssp EEEEEETTTEEEEEEE-TTSBHHHHH
T ss_pred eEEEECCCCCEEEEEEcCCCCHHHHH
Confidence 57899999999999999999998743
No 115
>cd03709 lepA_C lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits significant homology to elongation factors (EFs) Tu and G. The function(s) of the proteins in this family are unknown. The N-terminal domain of LepA is homologous to a domain of similar size found in initiation factor 2 (IF2), and in EF-Tu and EF-G (factors required for translation in Escherichia coli). Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including S. cerevisiae GUF1) originated within the bacterial LepA family. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=22.34 E-value=26 Score=19.94 Aligned_cols=18 Identities=33% Similarity=0.484 Sum_probs=14.2
Q ss_pred eeEEEEEecCCceeeEEe
Q psy14680 13 VCQIKILVPSYAAGAIIG 30 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIG 30 (78)
-..+++.+|.+++|.|++
T Consensus 3 i~~v~i~vP~e~~G~V~~ 20 (80)
T cd03709 3 FVKATIITPSEYLGAIME 20 (80)
T ss_pred EEEEEEEeCHHhhHHHHH
Confidence 357889999999987654
No 116
>TIGR03021 pilP_fam type IV pilus biogenesis protein PilP. Members of this protein family are found in type IV pilus biogenesis loci and include proteins designated PilP.
Probab=20.65 E-value=60 Score=20.38 Aligned_cols=43 Identities=19% Similarity=0.263 Sum_probs=33.9
Q ss_pred eeeEEecCCchHHHHHHHhCCeEEEecCCCCCCCCceeEEEEec
Q psy14680 25 AGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITLFLLS 68 (78)
Q Consensus 25 vG~IIGk~G~~Ik~i~~~Tga~I~i~~~~~~~~g~~er~v~I~G 68 (78)
+=.|.|++|.-...|+--.|..+.|. .++.+||+..++..|+-
T Consensus 71 v~~I~G~~~~l~A~l~l~~G~~~~v~-~G~~lpgt~~~V~~I~~ 113 (119)
T TIGR03021 71 VVEIFGRGGRLTATLRLPGGREVDVQ-VGDSLPGTGYKVKSITL 113 (119)
T ss_pred EEEEEccCCCeEEEEEeCCCcEEEec-CCCccCCCCcEEEEEeC
Confidence 55788999888888887778777775 56778888889988864
No 117
>PHA01707 dut 2'-deoxyuridine 5'-triphosphatase
Probab=20.29 E-value=1.2e+02 Score=19.68 Aligned_cols=25 Identities=8% Similarity=-0.133 Sum_probs=19.7
Q ss_pred eeEEEEEecCCceeeEEecCCchHH
Q psy14680 13 VCQIKILVPSYAAGAIIGKGGETIA 37 (78)
Q Consensus 13 ~~~~~l~vP~~~vG~IIGk~G~~Ik 37 (78)
...+.+.+|.+.+|.+.+|.+---+
T Consensus 66 ~T~E~i~lP~~~~~~i~~RSslaR~ 90 (158)
T PHA01707 66 TTKEYIKLPNDIIAFCNLRSTFARK 90 (158)
T ss_pred EEeEEEECCCCEEEEEECcchhhhC
Confidence 3556778899999999999875443
No 118
>PRK00416 dcd deoxycytidine triphosphate deaminase; Reviewed
Probab=20.10 E-value=1.3e+02 Score=19.76 Aligned_cols=23 Identities=13% Similarity=0.157 Sum_probs=18.8
Q ss_pred eEEEEEecCCceeeEEecCCchH
Q psy14680 14 CQIKILVPSYAAGAIIGKGGETI 36 (78)
Q Consensus 14 ~~~~l~vP~~~vG~IIGk~G~~I 36 (78)
..+.+.+|...+|.+.+|.+-.-
T Consensus 83 t~e~i~lP~~~~~~i~~RSslar 105 (177)
T PRK00416 83 TLEYFKLPDDVVGILEGRSSLAR 105 (177)
T ss_pred eeeEEECCCCeEEEEEeCchhhc
Confidence 45667889999999999988553
Done!